AbstractThe red-legged partridge Alectoris rufa plays a crucial role in the ecosystem of southwestern Europe, and understanding its genetics is vital for conservation and management. Here we sequence, assemble, and annotate a highly contiguous and nearly complete version of its genome. This assembly encompasses 96.9% of the avian genes flagged as essential in the BUSCO aves_odb10 dataset.

摘要红腿鹧鸪Alectoris rufa在欧洲西南部的生态系统中起着至关重要的作用，了解其遗传学对于保护和管理至关重要。在这里，我们对其基因组的高度连续且几乎完整的版本进行测序，组装和注释。该装配包含BUSCO aves\u odb10数据集中标记为必需的96.9%的禽类基因。

Moreover, we pinpointed RNA and protein-coding genes, 95% of which had functional annotations. Notably, we observed significant chromosome rearrangements in comparison to quail (Coturnix japonica) and chicken (Gallus gallus). In addition, a comparative phylogenetic analysis of these genomes suggests that A.

此外，我们确定了RNA和蛋白质编码基因，其中95%具有功能注释。值得注意的是，与鹌鹑（Coturnix japonica）和鸡（Gallus Gallus）相比，我们观察到显着的染色体重排。此外，对这些基因组的比较系统发育分析表明，a。

rufa and C. japonica diverged roughly 20 million years ago and that their common ancestor diverged from G. gallus 35 million years ago. Our assembly represents a significant advancement towards a complete reference genome for A. rufa, facilitating comparative avian genomics, and providing a valuable resource for future research and conservation efforts for the red-legged partridge..

rufa和C.japonica大约在2000万年前分化，他们的共同祖先在3500万年前与G.gallus分化。我们的大会代表了对a.rufa完整参考基因组的重大进步，促进了比较鸟类基因组学，并为红腿鹧鸪的未来研究和保护工作提供了宝贵的资源。。

IntroductionAlectoris rufa, also known as red-legged partridge, is a game bird that holds significant ecological and economic importance for rural areas in southwestern Europe1. Habitat degradation, captive breeding, and hunting management have led to the creation of a complex species situation, impacting both the ecosystems and society of the region.

简介红腿鹧鸪，也称为红腿鹧鸪，是一种猎鸟，对西南欧的农村地区具有重要的生态和经济意义1。栖息地退化、圈养繁殖和狩猎管理导致了复杂的物种状况，影响了该地区的生态系统和社会。

Across various hunting grounds, wild, farmed, and hybrid partridges coexist in varying proportions. While these partridges exhibit distinctions in behavior, physiology, morphology, anatomy, and genetics, the absence of a reference genome hinders our ability to molecularly differentiate these ecotypes, spanning from wild to domestic2.

在各种狩猎场，野生、养殖和杂交鹧鸪以不同的比例共存。虽然这些鹧鸪在行为，生理学，形态学，解剖学和遗传学方面表现出差异，但缺乏参考基因组阻碍了我们从野生到家养的分子分化这些生态型的能力2。

The haploid genome of A. rufa has 9 macro chromosomes and 30 micro chromosomes3,4. The advent of Next-Generation Sequencing (NGS) technologies, mainly based on short-read sequencing data, combined with decreasing DNA sequencing costs, led to an increase in the number of available genome sequences. However, those genomes were still highly fragmented due to the limitations inherent to short reads, where for example repetitive regions can lead to genome misassembly.

A.rufa的单倍体基因组具有9条宏染色体和30条微染色体3,4。主要基于短读测序数据的下一代测序（NGS）技术的出现，加上DNA测序成本的降低，导致可用基因组序列数量的增加。然而，由于短读固有的局限性，这些基因组仍然高度碎片化，例如重复区域可能导致基因组错误组装。

The emergence of third-generation sequencing technologies partially overcame those limitations by generating long-read sequencing data. These long-reads helped to reduce assembly fragmentation and increase contiguity, greatly improving the quality of whole-genome assemblies5. Still, early long-read technologies had base-calling error rates of 10–14%, that are much higher than the less than 1% error rate found in short-read technologies6.

第三代测序技术的出现通过产生长读取测序数据部分克服了这些限制。这些长读取有助于减少装配碎片并增加连续性，从而大大提高全基因组装配的质量5。尽管如此，早期的长读技术的基本呼叫错误率为10-14%，远高于短读技术中不到1%的错误率6。

In addition, the error profiles of both technologies are different. Errors in short-reads are mostly at the level of incorrect nucleotide substitutions, while errors in long-reads mostly involve incor.

另外，两种技术的误差分布是不同的。短读中的错误主要是不正确的核苷酸取代水平，而长读中的错误主要涉及incor。

A. rufa genome assembly, annotation and quality assessmentWe tested and evaluated various pipelines to assemble the genome of the red-legged partridge. The NextDenovo pipeline produced a primary assembly with the best metrics. This assembly comprised 116 contigs, with an N50 length of 74 Mb and an N90 of 10 Mb (Supplementary Table S1).

A、 rufa基因组组装，注释和质量评估我们测试和评估了各种管道，以组装红腿鹧鸪的基因组。NextDenovo管道产生了一个具有最佳度量的主程序集。该组件由116个重叠群组成，N50长度为74 Mb，N90长度为10 Mb（补充表S1）。

We further refined this assembly, recovering 96.8% (8078 out of 8332) of the single-copy genes found in the BUSCO dataset of avian single copy orthologous genes (aves_odb10, N = 8332 genes) (Supplementary Table S2). The contigs were then used as the basis for genome scaffolding, resulting in a final genome assembly of 115 scaffolds and 1.03 Gb.

我们进一步改进了这个组装，回收了在鸟类单拷贝直系同源基因（aves u odb10，N=8332个基因）的BUSCO数据集中发现的96.8%（8332个中的8078个）的单拷贝基因（补充表S2）。然后将重叠群用作基因组支架的基础，最终产生115个支架和1.03 Gb的基因组组装。

Table 1 summarizes the most relevant contiguity metrics of this assembly and its annotation.Table 1 Statistic for the Alectoris rufa genome assembly and annotation.Full size tableThe final assembly significantly improves the statistical metrics of contiguity of the earlier available assemblies (Table 2).

表1总结了此程序集及其注释的最相关的邻接度量。。全尺寸表最终装配显着提高了早期可用装配的连续性统计指标（表2）。

Our L90 is 23, closer to the 9 macro-chromosomes present in the haploid genome of A. rufa, and at least five times smaller than that for assemblies GCA_947331505.1 (based on short-reads) and GCA_019345075.1 (based on long-reads). Our N50 (74 Mb) is twice that of the GCA_019345075.1 assembly and seven times that of the GCA_947331505.1 assembly.

我们的L90是23，更接近A.rufa单倍体基因组中存在的9条宏染色体，并且比组件GCA\U 947331505.1（基于短读数）和GCA\U 019345075.1（基于长读数）小至少五倍。我们的N50（74 Mb）是GCA\U 019345075.1组件的两倍，是GCA\U 947331505.1组件的七倍。

Our assembly contained 96.78% (n = 8053 genes) of complete and single-copy genes without duplications present in the BUSCO avian dataset, surpassing both the short-read (95.1%; n = 7933 genes) and the long read (96.58%; n = 7378) genome assemblies. Table 2 summarizes the main differences in terms of the genome contiguity and completeness metrics between those assemblies.Table 2 Comparing Alectoris rufa genome assemblies.Full size tableAdditionally, we compare.

我们的装配包含96.78%（n=8053个基因）的完整和单拷贝基因，在BUSCO禽类数据集中没有重复，超过了短读（95.1%；n=7933个基因）和长读（96.58%；n=7378）基因组装配。表2总结了这些组件之间在基因组连续性和完整性指标方面的主要差异。。全尺寸表另外，我们进行了比较。

gallus

鸡

A. rufa belongs to the Phasianidae (pheasants, partridges, chickens, turkeys, etc.) family of the Galliformes clade. While many relationships within Galliformes are well-supported, some uncertainties remain, particularly regarding the branching order within the species-rich Phasianidae family. One of the uncertainties in this family is the relationship between A.

A、 。虽然鸡形目内的许多关系得到了很好的支持，但仍然存在一些不确定性，特别是关于物种丰富的Phasianidae科内的分支顺序。这个家庭的不确定性之一是A之间的关系。

rufa, C. japonica, and G. gallus. The three birds are closely related and exhibit a shared karyotype of n = 39 chromosomes22. This karyotype similarity motivated us to compare the sequence of the largest 23 scaffolds of A. rufa (containing at least 90% of the assembled genome) across the three species.

rufa，C.japonica和G.gallus。这三种鸟密切相关，并表现出n=39染色体的共同核型22。这种核型相似性促使我们比较三个物种中最大的23个A.rufa支架（包含至少90%的组装基因组）的序列。

Figure 3 highlights significant syntenic regions across the three genomes. Scaffolds 2 and 5 of A. rufa align with chromosome 1 in the two other species. Similarly, scaffolds 1, 3 and 4 respectively align to chromosomes 2, 4 and 3 of both birds. Furthermore, A. rufa scaffolds 6 and 10 display near complete synteny with C.

