Mitochondrial genome of Chthamalus challengeri(Crustacea:Sessilia): gene order comparison within Chthamalidae and phylogenetic consideration within Balanomorpha
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摘要
Acorn barnacles are important model species in researches on intertidal ecology, larval development and biofouling. At present, with the development of mitochondrial genomics, it is helpful to understand the phylogenetic relationship from the mitogenomic level. The complete mitochondrial genome of Chthamalus challengeri was presented. The genome is a circular molecule of 15 358 bp. Compared with other species in Balanomorpha, the non-coding region is longer, while the length of the genes is similar to the other species. The overall A+T content of the mitochondrial genome of C. challengeri is 70.5%. There are variations of initiation and stop codons in the known Balanomorpha mitochondrial genomes. The C. challengeri and C. antennatus within the same genus share the identical gene arrangement. However, the gene arrangement of different genera in Chthamalidae is different,as there is a translocation between two tRNA genes and an inversion involving a large gene block. In particular,both srRNA and lrRNA of the two species in Chthamalus are encoded in the heavy strand, differing from the former Balanomorpha species. The topology and gene arrangement in Chthamalidae support each other.Phylogenetic analysis indicates that the Chthamalidae is monophyletic, while the Balanidae and Archaeobalanidae are polyphyletic.
Acorn barnacles are important model species in researches on intertidal ecology, larval development and biofouling. At present, with the development of mitochondrial genomics, it is helpful to understand the phylogenetic relationship from the mitogenomic level. The complete mitochondrial genome of Chthamalus challengeri was presented. The genome is a circular molecule of 15 358 bp. Compared with other species in Balanomorpha, the non-coding region is longer, while the length of the genes is similar to the other species. The overall A+T content of the mitochondrial genome of C. challengeri is 70.5%. There are variations of initiation and stop codons in the known Balanomorpha mitochondrial genomes. The C. challengeri and C. antennatus within the same genus share the identical gene arrangement. However, the gene arrangement of different genera in Chthamalidae is different,as there is a translocation between two tRNA genes and an inversion involving a large gene block. In particular,both srRNA and lrRNA of the two species in Chthamalus are encoded in the heavy strand, differing from the former Balanomorpha species. The topology and gene arrangement in Chthamalidae support each other.Phylogenetic analysis indicates that the Chthamalidae is monophyletic, while the Balanidae and Archaeobalanidae are polyphyletic.
Acorn barnacles are important model species in researches on intertidal ecology, larval development and biofouling. At present, with the development of mitochondrial genomics, it is helpful to understand the phylogenetic relationship from the mitogenomic level. The complete mitochondrial genome of Chthamalus challengeri was presented. The genome is a circular molecule of 15 358 bp. Compared with other species in Balanomorpha, the non-coding region is longer, while the length of the genes is similar to the other species. The overall A+T content of the mitochondrial genome of C. challengeri is 70.5%. There are variations of initiation and stop codons in the known Balanomorpha mitochondrial genomes. The C. challengeri and C. antennatus within the same genus share the identical gene arrangement. However, the gene arrangement of different genera in Chthamalidae is different,as there is a translocation between two tRNA genes and an inversion involving a large gene block. In particular,both srRNA and lrRNA of the two species in Chthamalus are encoded in the heavy strand, differing from the former Balanomorpha species. The topology and gene arrangement in Chthamalidae support each other.Phylogenetic analysis indicates that the Chthamalidae is monophyletic, while the Balanidae and Archaeobalanidae are polyphyletic.
