Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization
Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization
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DOI：
10.1101/2022.10.17.512540
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发表时间：
2022-10
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通讯作者：
Kazuaki Yamaguchi;Y. Uno;M. Kadota;Osamu Nishimura;R. Nozu;K. Murakumo;R. Matsumoto;Keiichi Sato;Shigehiro Kuraku
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作者：
Kazuaki Yamaguchi;Y. Uno;M. Kadota;Osamu Nishimura;R. Nozu;K. Murakumo;R. Matsumoto;Keiichi Sato;Shigehiro Kuraku
脊椎动物染色体进化的基因组学研究长期以来一直受到一些关键类群染色体尺度DNA序列缺乏的阻碍。其中一个限制性的类群是板鳃类（鲨鱼和鳐），这些物种通常具有大量的染色体和扩大的基因组。在这里，我们报告了斑马鲨鱼Stegostoma tigrinum的染色体规模的基因组组装，这是一种濒危物种，具有迄今为止鲨鱼中最小的基因组测序（3.71 Gb），以及鲸鲨Rhincodon typus。我们的分析采用了男性-女性比较确定了X染色体，第一个基因组特征的鲨鱼性染色体。X染色体含有一个Hox C簇，其完整的连锁尚未显示为板鳃鱼。测序鲨鱼基因组显示出显着的长度依赖性特征的染色体长度的渐变性，较短的染色体往往有较高的GC含量，基因密度，同义替换率，简单串联重复序列的含量以及较小的基因长度，这类似于较长的染色体的边缘。这种基因组内异质性的模式，以前被认为是特有的物种与所谓的微染色体，发生在更多的脊椎动物，包括板鳃类。我们挑战了传统的核型的二元分类，即有和没有微染色体，因为即使没有微染色体，较短的染色体往往具有较高的GC和简单串联重复序列的含量，并且具有较短和更快速进化的基因。这些特征也出现在较长染色体的边缘。我们的调查板鳃类核型的基础上，其独特的特点，并提供了线索，了解脊椎动物核型如何适应基因组内的异质性，实现复杂的读出。
Genomic studies of vertebrate chromosome evolution have long been hindered by the scarcity of chromosome-scale DNA sequences of some key taxa. One of those limiting taxa has been the elasmobranchs (sharks and rays), which harbor species often with numerous chromosomes and enlarged genomes. Here, we report the chromosome-scale genome assembly for the zebra shark Stegostoma tigrinum, an endangered species that has the smallest genome sequenced to date among sharks (3.71 Gb), as well as for the whale shark Rhincodon typus. Our analysis employing a male–female comparison identified an X chromosome, the first genomically characterized shark sex chromosome. The X chromosome harbors a Hox C cluster whose intact linkage has not been shown for an elasmobranch fish. The sequenced shark genomes exhibit a gradualism of chromosome length with remarkable length-dependent characteristics—shorter chromosomes tend to have higher GC content, gene density, synonymous substitution rate, and simple tandem repeat content as well as smaller gene length, which resemble the edges of longer chromosomes. This pattern of intragenomic heterogeneity, previously recognized as peculiar to species with so-called microchromosomes, occurs in more vertebrates including elasmobranchs. We challenge the traditional binary classification of karyotypes as with and without microchromosomes, as even without microchromosomes, shorter chromosomes tend to have higher contents of GC and simple tandem repeats and harbor shorter and more rapid-evolving genes. Such characteristics also appear on the edges of longer chromosomes. Our investigation of elasmobranch karyotypes underpins their unique characteristics and provides clues for understanding how vertebrate karyotypes accommodate intragenomic heterogeneity to realize a complex readout.