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Li Bian,Changlin Liu,Siqing Chen,Fazhen Zhao,Jianlong Ge,Jie Tan 한국유전학회 2018 Genes & Genomics Vol.40 No.3
Golden cuttlefish (Sepia esculenta) is an important economic species in China. Because of the rapid decline of its natural resource, researchers are exploring breeding technique for this species. The major obstacle that hinders artificial breeding of S. esculenta is the low larvae survival rate. Mortality is especially high during the mouth-opening stage. Investigating the embryogenesis before the first feed could provide theoretical guidance for reproduction control and breeding of S. esculenta and other Sepia species. In this study, we analyzed the dynamics of the S. esculenta transcriptome along different stages of embryonic development by mRNA-sEq. Our bioinformatics protocol identified 1492 differentially expressed genes (DEGs) across the early developmental stages. Gene ontology enrichment analysis showed that the DEGs were significantly involved in developmental processes and molecular functions, including chitin metabolic process, peptidase activity, catalytic activity, and calcium ion binding. Our results indicated that genes related to cuttlebone development and gene regulation functions were active during the early life phase of S. esculenta. Hierarchical clustering of the DEGs reflected the successiveness of the developmental stages, revealing that gene expression patterns of neighboring stages were similar. The DEG analysis allowed us to identify specific genes and relevant biological pathways to better understand the molecular mechanisms during each developmental stage. This study provides novel insights into the processes underlying the early developmental stages of S. esculenta. The transcriptomic data and identified genes will serve as valuable references for the developmental biology of this species and will help promote its aquaculture research.
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Jiajia Wang,Qianqian Ge,Jitao Li,Haiyu Gao,Jian Li,Fazhen Zhao 한국유전학회 2018 Genes & Genomics Vol.40 No.2
The ridgetail white prawn Exopalaemon carinicauda is one of the major commercial mariculture species in eastern China. However, only limited molecular markers are currently available due to the lack of genome information, which hinders its genetic and breeding studies. In this study, we identified new simple sequence repeats from transcriptome sequences by Illumina Hiseq 2500 platform. A total of 14273 SSR loci were identified from 130,082 assembled transcripts, with 6590 pairs of PCR primers designed. A total of 12,155 sequences containing SSR were predicted; and 2764 (22.74%) transcripts had significant matches to the NCBI non redundant protein (Nr) database. 11,563 transcripts were assigned into gene ontology (GO) categories. A set of 200 primers selected randomly were synthesized, of which 152 (76.0%) were successfully amplified. Further test with 60 pairs of polymorphic SSR primers to evaluate the genetic diversity of 30 wild populations and 43 loci were polymorphic, which had a polymorphic information content between 0.204 and 0.911. The results enriched genomic resources of E. carinicauda and provided powerful information for future conservation and breeding researches.
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