不同大小规格墨西哥湾扇贝(Argopecten irradians concentricus)转录组分析及生长相关基因筛选

Transcriptome Analysis and Growth-Related Genes Screening of Argopecten irradians concentricus of Different Sizes

墨西哥湾扇贝(Argopecten irradians concentricus)是中国双壳贝类养殖的重要经济品种,具有较高的研究价值,然而,转录组学及基因组学信息的匮乏,严重制约了该贝的遗传改良进程。本研究基于Illumina Hi SeqTM2000平台,对5月龄大规格(平均体质量16.05 g)和小规格(平均体质量5.57 g)墨西哥湾扇贝进行转录组测序,经de nove组装,大、小规格墨西哥湾扇贝分别获得120 563和118 794条高质量unigenes,unigene的平均长度分别为944 bp和969 bp;按照FDR≤0.001且|log2Ratio|≥1的原则,共筛选出9 901个差异表达基因,其中,大规格组相对于小规格组,上调基因4 976个(50.26%),下调基因4 925个(49.74%);六大公共数据库Blast比对结果显示,差异表达基因在Nr数据库的注释率最高,其次是GO数据库;从已获功能注释的差异表达基因中筛选得到47个生长相关候选基因,涉及多个生长因子及其受体;GO功能富集结果显示,膜、L-氨基酸运输和糖基键水解酶活性分别是细胞组分、生物过程和分子功能富集unigene最多的条目;Pathway富集分析发现,3 699条差异表达基因被成功注释到252条代谢通路中,其中33条为显著性富集通路(p<0.05),富集度最高的是焦点粘附;大规格组中共鉴定出10 870个SSRs和242 551个SNPs,小规格组中共鉴定出10 857个SSRs和228 121个SNPs。研究结果为墨西哥湾扇贝分子标记批量开发、功能相关基因挖掘以及分子遗传育种提供了理论数据支撑。

Argopecten irradians concentricus is a commercially important bivalve species for aquaculture in China,with high research value. However, the scarcity of transcriptome and genomic resources have severely constrained the progress of its genetic improvement. This study was based on the Illumina HiSeqTM2000 platform to perform transcriptome sequencing for the large size(average body weight was 16.05 g) and the small size(average body weight was 5.57 g) of A. i. concentricus. By de nove assembly, large and small sizes of A. i. concentricus obtained120 563 and 118 794 high-quality unigenes, and the average length of these unigenes were 944 bp and 969 bp,respectively;According to the principle of FDR≤0.001 and |log2Ratio|≥1, a total of 9 901 differentially expressed genes(DEGs) were screened. Among them, the large-size group compared with the small-size group, there were 4 976(50.26%) up-regulated genes, 4 925(49.74%) down-regulated genes. The results of blast comparison between six major public databases showed that the DEGs have the highest annotation rate in Nr database, followed by GO database. 47 growth-related candidate genes were screened from the DEGs that have been functionally annotated,involving multiple growth factors and their receptors. GO functional enrichment results showed that membrane,L-amino acid transport and sugar-based key hydrolase activity were enriched with the largest number of unigene entries of cell composition, biological processes and molecular function. Pathway enrichment analysis showed that 3 699 differentially expressed genes were successfully annotated into 252 metabolic pathways, 33 of which were significantly enriched(p<0.05), and the highest enrichment was focal adhesion. In the large size group, a total of10 870 SSRs and 242 551 SNPs were identified, and 10 857 SSRs and 228 121 SNPs were identified in the small size group. The results could provide theoretical data support for A. i. concentricus on batch development of molecular markers, deep excavation of functional related genes and molecular genetic breeding.