Developmental transcriptome analysis and identification of genes involved in formation of intestinal air-breathing function of Dojo loach, Misgurnus anguillicaudatus

Abstract

Dojo loach, Misgurnus anguillicaudatus is a freshwater fish species of the loach family Cobitidae, using its posterior intestine as an accessory air-breathing organ. Little is known about the molecular regulatory mechanisms in the formation of intestinal air-breathing function of M. anguillicaudatus. Here high-throughput sequencing of mRNAs was performed from six developmental stages of posterior intestine of M. anguillicaudatus: 4-Dph (days post hatch) group, 8-Dph group, 12-Dph group, 20-Dph group, 40-Dph group and Oyd (one-year-old) group. These six libraries were assembled into 81300 unigenes. Totally 40757 unigenes were annotated. Subsequently, 35291 differentially expressed genes (DEGs) were scanned among different developmental stages and clustered into 20 gene expression profiles. Finally, 15 key pathways and 25 key genes were mined, providing potential targets for candidate gene selection involved in formation of intestinal air-breathing function in M. anguillicaudatus. This is the first report of developmental transcriptome of posterior intestine in M. anguillicaudatus, offering a substantial contribution to the sequence resources for this species and providing a deep insight into the formation mechanism of its intestinal air-breathing function. This report demonstrates that M. anguillicaudatus is a good model for studies to identify and characterize the molecular basis of accessory air-breathing organ development in fish.

Full-length transcriptome of Misgurnus anguillicaudatus provides insights into evolution of genus Misgurnus

“…In this study, we generated 33,300 transcripts using the PacBio Iso-Seq, which was much smaller than 81,300 transcripts de novo assembled in Luo et al . 18 and showed high-efficiency in recovering full-length transcript. Even though the number of predicted ORFs in the PacBio dataset was less than that in the de novo dataset, the full-length transcripts included longer coding transcripts (26,683 ORFs with average length of 1457 bp) while the average length of ORFs in assembled transcripts was only 661 bp in the previous RNA-seq study 12 of M .…”

“…Many transcriptome studies of M . anguillicaudatus based on Illumina platform have been reported 12 , 18 – 20 . Compared with those studies, our study produced a more comprehensive transcriptome data set with several features.…”

Comparative Transcriptomic Analysis Reveals Candidate Genes and Pathways Involved in Larval Settlement of the Barnacle Megabalanus volcano

“…Unigenes that had no hits to any databases were used to predict coding regions and figure out the sequence direction by ESTScan 3.0.2 [ 52 ]. Gene Ontology annotation was analyzed by Blast2go [ 53 ], following functional classification by WEGO [ 54 ].…”

Molecular characterization of three muscle alpha actin genes in mud loach (Misgurnus mizolepis; Cypriniformes)

“…Previously, a histological analysis has reported that loach would possess the proximal intestine consisting of intermingled striated and smooth muscle cells (Hara et al 1989). One plausible, but untested, assumption on this finding (i.e., the considerably active expression of ACTA1 in the intestine) is that this species uses its intestine as an accessory air-breathing organ (Luo et al 2016), and thereby mud loach may require a unique contractility in order to eject air bubbles from its intestine.…”