Chromosome Level Genome Assembly and Comparative Genomics between Three Falcon Species Reveals an Unusual Pattern of Genome Organisation
Chromosome Level Genome Assembly and Comparative Genomics between Three Falcon Species Reveals an Unusual Pattern of Genome Organisation
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DOI：
10.3390/d10040113
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发表时间：
2018-12-01
期刊：
影响因子：
2.4
通讯作者：
Griffin, Darren K.
中科院分区：
文献类型：
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作者：
Joseph, Sunitha;O'Connor, Rebecca E.;Griffin, Darren K.
全基因组组装对于了解猎鹰生物学的各个方面至关重要，包括形态学、生态学和生理学，因此对它们的护理和保护至关重要。任何物种基因组的一个关键方面是它的核型，核型可以与整个基因组序列联系起来，从而产生所谓的染色体水平组装。染色体水平的组装对于育种制度中的标记辅助选择和基因型-表型相关性以及确定总体基因组进化模式至关重要。迄今为止，只有两种猎鹰被测序，最初都没有组装到染色体水平。猎鹰具有非典型的鸟类核型，染色体比其他鸟类少，可能是由于大规模融合造成的。然而，到目前为止，已发表的染色体制备质量很差，很少有染色体被区分出来，也没有制作出标准的表意文字。本研究的目的是建立游隼、saker隼和gyr隼可分析的核型和表意符号，报道我们最近一代游隼和saker隼的染色体水平序列组合，并首次对gyr隼基因组进行测序。最后，我们的目标是生成所有三种鸡和参考鸡基因组之间的比较基因组数据。结果表明，游隼的二倍体数量为2n = 50， saker和gyr的二倍体数量为2n = 52。这里生成的标准表意文字有助于将预测的染色体片段（pcf）从基因组序列直接映射到染色体上，从而生成游隼和saker猎鹰的染色体水平序列集合。gyr falcon的全基因组测序是成功的，但读取深度和覆盖范围不足以产生染色体水平的组装。尽管如此，比较基因组学显示gyr和saker猎鹰之间的基因组组织没有差异。与游隼相比，saker/gyr基因组存在1次染色体间重排和7次染色体内重排（1次融合加7次倒位）的差异，而游隼和saker/gyr基因组与参考鸡基因组存在14/13次融合（11次微染色体）和6次分裂的差异。物种间的染色体差异可能为杂交动物的筛选试验提供潜在的基础。
Whole genome assemblies are crucial for understanding a wide range of aspects of falcon biology, including morphology, ecology, and physiology, and are thus essential for their care and conservation. A key aspect of the genome of any species is its karyotype, which can then be linked to the whole genome sequence to generate a so-called chromosome-level assembly. Chromosome-level assemblies are essential for marker assisted selection and genotype-phenotype correlations in breeding regimes, as well as determining patterns of gross genomic evolution. To date, only two falcon species have been sequenced and neither initially were assembled to the chromosome level. Falcons have atypical avian karyotypes with fewer chromosomes than other birds, presumably brought about by wholesale fusion. To date, however, published chromosome preparations are of poor quality, few chromosomes have been distinguished and standard ideograms have not been made. The purposes of this study were to generate analyzable karyotypes and ideograms of peregrine, saker, and gyr falcons, report on our recent generation of chromosome level sequence assemblies of peregrine and saker falcons, and for the first time, sequence the gyr falcon genome. Finally, we aimed to generate comparative genomic data between all three species and the reference chicken genome. Results revealed a diploid number of 2n = 50 for peregrine falcon and 2n = 52 for saker and gyr through high quality banded chromosomes. Standard ideograms that are generated here helped to map predicted chromosomal fragments (PCFs) from the genome sequences directly to chromosomes and thus generate chromosome level sequence assemblies for peregrine and saker falcons. Whole genome sequencing was successful in gyr falcon, but read depth and coverage was not sufficient to generate a chromosome level assembly. Nonetheless, comparative genomics revealed no differences in genome organization between gyr and saker falcons. When compared to peregrine falcon, saker/gyr differed by one interchromosomal and seven intrachromosomal rearrangements (a fusion plus seven inversions), whereas peregrine and saker/gyr differ from the reference chicken genome by 14/13 fusions (11 microchromosomal) and six fissions. The chromosomal differences between the species could potentially provide the basis of a screening test for hybrid animals.