图3突出显示了三个基因组中重要的同线性区域。A.rufa的支架2和5与另外两个物种的1号染色体对齐。类似地，支架1、3和4分别与两只鸟的染色体2、4和3对齐。此外，A.rufa支架6和10与C显示出接近完全的同线性。

japonica’s sex chromosome Z, while scaffold 10 showing synteny with G. gallus’ Z chromosome. Scaffolds 7 and 15 of A. rufa display considerable synteny with chromosome 5 of the other birds. The remaining 14 A. rufa scaffolds exhibit strong synteny with individual chromosomes of the other two bird species.

粳稻的性染色体Z，而支架10与G.gallus的Z染色体显示出同线性。A.rufa的支架7和15与其他鸟类的5号染色体显示出相当大的同线性。其余14个A.rufa支架与其他两种鸟类的个体染色体表现出强烈的同线性。

Notably, twelve micro chromosomes from C. japonica and 20 micro chromosomes from G. gallus did not exhibit significant homology with any of the assembled A. rufa scaffolds.Figure 3Circus plots comparing sequence homology between the largest 23 A. rufa scaffolds and the reference chromosomes of A C. japonica, and B G.

值得注意的是，来自C.japonica的12条微染色体和来自G.gallus的20条微染色体与任何组装的A.rufa支架均未显示出显着的同源性。图3Circus图比较了最大的23个A.rufa支架与A.japonica和B G的参考染色体之间的序列同源性。

gallus. Each line within the circle represents 10 Kb of sequence homology. Chromosomes are color coded to facilitate visualizing the synteny regions between A. rufa and the other t.

加卢斯。圆圈内的每条线代表10 Kb的序列同源性。染色体进行颜色编码，以便于可视化A.rufa和其他t.之间的同线性区域。

gallus

鸡

The scaffold-to-chromosome alignments revealed significant large-scale genomic rearrangements between A. rufa and both C. japonica and G. gallus genomes (Supplementary Fig. S5, Supplementary Table S6). Scaffold 2 exhibits a small 2.52 Mb inversion within the 105.87–108.07 Mb region of C. japonica's chromosome 1.

支架与染色体比对揭示了A.rufa与C.japonica和G.gallus基因组之间显着的大规模基因组重排（补充图S5，补充表S6）。支架2在日本血吸虫1号染色体的105.87–108.07 Mb区域内显示出一个小的2.52 Mb反转。

Scaffold 5 presents two similar-sized inversions, occurring at regions 19.06–20.95 Mb and 50.02–57.48 Mb of chromosome 1. Scaffold 1 displays a substantial inversion in its center relative to the centromeric region of C. japonica's chromosome 2 (42.9–77.77 Mb). Scaffold 3 features two inversions near one of its ends compared to chromosome 3.

支架5呈现两个相似大小的倒位，发生在1号染色体的19.06–20.95 Mb和50.02–57.48 Mb区域。相对于日本血吸虫2号染色体的着丝粒区域（42.9–77.77 Mb），支架1的中心显示出明显的倒置。与3号染色体相比，支架3在其一端附近有两个倒位。

Similarly, scaffolds 4 and 18 exhibit inversions when aligned to chromosomes 4 and 15, respectively.Pairwise alignment of our scaffolds with G. gallus chromosomes unveiled repeated inversions, particularly at telomeric regions. Notably, scaffold 4 included two inversions totaling 4.37 Mb within regions 1.76–4.29 Mb and 0.02–1.77 Mb of chromosome 4.

类似地，支架4和18分别与染色体4和15对齐时表现出倒置。我们的支架与G.gallus染色体的成对比对揭示了重复的倒位，特别是在端粒区域。值得注意的是，脚手架4在4号染色体的1.76–4.29 Mb和0.02–1.77 Mb区域内包括两个总计4.37 Mb的倒位。

Similarly, scaffold 8 exhibited three inversions totaling 3.23 Mb between regions 7.3–8.46 Mb, 9.97–11.06 Mb, and 11.81–12.72 Mb, aligning with chromosome 6 of the G. gallus genome. Additionally, scaffold 11 featured a substantial 8.35 Mb inversion relative to the 0.06–8.07 Mb region of chromosome 8.Overall, these results suggest that A.

同样，scaffold 8在7.3–8.46 Mb，9.97–11.06 Mb和11.81–12.72 Mb区域之间表现出三个倒位，总计3.23 Mb，与鸡G.gallus基因组的6号染色体对齐。此外，相对于8号染色体的0.06–8.07 Mb区域，支架11具有显着的8.35 Mb倒置。总体而言，这些结果表明a。

rufa’s genome is more similar to that of C. japonica than to that of G. gallus, indicating a closer evolutionary relationship between A. rufa and C. japonica when compared to the G. gallus. The similarities in genomic structures and rearrangements between A. rufa and C. japonica genomes imply a closer evolutionary proximity between the two birds with respect to G.

rufa的基因组与C.japonica的基因组比G.gallus的基因组更相似，表明与G.gallus相比，a.rufa和C.japonica之间的进化关系更为密切。A.rufa和C.japonica基因组之间基因组结构和重排的相似性意味着这两只鸟相对于G更接近进化。

gallus.Comparative proteome of A. rufa, C. japonica, G. gallus, and M. gallopavo.

加卢斯。A.rufa，C.japonica，G.gallus和M.gallopavo的比较蛋白质组。

Comparing the ortholog clusters of protein coding genes in the high confidence dataset between the four species reveals 10,111 shared orthologous gene families (Fig. 4A). We have also identified 113 gene families that are exclusive to A. rufa. Among these, 101 genes could be functionally associated to general biological processes using GO (Supplementary data file S1, summarized in Fig. 4B).

比较四个物种之间高可信度数据集中蛋白质编码基因的直系同源簇，发现10111个共享的直系同源基因家族（图4A）。我们还确定了A.rufa独有的113个基因家族。其中，使用GO（补充数据文件S1，总结在图4B中），101个基因可能在功能上与一般生物过程相关。

Among the gene families linked to more specific GO components, 1 gene was associated with membranes, and 2 genes were associated with structural activities. The set of genes unique to A. rufa (Fig. 4C) is significantly enriched in genes related to viral processes (5 genes) regulation of immune response (8 genes) and microtubule depolymerization (16 genes).Figure 4Functional comparison of the protein genes annotated with higher confidence in A.

。A.rufa特有的一组基因（图4C）显着富集了与病毒过程（5个基因）调节免疫应答（8个基因）和微管解聚（16个基因）相关的基因。图4在A中以更高的可信度注释的蛋白质基因的功能比较。

rufa’s proteome to the annotated NCBI proteomes of C. japonica, G. gallus, and M. gallopavo. A Comparison of orthologous gene families between A. rufa, C. japonica, G. gallus and M. gallopavo. B Generic GO enrichment terms for gene families that are unique to A. rufa. C Specific GO enrichment terms for gene families that are unique to A.

rufa的蛋白质组到C.japonica，G.gallus和M.gallopavo的注释NCBI蛋白质组。A.rufa，C.japonica，G.gallus和M.gallopavo之间直系同源基因家族的比较。B A.rufa特有的基因家族的通用GO富集术语。C A特有的基因家族的特定GO富集术语。

rufa. Only GO categories that are associated to more than one gene were included in panels (B) and (C).Full size imagePhylogenetic analysis of A. rufa within the Galliformes cladeThe phylogenetic tree (Fig. 5), constructed through the alignment of 8212 single-copy BUSCO genes found across thirteen genomes (Supplementary Table S3 and our A.

鲁法。面板（B）和（C）中仅包含与多个基因相关的GO类别。Galliformes进化枝内A.rufa的全尺寸图像系统发育分析系统发育树（图5），通过在13个基因组中发现的8212个单拷贝BUSCO基因的比对构建（补充表S3和我们的A。

rufa assembly), unveils pivotal points in evolutionary history measured in million years ago (Mya). The divergence between birds and reptiles occurred roughly 300 Mya. Anseriformes and Galliformes parted ways around 75 (95% credibility interval 46.14–106.85) Mya, with the Gui.

rufa大会），揭示了以百万年前（Mya）为单位的进化历史中的关键点。。Anseriformes和Galliformes在75（95%可信区间46.14-106.85）Mya左右分开，使用Gui。

1-

1-

We ran Miniprot v.0.10-r22576 for homology-based gene prediction. A dataset comprising 3,044,546 protein sequences was generated. These sequences were obtained from the NCBI reference sequence of proteins (accessed on April 15, 2023). Specifically, we focused on the Aves NCBI:txid8782 lineage to ensure retrieval of only avian proteins.

