Analysis of Chromosomal Numbers, Mitochondrial Genome, and Full-Length Transcriptome of Onychostoma brevibarba

Abstract

Onychostoma brevibarba is a new discovered species which is distributed in Xiang Jiang River of the middle Chang Jiang basin in Hunan Province, South China. In this study, the ploidy levels of O. brevibarba were confirmed by counting chromosomal numbers and analyzing karyotype. The complete mitochondrial genome of O. brevibarba was determined and analyzed. Besides, we firstly performed the full-length transcriptome of O. brevibarba derived from 5 different tissues using the PacBio SMRT sequencing. The result shows that O. brevibarba was a diploid with 48 chromosomes. The complete mitogenome of O. brevibarba was 16,602 bp in size and very similar (89.1–91.3%) to that of other Onychostoma species but was distinct from all congeners. The full-length transcriptome dataset of O. brevibarba comprised 120,239 unigenes. Among the unigenes, 91,542 were functionally annotated, whereas 26,794 were found to have two or more isoforms. This study could provide many new insights into cytology and molecular characteristics of O. brevibarba ; it laid the foundation for further exploration of the genomic signatures of species of Onychostoma . Electronic supplementary material The online version of this article (10.1007/s10126-019-09899-6) contains supplementary material, which is available to authorized users.

Chromosome‐level genome assembly of a cyprinid fish Onychostoma macrolepis by integration of nanopore sequencing, Bionano and Hi‐C technology

“…Ultimately, 881.3 Mb data in 526 scaffolds were anchored and orientated onto 25 chromosomes by agglomerative hierarchical clustering, which was consistent with the chromosome numbers in our karyotype analyses. The same chromosome numbers were also reported in other species from the same genus (Hu et al., 2019). The 25 chromosomes ranged in size from 25.27 to 56.49 Mb (Table S9), and covered ~99.4% of the whole genome sequences.…”

“…Polyploids usually harbour more complex genome organization and gene content than diploids (Xu et al., 2019). The Cyprininae contains around 400 polyploidy species (Arai, 2011), while most of species in Onychostoma genus are diploids with 50 chromsomes (Hu et al., 2019; Yin & Dai, 2014). Onychostoma macrolepis (Bleeker, 1871), distributed mainly in the river system of the Yangtze River, the Huaihe River, the Weihe River and the Haihe River in China, is an emerging commercial fish.…”

Dynamic Transcriptional Landscape of Grass Carp (Ctenopharyngodon idella) Reveals Key Transcriptional Features Involved in Fish Development

“…Sequences in gc.v2 (3281 bp, median) are much longer than in gc.v1 (1642 bp) and are longer than the sequences both in loach ( Misgurnus anguillicaudatus ) transcriptome (3054) [ 28 ] and in Onychostoma brevibarba transcriptome (3054) [ 29 ], which were sequenced using SMRT technology. In addition to this, it was significantly longer than the RNAs that were found in the zebrafish transcriptome (2103) (GRCz11) ( Supplemental Table S2 ).…”

“…Single-molecular real-time (SMRT)-based RNA-seq has been used a lot in fish studies to look at alternative splicing events. However, these studies have mostly focused on transcriptome assembly [ 28 , 29 , 30 , 31 ] and specific study subjects [ 32 , 33 , 34 , 35 , 36 , 37 , 38 ], and they have not looked at how alternatively spliced transcripts change in expression over time in a systematic way.…”