Transcriptome Analysis Of Developing Embryos In The Blunt Snout Bream

The blunt snout bream is a freshwater fish and farmed widely in China. By distant hybridization of Carassius auratus red var.(RR, 2n=100)(female) x Megalobrama amblycephala(BB, 2n=48)(male), we gained normal offspring, but it didn’t work otherwise. The BB x RR offspring, which we called FJ, died at 34 hours post fertilized. In order to understand why, we explored the difference of embryonic gene expression of the female parent bream blunt snout bream. The contents are as follows:1.RNAs were prepared from 6 embryogenesis stages(0, 4, 6, 12, 24 and 34hpf) from the zygote and used for RNA-seq by using the Illumina Hi Seq2000 platform. A total of 26.98 Gb data were gained. 54,821,138 clean reads were obtained from 359,951,288 raw reads. All data were used to assemble the embryo transcriptome file called “All Unigene”,which were clustered into 64,402 Unigenes with an average length of 1,077 bp. Unigenes of different stages have an average length longer than 698 bp.2.Contigs were aligned by BLASTX(e-value?1e-5) to the NCBI-NR, Swiss-Prot, KEGG and COG step by step for extracting the ORFs using a Perl script. ESTScan produced nucleotide sequences with direction(5’-3’) and CDS sequences. SSR and SNP analysis were done by Micro SAtellite(MISA) and SOAPsnp. The associated gene name were obtained from BLASTX alignment(e-values?1e-6) with zebrafish in Ensembl Bio Mart.3.FPKM(Fragments Per kb per Million fragments) was used as ruler to calculate the gene expression. 10 couples were used to compare with each other. We identified Unigenes as different expressed and constantly expressed. GO analysis were done to them.