我们运行了Miniprot v.0.10-r22576进行基于同源性的基因预测。产生了包含3044546个蛋白质序列的数据集。这些序列是从NCBI蛋白质参考序列（2023年4月15日访问）获得的。具体而言，我们专注于Aves NCBI:txid8782谱系，以确保仅检索禽类蛋白质。

Additional details about this dataset can be found in Supplementary Table S11..

有关此数据集的其他详细信息，请参见补充表S11。。

2-

2-

We ran PASApipeline v.2.5.377 to perform gene prediction based on the transcriptional evidence provided by the transcriptome assembly of A. rufa published in 201736.

。

3-

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For ab initio gene prediction, we ran BRAKER2 v.2.1.678, training it with the same dataset we used for Miniprot.

对于从头算基因预测，我们运行了BRAKER2 v.2.1.678，并使用与Miniprot相同的数据集对其进行了训练。

The annotation results of the three approaches were then combined using EVidenceModeler v.2.1.077 to produce a consensus gene set model of the assembled A.rufa genome. The pipeline is summarized in Supplementary Fig. S8.We then took the annotated proteome of A. rufa and BLASTed it against the annotated proteome of G.

然后使用EVidenceModeler v.2.1.077组合这三种方法的注释结果，以产生组装的a.rufa基因组的共有基因组模型。该管道总结在补充图S8中。然后，我们取了A.rufa的注释蛋白质组，并将其与G的注释蛋白质组进行了对比。

gallus, to identify all pairs of orthologs, filtering by e-values ≤ 10–30, mutual best BLAST result, and mutual alignments over more than 80% of query and target proteins. Finally, we mapped each ortholog to its corresponding genome, to compare intron structures between orthologous genes. We repeated this comparison between A.

gallus，以识别所有直系同源物对，通过e值≤10-30过滤，相互最佳BLAST结果，以及超过80%的查询和靶蛋白的相互比对。最后，我们将每个直系同源物映射到其相应的基因组，以比较直系同源基因之间的内含子结构。我们在A之间重复了这个比较。

rufa and C. japonica.Non-coding RNA gene annotationWe also annotated non-coding RNA genes (ncRNAs) in our genome assembly. We used tRNAscan-SE2 v.2.0.1179 to identify transfer RNAs (tRNAs). Infernal v.1.1.480 was run to identify microRNAs (miRNAs), ribosomal RNAs (rRNAs) and small nuclear RNAs (snRNAs), based on the Rfam database (release 14.0)81.Functional annotationWe assigned functions to the predicted gene models combining various approaches.

rufa和C.japonica。非编码RNA基因注释我们还在基因组装配中注释了非编码RNA基因（ncRNA）。我们使用tRNAscan-SE2 v.2.0.1179来鉴定转移RNA（tRNA）。基于Rfam数据库（版本14.0）81，运行Infernal v.1.1.480以鉴定microRNA（miRNA），核糖体RNA（rRNA）和小核RNA（snRNA）。功能注释我们将功能分配给结合各种方法的预测基因模型。

A standard e-value cutoff of 1e-6 was applied for sequence comparisons, unless otherwise specified. Initially, we utilized eggnog-mapper v.2.1.1082 against the eggNOG database83 to assign Gene Ontology terms. Subsequently, Blastp v2.12.0 + was employed against SwissProt, TrEMBL84, and NCBI NR85 databases for homology-based functional annotation (all the public protein databases mentioned above were downloaded on April 15, 2023).

除非另有说明，否则将1e-6的标准e值截止值用于序列比较。最初，我们利用eggnog mapper v.2.1.1082对抗eggnog数据库83来分配基因本体术语。随后，针对SwissProt，TrEMBL84和NCBI NR85数据库使用Blastp v2.12.0+，进行基于同源性的功能注释（上述所有公共蛋白质数据库均于2023年4月15日下载）。

Priority was given to matches with over 95% identity from SwissProt and TrEMBL, as annotation of proteins in these databases is more reliable because of manual curation. The resulting functional annotations were combined with InterProScan v5.64.-96.086. InterProScan i.

优先考虑来自SwissProt和TrEMBL的95%以上同一性的匹配，因为这些数据库中蛋白质的注释由于手动管理而更可靠。产生的功能注释与InterProScan v5.64。-96.086相结合。InterProScan i。

gallus

鸡

We used MUMMER v.493 to perform whole-genome alignment between our assembly and the fully sequenced genomes of C. japonica and G. gallus. The genome pairwise alignment results and synteny blocks of 10 kb were visualized with DOT-PLOT viewer94 and Circos v.0.69-895.Gene family analysisWe used the OrthoVenn3 pipeline96 to compare gene families between A.

我们使用MUMMER v.493在我们的装配体与日本血吸虫和鸡胆吸虫的完全测序基因组之间进行全基因组比对。使用DOT-PLOT viewer94和Circos v.0.69-895可视化基因组成对比对结果和10 kb的同步块。基因家族分析我们使用OrthoVenn3管线96比较A之间的基因家族。

rufa, C. japonica, G. gallus, and G. pavo. In brief, Orthofinder97 was used to compute the orthologs between the species of interest and to cluster gene families based on GO functional annotation categories. Additionally, we also used the pipeline to automatically conduct GO terms enrichment analysis by considering the evolutionary relationship between the four species.Phylogenomic analysis and divergence time tree buildingWe performed phylogenetic analysis to infer the divergence time of A.

rufa，C.japonica，G.gallus和G.pavo。简而言之，Orthofinder97用于计算目标物种之间的直系同源物，并基于GO功能注释类别对基因家族进行聚类。此外，我们还使用管道通过考虑四个物种之间的进化关系来自动进行GO术语富集分析。系统发育基因组分析和发散时间树构建我们进行了系统发育分析，以推断A的发散时间。

rufa with respect to other birds with fully sequenced genomes within the Galliformes order, in a way that is similar to previous reports14,98,99. We included all Galliformes reference genomes available at the NCBI RefSeq database at the time of submission. In addition to A. rufa, we included 8 genome protein sequences of Galliformes species, of which 7 species belong to Phasianidae family and one to Numididae family (Numida meleagris).

rufa与其他在鸡形目中具有完全测序基因组的鸟类相比，其方式类似于先前的报道14,98,99。我们包括了提交时NCBI RefSeq数据库中可用的所有鸡形目参考基因组。除A.rufa外，我们还包括了鸡形目物种的8个基因组蛋白质序列，其中7个物种属于Phasianidae家族，一个属于Numidae家族（Numidameleagris）。

We also included one genome from the Anseriformes order (Anas platyrhynchos), and another bird species for the Falconiformes order (Falco cherrug). As an outgroup we used Anolis carolinensis100 from the Reptilia class.Genome assemblies for the birds and outgroup (Anolis carolinensis) from Reptilia were downloaded from the NCBI.

我们还包括了一个来自雁形目（Anas platyrhynchos）的基因组，以及另一种来自隼形目（Falco cherrug）的鸟类。作为外群，我们使用了爬行动物类的Anolis carolinensis100。爬行动物的鸟类和外群（Anolis carolinensis）的基因组组装从NCBI下载。

Detailed information about those species can be found in Supplementary Table S3. We started by using the aves_odb10 database of the BUSCO tool28 to identify shared single-copy ge.

关于这些物种的详细信息可以在补充表S3中找到。我们首先使用BUSCO工具28的aves\u odb10数据库来识别共享的单拷贝ge。

Data availability

数据可用性

Data Availability This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession JBCGZB000000000. The version described in this paper is version JBCGZB010000000. The Nanopore raw read data are available via ENA (Bioproject accession PRJEB67643, Biosample: ERS16499794, ERS16499793, ERS16499792, ERS16499791, ERS16499790).

数据可用性该全基因组鸟枪计划已以JBCGZB000000的登录号保存在DDBJ/ENA/GenBank中。本文描述的版本是JBCGZB01000000版本。。

The sixty Illumina sample of the partridge sequencing raw reads used for polishing have been deposited in the NCBI database under BioProject PRJNA824288. The high confidence gene annotation dataset is available at https://figshare.com/articles/dataset/Filtered_gene_set_model_of_the_i_Alectoris_rufa_i_genome/25982689.

用于抛光的鹧鸪测序原始读数的60个Illumina样品已保存在生物项目PRJNA824288下的NCBI数据库中。https://figshare.com/articles/dataset/Filtered_gene_set_model_of_the_i_Alectoris_rufa_i_genome/25982689.

The complete annotation dataset is available as supplementary material. The source code and relevant data files used to generate each figure in this manuscript are available on the GitHub repository page of the Systems Biology and Statistical Methods Group at https://github.com/BioModelLab/A.rufa_genome.git This work was performed under the scope of the Catalan Biogenome Project (CBP)..

