|Table of Contents|

First Complete Mitochondrial Genome of Lauridromia dehaaniand Phylogenetic Analysis of Brachyura(PDF)

《南京师大学报（自然科学版）》[ISSN:1001-4616/CN:32-1239/N]

Issue:
2021年01期
Page:
79-90
Research Field:
·生物学·
Publishing date:

Info

Title:
First Complete Mitochondrial Genome of Lauridromia dehaaniand Phylogenetic Analysis of Brachyura
Author(s):
Xing Yuhui1; Zhou Hao1; Zou Yongmei2; Yao Wenjia3; Zhang Chenling2; Ying Xuechen1; Zou Xiuwen1; Chen Jianqin2
(1.Nanjing Normal University Zhongbei College,Zhenjiang 212310,China)(2.School of Life Sciences,Chemistry and Chemical Engineering,Jiangsu Second Normal University,Nanjing 210013,China)(3.School of Life Sciences,Nanjing Normal University,Nanjing 210023,China)
Keywords:
Lauridromia dehaani; mitochondrial genome; Podotremata; Dromiidea
PACS:
Q959.223+.63
DOI:
10.3969/j.issn.1001-4616.2021.01.012
Abstract:
The mitochondrial genome of Lauridromia dehaani was firstly determined by using high-throughput sequencing in this research. The results indicated that the complete mitogenome of L.dehaani was 15 755 bp in length,containing 37 genes. Comparative mitogenomic features including the secondary structures of tRNAs,nucleotide composition,start/stop codons and selective pressures for protein coding genes indicated special evolution that trnS1 lack DHU stem arm,which has been commonly observed in brachyuran mitogenomes. AT nucleotide content and selective pressures varied among different functional protein coding genes. Unusual start codon ACG for cox1 was commonly found in the published primitive crabs. Longer intergenic intervals(32 bp-130 bp)were observed in break point where gene rearranged and guided for deducing the generation of rearrangement. With respect to the ancestral brachyuran mitochondrial gene order,two protein coding genes(nad6 and cob),and 4 tRNA genes(trnH,trnF,trnS2 and trnT)were rearranged,which is a novel mitogenomic arrangement pattern. Two dromiids shared a translocation of trnH common in brachyuran mitogenomes,and formed a sister group with species from Homoloidea as basal branch of Brachyura in phylogenetic trees,reconfirming Dromioidea belong to Brachyura. The robust phylogenetic tree among brachyuran section and subsection were generated by using mitochondrial DNA sequence and exhibited relationships as:(Dromioidea,Homoloidea),(Raninoidea,Eubrachyura).

References:

[1] DAVIE P J F,GUINOT D,NG P K L. Systematics and classification of brachyura[M]//Treatise on zoology antomy,taxonomy,biology. Decapoda:The Crustacea,2015.
[2]MARTIN J W,DAVIS G E. An updated classification of the recent crustacea[J]. Natural history museum of Los Angeles country science series,2001,39:1-124.
[3]GUINOT D,TAVARES M. Une nouvelle famille de Crabes du Crétacé,et la notion de Podotremata Guinot,1977(Crustacea,Decapoda,Brachyura)[J]. Zoosystema,2001,23:507-546.
[4]GUINOT D,JAMIESON B G M,FORGES B R D. Relationship of Homolidae and Dromiidae:evidence from spermatozoal ultrastructure(Crustacea,Decapoda)[J]. Acta zoologica,1994,75(3):255-267.
[5]GUINOT D. Propositions pour une nouvelle classification des Crustacés Décapodes Brachyoures[J]. Comptes rendus hebdomadaires des séances de académie des sciences,1977,285:1049-1052.
[6]DE SAINT L M. Sur la classification et la,phylogenie des Crustacés Décapodes Brachyoures. I. Podotremata Guinot,1977,et Eubrachyura sect,nov[J]. Comptes Rendus de I’ academie des sciences paris D,1980,290:1265-1268.
[7]NG P K L,GUINOT D,DAVIE P J F. Systema Brachyurorum:part 1. An annotated checklist of extant brachyuran crabs of the world[J]. The raffles bulletin of zoology,2008,17:1-286.
[8]陈惠莲,孙海宝. 中国动物志无脊椎动物第三十卷节肢动物门甲壳动物亚门短尾次目低等海洋蟹类[M]. 北京:科学出版社,2012.
[9]刘瑞玉. 中国海洋生物名录[M]. 北京:科学出版社,2008.
[10]TSANG L M,SCHUBART C D,AHYONG S T,et al. Evolutionary history of true crabs(Crustacea:Decapoda:Brachyura)and the origin of freshwater crabs[J]. Molecular biology and evolution,2014,31(5):1173-1187.
[11]AHYONG S T,LAI J C,SHARKEY D,et al. Phylogenetics of the brachyuran crabs(Crustacea:Decapoda):the status of Podotremata based on small subunit nuclear ribosomal RNA[J]. Molecular phylogenetics and evolution,2007,45(2):576-586.
[12]师国慧. 五种肢孔派(Podotremata)蟹类线粒体基因组测定及短尾类系统发生研究[D]. 北京:中国科学院大学,2015.
[13]MCLAY C L. Crustacea decapoda:revision of the family dynomenidae[J]//Crosnier,A. Résultats des campagnes Musorstomzo 20. Mémoires du muséum national d’ histoire natureue,1999,180:427-569.
[14]AHYONG S T,O’MEALLY D. Phylogeny of the Decapoda Reptantia:resolution using three molecular loci and morphology[J]. The raffles bulletin of zoology,2004,52(2):673-693.
[15]KARASAWA H,SCHWEITZER C E,FELDMANN R M. Phylogenetic analysis and revised classification of podotrematous Brachyura(Decapoda)including extinct and extant families[J]. Journal of crustacean biology,2011,31:523-565.