引文
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Boore J L.1999.Animal mitochondrial genomes.Nucleic Acids Research,27(8):1767-1780,doi:10.1093/nar/27.8.1767
Chan B K K,Corbari L,Moreno P A R,et al.2017.Molecular phylogeny of the lower acorn barnacle families(Bathylasmatidae,Chionelasmatidae,Pachylasmatidae and Waikalasmatidae)(Cirripedia:Balanomorpha)with evidence for revisions in family classification.Zoological Journal of the Linnean Society,180(3):542-555,doi:10.1093/zoolinnean/zlw005
Corradi N,Bonen L.2012.Mitochondrial genome invaders:an unselfish role as molecular markers.New Phytologist,196(4):963-965,doi:10.1111/j.1469-8137.2012.04354.x
Guindon S,Dufayard J F,Lefort V,et al.2010.New algorithms and methods to estimate maximum-likelihood phylogenies:assessing the performance of PhyML 3.0.Systematic Biology,59(3)307-321,doi:10.1093/sysbio/syq010
Kumar S,Stecher G,Tamura K.2016.MEGA7:Molecular evolutionary genetics analysis version 7.0 for bigger datasets.Molecular Biology and Evolution,33(7):1870-1874,doi:10.1093/molbev/msw054
Lavrov D V,Brown W M,Boore J L.2004.Phylogenetic position of the Pentastomida and(pan)crustacean relationships.Proceedings of the Royal Society of London.Series B:Biological Sciences,271(1538):537-544,doi:10.1098/rspb.2003.2631
Librado P,Rozas J.2009.DnaSP v5:a software for comprehensive analysis of DNA polymorphism data.Bioinformatics,25(11):1451-1452,doi:10.1093/bioinformatics/btp187
Lim J T,Hwang U W.2006.The complete mitochondrial genome of Pollicipes mitella(Crustacea,Maxillopoda,Cirripedia):nonmonophylies of maxillopoda and crustacea.Molecules and Cells,22(3):314-322
Liu Qiuning,Chai Xinyue,Bian Dandan,et al.2016.The complete mitochondrial genome of Plodia interpunctella(Lepidoptera Pyralidae)and comparison with other Pyraloidea insects.Genome,59(1):37-49,doi:10.1139/gen-2015-0079
Liu Ruiyu,Ren Xianqiu.2007.Fauna Sinica(in Chinese).Beijing:Science Press,293-296.
Lohse M,Drechsel O,Kahlau S,et al.2013.OrganellarGenomeDRAW-a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets.Nucleic Acids Research,41(Web Server issue):W575-W581
Perna N T,Kocher T D.1995.Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes.Journal of Molecular Evolution,41(3):353-358,doi:10.1007/BF01215182
Shen Xin,Chan B K K,Tsang L M.2015a.The complete mitochondrial genome of common fouling barnacle Amphibalanus amphitrite(Darwin,1854)(Sessilia:Balanidae)reveals gene rearrangements compared to pancrustacean ground pattern.Mitochondrial DNA,26(5):773-774,doi:10.3109/19401736.2013.855745
Shen Xin,Chan B K K,Tsang L M.2016a.The mitochondrial genome of Nobia grandis Sowerby,1839(Cirripedia:Sessilia):the first report from the coral-inhabiting barnacles family Pyrgomatidae.Mitochondrial DNA,27(1):339-341,doi:10.3109/194017362014.892106
Shen Xin,Chu Kahou,Chan B K K,et al.2016b.The complete mitochondrial genome of the fire coral-inhabiting barnacle Megabalanus ajax(Sessilia:Balanidae):gene rearrangements and atypical gene content.Mitochondrial DNA,27(2):1173-1174doi:10.3109/19401736.2014.936424
Shen Xin,Ma Xiaoyin,Ren Jianfeng,et al.2009.A close phylogenetic relationship between Sipuncula and Annelida evidenced from the complete mitochondrial genome sequence of Phascolosoma esculenta.BMC Genomics,10:136,doi:10.1186/1471-2164-10-136
Shen Xin,Sun Song,Zhao Fangqing,et al.2016c.Phylomitogenomic analyses strongly support the sister relationship of the Chaetognatha and Protostomia.Zoologica Scripta,45(2):187-199,doi10.1111/zsc.12140
Shen Xin,Tian Mei,Meng Xueping,et al.2012.Complete mitochondrial genome of Membranipora grandicella(Bryozoa:Cheilostomatida)determined with next-generation sequencing:The first representative of the suborder Malacostegina.Comparative Biochemistry and Physiology Part D:Genomics and Proteomics,7(3):248-253,doi:10.1016/j.cbd.2012.03.003