完整的注释数据集可作为补充材料使用。用于生成本手稿中每个数字的源代码和相关数据文件可在系统生物学和统计方法组的GitHub存储库页面上找到https://github.com/BioModelLab/A.rufa_genome.git这项工作是在加泰罗尼亚生物基因组项目（CBP）的范围内进行的。。

Code availability

代码可用性

The source code and relevant data files used to generate each figure in this manuscript are available on the GitHub repository page of the Systems Biology and Statistical Methods Group at https://github.com/BioModelLab/A.rufa_genome.git

用于生成本手稿中每个数字的源代码和相关数据文件可在系统生物学和统计方法组的GitHub存储库页面上找到https://github.com/BioModelLab/A.rufa_genome.git

ReferencesFarfán, M. Á. et al. The red-legged partridge: A historical overview on distribution, status, research and hunting. In The Future of the Red-legged Partridge: Science, Hunting and Conservation (eds Casas, F. & García, J. T.) 1–19 (Springer International Publishing, Cham, 2022). https://doi.org/10.1007/978-3-030-96341-5_1.Chapter .

参考文献Farfán，M。红腿鹧鸪：关于分布、地位、研究和狩猎的历史概述。《红腿鹧鸪的未来：科学、狩猎和保护》（eds Casas，F.＆García，J.T.）1-19（Springer International Publishing，Cham，2022）。https://doi.org/10.1007/978-3-030-96341-5_1.Chapter。

Google Scholar

谷歌学者

Ros-Freixedes, R., Pena, R. N., Richart, C. & Nadal, J. Genomic diversity and signals of selection processes in wild and farm-reared red-legged partridges (Alectoris rufa). Genomics 115, 110591 (2023).Article

Ros Freixedes，R.，Pena，R.N.，Richart，C。＆Nadal，J。野生和农场饲养的红腿鹧鸪（Alectoris rufa）的基因组多样性和选择过程的信号。基因组学115110591（2023）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Arruga, V. et al. Estudios genéticos en ‘alectoris rufa’ y ‘a. graeca’ en España. Arch. Zootec. 45(170–171), 339–344 (1996).Kasai, F., Garcia, C., Arruga, M. V. & Ferguson-Smith, M. A. Chromosome homology between chicken (Gallus gallus domesticus) and the red-legged partridge (Alectoris rufa); evidence of the occurrence of a neocentromere during evolution.

Arruga，V。等人，Estudios genéticos en’alectoris rufa‘y’a。格拉埃卡·恩埃斯帕尼亚。拱门。Zootec公司。45（170-171），339-344（1996）。Kasai，F.，Garcia，C.，Arruga，M.V。和Ferguson-Smith，M.A。鸡（Gallus Gallus domesticus）和红腿鹧鸪（Alectoris rufa）之间的染色体同源性；进化过程中新着丝粒发生的证据。

Cytogenet. Genome Res. 102, 326–330 (2003).Article .

细胞遗传学。《基因组研究》102326-330（2003）。第[UNK]条。

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Pollard, M. O., Gurdasani, D., Mentzer, A. J., Porter, T. & Sandhu, M. S. Long reads: Their purpose and place. Hum. Mol. Genet. 27, R234–R241 (2018).Article

波拉德（Pollard，M.O.），古尔达萨尼（Gurdasani，D.），门泽（Mentzer），A.J。，波特（Porter），T。和桑德胡（Sandhu），M.S。朗（Long）读到：他们的目的和地位。嗯，摩尔·吉内特。27，R234–R241（2018）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Nagarajan, N. & Pop, M. Sequence assembly demystified. Nat. Rev. Genet. 14, 157–167 (2013).Article

。Genet自然Rev。14157-167（2013）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Ma, X. et al. Analysis of error profiles in deep next-generation sequencing data. Genome Biol. 20, 50 (2019).Article

Ma，X。等人。深层下一代测序数据中误差分布的分析。基因组生物学。20,50（2019）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Pfeiffer, F. et al. Systematic evaluation of error rates and causes in short samples in next-generation sequencing. Sci. Rep. 8, 10950 (2018).Article

Pfeiffer，F。等人。下一代测序中短样本错误率和原因的系统评估。科学。众议员810950（2018）。文章

ADS

广告

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Weissensteiner, M. H. et al. Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications. Genome Res. 27, 697–708 (2017).Article

Weissensteiner，M.H.等人。短读，长读和光学作图组件的组合揭示了具有群体遗传意义的大规模串联重复阵列。基因组研究27697-708（2017）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

De Maio, N. et al. Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes. Microb. Genomics https://doi.org/10.1099/mgen.0.000294 (2019).Article

De Maio，N.等人。复杂细菌基因组杂交组装中长读测序技术的比较。微生物。基因组学https://doi.org/10.1099/mgen.0.000294（2019年）。文章

Google Scholar

谷歌学者

Rhoads, A. & Au, K. F. PacBio sequencing and its applications. Genomics Proteomics Bioinform. 1, 3. https://doi.org/10.1016/j.gpb.2015.08.002 (2015).Article

Rhoads，A。＆Au，K.F。PacBio测序及其应用。基因组学蛋白质组学Bioinform。1，3。https://doi.org/10.1016/j.gpb.2015.08.002（2015年）。文章

Google Scholar

谷歌学者

Jain, M., Olsen, H. E., Paten, B. & Akeson, M. The Oxford Nanopore MinION: Delivery of nanopore sequencing to the genomics community. Genome Biol. https://doi.org/10.1186/s13059-016-1103-0 (2016).Article

Jain，M.，Olsen，H.E.，Paten，B。＆Akeson，M。牛津纳米孔MinION：向基因组学界提供纳米孔测序。基因组生物学。https://doi.org/10.1186/s13059-016-1103-0（2016年）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Jaiswal, S. K. et al. Genome sequence of peacock reveals the peculiar case of a glittering bird. Front. Genet. 9, 392 (2018).Article

Jaiswal，S.K。等人。孔雀的基因组序列揭示了一种闪闪发光的鸟的特殊情况。正面。基因。9392（2018）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Dalloul, R. A. et al. Multi-platform next-generation sequencing of the domestic Turkey (Meleagris gallopavo): GENzOME assembly and analysis. PLoS Biol. 8, e1000475 (2010).Article

Dalloul，R.A.等人。国内火鸡（Meleagris gallopavo）的多平台下一代测序：GENzOME组装和分析。《公共科学图书馆·生物学》。8，e1000475（2010）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Xuejuan, L. I. et al. A de novo assembled genome of the Tibetan Partridge (Perdix hodgsoniae) and its high-altitude adaptation. Integr. Zool. 18, 225–236 (2023).Article

Xuejuan，L.I.等人。西藏鹧鸪（Perdix hodgsoniae）的从头组装基因组及其高原适应。整数。佐尔。18225-236（2023）。文章

Google Scholar

谷歌学者

Dhar, R. et al. De novo assembly of the Indian blue peacock (Pavo cristatus) genome using Oxford Nanopore technology and Illumina sequencing. GigaScience 8, 1–13 (2019).Article

Dhar，R.等人。使用牛津纳米孔技术和Illumina测序从头组装印度蓝孔雀（Pavo cristatus）基因组。GigaScience 8,1-13（2019）。文章

CAS

中科院

Google Scholar

谷歌学者

Liu, S. et al. A high-quality assembly reveals genomic characteristics, phylogenetic status, and causal genes for leucism plumage of Indian peafowl. GigaScience 11, 1–16 (2022).Article

Liu，S。等人。高质量的组装揭示了印度孔雀的基因组特征，系统发育状态和亮氨酸羽毛的致病基因。GigaScience 11,1-16（2022）。文章

Google Scholar

谷歌学者

Liu, Y. et al. Genome assembly of the common pheasant phasianus colchicus: A model for speciation and ecological genomics. Genome Biol. Evol. 11, 3326–3331 (2019).CAS

Liu，Y.等人。秋水仙雉的基因组组装：物种形成和生态基因组学模型。基因组生物学。进化。113326-3331（2019）。中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Chattopadhyay, B. et al. Novel genome reveals susceptibility of popular gamebird, the red-legged partridge (Alectoris rufa, Phasianidae), to climate change. Genomics 113, 3430–3438 (2021).Article

Chattopadhyay，B。等人的新基因组揭示了流行的猎鸟红腿鹧鸪（Alectorisrufa，Phasianidae）对气候变化的敏感性。基因组学1133430–3438（2021）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

González-Prendes, R., Pena, R. N., Richart, C., Nadal, J. & Ros-Freixedes, R. Long-read de novo assembly of the red-legged partridge (Alectoris rufa) genome. 2024.01.23.576805 Preprint at https://doi.org/10.1101/2024.01.23.576805 (2024).Smit, A. F. A., Hubley, R. & Green, P. RepeatMasker Open-4.0.

