The triangle sail mussel Hyriopsis cumingii (Lea) is the most important mussel species used for commercial freshwater pearl production in China. Mussel color is an important indicator of pearl quality. To identify genes involved in the nacre coloring, we conducted RNA-seq and obtained 541,268 sequences (298 bp average size) and 440,034 sequences (293 bp average size) in secreting purple and white nacre libraries (P- and W-libraries), respectively. The 981,302 Expressed Sequence Tags (ESTs) were assembled into 47,812 contigs and 289,386 singletons. In BLASTP searches of the deduced protein, 22,495 were proteins with functional annotations. Thirty-three genes involved in pearl or shell formation were identified. Digital expression analysis identified a total of 358 differentially expressed genes, and 137 genes in the P-library and 221 genes in the W-library showed significantly higher expression. Furthermore, a set of SSR motifs and SNPs between the two samples was identified from the ESTs, which provided the markers for genetic linkage, QTL analysis and future breeding. These EST sequences provided valuable information to further understand the molecular mechanisms involved in the formation, color determination and evolution of the pearl or shell.
Fishes live in aquatic environments and several aquatic environmental factors have undergone recent alterations. The molecular mechanisms underlying fish responses to hypoxia and acidification stress have become a serious concern in recent years. This study revealed that hypoxia and acidification stress suppressed the growth of body length and height of the large yellow croaker (Larimichthys crocea). Subsequent transcriptome analyses of L. crocea juveniles under hypoxia, acidification, and hypoxia–acidification stress led to the identification of 5897 differentially expressed genes (DEGs) in the five groups. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed that several DEGs were enriched in the ‘protein digestion and absorption’ pathway. Enrichment analysis revealed that this pathway was closely related to hypoxia and acidification stress in the five groups, and we found that genes of the collagen family may play a key role in this pathway. The zf-C2H2 transcription factor may play an important role in the hypoxia and acidification stress response, and novel genes were additionally identified. The results provide new clues for further research on the molecular mechanisms underlying hypoxia–acidification tolerance in L. crocea and provides a basic understanding of the potential combined effects of reduced pH and dissolved oxygen on Sciaenidae fishes.
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