Turn off MathJax
Article Contents
Jian Zheng, Bingjie Chen, Tianxiang Gao, Na Song. The mitochondrial genome of Chaeturichthys stigmatias provides novel insight into the interspecific difference with Amblychaeturichthys hexanema[J]. Acta Oceanologica Sinica. doi: 10.1007/s13131-021-1787-1
Citation: Jian Zheng, Bingjie Chen, Tianxiang Gao, Na Song. The mitochondrial genome of Chaeturichthys stigmatias provides novel insight into the interspecific difference with Amblychaeturichthys hexanema[J]. Acta Oceanologica Sinica. doi: 10.1007/s13131-021-1787-1

The mitochondrial genome of Chaeturichthys stigmatias provides novel insight into the interspecific difference with Amblychaeturichthys hexanema

doi: 10.1007/s13131-021-1787-1
Funds:  The National Key R&D Program of China under contract No. 2018YFD0900905; the National Natural Science Foundation of China under contract No. 41776171.
More Information
  • Corresponding author: E-mail: songna624@163.com
  • Received Date: 2020-06-17
  • Accepted Date: 2020-08-24
  • Available Online: 2021-07-23
  • Chaeturichthys stigmatias and Amblychaeturichthys hexanema belong to the family Gobiidae, which are offshore warm fish species and widely distribute in the western Pacific Ocean. In this study, the mitochondrial cytochrome c oxidase subunit I (COI) sequences and 12S ribosomal RNA (12S rRNA) sequences were used to analyze the interspecific differences between the two species. The phylogenetic analysis showed that the interspecific distance was significantly higher than the intraspecific genetic distance. The Neighbor-Joining tree showed two separate clusters, without sharing haplotype. The mitochondrial genome sequence of C. stigmatias was also reported. This genome was 17 134 bp in size, with a high A+T content of 55.9%. The phylogenetic analysis based on the tandem 13 coding protein genes nucleotide sequences indicated that C. stigmatias showed a close relationship with A. hexanema. This study can provide the basic genetic data for two species and will help for constructing the phylogeny of the Gobiiade.
  • loading
  • [1]
    Boore J L. 2006. The use of genome-level characters for phylogenetic reconstruction. Trends in Ecology & Evolution, 21(8): 439–446
    [2]
    Burland T G. 2000. DNASTAR’s lasergene sequence analysis software. In: Misener S, Krawetz S A, eds. Bioinformatics Methods and Protocols. Totowa, NJ: Humana Press, 71–91
    [3]
    Chen Fenfang, Ma Hongyu, Ma Chunyan, et al. 2016. The complete mitochondrial genome sequence and gene organization of Amblychaeturichthys hexanema (Gobiidae: Amblychaeturichthys) with phylogenetic consideration. Mitochondrial DNA Part A, 27(6): 4687–4688. doi: 10.3109/19401736.2015.1106503
    [4]
    Cywinska A, Hunter F F, Hebert P D N. 2006. Identifying Canadian mosquito species through DNA barcodes. Medical and Veterinary Entomology, 20(4): 413–424. doi: 10.1111/j.1365-2915.2006.00653.x
    [5]
    East China Sea Fishery Research Institute of Chinese Academy of Fishery Sciences. 1990. The Fishes of Shanghai (in Chinese). Shanghai: Shanghai Scientific & Technical Publishers
    [6]
    Excoffier L, Laval G, Schneider S. 2005. Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online, 1: 47–50
    [7]
    Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39(4): 783–791. doi: 10.1111/j.1558-5646.1985.tb00420.x
    [8]
    Gao Tianxiang, Ji Dongping, Xiao Yongshuang, et al. 2011. Description and DNA barcoding of a new Sillago species, Sillago sinica (Perciformes: Sillaginidae), from coastal waters of China. Zoological Studies, 50(2): 254–263
    [9]
    Guo Enmian, Liu Yuan, Liu Jing, et al. 2010. DNA barcoding discriminates Pampus minor (Liu et al., 1998) from Pampus species. Chinese Journal of Oceanology and Limnology, 28(6): 1266–1274. doi: 10.1007/s00343-010-9917-1
    [10]
    Han Dongyan, Xue Ying, Ji Yupeng, et al. 2013. Feeding ecology of Amblychaeturichthys hexanema in Jiaozhou Bay, China. Chinese Journal of Applied Ecology (in Chinese), 24(5): 1446–1452