González Prendes，R.，Pena，R.N.，Richart，C.，Nadal，J。＆Ros Freixedes，R。Long read从头组装红腿鹧鸪（Alectoris rufa）基因组。2024.01.23.576805预印本https://doi.org/10.1101/2024.01.23.576805（2024年）。Smit，A.F.A.，Hubley，R。＆Green，P。RepeatMasker Open-4.0。

(2013).Schmid, M. et al. Second report on chicken genes and chromosomes 2005. Cytogenet. Genome Res. https://doi.org/10.1159/000084205 (2005).Article .

（2013年）。Schmid，M.等人，《2005年关于鸡基因和染色体的第二份报告》。细胞遗传学。基因组研究。https://doi.org/10.1159/000084205（2005年）。文章。

ADS

广告

PubMed

PubMed

Google Scholar

谷歌学者

O’Connor, R. E. et al. Chromosome-level assembly reveals extensive rearrangement in saker falcon and budgerigar, but not ostrich, genomes. Genome Biol. https://doi.org/10.1186/s13059-018-1550-x (2018).Article

染色体水平的组装揭示了猎鹰和鹦鹉基因组的广泛重排，但鸵鸟基因组没有。基因组生物学。https://doi.org/10.1186/s13059-018-1550-x（2018年）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Palacios, C. et al. Genomic variation, population history, and long-term genetic adaptation to high altitudes in tibetan partridge (Perdix hodgsoniae). Mol. Biol. Evol. 40, msad214 (2023).Article

Palacios，C.等人。西藏鹧鸪（Perdix hodgsoniae）的基因组变异，种群历史和对高海拔的长期遗传适应。分子生物学。进化。40，msad214（2023）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Luo, H. et al. A high-quality genome assembly highlights the evolutionary history of the great bustard (Otis tarda, Otidiformes). Commun. Biol. 6, 1–11 (2023).Article

。Commun公司。生物学杂志6,1-11（2023）。文章

Google Scholar

谷歌学者

Mirarab, S. et al. A region of suppressed recombination misleads neoavian phylogenomics. Proc. Natl. Acad. Sci. 121, e2319506121 (2024).Article

Mirarab，S。等人。抑制重组的区域误导了新禽系统发育基因组学。程序。纳特尔。阿卡德。科学。121，e2319506121（2024）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Stiller, J. et al. Complexity of avian evolution revealed by family-level genomes. Nature https://doi.org/10.1038/s41586-024-07323-1 (2024).Article

Stiller，J.等人。家族级基因组揭示的鸟类进化的复杂性。自然https://doi.org/10.1038/s41586-024-07323-1（2024年）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Manni, M., Berkeley, M. R., Seppey, M. & Zdobnov, E. M. BUSCO: Assessing genomic data quality and beyond. Curr. Protoc. 1, e323 (2021).Article

Manni，M.，Berkeley，M.R.，Seppey，M。＆Zdobnov，E.M.BUSCO：评估基因组数据质量及其后。货币。普罗托克。1，e323（2021）。文章

PubMed

PubMed

Google Scholar

谷歌学者

Waterhouse, R. M. et al. BUSCO applications from quality assessments to gene prediction and phylogenomics. Mol. Biol. Evol. 35, 543–548 (2018).Article

Waterhouse，R.M.等人，BUSCO从质量评估到基因预测和系统发育基因组学的应用。分子生物学。进化。35543-548（2018）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Zerbino, D. R., Frankish, A. & Flicek, P. Progress, challenges, and surprises in annotating the human genome. Annu. Rev. Genomics Hum. Genet. 21, 55–79 (2020).Article

Zerbino，D.R.，Frankish，A。＆Flicek，P。注释人类基因组的进展，挑战和惊喜。年。基因组学评论Hum.Genet。21,55-79（2020）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Wicker, T. et al. The repetitive landscape of the chicken genome. Genome Res. 15, 126–136 (2005).Article

Wicker，T.等人，《鸡基因组的重复景观》。。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Kulak, M. et al. Genome organization of major tandem repeats and their specificity for heterochromatin of macro- and microchromosomes in Japanese quail. Genome 65, 391–403 (2022).Article

Kulak，M.等人。日本鹌鹑主要串联重复序列的基因组组织及其对大染色体和微染色体异染色质的特异性。基因组65391-403（2022）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Benham, P. M. et al. A highly contiguous genome assembly for the California quail (Callipepla californica). J. Hered. https://doi.org/10.1093/jhered/esad008 (2023).Article

Benham，P.M.等人。加利福尼亚鹌鹑（Callipepla californica）的高度连续的基因组组装。J、 埃德。https://doi.org/10.1093/jhered/esad008（2023年）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Galbraith, J. D. & Hayward, A. The influence of transposable elements on animal colouration. Trends Genet. 39, 624–638 (2023).Article

Galbraith，J.D。和Hayward，A。转座因子对动物着色的影响。趋势Genet。39624-638（2023）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Mundy, N. I., Kelly, J., Theron, E. & Hawkins, K. Evolutionary genetics of the melanocortin-1 receptor in vertebrates. Ann. N. Y. Acad. Sci. 994, 307–312 (2003).Article

Mundy，N.I.，Kelly，J.，Theron，E。和Hawkins，K。脊椎动物黑皮质素-1受体的进化遗传学。安·N·Y·阿卡德。科学。。文章

ADS

广告

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Sevane, N., Cañon, J., Gil, I. & Dunner, S. Transcriptomic characterization of innate and acquired immune responses in red-legged partridges (Alectoris rufa): A resource for immunoecology and robustness selection. PLoS One https://doi.org/10.1371/journal.pone.0136776 (2015).Article

Sevane，N.，Cañon，J.，Gil，I。＆Dunner，S。红腿鹧鸪（Alectoris rufa）先天性和获得性免疫反应的转录组学表征：免疫生态学和稳健性选择的资源。公共科学图书馆一号https://doi.org/10.1371/journal.pone.0136776（2015年）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Sanchez-Donoso, I. et al. Massive genome inversion drives coexistence of divergent morphs in common quails. Curr. Biol. https://doi.org/10.1016/j.cub.2021.11.019 (2022).Article

Sanchez-Donoso，I。等人。大规模基因组倒位驱动普通鹌鹑中不同形态的共存。货币。生物。https://doi.org/10.1016/j.cub.2021.11.019（2022年）。文章

PubMed

PubMed

Google Scholar

谷歌学者

Jackson, C. E. et al. Chromosomal rearrangements preserve adaptive divergence in ecological speciation. 2021.08.20.457158 Preprint at https://doi.org/10.1101/2021.08.20.457158 (2021).Pimm, S. L. et al. The biodiversity of species and their rates of extinction, distribution, and protection.

染色体重排保留了生态物种形成中的适应性差异。2021.08.20.457158预印本https://doi.org/10.1101/2021.08.20.457158（2021年）。Pimm，S.L.等人，《物种的生物多样性及其灭绝率、分布和保护》。

Science 344, 1246752–1246752 (2014).Article .

科学3441246752–1246752（2014）。文章。

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Prum, R. O. et al. A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing. Nature 526, 569–573 (2015).Article

Prum，R.O.等人。使用靶向下一代DNA测序的鸟类（鸟类）的全面系统发育。《自然》526569–573（2015）。文章

ADS

广告

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Meseguer, A. S., Lobo, J. M., Ree, R., Beerling, D. J. & Sanmartín, I. Integrating fossils, phylogenies, and niche models into biogeography to reveal ancient evolutionary history: The case of hypericum (Hypericaceae). Syst. Biol. 64, 215–232 (2015).Article

Meseguer，A.S.，Lobo，J.M.，Ree，R.，Beerling，D.J。＆Sanmartin，I。将化石，系统发育和生态位模型整合到生物地理学中以揭示古代进化史：金丝桃属（金丝桃科）的情况。系统。生物学64215-232（2015）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Kan, X.-Z. et al. Phylogeny of major lineages of galliform birds (Aves: Galliformes) based on complete mitochondrial genomes. Genet. Mol. Res. GMR 9, 1625–1633 (2010).Article

Kan，X.-Z.等人。基于完整线粒体基因组的鸡形鸟类（鸟类：鸡形目）主要谱系的系统发育。基因。Mol.Res.GMR 91625–1633（2010）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Martínez-Fresno, M., Henriques-Gil, N. & Arana, P. Mitochondrial DNA sequence variability in red-legged partridge, Alectoris rufa, Spanish populations and the origins of genetic contamination from A. chukar. Conserv. Genet. 9, 1223–1231 (2008).Article

Martínez Fresno，M.，Henriques Gil，N。和Arana，P。红腿鹧鸪，Alectoris rufa，西班牙种群的线粒体DNA序列变异性以及A.chukar遗传污染的起源。保存。基因。91223-1231（2008）。文章

Google Scholar

谷歌学者

Huerta-Cepas, J., Dopazo, H., Dopazo, J. & Gabaldón, T. The human phylome. Genome Biol. 8, R109 (2007).Article

Huerta Cepas，J.、Dopazo，H.、DopazoJ.和Gabaldón，T.人类门。基因组生物学。8，R109（2007）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Castresana, J. Topological variation in single-gene phylogenetic trees. Genome Biol. 8, 216 (2007).Article