Shen Xin,Tsang L M,Chu Kahou,et al.2015b.Mitochondrial genome of the intertidal acorn barnacle Tetraclita serrata Darwin1854(Crustacea:Sessilia):Gene order comparison and phylogenetic consideration within Sessilia.Marine Genomics,22:63-69,doi:10.1016/j.margen.2015.04.004
Shen Xin,Tsang L M,Chu Kahou,et al.2017.A unique duplication of gene cluster(S2-C-Y)in Epopella plicata(Crustacea)mitochondrial genome and phylogeny within Cirripedia.Mitochondrial DNA,28(2):285-287,doi:10.3109/19401736.2015.1118082
Shen Xin,Tsoi K H,Cheang C C.2016d.The model barnacle Balanus balanus Linnaeus,1758(Crustacea:Maxillopoda:Sessilia)mitochondrial genome and gene rearrangements within the family Balanidae.Mitochondrial DNA,27(3):2112-2114
Tsang L M,Chu Kahou,Nozawa Y,et al.2014.Morphological and host specificity evolution in coral symbiont barnacles(Balanomorpha:Pyrgomatidae)inferred from a multi-locus phylogeny Molecular Phylogenetics and Evolution,77:11-22,doi:10.1016/j.ympev.2014.03.002
Tsang L M,Shen Xin,Cheang C C,et al.2017.Gene rearrangement and sequence analysis of mitogenomes suggest polyphyly of Archaeobalanid and Balanid barnacles(Cirripedia:Balanomorpha).Zoologica Scripta,46(6):729-739,doi:10.1111/zsc.12246
Tsang L M,Shen Xin,Chu Kahou,et al.2015.Complete mitochondrial genome of the acorn barnacle Striatobalanus amaryllis(Crustacea:Maxillopoda):the first representative from Archaeobalanidae.Mitochondrial DNA,26(5):761-762,doi:10.3109/19401736.2013.855739
Wares J P.2015.Mitochondrial evolution across lineages of the vampire barnacle Notochthamalus scabrosus.Mitochondrial DNA26(1):7-10,doi:10.3109/19401736.2013.825791
Zhang Wenqi,Zhang Minghao.2012.Phylogeny and evolution of Cervidae based on complete mitochondrial genomes.Genetics and Molecular Research,11(1):628-635,doi:10.4238/2012.March.14.6
Boore J L.1999.Animal mitochondrial genomes.Nucleic Acids Research,27(8):1767-1780,doi:10.1093/nar/27.8.1767
Chan B K K,Corbari L,Moreno P A R,et al.2017.Molecular phylogeny of the lower acorn barnacle families(Bathylasmatidae,Chionelasmatidae,Pachylasmatidae and Waikalasmatidae)(Cirripedia:Balanomorpha)with evidence for revisions in family classification.Zoological Journal of the Linnean Society,180(3):542-555,doi:10.1093/zoolinnean/zlw005
Corradi N,Bonen L.2012.Mitochondrial genome invaders:an unselfish role as molecular markers.New Phytologist,196(4):963-965,doi:10.1111/j.1469-8137.2012.04354.x
Guindon S,Dufayard J F,Lefort V,et al.2010.New algorithms and methods to estimate maximum-likelihood phylogenies:assessing the performance of PhyML 3.0.Systematic Biology,59(3)307-321,doi:10.1093/sysbio/syq010
Kumar S,Stecher G,Tamura K.2016.MEGA7:Molecular evolutionary genetics analysis version 7.0 for bigger datasets.Molecular Biology and Evolution,33(7):1870-1874,doi:10.1093/molbev/msw054
Lavrov D V,Brown W M,Boore J L.2004.Phylogenetic position of the Pentastomida and(pan)crustacean relationships.Proceedings of the Royal Society of London.Series B:Biological Sciences,271(1538):537-544,doi:10.1098/rspb.2003.2631
Librado P,Rozas J.2009.DnaSP v5:a software for comprehensive analysis of DNA polymorphism data.Bioinformatics,25(11):1451-1452,doi:10.1093/bioinformatics/btp187
Lim J T,Hwang U W.2006.The complete mitochondrial genome of Pollicipes mitella(Crustacea,Maxillopoda,Cirripedia):nonmonophylies of maxillopoda and crustacea.Molecules and Cells,22(3):314-322
Liu Qiuning,Chai Xinyue,Bian Dandan,et al.2016.The complete mitochondrial genome of Plodia interpunctella(Lepidoptera Pyralidae)and comparison with other Pyraloidea insects.Genome,59(1):37-49,doi:10.1139/gen-2015-0079
Liu Ruiyu,Ren Xianqiu.2007.Fauna Sinica(in Chinese).Beijing:Science Press,293-296.