[16]JI Y K,WANG A,LU J J,et al. Mitochondrial genomes of two brachyuran crabs(Crustacea:Decapoda)and phylogenetic analysis[J]. Journal of crustacean biology,2014,34(4):494-503.

[17]陈建琴,张振华,邢雨辉,等. 光滑异装蟹(Heteropanope glabra)线粒体基因组测定及其在系统发生研究中的意义[J]. 南京师大学报(自然科学版),2018,41(4):114-120.
[18]BOORE J L. Animal mitochondrial genomes[J]. Nucleic acids research,1999,27(8):1767-1780.
[19]TAN M H,GAN H M,LEE Y P,et al. Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition[J]. Scientific reports,2019,9:10756.
[20]SUN H Y,ZHOU K Y,SONG D X. Mitochondrial genome and phylogenetic reconstruction of arthropods[J]. Zoological research,2003,24(6):467-479.
[21]SUN H Y,ZHOU K Y,SONG D X. Mitochondrial genome of the Chinese mitten crab Eriocheir japonica sinenesis(Brachyura:Thoracotremata:Grapsoidea)reveals a novel gene order and two target regions of gene rearrangements[J]. Gene,2005,349:207-217.
[22]XING Y H,ZHOU L J,HOU Y,et al. Complete mitochondrial genomes from two species of Chinese freshwater crabs of the genus Sinopotamon recovered using next-generation sequencing reveal a novel gene order(Brachyura,Potamidae)[J]. ZooKeys,2017,705:41-60.
[23]CHEN J Q,XING Y H,YAO W J,et al. Characterization of four new mitogenomes from Ocypodoidea and Grapsoidea,and phylomitogenomic insights into thoracotreme evolution[J]. Gene,2018,675(30):27-35.
[24]TAN M H,GAN H M,LEE Y P,et al. ORDER within the chaos:insights into phylogenetic relationships within the Anomura(Crustacea:Decapoda)from mitochondrial sequences and gene order rearrangements[J]. Molecular phylogenetics and evolution,2018,127:320-331.
[25]BASSO A,BABBUCCI M,PAULETTO M,et al. The highly rearranged mitochondrial genomes of the crabs Maja crispate and Maja squinado(Majidae)and gene order evolution in Brachyura[J]. Scientific reports,2017(7):4096.
[26]戴爱云,杨思谅,宋玉枝,等. 中国海洋蟹类[M]. 北京:海洋出版社,1986.
[27]BERNT M,DONATH A,JüHLING F,et al. MITOS:improved de novo metazoan mitochondrial genome annotation[J]. Molecular phylogenetics and evolution,2013,69(2):313-319.
[28]WANG D,ZHANG Y,ZHANG Z,et al. KaKs_Calculator 2.0:a toolkit incorporating gamma-series methods and sliding window strategies[J]. Genomics,proteomics and bioinformatics,2010,8(1):77-80.
[29]KATOH K,STANDLEY D M. MAFFT multiple sequence alignment software version 7:improvements in performance and usability[J]. Molecular biology and evolution,2013,30(4):772-780.
[30]TALAVERA G,CASTRESANA J. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments[J]. Systematic biology,2007,56(4):564-577.
[31]LANFEAR R,CALCOTT B,HO S Y,et al. Partitionfinder:combined selection of partitioning schemesand substitution models for phylogenetic analyses[J]. Molecular biology and evolution,2012,29(6):1695-1701.
[32]HOANG D T,CHERNOMOR O,VON HAESELER A,et al. UFBoot2:Improving the ultrafast bootstrap approximatio molecular[J]. Biology and evolution,2017,35(2):518-522.
[33]NGUYEN L T,SCHMIDT H A,VON HAESELER A,et al. IQ-TREE:a fast and effective stochastic algorithm for estimating Maximum-Likelihood phylogenies[J]. Molecular biology and evolution,2015,32(1):268-274.
[34]HUELSENBECK J P,RONQUIST F. MRBAYES:Bayesian inference of phylogenetic trees[J]. Bioinformatics,2001,17(8):754-755.
[35]SHI G H,CUI Z X,HUI M,et al. Unusual sequence features and gene rearrangements of primitive crabs revealed by three complete mitochondrial genomes of Dromiacea[J]. Comparative biochemistry and physiology part D genomics and proteomics,2016,20:65-73.
