Chromosome-level genome assembly for giant panda provides novel insights into Carnivora chromosome evolution
Chromosome-level genome assembly for giant panda provides novel insights into Carnivora chromosome evolution
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DOI：
10.1186/s13059-019-1889-7
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发表时间：
2019-12-06
期刊：
影响因子：
12.3
通讯作者：
Hu, Yibo
中科院分区：
文献类型：
--
作者：
Fan, Huizhong;Wu, Qi;Hu, Yibo
背景染色体进化是物种形成和物种进化的重要驱动力。先前的研究已经检测到染色体重排事件之间的不同食肉动物物种使用染色体彩绘策略。然而，这些研究很少集中在染色体进化的核苷酸分辨率由于有限的染色体水平食肉动物基因组的可用性。虽然大熊猫的从头基因组组装是可用的，但目前基于短读的组装仅限于中等大小的支架，使得染色体进化的研究变得困难。结果获得了大熊猫染色体水平的基因组草图，总大小为2.29Gb。基于大熊猫基因组和已发表的染色体水平的狗和猫基因组，我们进行了六个大规模的成对同线性比对，并确定了进化断点区域。有趣的是，基因功能富集分析表明，对于所有三个食肉目基因组，位于进化断点区域的一些基因在与嗅觉感官感知相关的途径或术语中显着富集。此外，我们还发现猫基因组中已被证实为假基因的甜味受体基因TAS1R2位于大熊猫的一个进化断点区域，提示染色体间重排可能在猫TAS1R2的假基因化过程中发挥作用。结论我们表明，在这项研究中采用的组合策略可以用来产生有效的染色体水平的基因组组装。此外，我们的比较基因组学分析提供了新的见解食肉动物染色体进化，染色体进化功能基因的进化。
Background Chromosome evolution is an important driver of speciation and species evolution. Previous studies have detected chromosome rearrangement events among different Carnivora species using chromosome painting strategies. However, few of these studies have focused on chromosome evolution at a nucleotide resolution due to the limited availability of chromosome-level Carnivora genomes. Although the de novo genome assembly of the giant panda is available, current short read-based assemblies are limited to moderately sized scaffolds, making the study of chromosome evolution difficult. Results Here, we present a chromosome-level giant panda draft genome with a total size of 2.29 Gb. Based on the giant panda genome and published chromosome-level dog and cat genomes, we conduct six large-scale pairwise synteny alignments and identify evolutionary breakpoint regions. Interestingly, gene functional enrichment analysis shows that for all of the three Carnivora genomes, some genes located in evolutionary breakpoint regions are significantly enriched in pathways or terms related to sensory perception of smell. In addition, we find that the sweet receptor gene TAS1R2, which has been proven to be a pseudogene in the cat genome, is located in an evolutionary breakpoint region of the giant panda, suggesting that interchromosomal rearrangement may play a role in the cat TAS1R2 pseudogenization. Conclusions We show that the combined strategies employed in this study can be used to generate efficient chromosome-level genome assemblies. Moreover, our comparative genomics analyses provide novel insights into Carnivora chromosome evolution, linking chromosome evolution to functional gene evolution.