Castresana，J。单基因系统发育树的拓扑变异。基因组生物学。8216（2007）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Hahn, M. W. Bias in phylogenetic tree reconciliation methods: Implications for vertebrate genome evolution. Genome Biol. 8, R141 (2007).Article

Hahn，M.W。系统发育树协调方法中的偏见：对脊椎动物基因组进化的影响。基因组生物学。8，R141（2007）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Rosenberg, N. A. & Nordborg, M. Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nat. Rev. Genet. 3, 380–390 (2002).Article

Rosenberg，N.A。＆Nordborg，M。家谱树，聚结理论和遗传多态性分析。Genet自然Rev。3380-390（2002）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Wang, N., Kimball, R. T., Braun, E. L., Liang, B. & Zhang, Z. Ancestral range reconstruction of Galliformes: The effects of topology and taxon sampling. J. Biogeogr. 44, 122–135 (2017).Article

Wang，N.，Kimball，R.T.，Braun，E.L.，Liang，B。＆Zhang，Z。鸡形目的祖先范围重建：拓扑和分类群采样的影响。J、 生物地理学。44122-135（2017）。文章

Google Scholar

谷歌学者

Chen, D. et al. Divergence time estimation of Galliformes based on the best gene shopping scheme of ultraconserved elements. BMC Ecol. Evol. 21, 209 (2021).Article

Chen，D.等人。基于超保守元件的最佳基因购物方案的鸡形目发散时间估计。BMC Ecol。进化。21209（2021）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Kimball, R. T., Hosner, P. A. & Braun, E. L. A phylogenomic supermatrix of Galliformes (Landfowl) reveals biased branch lengths. Mol. Phylogenet. Evol. 158, 107091 (2021).Article

Kimball，R.T.，Hosner，P.A。＆Braun，E.L。鸡形目（陆地猫头鹰）的系统发育基因组超矩阵揭示了偏向的分支长度。分子系统发育。进化。158107091（2021）。文章

PubMed

PubMed

Google Scholar

谷歌学者

Wang, N., Kimball, R. T., Braun, E. L., Liang, B. & Zhang, Z. Assessing phylogenetic relationships among galliformes: A multigene phylogeny with expanded taxon sampling in Phasianidae. PLoS One 8, e64312 (2013).Article

Wang，N.，Kimball，R.T.，Braun，E.L.，Liang，B。＆Zhang，Z。评估鸡形目之间的系统发育关系：在Phasianidae中扩展分类群采样的多基因系统发育。PLoS One 8，e64312（2013）。文章

ADS

广告

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Brown, J. W., Wang, N. & Smith, S. A. The development of scientific consensus: Analyzing conflict and concordance among avian phylogenies. Mol. Phylogenet. Evol. 116, 69–77 (2017).Article

Brown，J.W.，Wang，N。＆Smith，S.A。科学共识的发展：分析鸟类系统发育之间的冲突和一致性。分子系统发育。进化。116,69-77（2017）。文章

PubMed

PubMed

Google Scholar

谷歌学者

Babraham Bioinformatics - FastQC A Quality Control tool for High Throughput Sequence Data.rrwick/Porechop: adapter trimmer for Oxford Nanopore reads. https://github.com/rrwick/Porechop.De Coster, W., D’Hert, S., Schultz, D. T., Cruts, M. & Van Broeckhoven, C. NanoPack: Visualizing and processing long-read sequencing data.

Babraham生物信息学-FastQC是高通量序列数据的质量控制工具。rrwick/Porecop：用于牛津纳米孔读数的适配器修剪器。https://github.com/rrwick/Porechop.DeCoster，W.，D'Hert，S.，Schultz，D.T.，Cruts，M。＆Van Broeckhoven，C。NanoPack：可视化和处理长读取测序数据。

Bioinformatics 34, 2666–2669 (2018).Article .

生物信息学342666-2669（2018）。文章。

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

rrwick/Filtlong: quality filtering tool for long reads. https://github.com/rrwick/Filtlong.Marçais, G. & Kingsford, C. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27, 764–770 (2011).Article

rrwick/Filtlong：用于长读取的质量过滤工具。https://github.com/rrwick/Filtlong.Marçais，G。＆Kingsford，C。一种快速，无锁的方法，用于有效并行计数k聚体的出现。生物信息学27764-770（2011）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Ranallo-Benavidez, T. R., Jaron, K. S. & Schatz, M. C. GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes. Nat. Commun. https://doi.org/10.1038/s41467-020-14998-3 (2020).Article

Ranallo Benavidez，T.R.，Jaron，K.S。＆Schatz，M.C。GenomeScope 2.0和Smudgeplot用于多倍体基因组的无参考分析。国家公社。https://doi.org/10.1038/s41467-020-14998-3（2020年）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Kolmogorov, M., Yuan, J., Lin, Y. & Pevzner, P. A. Assembly of long, error-prone reads using repeat graphs. Nat. Biotechnol. 37, 540–546 (2019).Article

Kolmogorov，M.，Yuan，J.，Lin，Y。＆Pevzner，P.A。使用重复图组装长而容易出错的读物。美国国家生物技术公司。37540-546（2019）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Koren, S. et al. Canu: Scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 27, 722–736 (2017).Article

Koren，S。等人。Canu：通过自适应k-mer加权和重复分离可扩展且准确的长读取组装。基因组研究27722-736（2017）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Ruan, J. & Li, H. Fast and accurate long-read assembly with wtdbg2. Nat. Methods 17, 155–158 (2019).Article

阮，J。＆Li，H。使用wtdbg2快速准确地进行长读取组装。自然方法17155-158（2019）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Hu, J. et al. An efficient error correction and accurate assembly tool for noisy long reads. bioRxiv 2023.03.09.531669 (2023) https://doi.org/10.1101/2023.03.09.531669.Mikheenko, A., Prjibelski, A., Saveliev, V., Antipov, D. & Gurevich, A. Versatile genome assembly evaluation with QUAST-LG.

Hu，J.等人。一种有效的纠错和准确的组装工具，用于嘈杂的长读取。bioRxiv 2023.03.09.531669（2023）https://doi.org/10.1101/2023.03.09.531669.Mikheenko。

Bioinformatics 34, i142–i150 (2018).Article .

生物信息学34，i142-i150（2018）。文章。

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Li, H. Minimap2: Pairwise alignment for nucleotide sequences. Bioinformatics 34, 3094–3100 (2018).Article

Li，H。Minimap2：核苷酸序列的成对比对。。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Vaser, R., Sović, I., Nagarajan, N. & Šikić, M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. https://doi.org/10.1101/gr.214270.116 (2017).Article

Vaser，R.，Sović，I.，Nagarajan，N。＆Šikić，M。从长时间未校正的读数快速准确地从头组装基因组。基因组研究。https://doi.org/10.1101/gr.214270.116（2017年）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Jung, Y. & Han, D. BWA-MEME: BWA-MEM emulated with a machine learning approach. Bioinformatics 38, 2404–2413 (2022).Article

Jung，Y.＆Han，D。BWA-MEM：BWA-MEM采用机器学习方法进行仿真。生物信息学382404-2413（2022）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Wick, R. R. & Holt, K. E. Polypolish: Short-read polishing of long-read bacterial genome assemblies. PLoS Comput. Biol. 18, e1009802 (2022).Article

Wick，R。R。＆Holt，K。E。Polypolish：长读细菌基因组组装的短读抛光。PLoS计算机。生物学18，e1009802（2022）。文章

ADS

广告

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Pryszcz, L. P. & Gabaldón, T. Redundans: An assembly pipeline for highly heterozygous genomes. Nucleic Acids Res. 44, e113 (2016).Article

Pryszcz，L.P。＆Gabaldón，T.Redundans：高度杂合基因组的组装管道。核酸研究44，e113（2016）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Astashyn, A. et al. Rapid and sensitive detection of genome contamination at scale with FCS-GX. 2023.06.02.543519 Preprint at https://doi.org/10.1101/2023.06.02.543519 (2023).Ou, S. et al. Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline.

Astashyn，A。等人。使用FCS-GX快速灵敏地检测大规模基因组污染。2023.06.02.543519预印本https://doi.org/10.1101/2023.06.02.543519（2023年）。Ou，S.等人。基准测试转座因子注释方法，以创建简化的综合管道。

Genome Biol. 20, 1–18 (2019).Article .

