Characteristics of Mitochondrial Genomes of <i>Semilabeo obscures</i> Analyzed Using Illumina Hiseq 4000 High-throughput Sequencing Technique

HAN Yao-quan; HUANG Li; ZHU Qiong-hua; WU Wei-jun; HE An-you; SHI Jun; LI Yu-sen

doi:10.19303/j.issn.1008-0384.2020.02.003

Volume 35 Issue 2

Feb. 2020

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Article Navigation > Fujian Journal of Agricultural Sciences > 2020 > 35(2): 130-139

HAN Y Q, HUANG L, ZHU Q H, et al. Characteristics of Mitochondrial Genomes of Semilabeo obscures Analyzed Using Illumina Hiseq 4000 High-throughput Sequencing Technique [J]. Fujian Journal of Agricultural Sciences，2020，35（2）：130−139 doi: 10.19303/j.issn.1008-0384.2020.02.003

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HAN Y Q, HUANG L, ZHU Q H, et al. Characteristics of Mitochondrial Genomes of Semilabeo obscures Analyzed Using Illumina Hiseq 4000 High-throughput Sequencing Technique [J]. Fujian Journal of Agricultural Sciences，2020，35（2）：130−139 doi: 10.19303/j.issn.1008-0384.2020.02.003

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Characteristics of Mitochondrial Genomes of Semilabeo obscures Analyzed Using Illumina Hiseq 4000 High-throughput Sequencing Technique

doi: 10.19303/j.issn.1008-0384.2020.02.003

1.
Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture/Guangxi Academy of Fishery Sciences, Nanning, Guangxi　530021, China
2.
Guangxi International Business Vocational College, Nanning, Guangxi　530007, China
3.
Science Corporation of Gene, Guangzhou, Guangdong　510540, China

Received Date: 2019-11-15
Rev Recd Date: 2020-01-07
Publish Date: 2020-02-01

Abstract

Abstract

Objective Molecular genetics of various Dusky Labiaet-barbel (Semilabeo obscures) was studied. Method The second-generation Illumina Hiseq 4000 high-throughput sequencing technology was employed to determine the sequences of the mitochondrial genomes of different species of S. obscures. Result The length of the individual mitochondrial genome was determined to be 16 598–16 599 bp containing 42.65%–42.7% GC. There were 13 protein-coding genes, 22 tRNA, 2 rRNA (i.e., 12S-rRNA and 16S-rRNA), and one control region. Except for the coded ND6, the values of GC-skew of the genomes were all negative; while those of AT-skew in COXI, ND3 and ND6 were negative as well; but those of AT-skew in others were positive. The 13 protein-coding genes consisted of 3 794 aa with the preference codon (RSCU＞2) including the termination codon Arg (CGA), Gly (GGA), Leu (CTA), Pro (CCA), Ser (TCA) and the termination codon Stp (TAA). These S. obscures appeared to relate most closely with Pseudogyrinocheilus prochilus and somewhat with Ptychidio jordani, Rectoris posehensis and Parasinilabeo assimilis. Conclusion The structures and sequences of the mitochondrial genomes of S. obscures as determined were in line with those of typical fish counterparts.
- Semilabeo obscures,
- mitochondrial genome,
- structure and characteristics,
- phylogeny

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References(34)