    [11]
    Hebert P D N, Cywinska A, Ball S L, et al. 2003a. Biological identifications through DNA barcodes. Proceedings of the Royal Society B: Biological Sciences, 270(1512): 313–321. doi: 10.1098/rspb.2002.2218
    [12]
    Hebert P D N, Ratnasingham S, Dewaard J R. 2003b. Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society B: Biological Sciences, 270(Suppl 1): S96–S99
    [13]
    Inoue J G, Miya M, Tsukamoto K, et al. 2001. A mitogenomic perspective on the basal teleostean phylogeny: resolving higher-level relationships with longer DNA sequences. Molecular Phylogenetics and Evolution, 20(2): 275–285. doi: 10.1006/mpev.2001.0970
    [14]
    Jin Xiaoxiao, Wang Rixin, Xu Tianjun, et al. 2012. Complete mitochondrial genome of Oxuderces dentatus (Perciformes, Gobioidei). Mitochondrial DNA, 23(2): 142–144. doi: 10.3109/19401736.2012.660930
    [15]
    Lavoué S, Miya M, Saitoh K, Ishiguro N B, et al. 2007. Phylogenetic relationships among anchovies, sardines, herrings and their relatives (Clupeiformes), inferred from whole mitogenome sequences. Molecular Phylogenetics and Evolution, 43(3): 1096–1105. doi: 10.1016/j.ympev.2006.09.018
    [16]
    Li Yongzhen, Chen Guobao, Sun Dianrong. 2000. Analysis of the composition of fishes in the Pearl River estuarine waters. Journal of Fisheries of China (in Chinese), 24(4): 312–317
    [17]
    Liu Jinxian, Gao Tianxiang, Wu Shifang, et al. 2007. Pleistocene isolation in the Northwestern Pacific marginal seas and limited dispersal in a marine fish, Chelon haematocheilus (Temminck & Schlegel, 1845). Molecular Ecology, 16(2): 275–288
    [18]
    Liu Lianwei, Xu Qianghua, Chen Xinjun. 2012. Population genetic structure of Ommastrephes bartramii in the North Pacific Ocean based on the COI and Cytb gene sequences analysis. Journal of Fisheries of China (in Chinese), 36(11): 1675–1684. doi: 10.3724/SP.J.1231.2012.27955
    [19]
    Lu Zhichuang, Xu Shengyong, Song Na, et al. 2016. Analysis of the diet of finless porpoise (Neophocaena asiaeorientalis sunameri) based on prey morphological characters and DNA barcoding. Conservation Genetics Resources, 8(4): 523–531. doi: 10.1007/s12686-016-0575-2
    [20]
    Masaki M, Yukuto S, Fukunaga, et al. 2015. Analytical pipeline for DNA sequences amplified by mifish primers. Biological Journal of the Linnean Society, 73: 259–316
    [21]
    Mei Chun, Xu Binduo, Xue Ying, et al. 2010. Fish community structure and species diversity during autumn and winter in the central waters of Jiaozhou Bay. Journal of Fishery Sciences of China (in Chinese), 17(1): 110–118
    [22]
    Meng Kuankuan, Wang Jing, Zhang Chongliang, et al. 2017. The fishery biological characteristics of Chaeturichthys stigmatias in the Yellow River Estuary and its adjacent waters. Journal of Fishery Sciences of China (in Chinese), 24(5): 939–945. doi: 10.3724/SP.J.1118.2017.17083
    [23]
    Meusnier I, Singer G A C, Landry J F, et al. 2008. A universal DNA mini-barcode for biodiversity analysis. BMC Genomics, 9: 214. doi: 10.1186/1471-2164-9-214
    [24]
    Miya M, Satoh T P, Nishida M. 2005. The phylogenetic position of toadfishes (Order Batrachoidiformes) in the higher ray-finned fish as inferred from partitioned Bayesian analysis of 102 whole mitochondrial genome sequences. Biological Journal of the Linnean Society, 85(3): 289–306. doi: 10.1111/j.1095-8312.2005.00483.x
    [25]
    Miya M, Takeshima H, Endo H, et al. 2003. Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Molecular Phylogenetics and Evolution, 26(1): 121–138. doi: 10.1016/S1055-7903(02)00332-9
    [26]
    Nelson J S, Grande T C, Wilson M V H. 2006. Fishes of the World. 4th ed. New York: John Wiley and Sons, 601
    [27]
    Pfenninger M, Nowak C, Kley C, et al. 2007. Utility of DNA taxonomy and barcoding for the inference of larval community structure in morphologically cryptic Chironomus (Diptera) species. Molecular Ecology, 16(9): 1957–1968. doi: 10.1111/j.1365-294X.2006.03136.x
    [28]
