The vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in the wild. First described in 1958, the vaquita has been in rapid decline resulting from inadvertent deaths due to the increasing use of large-mesh gillnets for more than 20 years. To understand the evolutionary and demographic history of the vaquita, we used combined long-read sequencing and long-range scaffolding methods with long- and short-read RNA sequencing to generate a near error-free annotated reference genome assembly from cell lines derived from a female individual. The genome assembly consists of 99.92% of the assembled sequence contained in 21 nearly gapless chromosome-length autosome scaffolds and the X-chromosome scaffold, with a scaffold N50 of 115 Mb. Genome-wide heterozygosity is the lowest (0.01%) of any mammalian species analyzed to date, but heterozygosity is evenly distributed across the chromosomes, consistent with long-term small population size at genetic equilibrium, rather than low diversity resulting from a recent population bottleneck or inbreeding. Historical demography of the vaquita indicates long-term population stability at less than 5000 (Ne) for over 200,000 years. Together, these analyses indicate that the vaquita genome has had ample opportunity to purge highly deleterious alleles and potentially maintain diversity necessary for population health.

中文翻译：

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最濒临灭绝的海洋哺乳动物vaquita的参考基因组和人口历史

迷迭香是濒临灭绝的海洋哺乳动物，在野外只剩下不到19只。自1958年首次描述以来，由于大网状刺网的使用增加了20多年，由于无意死亡而导致的迷迭香迅速减少。为了了解vaquita的进化史和人口统计学历史，我们使用了长读测序和长距离支架方法以及长读和短读RNA测序相结合的方法，从来源于a的细胞系中生成了几乎没有错误的带注释的参考基因组。女性。基因组装配体由21个几乎无间隙的染色体长度常染色体支架和X染色体支架所含的装配序列的99.92％组成，支架的N50为115 Mb。全基因组杂合度是迄今为止分析的所有哺乳动物中最低的（0.01％），但是杂合性在整个染色体上均匀分布，这与遗传平衡时长期的小种群规模相符，而不是由于最近的种群瓶颈或近交导致的低多样性。vaquita的历史人口统计数据表明，超过200,000年的时间，长期人口稳定在5000（Ne）以下。总之，这些分析表明，vaquita基因组有足够的机会清除高度有害的等位基因，并有可能维持种群健康所必需的多样性。vaquita的历史人口统计数据表明，超过200,000年的时间，长期人口稳定在5000（Ne）以下。总之，这些分析表明，vaquita基因组有足够的机会清除高度有害的等位基因，并有可能维持种群健康所必需的多样性。vaquita的历史人口统计数据表明，超过200,000年的时间，长期人口稳定在5000（Ne）以下。总之，这些分析表明，vaquita基因组有足够的机会清除高度有害的等位基因，并有可能维持种群健康所必需的多样性。