References

[1]	乐佩琦. 中国动物志硬骨鱼纲鲤形目（下卷）[M]. 北京: 科学出版社, 2000: 171-272.
[2]	周解, 张春光. 广西淡水鱼类志（第二版）[M]. 南宁: 广西人民出版社, 2006: 276-279.
[3]	褚新洛, 陈银瑞. 云南鱼类志（上册）[M]. 北京: 科学出版社, 1990: 238-243.
[4]	郑慈英. 珠江鱼类志[M]. 北京: 科学出版社, 1989: 210-213.
[5]	乐佩琦, 陈宜瑜. 中国濒危动物红皮书鱼类卷[M]. 北京: 科学出版社, 1998: 167-169.
[6]	汪松, 解焱. 中国物种红色名录[M]. 北京: 高等教育出版社, 2009.
[7]	刘霆, 杨兴, 李道友, 等. 唇鲮的引种及人工驯养技术研究 [J]. 水利渔业, 2008, 29(1):56, 98. LIU T, YANG X, LI D Y, et al. Research on introduction and artificial domestication of the Semilabeo notabilis [J]. Reservoir Fisheries, 2008, 29(1): 56, 98.(in Chinese)
[8]	安苗, 潘光群. 唇鲮染色体核型的研究 [J]. 山地农业生物学报, 2008, 27(6):508−511, 521. doi: 10.3969/j.issn.1008-0457.2008.06.008 AN M, PAN G Q. Studies on karyotype of Semilabeo notabilis Peters [J]. Journal of Mountain Agriculture and Biology, 2008, 27(6): 508−511, 521.(in Chinese) doi: 10.3969/j.issn.1008-0457.2008.06.008
[9]	刘霆, 李建光, 胡世然, 等. 唇鲮的人工繁殖技术 [J]. 水产科技情报, 2011, 38(4):216−218. doi: 10.3969/j.issn.1001-1994.2011.04.013 LIU T, LI J G, HU S R, et al. The artificial breeding of Semilabeo notabilis [J]. Fisheries Science & Technology Information, 2011, 38(4): 216−218.(in Chinese) doi: 10.3969/j.issn.1001-1994.2011.04.013
[10]	王晓爱, 潘晓赋, 杨君兴, 等. 一种暗色唇鱼精子超低温冷冻保存方法: 201210277522.7[P].2012-08-07.
[11]	杨君兴, 潘晓赋, 李再云, 等. 一种暗色唇鱼的人工繁殖方法: 201210111579.X[P]. 2013-11-27.
[12]	刘兴, 许洪亮, 李光华, 等. 一种暗色唇鲮的鱼苗培育方法: 201610837430.8[P]. 2016-09-21.
[13]	王晓爱, 杨君兴, 陈小勇, 等. 4种渗透性抗冻剂对暗色唇鱼精子冷冻保存的影响 [J]. 水生态学杂志, 2012, 33(5):88−93. WANG X A, YANG J X, CHEN X Y, et al. Effects of four penetrating cryoprotectants on cryopreservation of Semilabeo obscurus sperm [J]. Journal of Hydroecology, 2012, 33(5): 88−93.(in Chinese)
[14]	韩耀全, 黄博, 何安尤, 等. 濒危鱼类暗色唇鲮的表型特征解构及内部结构测度 [J]. 福建农业学报, 2018, 33(9):899−905. HAN Y Q, HUANG B, HE A Y, et al. Phenotype and interior of endangered species, Semilabeo obscurus [J]. Fujian Journal of Agricultural Sciences, 2018, 33(9): 899−905.(in Chinese)
[15]	崔鹏, 徐海根, 吴军, 等. 中国脊椎动物红色名录指数评估 [J]. 生物多样性, 2014, 22(5):589−595. doi: 10.3724/SP.J.1003.2014.14085 CUI P, XU H G, WU J, et al. Assessing the red list index for vertebrate species in China [J]. Biodiversity Science, 2014, 22(5): 589−595.(in Chinese) doi: 10.3724/SP.J.1003.2014.14085
[16]	沙淼, 林立亮, 李雪娟, 等. 线粒体基因组测序策略和方法 [J]. 应用昆虫学报, 2013, 50(1):293−297. doi: 10.7679/j.issn.2095-1353.2013.039 SHA M, LIN L L, LI X J, et al. Strategy and methods for sequencing mitochondrial genome [J]. Chinese Journal of Applied Entomology, 2013, 50(1): 293−297.(in Chinese) doi: 10.7679/j.issn.2095-1353.2013.039
[17]	刘连为, 许强华, 陈新军. 基于线粒体COI和Cytb基因序列的北太平洋柔鱼种群遗传结构研究 [J]. 水产学报, 2012, 36(11):1675−1684. doi: 10.3724/SP.J.1231.2012.27955 LIU L W, XU Q H, CHEN X J. Population genetic structure of Ommastrephes bartramii in the North Pacific Ocean based on the COI and Cytb gene sequences analysis [J]. Journal of Fisheries of China, 2012, 36(11): 1675−1684.(in Chinese) doi: 10.3724/SP.J.1231.2012.27955
[18]	司从利, 章群, 马奔, 等. 基于线粒体细胞色素b基因序列分析的泉水鱼遗传多样性研究 [J]. 广东农业科学, 2012, 39(1):6−8. doi: 10.3969/j.issn.1004-874X.2012.01.002 SI C L, ZHANG Q, MA B, et al. Genetic diversity of Pseudogrincheilus procheiluys based on mitochondrial cytochrome b sequence analysis [J]. Guangdong Agricultural Sciences, 2012, 39(1): 6−8.(in Chinese) doi: 10.3969/j.issn.1004-874X.2012.01.002