基因组生物学。20,1-18（2019）。文章。

Google Scholar

谷歌学者

Liao, X. et al. msRepDB: A comprehensive repetitive sequence database of over 80 000 species. Nucleic Acids Res. 50, D236–D245 (2022).Article

Liao，X。et al。msRepDB：一个包含8万多个物种的综合重复序列数据库。核酸研究50，D236–D245（2022）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Cunningham, F. et al. Ensembl 2022. Nucleic Acids Res. 50, D988–D995 (2022).Article

Cunningham，F.等人，Ensembl 2022。核酸研究50，D988–D995（2022）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Flynn, J. M. et al. RepeatModeler2 for automated genomic discovery of transposable element families. Proc. Natl. Acad. Sci. U. S. A. 117, 9451–9457 (2020).Article

Flynn，J.M.等人，RepeatModeler2，用于转座因子家族的自动基因组发现。程序。纳特尔。阿卡德。科学。U、 S.A.1179451–9457（2020）。文章

ADS

广告

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

GitHub - 4ureliek/Parsing-RepeatMasker-Outputs: Few scripts facilitating the extraction of info from Repeat Masker .out files. https://github.com/4ureliek/Parsing-RepeatMasker-Outputs.Storer, J., Hubley, R., Rosen, J., Wheeler, T. J. & Smit, A. F. The Dfam community resource of transposable element families, sequence models, and genome annotations.

GitHub-4ureliek/Parsing-RepeatMasker输出：很少有脚本可以帮助从RepeatMasker.out文件中提取信息。https://github.com/4ureliek/Parsing-RepeatMasker-Outputs.Storer，J.，Hubley，R.，Rosen，J.，Wheeler，T.J。＆Smit，A.F。转座因子家族，序列模型和基因组注释的Dfam社区资源。

Mob. DNA 12, 1–14 (2021).Article .

暴徒。DNA 12,1-14（2021）。文章。

Google Scholar

谷歌学者

Li, H. Protein-to-genome alignment with miniprot. Bioinform. Oxf. Engl. 3, 9. https://doi.org/10.1093/bioinformatics/btad014 (2022).Article

Li，H。蛋白质与miniprot的基因组比对。生物信息。Oxf。英语。3，9。https://doi.org/10.1093/bioinformatics/btad014（2022年）。文章

CAS

中科院

Google Scholar

谷歌学者

Haas, B. J. et al. Automated eukaryotic gene structure annotation using EVidenceModeler and the program to assemble spliced alignments. Genome Biol. https://doi.org/10.1186/gb-2008-9-1-r7 (2008).Article

。基因组生物学。https://doi.org/10.1186/gb-2008-9-1-r7（2008年）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Brůna, T., Hoff, K. J., Lomsadze, A., Stanke, M. & Borodovsky, M. BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP+ and AUGUSTUS supported by a protein database. NAR Genomics Bioinform. 3, lqaa108 (2021).Article

Brůna，T.，Hoff，K.J.，Lomsadze，A.，Stanke，M。＆Borodovsky，M.BRAKER2：由蛋白质数据库支持的GeneMark EP+和AUGUSTUS的自动真核基因组注释。NAR Genomics Bioinform。3，lqaa108（2021）。文章

Google Scholar

谷歌学者

Chan, P. P., Lin, B. Y., Mak, A. J. & Lowe, T. M. tRNAscan-SE 2.0: Improved detection and functional classification of transfer RNA genes. Nucleic Acids Res. 49, 9077–9096 (2021).Article

Chan，P.P.，Lin，B.Y.，Mak，A.J。＆Lowe，T.M。tRNAscan SE 2.0：改进转移RNA基因的检测和功能分类。核酸研究499077-9096（2021）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Nawrocki, E. P. & Eddy, S. R. Infernal 1.1: 100-fold faster RNA homology searches. Bioinformatics 29, 2933–2935 (2013).Article

Nawrocki，E.P。＆Eddy，S.R。Infernal 1.1：RNA同源性搜索速度快100倍。生物信息学292933-2935（2013）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Kalvari, I. et al. Rfam 14: Expanded coverage of metagenomic, viral and microRNA families. Nucleic Acids Res. https://doi.org/10.1093/nar/gkaa1047 (2021).Article

Kalvari，I。等人，Rfam 14：扩大了宏基因组，病毒和microRNA家族的覆盖范围。核酸研究。https://doi.org/10.1093/nar/gkaa1047（2021年）。文章

PubMed

PubMed

Google Scholar

谷歌学者

Cantalapiedra, C. P., Hern̗andez-Plaza, A., Letunic, I., Bork, P. & Huerta-Cepas, J. eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale. Mol. Biol. Evol. 38, 5825–5829 (2021).Article

Cantalapiedra，C.P.，Hern̗andez Plaza，A.，Letunic，I.，Bork，P。＆Huerta Cepas，J。eggNOG mapper v2：宏基因组规模的功能注释，正畸分配和域预测。分子生物学。进化。385825-5829（2021）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Huerta-Cepas, J. et al. eggNOG 50: A hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 47, D309–D314 (2019).Article

Huerta-Cepas，J.等人，《eggNOG 50：基于5090种生物体和2502种病毒的分层，功能和系统发育注释的直系同源资源》。核酸研究47，D309–D314（2019）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Bairoch, A. & Apweiler, R. The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res. https://doi.org/10.1093/nar/28.1.45 (2000).Article

Bairoch，A。＆Apweiler，R。SWISS-PROT蛋白质序列数据库及其补充TrEMBL于2000年。核酸研究。https://doi.org/10.1093/nar/28.1.45（2000年）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

O’Leary, N. A. et al. Reference sequence (RefSeq) database at NCBI: Current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. https://doi.org/10.1093/nar/gkv1189 (2016).Article

O'Leary，N.A。等人。NCBI的参考序列（RefSeq）数据库：现状，分类学扩展和功能注释。核酸研究。https://doi.org/10.1093/nar/gkv1189（2016年）。文章

PubMed

PubMed

Google Scholar

谷歌学者

Jones, P. et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 30, 1236–1240 (2014).Article

Jones，P.等人，《InterProScan 5：基因组规模的蛋白质功能分类》。生物信息学301236-1240（2014）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Aramaki, T. et al. KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics 36, 2251–2252 (2020).Article

Aramaki，T。等。KofamKOALA：基于轮廓HMM和自适应评分阈值的KEGG直系同源分配。生物信息学362251-2252（2020）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Kanehisa, M., Furumichi, M., Sato, Y., Kawashima, M. & Ishiguro-Watanabe, M. KEGG for taxonomy-based analysis of pathways and genomes. Nucleic Acids Res. 51, D587–D592 (2023).Article

Kanehisa，M.，Furumichi，M.，Sato，Y.，Kawashima，M。＆Ishiguro Watanabe，M。KEGG用于基于分类学的途径和基因组分析。核酸研究51，D587–D592（2023）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Geib, S. M. et al. Genome annotation generator: A simple tool for generating and correcting WGS annotation tables for NCBI submission. GigaScience 7, giy018 (2018).Article

Genome annotation generator：一种用于生成和校正NCBI提交的WGS注释表的简单工具。GigaScience 7，giy018（2018）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Rhie, A., Walenz, B. P., Koren, S. & Phillippy, A. M. Merqury: Reference-free quality, completeness, and phasing assessment for genome assemblies. Genome Biol. 21, 245 (2020).Article

Rhie，A.，Walenz，B.P.，Koren，S。＆Phillippy，A.M.Merqury：基因组装配的无参考质量，完整性和定相评估。基因组生物学。21245（2020）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Dobin, A. et al. STAR: Ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).Article

Dobin，A。等人STAR：超快通用RNA-seq比对仪。生物信息学29,15-21（2013）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Pertea, G. & Pertea, M. GFF utilities: GffRead and GffCompare. F1000research. https://doi.org/10.12688/f1000research.23297.2 (2020).Article

Pertea，G。和Pertea，M。GFF实用程序：GffRead和GffCompare。F1000研究。https://doi.org/10.12688/f1000research.23297.2（2020年）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Marçais, G. et al. MUMmer4: A fast and versatile genome alignment system. PLoS Comput. Biol. 14, e1005944 (2018).Article

Marçais，G。等人。MUMmer4：一种快速且通用的基因组比对系统。PLoS计算机。生物学14，e1005944（2018）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

MariaNattestad/dot: Dot: An interactive dot plot viewer for comparative genomics. https://github.com/marianattestad/dot.Krzywinski, M. I. et al. Circos: An information aesthetic for comparative genomics. Genome Res. https://doi.org/10.1101/gr.092759.109 (2009).Article

MarianaTestad/dot:dot：用于比较基因组学的交互式点图查看器。https://github.com/marianattestad/dot.Krzywinski，M.I.等人，《Circos：比较基因组学的信息美学》。基因组研究。https://doi.org/10.1101/gr.092759.109（2009年）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Sun, J. et al. OrthoVenn3: An integrated platform for exploring and visualizing orthologous data across genomes. Nucleic Acids Res. 51, W397–W403 (2023).Article

Sun，J。等人。OrthoVenn3：用于探索和可视化跨基因组直系同源数据的集成平台。核酸研究51，W397–W403（2023）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Emms, D. M. & Kelly, S. OrthoFinder: Phylogenetic orthology inference for comparative genomics. Genome Biol. 20, 1–14 (2019).Article

