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绿鲍和西氏鲍的全长转录组测序分析

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为丰富绿鲍(Haliotis fulgens)和西氏鲍(H.sieboldii)的遗传信息、挖掘其功能基因、解析生物学性状的遗传基础,采用PacBio三代测序平台对两种鲍鱼进行了全长转录组测序,首次获得两种鲍鱼的全长转录本文库.通过测序拼接和去冗余,分别获得37 533条绿鲍和67 070条西氏鲍基因序列.通过与NR、SwissProt、KEGG、KOG、GO、NT和Pfam数据库比对,分别注释到20 051个绿鲍和31 421个西氏鲍基因,这些基因主要与细胞生长与代谢、信号转导有关.通过基因结构分析,在绿鲍和西氏鲍全长转录本中各检测到21 133和32 827个蛋白质编码区,并分别预测了 771和1 190个转录因子.在绿鲍和西氏鲍中分别发掘了 5 941个和11 183个微卫星;得到535条和765条长链非编码RNA;并鉴定到119和556个可变剪切事件.研究结果为进一步探究绿鲍和西氏鲍的生物学特性、基因功能以及遗传机制等方面提供了可靠的分子数据基础.
Full-length transcriptome analysis of Haliotis fulgens and H.sieboldii
The Pacific abalone Haliotis discus hannai is the main native farmed species in China.Hybridization is an effective method of genetic improvement in aquaculture,which can introduce improved traits to the hybrids.To improve the growth rate,survival rate,food conversion and stress resistance of abalone,China has introduced a number of new abalone varieties from abroad.The green abalone,H.fulgens is naturally distributed in California,USA and Baja California,Mexico.It has a wide range of temperature adaptability.H.sieboldii is a Japanese warm-water species with tender meat and excellent disease resistance ability.The hybrid abalone species,H.discus hannai ♀ × H.fulgens ♂ and H.sieboldii ♀ × H.discus hannai ♂,were both new varieties with significant heterosis.To enrich the genetic information and explore the genetic basis for important traits of H.fulgens and H.sieboldii,their full-length transcriptome was sequenced by the PacBio platform.Compared to the second-generation sequencing technologies,the third-generation sequencing technology has many advantages,such as longer sequencing length,high accuracy and throughput,and direct sequencing without fragmentation or post-sequencing assembly.To date,the application of the third-generation sequencing technology in abalone is scare.In this study,cDNA libraries of H.fulgens and H.sieboldii composed of several different tissues including muscle,head,gill,hepatopancreas,and mantle,were constructed and sequenced.After the functional annotation of transcripts in 7 databases(NR,SwissProt,KEGG,KOG,GO,NT,Pfam),the characteristics and sequence structure of these genes including coding sequence(CDS),transcription factor(TF),simple sequence repeat(SSR),long non-coding RNA(LncRNA)and alternative splicing(AS)were analyzed.A total of 37 533 and 67 070 polished consensus sequences were generated in H.fulgens and H.sieboldii,respectively.According to annotation,20 051 and 32 827 genes were found in H.fulgens and H.sieboldii,respectively,and these genes were mainly related to cell growth,metabolism and signal transduction.Gene structure analysis showed that a total of 21 133 and 32 506 protein CDs were found in H.fulgens and H.sieboldii,respectively.In addition,771 and 1 190 TFs were predicted.There were 5 941 and 11 183 SSRs in full-length transcriptome of H.fulgens and H.sieboldii,respectively.In addition,there were 535 and 765 long-noncoding RNA in H.fulgens and H.sieboldii library,respectively.It was also predicted that there were 119 and 556 AS events in the two abalone species.The full-length transcription libraries of these two abalone species were obtained for the first time,which would further enrich the genetic information of abalone.The results of this study lay the foundation for the further exploration of biological characteristics,functional genes and genetic mechanisms of H.fulgens and H.sieboldii.The key genes will also facilitate the development of molecular markers for studies of two abalone species.

Haliotis fulgensH.sieboldiifull-length transcriptomegene analysisfunctional annotation

傅仰涛、张倩、陈建明

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闽江学院地理与海洋学院,福州 350108

绿鲍 西氏鲍 全长转录组 基因分析 功能注释

2024

海洋渔业
中国水产学会 中国水产科学研究院东海水产研究所

海洋渔业

CSTPCD北大核心
影响因子:1.063
ISSN:1004-2490
年,卷(期):2024.46(5)