[19]	WYMAN S K, JANSEN R K, BOORE J L. Automatic annotation of organellar genomes with DOGMA [J]. Bioinformatics, 2004, 20(17): 3252−3255. doi: 10.1093/bioinformatics/bth352
[20]	LOWE T M, CHAN P P. tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes [J]. Nucleic Acids Research, 2016, 44(W1): W54−W57. doi: 10.1093/nar/gkw413
[21]	LASLETT D, CANBACK B. ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences [J]. Bioinformatics, 2008, 24(2): 172−175. doi: 10.1093/bioinformatics/btm573
[22]	SHARP P M, LI W H. The Codon adaptation index-a measure of directional synonymous Codon usage bias, and its potential applications [J]. Nucleic Acids Research, 1987, 15(3): 1281−1295. doi: 10.1093/nar/15.3.1281
[23]	陈宜瑜, 等. 中国动物志硬骨鱼纲鲤形目（中卷）[M]. 北京: 科学出版社, 1998.
[24]	EDGAR R C. MUSCLE: multiple sequence alignment with high accuracy and high throughput [J]. Nucleic Acids Research, 2004, 32(5): 1792−1797. doi: 10.1093/nar/gkh340
[25]	POSADA D. jModelTest: phylogenetic model averaging [J]. Molecular Biology and Evolution, 2008, 25(7): 1253−1256. doi: 10.1093/molbev/msn083
[26]	STAMATAKIS A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models [J]. Bioinformatics, 2006, 22(21): 2688−2690. doi: 10.1093/bioinformatics/btl446
[27]	MEYER A. DNA technology and phylogeny of fish. In: Beaumont A R. Genetics and Evolution of Aquatic Organisms [M]. London: Chapman and Hall, 1994, 219–249.
[28]	BROUGHTON R E, MILAM J E, ROE B A. The complete sequence of the zebrafish (Danio rerio) mitochondrial genome and evolutionary patterns in vertebrate mitochondrial DNA [J]. Genome Research, 2001, 11(11): 1958−1967. doi: 10.1101/gr.156801
[29]	ANDERSON S, BANKIER A T, BARRELL B G, et al. Sequence and organization of the human mitochondrial genome [J]. Nature, 1981, 290(5806): 457−465. doi: 10.1038/290457a0
[30]	OJALA D, MONTOYA J, ATTARDI G. tRNA punctuation model of RNA processing in human mitochondria [J]. Nature, 1981, 290(5806): 470−474. doi: 10.1038/290470a0
[31]	KOTLíK P, BERREBI P. Genetic subdivision and biogeography of the Danubian rheophilic barb Barbus petenyi inferred from phylogenetic analysis of mitochondrial DNA variation [J]. Molecular Phylogenetics and Evolution, 2002, 24(1): 10−18. doi: 10.1016/S1055-7903(02)00264-6
[32]	VON DER HEYDEN S, LIPINSKI M R, MATTHEE C A. Mitochondrial DNA analyses of the Cape hakes reveal an expanding, panmictic population for Merluccius capensis and population structuring for mature fish in Merluccius paradoxus [J]. Molecular Phylogenetics and Evolution, 2007, 42(2): 517−527. doi: 10.1016/j.ympev.2006.08.004
[33]	王中铎, 郭昱嵩, 陈荣玲, 等. 南海常见硬骨鱼类COI条码序列 [J]. 海洋与湖沼, 2009, 40(5):608−614. doi: 10.3321/j.issn:0029-814X.2009.05.014 WANG Z D, GUO Y S, CHEN R L, et al. COI barcoding sequences of teleosts in the South China Sea [J]. Oceanologia et Limnologia Sinica, 2009, 40(5): 608−614.(in Chinese) doi: 10.3321/j.issn:0029-814X.2009.05.014
[34]	刘思情, 张家波, 唐琼英, 等. 基于ND4和ND5基因序列分析的鳅超科鱼类系统发育关系 [J]. 动物学研究, 2010, 31(3):221−229. LIU S Q, ZHANG J B, TANG Q Y, et al. Phylogenetic relationships among cobitoidea based on mitochondrial ND4 and ND5 gene sequences [J]. Zoological Research, 2010, 31(3): 221−229.(in Chinese)