Transcriptome Analysis and SSR/SNP Markers Information of the Blunt Snout Bream (Megalobrama amblycephala)

Abstract

BackgroundBlunt snout bream (Megalobrama amblycephala) is an herbivorous freshwater fish species native to China and has been recognized as a main aquaculture species in the Chinese freshwater polyculture system with high economic value. Right now, only limited EST resources were available for M. amblycephala. Recent advances in large-scale RNA sequencing provide a fast, cost-effective, and reliable approach to generate large expression datasets for functional genomic analysis, which is especially suitable for non-model species with un-sequenced genomes.Methodology and Principal FindingsUsing 454 pyrosequencing, a total of 1,409,706 high quality reads (total length 577 Mbp) were generated from the normalized cDNA of pooled M. amblycephala individuals. These sequences were assembled into 26,802 contigs and 73,675 singletons. After BLAST searches against the NCBI non-redundant (NR) and UniProt databases with an arbitrary expectation value of E−10, over 40,000 unigenes were functionally annotated and classified using the FunCat functional annotation scheme. A comparative genomics approach revealed a substantial proportion of genes expressed in M. amblycephala tanscriptome to be shared across the genomes of zebrafish, medaka, tetraodon, fugu, stickleback, human, mouse, and chicken, and identified a substantial number of potentially novel M. amblycephala genes. A total number of 4,952 SSRs were found and 116 polymorphic loci have been characterized. A significant number of SNPs (25,697) and indels (23,287) were identified based on specific filter criteria in the M. amblycephala.ConclusionsThis study is the first comprehensive transcriptome analysis for a fish species belonging to the genus Megalobrama. These large EST resources are expected to be valuable for the development of molecular markers, construction of gene-based linkage map, and large-scale expression analysis of M. amblycephala, as well as comparative genome analysis for the genus Megalobrama fish species. The identified SSR and SNP markers will greatly benefit its breeding program and whole genome association studies.

Characterization of GHRs, IGFs and MSTNs, and analysis of their expression relationships in blunt snout bream, Megalobrama amblycephala

“…According to the manufacturer's instructions, first strand cDNA was reverse-transcribed from the total RNA using reverse transcriptase M-MLV (Fermentas, Canada). The partial cDNA sequences of M. amblycephala GHR 1, GHR 2, IGF-I, IGF-II, MSTN a and MSTN b, were obtained by our previous study on M. amblycephala transcriptome data using 454 pyrosequencing (Gao et al, 2012). The 5′ and 3′ end sequences of these genes cDNA were amplified using the 5′-/3′-Full RACE kit (Takara, Japan) following the manufacturer's instructions (special amplified primers were shown in Table 1).…”

“…Blunt snout bream (Megalobrama amblycephala Yih, 1955), also known as Wuchang fish, is a herbivorous cyprinid fish and endemic to limited lakes in the middle and lower reaches of the Yangtze River (Gao et al, 2012). Due to its widely-favored delicacy, nationwide fame, easy-recognized morphology and high economic value, it has been recognized as a main important aquaculture species in the freshwater polyculture system since the 1960s in China (Zhao et al, 2011).…”

Transcriptomic comparison of invasive bigheaded carps (Hypophthalmichthys nobilis and Hypophthalmichthys molitrix) and their hybrids

“…The difference between the total number of transcripts in native and invasive silver carp could be attributed to the number of tissues used for analysis and/or the number of raw reads produced. The transcriptomes of several other cyprinid species have been reported, including common carp, crucian carp, blunt snout bream ( Megalobrama amblycephala ), and many other species, and the number of annotated transcripts among them including bigheaded carps ranges from 22,000 to 25,000, except for blunt snout bream (Gao et al., 2012; Liao et al., 2013; Wang et al., 2012). Transcriptomes are known to vary in different tissues, developmental stages, and physiological conditions.…”

Transcriptome analysis of the plateau fish (Triplophysa dalaica): Implications for adaptation to hypoxia in fishes

“…Compared with other fish transcriptomes sequenced within Cypriniformes (Fu and He, 2012;Gao et al, 2012;Ji et al, 2012;Liao et al, 2013;Long et al, 2013;Zou et al, 2014), the de novo assembly and annotations of T. dalaica transcriptome were best (Table 2). In terms of the gene expression level, T. dalaica transcriptome showed the highest similarity to zebrafish, which can be explained by the fact that Triplophysa fishes and zebrafish belonging to the same order Cypriniformes.…”

“…To assess the quality of our assembled unigenes, we made comparisons with other fish transcriptomes sequenced within Cypriniformes, Carassius auratus, Megalobrama amblycephala, Hypophthalmichthys molitrix, Elopichthys bambusa and Cyprinus carpio (Fu and He, 2012;Gao et al, 2012;Ji et al, 2012;Liao et al, 2013;Long et al, 2013;Zou et al, 2014). Furthermore, cDNA template was prepared using highquality RNA with a first-strand DNA synthesis kit (Promega).…”