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

Overview

Journal Mar Biotechnol (NY)

Specialties Biology
Biotechnology

Date 2019 Jun 17

PMID 31203477

Citations 1

Authors

Fangzhou Hu

Jingjing Fan

Chang Wu

Ming Zhu

Yunfan Zhou

Shi Wang

Chun Zhang

Min Tao

Rurong Zhao

Chenchen Tang

Kaikun Luo

Qinbo Qin

Ming Ma

Bo Chen

Jinpu Wang

Aiguo Zhou

Liangxiong Bai

Shaojun Liu

Affiliations

Soon will be listed here.

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 50 chromosomes [corrected]. 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.

Citing Articles

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

Duan Y, Zhang Q, Jiang Y, Zhang W, Cheng Y, Shi M Int J Mol Sci. 2022; 23(19).

PMID: 36232849 PMC: 9569805. DOI: 10.3390/ijms231911547.

References

Tilgner H, Raha D, Habegger L, Mohiuddin M, Gerstein M, Snyder M . Accurate identification and analysis of human mRNA isoforms using deep long read sequencing. G3 (Bethesda). 2013; 3(3):387-97. PMC: 3583448. DOI: 10.1534/g3.112.004812. View

Xiao J, Kang X, Xie L, Qin Q, He Z, Hu F . The fertility of the hybrid lineage derived from female Megalobrama amblycephala × male Culter alburnus. Anim Reprod Sci. 2014; 151(1-2):61-70. DOI: 10.1016/j.anireprosci.2014.09.012. View

Jones P, Binns D, Chang H, Fraser M, Li W, McAnulla C . InterProScan 5: genome-scale protein function classification. Bioinformatics. 2014; 30(9):1236-40. PMC: 3998142. DOI: 10.1093/bioinformatics/btu031. View

Tan S, Wang W, Tian C, Niu D, Zhou T, Jin Y . Heat stress induced alternative splicing in catfish as determined by transcriptome analysis. Comp Biochem Physiol Part D Genomics Proteomics. 2018; 29:166-172. DOI: 10.1016/j.cbd.2018.11.008. View

Kijewska A, Malachowicz M, Wenne R . Alternatively spliced variants in Atlantic cod (Gadus morhua) support response to variable salinity environment. Sci Rep. 2018; 8(1):11607. PMC: 6072735. DOI: 10.1038/s41598-018-29723-w. View

Hu F, Xu K, Zhou Y, Wu C, Wang S, Xiao J . Different expression patterns of sperm motility-related genes in testis of diploid and tetraploid cyprinid fish†. Biol Reprod. 2017; 96(4):907-920. PMC: 5441299. DOI: 10.1093/biolre/iox010. View

Bar I, Cummins S, Elizur A . Transcriptome analysis reveals differentially expressed genes associated with germ cell and gonad development in the Southern bluefin tuna (Thunnus maccoyii). BMC Genomics. 2016; 17:217. PMC: 4785667. DOI: 10.1186/s12864-016-2397-8. View

Fujikake N, Nagai Y, Popiel H, Kano H, Yamaguchi M, Toda T . Alternative splicing regulates the transcriptional activity of Drosophila heat shock transcription factor in response to heat/cold stress. FEBS Lett. 2005; 579(17):3842-8. DOI: 10.1016/j.febslet.2005.05.074. View

Han C, Yen T, Chen N, Tseng M . Comparative Studies of 5S rDNA Profiles and Cyt b Sequences in two Onychostoma Species (Cyprinidae). Int J Mol Sci. 2015; 16(12):29663-72. PMC: 4691136. DOI: 10.3390/ijms161226193. View

10.

Sharma E, Kunstner A, Fraser B, Zipprich G, Kottler V, Henz S . Transcriptome assemblies for studying sex-biased gene expression in the guppy, Poecilia reticulata. BMC Genomics. 2014; 15:400. PMC: 4059875. DOI: 10.1186/1471-2164-15-400. View

11.

Huang Y, Zhao G, Peng Z . Mitochondrial genome of Onychostoma lini (Teleostei, Cypriniformes). Mitochondrial DNA. 2012; 23(3):173-5. DOI: 10.3109/19401736.2012.660935. View

12.

Weirather J, de Cesare M, Wang Y, Piazza P, Sebastiano V, Wang X . Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis. F1000Res. 2017; 6:100. PMC: 5553090. DOI: 10.12688/f1000research.10571.2. View

13.

Xu K, Wen M, Duan W, Ren L, Hu F, Xiao J . Comparative analysis of testis transcriptomes from triploid and fertile diploid cyprinid fish. Biol Reprod. 2015; 92(4):95. DOI: 10.1095/biolreprod.114.125609. View

14.

Tao W, Yuan J, Zhou L, Sun L, Sun Y, Yang S . Characterization of gonadal transcriptomes from Nile tilapia (Oreochromis niloticus) reveals differentially expressed genes. PLoS One. 2013; 8(5):e63604. PMC: 3643912. DOI: 10.1371/journal.pone.0063604. View

15.

Yang L, Jin Y, Huang W, Sun Q, Liu F, Huang X . Full-length transcriptome sequences of ephemeral plant Arabidopsis pumila provides insight into gene expression dynamics during continuous salt stress. BMC Genomics. 2018; 19(1):717. PMC: 6161380. DOI: 10.1186/s12864-018-5106-y. View

16.

Conesa A, Gotz S . Blast2GO: A comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics. 2008; 2008:619832. PMC: 2375974. DOI: 10.1155/2008/619832. View

17.

Liu S, Qin Q, Xiao J, Lu W, Shen J, Li W . The formation of the polyploid hybrids from different subfamily fish crossings and its evolutionary significance. Genetics. 2007; 176(2):1023-34. PMC: 1894572. DOI: 10.1534/genetics.107.071373. View

18.

Cheng H, Wu C, Tsai K, Liu A, Chiu Y, Tseng D . The complete mitochondrial genome sequence of Onychostoma alticorpus (Cypriniformes, Cyprinidae). Mitochondrial DNA. 2013; 25(3):188-9. DOI: 10.3109/19401736.2013.792069. View

19.

Zhang G, Sun M, Wang J, Lei M, Li C, Zhao D . PacBio full-length cDNA sequencing integrated with RNA-seq reads drastically improves the discovery of splicing transcripts in rice. Plant J. 2018; 97(2):296-305. DOI: 10.1111/tpj.14120. View

20.

LARKIN M, Blackshields G, Brown N, Chenna R, McGettigan P, McWilliam H . Clustal W and Clustal X version 2.0. Bioinformatics. 2007; 23(21):2947-8. DOI: 10.1093/bioinformatics/btm404. View