Comparative analysis of genome sequences of the two cultivated tetraploid cottons, Gossypium hirsutum (L.) and G. barbadense (L.)
Comparative analysis of genome sequences of the two cultivated tetraploid cottons, Gossypium hirsutum (L.) and G. barbadense (L.)
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DOI：
10.1016/j.indcrop.2023.116471
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发表时间：
2023-03-01
影响因子：
5.9
通讯作者：
Yuan，Daojun
中科院分区：
文献类型：
--
作者：
Meng，Qingying;Gu，Jiaqi;Yuan，Daojun
随着测序技术的创新和高性能计算系统的进步，现在对复杂基因组进行测序和组装相对简单。近年来，来自多个棉花物种的许多基因组已经被释放，其中两个栽培异源四倍体棉花的高度纯合的标准遗传系，即，陆地棉（Gossypium hirsutum TM-1）和棉（G. barbadense 3 -79，由不同的研究小组使用不同的测序技术多次组装。这些基因组之间的组装质量是可变的，甚至在相同物种的多个加入或版本之间，这可能在选择适当的基因组进行遗传分析时产生混乱，并且在比较不同参考基因组之间的结果时产生障碍。因此，许多棉花基因组序列的评估是必要的，以促进基因组序列的选择和不同版本或物种之间的比较。在这里，我们全面评估和比较基因组组装的准确性，完整性和连续性nineG。hirsutumassemblies和fourG. barbadenseassemblies使用具有相同条件的多个分析策略。我们确定了着丝粒区域和几个大规模的倒位基因组从同一个加入，表明结构错误引入序列排序和方向inG。多毛瘤和G.巴巴多斯基因组组装来自多个基因组的注释之间的基因关系在物种内和物种间被定义，并且结果可在棉花旁系同源物组搜索网站（https：//iphon.shinyapps.io/cottonParalogs/）上获得，这是用于转换基因ID和比较不同基因组版本之间的注释的方便资源。本研究全面评估和比较了两个栽培四倍体棉花品种不同组装策略的多个版本的组装质量，说明了复杂基因组测序和组装的挑战，并为棉花基因组学提供了资源。
With innovations in sequencing technology and the progress of high-performance computing systems, it is now relatively straightforward to sequence and assemble complex genomes. Many genomes from multiple cotton species have been released in recent years, with the highly homozygous standard genetic lines of two cultivated allotetraploid cottons,i.e., Gossypium hirsutumTM-1 andG. barbadense3–79, assembled multiple times by different research groups using diverse sequencing technologies. The assembly quality among these genomes is variable, even between multiple accessions or versions of the same species, which can generate both confusion in choosing the appropriate genome for genetic analysis and obstacles when comparing results among the different reference genomes. Accordingly, an assessment of the many cotton genome sequences is necessary to facilitate both choice of genome sequence and comparisons between different versions or species. Here we comprehensively assess and compare genome assembly accuracy, completeness, and contiguity for nineG. hirsutumassemblies and fourG. barbadenseassemblies using multiple analysis strategies with the same criteria. We identify centromeric regions and several large-scale inversions among genomes from the same accession, indicating structural errors introduced during sequence ordering and orientation inG. hirsutumandG. barbadensegenome assembly. Gene relationships between annotations from multiple genomes are defined within and across species, and the results are available at the Cotton Paralogs Groups Search website (https://ihope.shinyapps.io/cottonParalogs/), a convenient resource for converting gene ids and comparing annotations between different genome versions. This study comprehensively assesses and compares assembly quality among multiple versions of the two cultivated tetraploid cotton species with different assembly strategies, illustrating the challenges of sequencing and assembling complex genomes and providing a resource for cotton genomics.