Table_2_A new Merluccius polli reference genome to investigate the effects of global change in West African waters.xlsx

Genome resources have become crucial to assess genome-wide level of variation as well as to detect adaptive variation. This is particularly important for studying diversity in marine species inhabiting regions highly affected by accelerated climate warming and pollution, also known as global change. A greater awareness of the impacts of global change is urgently needed to ensure sustainable marine fisheries. Despite recent efforts, there are still many gaps in fish reference genomes, both geographical and taxonomic. Here, we sequence, assemble and annotate the genome of Merluccius polli. The total length of this new assembly (~582 Kb, N50 = 168Kb) is approximately 40% longer and much less fragmented than a previous version. Even though it might not be intrinsic of this species, low level of heterozygosity (1.16 SNPs/Kb) and low proportion of repeat content (9.21%) was found in this genome. This hake species has a wide latitudinal distribution; therefore, it is exposed to a changing temperature gradient and to a variety of contaminants in part of its distribution along West African coast. Special emphasis was laid on the identification and characterization of candidate genes known to respond to different stressors (depth, temperature, hypoxia, and heavy metals) happening along its geographical distribution. A total of 68 of the selected candidate genes known to be associated with responses to these stressors were found in the current assembly of the genome, and their predicted sequence can be considered as full-length. Therefore, it is expected that this genome would serve as a tool to further investigations of global change in one of the most stressed marine regions in the planet.

基因组资源已成为评估全基因组变异水平、检测适应性变异的核心支撑。这对于研究栖息于受加速气候变暖与污染（即全球变化）严重影响区域的海洋物种多样性尤为关键。为保障海洋渔业可持续发展，亟需深化对全球变化影响的认知。尽管近期已取得诸多进展，但鱼类参考基因组在地理覆盖与类群覆盖层面仍存在大量空白。本研究对波氏无须鳕（Merluccius polli）的基因组进行了测序、组装与注释。本次新组装的基因组总长度约为582千碱基对（Kb），N50值达168Kb，较此前版本长约40%，且碎片化程度大幅降低。尽管该特征或许并非该物种固有，但本基因组的杂合度水平较低（1.16个单核苷酸多态性位点/千碱基对，SNPs/Kb），重复序列占比仅为9.21%。该无须鳕物种具有广泛的纬度分布范围，在其沿西非海岸的部分分布区域中，会面临动态变化的温度梯度以及多种污染物的胁迫。研究重点聚焦于鉴定并表征已知可响应其地理分布范围内各类胁迫因子（水深、温度、低氧与重金属）的候选基因。在本次基因组组装中，共发现68个经筛选的、已知与上述胁迫响应相关的候选基因，且其预测序列均为全长序列。因此，该基因组有望成为研究工具，助力深入探究全球变化对地球上受胁迫最为严重的海洋区域之一的影响。