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

Abstract

Reconstruction and annotation of transcripts, particularly for a species without reference genome, plays a critical role in gene discovery, investigation of genomic signatures, and genome annotation in the pre-genomic era. This study generated 33,330 full-length transcripts of diploid M. anguillicaudatus using PacBio SMRT Sequencing. A total of 6,918 gene families were identified with two or more isoforms, and 26,683 complete ORFs with an average length of 1,497 bp were detected. Totally, 1,208 high-confidence lncRNAs were identified, and most of these appeared to be precursor transcripts of miRNAs or snoRNAs. Phylogenetic tree of the Misgurnus species was inferred based on the 1,905 single copy orthologous genes. The tetraploid and diploid M. anguillicaudatus grouped into a clade, and M. bipartitus showed a closer relationship with the M. anguillicaudatus. The overall evolutionary rates of tetraploid M. anguillicaudatus were significantly higher than those of other Misgurnus species. Meanwhile, 28 positively selected genes were identified in M. anguillicaudatus clade. These positively selected genes may play critical roles in the adaptation to various habitat environments for M. anguillicaudatus. This study could facilitate further exploration of the genomic signatures of M. anguillicaudatus and provide potential insights into unveiling the evolutionary history of tetraploid loach.

Full-length transcriptome sequencing and comparative transcriptomic analysis to uncover genes involved in early gametogenesis in the gonads of Amur sturgeon (Acipenser schrenckii)

“…For example, deciphering highly similar multigene family transcripts from Iso-Seq data with IsoCon has opened the door for gaining a deep understanding of genome evolution and human diseases [19], and the full-length transcripts from the Iso-Seq platform have provided new insight into the extreme metabolism of the ruby-throated hummingbird [20]. Meanwhile, the reconstruction and annotation of fulllength transcripts also plays a critical role in gene discovery, particularly for species with no reference genome, such as the transcript variants involved in the innate immune system in Litopenaeus vannamei [21], gene families with two and more isoforms in Misgurnus anguillicaudatus [22] and transcript diversity in bioactive compound biosynthesis of Astragalus membranaceus [23]. Full-length transcriptome analyses may also drive new innovative progress for understanding the mechanisms of reproduction regulation in sturgeon.…”

Reconstruction and functional annotation of Ascosphaera apis full-length transcriptome via PacBio single-molecule long-read sequencing

“…PacBio SMRT sequencing provides better completeness to the sequencing of both the 5’ and 3’ ends of cDNA molecules; thus, it is a superior strategy for the direct generation of a comprehensive transcriptome with precise AS isoforms and novel genes [36–37]. Yi et al identified 33,300 full-length transcripts (transcript N50 of 5234 bp) of Misgurnus anguillicaudatus based on SMRT sequencing, and constructed a transcriptome by performing functional annotations of the non-redundant transcripts with public databases [38]. By sequencing mixed samples of Agasicles hygrophila eggs, larvae, pupae, and adults using PacBio SMRT, Jia and colleagues constructed a transcripotome composed of 28,982 full-length transcripts (transcript N50 of 2331 bp) [5].…”

Transcriptome Atlas by Long-Read RNA Sequencing: Contribution to a Reference Transcriptome

“…The samples can be collected from various tissues (i.e., blood, gill, skin, muscle, liver, spleen, intestine, ovary, testis, kidney, heart, and brain of an animal) [21], or from certain developmental stages (developing rabbit at 21, 49, and 84 days of age) [22]. The high quality of RNA with enough purity and integrity is critical to reduce the amplification cycles required in large-scale PCR and improve the sequencing diversity.…”

“…The high quality of RNA with enough purity and integrity is critical to reduce the amplification cycles required in large-scale PCR and improve the sequencing diversity. RNA extraction is usually done through an easy-spin RNA extraction kit, or RNAiso Pure RNA Isolation kit [20][21][22]. In general, 2-5 μg of total RNA with an RNA integrity number (RIN) greater than 7 is required.…”