PDF(Pubmed)
Abstract：
Salmon lice, Lepeophtheirus salmonis (family Caligidae), are ectoparasites that have negatively impacted the salmon aquaculture industry and vulnerable wild salmon populations. Researchers have studied salmon lice to better understand their biology to develop effective control strategies. In this study, we updated the chromosome-level reference genome assembly of the Pacific subspecies of L. salmonis using Hi-C data. The previous version placed contigs/scaffolds using an Atlantic salmon louse genetic map. By utilizing Hi-C data from Pacific salmon lice, we were able to properly assign locations to contigs/scaffolds previously unplaced or misplaced. This resulted in a more accurate genome assembly and a more comprehensive characterization of the sex chromosome unique to females (W). We found evidence that the same ZW-ZZ mechanism is common in both Atlantic and Pacific subspecies of salmon lice using PCR assays. The W chromosome was approximately 800 kb in size, which is ∼30 times smaller than the Z chromosome (24 Mb). The W chromosome contained 61 annotated genes, including 32 protein-coding genes, 27 long noncoding RNA (lncRNA) genes, and 2 pseudogenes. Among these 61 genes, 39 genes shared homology to genes found on other chromosomes, while 20 were unique to the W chromosome. Two genes of interest on the W chromosome, prohibitin-2 and kinase suppressor of ras-2, were previously identified as potential sex-linked markers in the salmon louse. However, we prioritized the 20 unique genes on the W chromosome as sex-determining candidates. This information furthers our understanding of the biology of this ectoparasite and may help in the development of more effective management strategies.
摘要：
三文鱼虱子,沙门氏菌Lepeophtheirus（Calgidae家族），是对鲑鱼水产养殖业和脆弱的野生鲑鱼种群产生负面影响的外寄生虫。研究人员研究了鲑鱼虱子，以更好地了解它们的生物学特性，从而制定有效的控制策略。在这项研究中,我们使用Hi-C数据更新了沙门氏菌太平洋亚种的染色体水平参考基因组组装。以前的版本使用大西洋鲑鱼虱子遗传图谱放置了重叠群/支架。利用太平洋鲑鱼虱的Hi-C数据，我们能够正确地将位置分配给以前未放置或放错位置的重叠群/支架。这导致更准确的基因组组装和对女性（W）特有的性染色体的更全面表征。我们发现有证据表明，使用PCR测定法，在大西洋和太平洋鲑鱼虱亚种中，相同的ZW-ZZ机制是常见的。W染色体大小约为800kbp,比Z染色体(24Mbp)小30倍。W染色体包含61个注释基因，包括32个蛋白质编码基因，27个长链非编码RNA（lncRNA）基因，和2个伪基因.在这61个基因中,39个基因与其他染色体上的基因具有同源性，而20是W染色体特有的。W染色体上的两个感兴趣的基因,抑制素2和ras-2的激酶抑制剂先前被鉴定为鲑鱼虱中的潜在性别相关标记。然而,我们优先考虑W染色体上的20个独特基因作为性别决定候选基因.这些信息进一步加深了我们对这种外寄生虫生物学的理解，并可能有助于制定更有效的管理策略。