    Puckridge M, Andreakis N, Appleyard S A, et al. 2013. Cryptic diversity in flathead fishes (Scorpaeniformes: Platycephalidae) across the Indo-West Pacific uncovered by DNA barcoding. Molecular Ecology Resources, 13(1): 32–42. doi: 10.1111/1755-0998.12022
    [29]
    Qu Liyan. 2018. Phylogenetic analysis of 28 species of gobies in the East China Sea based on morphology, barcode and nuclear genes (in Chinese) [dissertation]. Shanghai: Shanghai Ocean University
    [30]
    Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4(4): 406–425
    [31]
    Sambrook J, Fritsch E F, Maniatis T. 1989. Molecular Cloning: A Laboratory Manual. 2nd ed. Harbor, NY: Cold Spring Harbor Laboratory Press
    [32]
    Shokralla S, Hellberg R S, Handy S M, et al. 2015. A DNA mini-barcoding system for authentication of processed fish products. Scientific Reports, 5: 15894. doi: 10.1038/srep15894
    [33]
    Smith P J, McVeagh S M, Steinke D. 2008. DNA barcoding for the identification of smoked fish products. Journal of Fish Biology, 72(2): 464–471. doi: 10.1111/j.1095-8649.2007.01745.x
    [34]
    Stoeckle M. 2003. Taxonomy, DNA, and the barcode of life. Bioscience, 53(9): 796–797. doi: 10.1641/0006-3568(2003)053[0796:TDATBC]2.0.CO;2
    [35]
    Suh K I, Hwang J M, Bae Y J, et al. 2019. Comprehensive DNA barcodes for species identification and discovery of cryptic diversity in mayfly larvae from South Korea: implications for freshwater ecosystem biomonitoring. Entomological Research, 49(1): 46–54. doi: 10.1111/1748-5967.12334
    [36]
    Sun Yuena, Wang Tao, Jin Xiaoxiao. 2015. Unusual features of control region and a novel NADH 6 genes in mitochondrial genome of the finespot goby, Chaeturichthys stigmatias (Perciformes, Gobiidae). Mitochondrial DNA, 26(5): 665–667. doi: 10.3109/19401736.2013.840598
    [37]
    Sun Peng, Yin Fei, Shi Zhaohong, et al. 2012. Phylogenetic relationships and population structure of Pampus in the South China Sea inferred from COI gene segments. Marine Sciences (in Chinese), 36(6): 15–21
    [38]
    Tamura K, Peterson D, Peterson N, et al. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28(10): 2731–2739. doi: 10.1093/molbev/msr121
    [39]
    Wang Lijuan, Wu Zhihao, Liu Mengxia, et al. 2018. DNA barcoding of marine fish species from Rongcheng Bay, China. PeerJ, 6: e5013. doi: 10.7717/peerj.5013
    [40]
    Ward R D, Holmes B H, Yearsley G K. 2008. DNA barcoding reveals a likely second species of Asian sea bass (barramundi) (Lates calcarifer). Journal of Fish Biology, 72(2): 458–463. doi: 10.1111/j.1095-8649.2007.01703.x
    [41]
    Ward R D, Zemlak T S, Innes B H, et al. 2005. DNA barcoding Australia’s fish species. Philosophical Transactions of the Royal Society B: Biological Sciences, 360(1462): 1847–1857. doi: 10.1098/rstb.2005.1716
    [42]
    Wu Hanlin, Zhong Junsheng. 2008. Fauna Sinica, Osfichthyes, Perciformes (V), Gobioidei. Beijing: Sdence Press, 211–215
    [43]
    Wyman S K, Jansen R K, Boore J L. 2004. Automatic annotation of organellar genomes with DOGMA. Bioinformatics, 20(17): 3252–3255. doi: 10.1093/bioinformatics/bth352
    [44]
    Xing Bingpeng, Lin Heshan, Zhang Zhilan, et al. 2018. DNA barcoding for identification of fish species in the Taiwan Strait. PLoS One, 13(6): e0198109. doi: 10.1371/journal.pone.0198109
    [45]
    Yu Xin. 2014. Methodology and case studies of fish otolith morphology and microchemistry analysis in stock discrimination (in Chinese) [dissertation]. Qingdao: Institute of Oceanography of Chinese Academy of Sciences
    [46]
    Zemlak T S, Ward R D, Connell A D, et al. 2009. DNA barcoding reveals overlooked marine fishes. Molecular Ecology Resources, 9(S1): 237–242
  • 加载中

Catalog

    通讯作者: 陈斌, bchen63@163.com
    • 1. 

      沈阳化工大学材料科学与工程学院 沈阳 110142

    1. 本站搜索
    2. 百度学术搜索
    3. 万方数据库搜索
    4. CNKI搜索

    Figures(4)  / Tables(5)

    Article Metrics

    Article views (44) PDF downloads(3) Cited by()
    Proportional views
    Related

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return