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The reference genome of the selfing fish Kryptolebias hermaphroditus: Identification of phases I and II detoxification genes.
Comparative Biochemistry and Physiology D: Genomics & Proteomics ( IF 3 ) Pub Date : 2020-04-12 , DOI: 10.1016/j.cbd.2020.100684
Beom-Soon Choi 1 , Jun Chul Park 2 , Min-Sub Kim 2 , Jeonghoon Han 2 , Duck-Hyun Kim 2 , Atsushi Hagiwara 3 , Yoshitaka Sakakura 3 , Un-Ki Hwang 4 , Bo-Young Lee 2 , Jae-Seong Lee 2
Affiliation  

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.



中文翻译:

自交鱼类Kryptolebias hermaphroditus的参考基因组:鉴定I和II期排毒基因。

自交的鱼类Kryptolebias hermaphroditus具有独特的繁殖系统,可以自我受精,使它们成为遗传纯合的后代。在这里,我们对高密度遗传图谱为基础的基因组装配用于报告K.赫马佛洛狄忒斯巴拿马线(PanRS)。支架数量为5212,基因组为683,992,224 bp(N50 = 27.45 Mb)。锚定在24个连接基团上的支架的长度为652,231,070 bp(基因组的95.3%),具有0.01%的缺口和39.33%的GC含量,完整的基准通用单拷贝直系同源物值为96.6%。带注释的基因数量为36,756(平均基因长度1368 bp),GC含量为54.1%。检查K虫属中两个姐妹物种之间的差异,我们在转座因子的组成上比较了K. hermaphroditus PanRS和Kryptolebias marmoratus PAN系的基因组。为了证明基因组库的应用,已经分析了I和II期排毒相关的基因家族,并比较了CYPGST基因位点在连接基团上的同源性。从鱼类环境生态毒理学的观点出发,此K.hermaphroditus基因组信息将有助于更好地了解全基因组的排毒机理和抗氧化剂相关基因,而不是进化论。

更新日期:2020-04-12
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