Emms，D。M。和Kelly，S。OrthoFinder：比较基因组学的系统发育正交推断。基因组生物学。20,1-14（2019）。文章

Google Scholar

谷歌学者

He, C. et al. Chromosome level assembly reveals a unique immune gene organization and signatures of evolution in the common pheasant. Mol. Ecol. Resour. 21, 897–911 (2021).Article

染色体水平的组装揭示了普通雉鸡独特的免疫基因组织和进化特征。摩尔Ecol。资源。。文章

PubMed

PubMed

Google Scholar

谷歌学者

Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., Von Haeseler, A. & Jermiin, L. S. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods 14, 587–589 (2017).Article

Kalyanamoorthy，S.，Minh，B.Q.，Wong，T.K.F.，Von Haeseler，A.＆Jermiin，L.S.ModelFinder：快速模型选择以进行准确的系统发育估计。自然方法14587-589（2017）。文章

CAS

中科院

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Alföldi, J. et al. The genome of the green anole lizard and a comparative analysis with birds and mammals. Nature 477, 587–591 (2011).Article

Alföldi，J.等人。绿色anole蜥蜴的基因组以及与鸟类和哺乳动物的比较分析。自然477587-591（2011）。文章

ADS

广告

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Edgar, R. C. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. https://doi.org/10.1093/nar/gkh340 (2004).Article

Edgar，R.C.MUSCLE：具有高精度和高通量的多序列比对。核酸研究。https://doi.org/10.1093/nar/gkh340（2004年）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics https://doi.org/10.1093/bioinformatics/btp348 (2009).Article

Capella Gutiérrez，S.，Silla Martínez，J.M。＆Gabaldón，T.trimAl：大规模系统发育分析中自动比对修剪的工具。生物信息学https://doi.org/10.1093/bioinformatics/btp348（2009年）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Nguyen, L. T., Schmidt, H. A., Von Haeseler, A. & Minh, B. Q. IQ-TREE: A fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol. Biol. Evol. 32, 268–274 (2015).Article

Nguyen，L.T.，Schmidt，H.A.，Von Haeseler，A。＆Minh，B.Q。IQ-TREE：一种快速有效的估计最大似然系统发育的随机算法。分子生物学。进化。32268-274（2015）。文章

CAS

中科院

PubMed

PubMed

Google Scholar

谷歌学者

Zhang, C., Rabiee, M., Sayyari, E. & Mirarab, S. ASTRAL-III: Polynomial time species tree reconstruction from partially resolved gene trees. BMC Bioinform. 19, 153 (2018).Article

Zhang，C.，Rabiee，M.，Sayyari，E。＆Mirarab，S。ASTRAL-III：从部分解析的基因树重建多项式时间物种树。BMC生物信息。19153（2018）。文章

Google Scholar

谷歌学者

Yang, Z. PAML 4: Phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. https://doi.org/10.1093/molbev/msm088 (2007).Article

Yang，Z。PAML 4：通过最大似然进行系统发育分析。分子生物学。进化。https://doi.org/10.1093/molbev/msm088（2007年）。文章

PubMed

PubMed

Google Scholar

谷歌学者

Kumar, S. et al. TimeTree 5: An expanded resource for species divergence times. Mol. Biol. Evol. https://doi.org/10.1093/molbev/msac174 (2022).Article

Kumar，S.等人，《时间树5：物种分化时间的扩展资源》。分子生物学。进化。https://doi.org/10.1093/molbev/msac174（2022年）。文章

PubMed

PubMed

PubMed Central

公共医学中心

Google Scholar

谷歌学者

Blair Hedges, S. & Poling, L. L. A molecular phylogeny of reptiles. Science 283, 998–1001 (1999).Article

Blair Hedges，S。＆Poling，L.L。爬行动物的分子系统发育。科学283998-1001（1999）。文章

ADS

广告

Google Scholar

谷歌学者

Download referencesAcknowledgementsWe are grateful for the contributions made by the Melgarejo family, Patricia, Luis and Ivan Maldonado and Tom Gullick. Thanks also to the “Las Ensanchas” staff, especially the game keepers, the Barranquero family and collaborators, the members of the Tom Gullick hunting team in Campo de Montiel and around the world, Federación de Caza de Castilla y León, Delegación Burgalesa, MUTUASPORT, and Real Federación Española de Caza (RFEC).

下载参考文献致谢我们感谢Melgarejo家族，Patricia，Luis和Ivan Maldonado以及Tom Gullick所做的贡献。还要感谢“Las Ensanchas”的工作人员，特别是猎场看守人、巴兰奎罗家族和合作者、蒙蒂埃尔坎波和世界各地的汤姆·古利克狩猎队成员、卡斯蒂利亚和莱昂联邦狩猎队、布尔加莱萨联邦狩猎队、穆图阿斯波特狩猎队和皇家西班牙狩猎队（RFEC）。

Carolina Ponz helped in sampling.FundingFundação para a Ciência e a Tecnologia (FCT), I.P., is acknowledged for funding A. Usié through Contrato–Programa (CEECINST/00100/2021/CP2774/CT0001) and for Projects UIDB/05183/2020 to Mediterranean Institute for Agriculture, Environment and Development (MED), and LA/P/0121/2020 to CHANGE—Global Change and Sustainability Institute.

Carolina Ponz协助取样。FundingFundaçãão para Ciência e a Tecnologia（FCT），I.P.因通过Contrato-Programa（CEECINST/00100/2021/CP2774/CT0001）资助a.Usié而获得认可，并为UIDB/05183/2020项目向地中海农业、环境与发展研究所（MED）提供资金，以及LA/P/0121/2020项目向全球变化与可持续发展研究所提供资金。

Fundación Universitat Rovira i Virgili funded the sequencing (grant no. 2060-398-454-455). The authors are member of 2021SGR135.Author informationAuthors and AffiliationsInstitut de Recerca Biomédica (IRBLleida), Lleida, SpainAbderrahmane Eleiwa, Ester Vilaprinyo, Alberto Marin-Sanguino, Albert Sorribas, Oriol Basallo, Abel Lucido & Rui AlvesUniversitat de Lleida (UdL), Lleida, SpainJesus Nadal, Ester Vilaprinyo, Alberto Marin-Sanguino, Albert Sorribas, Oriol Basallo, Abel Lucido, Ramona N.

罗维拉大学基金会（Fundación Universitat Rovira i Virgili）资助了测序（批准号2060-398-454-455）。作者是2021SGR135的成员。作者信息作者和附属机构研究所（IRBLleida），Lleida，SpainAbderrahmane Eleiwa，Ester Vilaprinyo，Alberto Marin Sanguino，Albert Sorribas，Oriol Basallo，Abel Lucido＆Rui Alves Universitat de Lleida（UdL），Lleida，SpainJesus Nadal，Ester Vilaprinyo，Alberto Marin Sanguino，Albert Sorribas，Oriol Basallo，Abel Lucido，Ramona N。

Pena, Roger Ros-Freixedes, Anabel Usie & Rui AlvesUniversitat Rovira i Virgili (URV), Tarragona, SpainCristobal RichartAGROTECNIO CERCA Center, Lleida, SpainRamona N. Pena & Roger Ros-FreixedesCentro de Biotecnologia Agrícola e Agro-Alimentar do Alentejo (CEBAL)/Instituto Politécnico de Beja (IPBeja), Beja, PortugalAnabel UsieMED–Instituto Mediterrâneo para a Agricultura, Ambiente e Desenvolvimento & CHANGE–Global Change and Sustainabilit.

Pena、Roger Ros Freixedes、Anabel Usie和Rui Alves Rovira i Virgili大学（URV）、塔拉戈纳、西班牙Cristobal Richart AGROTENIO CERCA中心、莱里达、西班牙Ramona N.Pena和Roger Ros-Freixedes阿连特茹农业和农业食品生物技术中心（CEBAL）/贝加政治学院（IPBeja）、贝加、葡萄牙-地中海农业、环境与发展与变革研究所-全球变化与可持续发展。

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PubMed Google ScholarContributionsA.E., J.N, and R.A. designed the study and performed the analysis. C.R., R.N.P., and R.R.F. performed DNA extraction and sequencing. E.V., A.M.S., A.S., O.B., A.L., and A.U. contributed to the analysis. A.E., A.U. and R.A. wrote the paper. All authors revised and approved the final version of the paper.Corresponding authorCorrespondence to.

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Reprints and permissionsAbout this articleCite this articleEleiwa, A., Nadal, J., Vilaprinyo, E. et al. Hybrid assembly and comparative genomics unveil insights into the evolution and biology of the red-legged partridge.

转载和许可本文引用本文Eleiwa，A.，Nadal，J.，Vilaprinyo，E。等人。杂交组装和比较基因组学揭示了对红腿鹧鸪进化和生物学的见解。

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