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.