9种硬骨鱼类转座组注释

Annotation of the mobilomes of nine teleost species

摘要:

通过生物信息学手段对9种硬骨鱼转座组进行注释。结果表明9种硬骨鱼类转座组大小和构成差异显著，其转座组含量从高到低分别为斑马鱼、矛尾鱼、青鳉鱼、罗非鱼、花斑剑尾鱼、大西洋鳕鱼、三刺鱼、金娃娃和红鳍东方鲀，转座子含量和基因组大小呈正相关。DNA转座子在硬骨鱼类中具有多样性高和含量差异大的特点 (0.50%–38.37%)，是硬骨鱼类转座组差异的主要决定因素，其中hAT和Tc/Mariner超家族是硬骨鱼类主要的DNA转座子。RNA转座子在硬骨鱼类中也具有多样性高的特点，其中LINE转座子占硬骨鱼类基因组的0.53%–5.75%，共检测到14个超家族分布，其中L1、L2、RTE和Rex转座子扩增较为明显，LTR转座子除了在斑马鱼和三刺鱼中含量达到5.58%和2.51%，在大多硬骨鱼类基因组中的含量低于2%，在硬骨鱼类中共检测到6个LTR转座子 (Copia、DIRS、ERV、Gypsy、Ngaro和Pao) 超家族分布，其中扩增最为明显的是Gypsy。而SINE转座子在硬骨鱼类中扩增最弱，仅在斑马鱼和矛尾鱼中分别达到3.28%和5.64%，在其他7个物种中低于1%。SINE中tRNA、5S和MIR三个超家族在部分硬骨鱼类中有一定程度扩增。本研究表明硬骨鱼类转座组具有多样性丰富、差异大的特点，转座组差异与硬骨鱼基因组大小有很强的相关性，转座组是决定硬骨鱼基因组大小的重要因素。

Abstract:

In this study, the mobilomes of nine teleost species were annotated by bioinformatics methods. Both of the mobilome size and constitute displayed a significant difference in 9 species of teleost fishes. The species of mobilome content ranking from high to low were zebrafish, medaka, tilapia, coelacanth, platyfish, cod, stickleback, tetradon and fugu. Mobilome content and genome size were positively correlated. The DNA transposons displayed higher diversity and larger variation in teleost (0.50% to 38.37%), was a major determinant of differences in teleost mobilomes, and hAT and Tc/Mariner superfamily were the major DNA transposons in teleost. RNA transposons also exhibited high diversity in teleost, LINE transposons accounted for 0.53% to 5.75% teleost genomic sequences, and 14 superfamilies were detected. L1, L2, RTE and Rex retrotransposons obtained significant amplification. While LTR displayed low amplification in most teleost with less than 2% of genome coverages, except in zebrafish and stickleback, where LTR reachs 5.58% and 2.51% of genome coverages respectively. And 6 LTR superfamilies (Copia, DIRS, ERV, Gypsy, Ngaro and Pao) were detected in the teleost, and Gypsy exhibits obvious amplication among them. While the SINE represents the weakest ampification types in teleost, only within zebrafish and coelacanth, it represents 3.28% and 5.64% of genome coverages, in the other 7 teleost, it occupies less than 1% of genomes, and tRNA, 5S and MIR families of SINE have a certain degree of amplification in some teleosts. This study shows that the teleost display high diversity and large variation of mobilome, there is a strong correlation with the size variations of genomes and mobilome contents in teleost, mobilome is an important factor in determining the teleost genome size.