[36]SHI G H,CUI Z X,HUI M,et al. The complete mitochondrial genomes of Umalia orientalis and Lyreidus brevifrons:the phylogenetic position of the family Raninidae within Brachyuran crabs[J]. Marine genomics,2015,21:53-61.
[37]OJALA D,MONTOYA J,ATTARDI G. tRNA punctuation model of RNA processing in human mitochondria[J]. Nature,1981,290(5806):470-474.
[38]YAMAUCHI M M,MIYA M U,NISHIDA M. Complete mitochondrial DNA sequence of the swimming crab,Portunus trituberculatus(Crustacea:Decapoda:Brachyura)[J]. Gene,2003,311:129-135.
[39]MILLER A D,MURPHY N P,BURRIDGE C P,et al. Complete mitochondrial DNA sequences of the decapod crustaceans Pseudocarcinus gigas(Menippidae)and Macrobrachium rosenbergii(Palaemonidae)[J]. Marine biotechnology,2005,7:339-349.
[40]MA H Y,MA CY,LI X C,et al. The complete mitochondrial genome sequence and gene organization of the mud crab(Scylla paramamosain)with phylogenetic consideration[J]. Gene,2013,519:120-127.
[41]MA C Y,MA H Y,REN G J,et al. Characterization of the complete mitochondrial genome of Portunus pelagicus with implications for phylogenomics[J]. Genetics and molecular research,2016,15(3):gmr.15038719.
[42]BAI J,XU S,NIE Z,et al. The complete mitochondrial genome of Huananpotamon lichuanense(Decapoda:Brachyura)with phylogenetic implications for freshwater crabs[J]. Gene,2018,646:217-226.
[43]JIA X N,XU S X,BAI J,et al. The complete mitochondrial genome of Somanniathelphusa boyangensis and phylogenetic analysis of Genus Somanniathelphusa(Crustacea:Decapoda:Parathelphusidae)[J]. PLoS one,2018,13(2):e0192601.
[44]WILLIAMSON D I. Larval characters and the origin of crabs(Crustacea,Decapoda,Brachyura)[J]. Thalassia jugoslavica,1976,10:401-414.
[45]WILLIAMSON D I. Evolutionary trends in larval form[J]//FINCHAM A A,RAINBOW P S. Aspects of decapod crustacean biology. Symposium of the zoological society of london,1988,59:1-375.[46]MARTIN J W. Crabs of the family Homolodromiidae,III. First record of the larvae[J]. Journal of crustacean biology,1991,11(1):156-161.[47]SPEARS T,ABELE L G,KIM W. The monophyly of brachyuran crabs:a phylogenetic study based on 18S rRNA[J]. Systematic biology,1992,41(4):446-461.[48]JAMIESON B G M,GUINOT D,FORGES B R D. Phylogeny of the Brachyura(Crustacea,Decapoda)evidence from spermatozoal ultrastructure[J]. Memoires du Muséum national d’ histoire naturelle pairs,1995,166:265-283.[49]SCHOLTZ G,RICHTER S. Phylogenetic systematics of the reptantian Decapoda(Crustacea,Malacostraca)[J]. Zoological journal of the linnean society,1995,113(3):289-328.[50]AHYONG S T,LOWRY J K,ALONSO M,et al. Subphylum Crustacea Brünnich,1772[J]//ZHANG Z Q. Animal biodiversity:an outline of higher-level classification and survey of taxonomic richness. Zootaxa,2011,3148:165-191.[51]GUINOT D,TAVARES M,CASTRO P. Significance of the sexual openings and supplementary structures on the phylogeny of brachyuran crabs(Crustacea,Decapoda,Brachyura),with new nomina for higher-ranked podotreme taxa[J]. Zootaxa,2013,3665(1):1-414.[52]VON STERNBERG R,CUMBERLIDGE N. On the Heterotreme-Thoracotreme distinction in the Eubrachyura de Saint Laurent,1980(Decapoda,Brachyura)[J]. Crustaceana,2001,74(4):321-338.[53]VON STERNBERG R,CUMBERLIDGE N. Notes on the position of the true freshwater crabs within the brachyrhynchan Eubrachyura(Crustacea:Decapoda:Brachyura)[J]. Hydrobiologia,2001,449:21-39.[54]KA M,JING Q,LIN C W,et al. Phylogenomic analyses of brachyuran crabs support early divergence of primary freshwater crabs[J]. Molecular phylogenetics and evolution,2019,135:62-66.

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Last Update: 2021-03-15