Phyzen Genomics Institute, Seongnam 13558, South Korea.
Department of Biological Sciences, College of Science, Sungkyunkwan University, Suwon 16419, South Korea.
Comp Biochem Physiol Part D Genomics Proteomics. 2020 Sep;35:100684. doi: 10.1016/j.cbd.2020.100684. Epub 2020 Apr 12.
The selfing fish Kryptolebias hermaphroditus has unique reproductive system for self-fertilization, making genetically homozygous offsprings. Here, we report on high density genetic map-based genome assembly for the K. hermaphroditus Panama line (PanRS). The numbers of scaffolds were 5212 and the genome was 683,992,224 bp (N50 = 27.45 Mb). The length of anchored scaffold onto 24 linkage groups was 652,231,070 bp (95.3% of genome) with 0.01% of the gap and 39.33% of GC content and complete Benchmarking Universal Single-Copy Orthologs value was 96.6%. The numbers of annotated genes were 36,756 (average gene length 1368 bp) with the GC content of 54.1%. To examine the difference between the two sister species in the genus Kryptolebias, we compared the genomes of K. hermaphroditus PanRS and Kryptolebias marmoratus PAN line on the composition of transposable elements. To demonstrate applications of genome library, phase I and II detoxification related gene families have been analyzed, and compared the syntenies containing loci of CYP and GST genes on linkage groups. This K. hermaphroditus genome information will be helpful for a better understanding on genome-wide mechanistic view of detoxification and antioxidant-related genes over evolution in the view of fish environmental ecotoxicology.
自交鱼类双色单棘鲀具有独特的自体受精生殖系统，可产生遗传同质的后代。在此，我们报告了基于高密度遗传图谱的双色单棘鲀巴拿马品系（PanRS）基因组组装。共组装了 5212 个 scaffolds，基因组大小为 683,992,224 bp（N50=27.45 Mb）。24 条连锁群上锚定 scaffolds 的长度为 652,231,070 bp（基因组的 95.3%），缺口大小为 0.01%，GC 含量为 39.33%，完整的 Benchmarking Universal Single-Copy Orthologs 值为 96.6%。注释基因数量为 36,756 个（平均基因长度 1368 bp），GC 含量为 54.1%。为了研究单棘鲀属两个姐妹种之间的差异，我们比较了双色单棘鲀 PanRS 和波纹单棘鲀 PAN 品系的基因组在转座元件组成上的差异。为了展示基因组文库的应用，我们分析了 Phase I 和 II 解毒相关基因家族，并比较了连锁群上 CYP 和 GST 基因座的基因同线性。该双色单棘鲀基因组信息将有助于更好地理解鱼类环境毒理学中进化过程中解毒和抗氧化相关基因的全基因组机制。