Lohse M,Drechsel O,Kahlau S,et al.2013.OrganellarGenomeDRAW-a suite of tools for generating physical maps of plastid and mitochondrial genomes and visualizing expression data sets.Nucleic Acids Research,41(Web Server issue):W575-W581
Perna N T,Kocher T D.1995.Patterns of nucleotide composition at fourfold degenerate sites of animal mitochondrial genomes.Journal of Molecular Evolution,41(3):353-358,doi:10.1007/BF01215182
Shen Xin,Chan B K K,Tsang L M.2015a.The complete mitochondrial genome of common fouling barnacle Amphibalanus amphitrite(Darwin,1854)(Sessilia:Balanidae)reveals gene rearrangements compared to pancrustacean ground pattern.Mitochondrial DNA,26(5):773-774,doi:10.3109/19401736.2013.855745
Shen Xin,Chan B K K,Tsang L M.2016a.The mitochondrial genome of Nobia grandis Sowerby,1839(Cirripedia:Sessilia):the first report from the coral-inhabiting barnacles family Pyrgomatidae.Mitochondrial DNA,27(1):339-341,doi:10.3109/194017362014.892106
Shen Xin,Chu Kahou,Chan B K K,et al.2016b.The complete mitochondrial genome of the fire coral-inhabiting barnacle Megabalanus ajax(Sessilia:Balanidae):gene rearrangements and atypical gene content.Mitochondrial DNA,27(2):1173-1174doi:10.3109/19401736.2014.936424
Shen Xin,Ma Xiaoyin,Ren Jianfeng,et al.2009.A close phylogenetic relationship between Sipuncula and Annelida evidenced from the complete mitochondrial genome sequence of Phascolosoma esculenta.BMC Genomics,10:136,doi:10.1186/1471-2164-10-136
Shen Xin,Sun Song,Zhao Fangqing,et al.2016c.Phylomitogenomic analyses strongly support the sister relationship of the Chaetognatha and Protostomia.Zoologica Scripta,45(2):187-199,doi10.1111/zsc.12140
Shen Xin,Tian Mei,Meng Xueping,et al.2012.Complete mitochondrial genome of Membranipora grandicella(Bryozoa:Cheilostomatida)determined with next-generation sequencing:The first representative of the suborder Malacostegina.Comparative Biochemistry and Physiology Part D:Genomics and Proteomics,7(3):248-253,doi:10.1016/j.cbd.2012.03.003
Shen Xin,Tsang L M,Chu Kahou,et al.2015b.Mitochondrial genome of the intertidal acorn barnacle Tetraclita serrata Darwin1854(Crustacea:Sessilia):Gene order comparison and phylogenetic consideration within Sessilia.Marine Genomics,22:63-69,doi:10.1016/j.margen.2015.04.004
Shen Xin,Tsang L M,Chu Kahou,et al.2017.A unique duplication of gene cluster(S2-C-Y)in Epopella plicata(Crustacea)mitochondrial genome and phylogeny within Cirripedia.Mitochondrial DNA,28(2):285-287,doi:10.3109/19401736.2015.1118082
Shen Xin,Tsoi K H,Cheang C C.2016d.The model barnacle Balanus balanus Linnaeus,1758(Crustacea:Maxillopoda:Sessilia)mitochondrial genome and gene rearrangements within the family Balanidae.Mitochondrial DNA,27(3):2112-2114
Tsang L M,Chu Kahou,Nozawa Y,et al.2014.Morphological and host specificity evolution in coral symbiont barnacles(Balanomorpha:Pyrgomatidae)inferred from a multi-locus phylogeny Molecular Phylogenetics and Evolution,77:11-22,doi:10.1016/j.ympev.2014.03.002
Tsang L M,Shen Xin,Cheang C C,et al.2017.Gene rearrangement and sequence analysis of mitogenomes suggest polyphyly of Archaeobalanid and Balanid barnacles(Cirripedia:Balanomorpha).Zoologica Scripta,46(6):729-739,doi:10.1111/zsc.12246
Tsang L M,Shen Xin,Chu Kahou,et al.2015.Complete mitochondrial genome of the acorn barnacle Striatobalanus amaryllis(Crustacea:Maxillopoda):the first representative from Archaeobalanidae.Mitochondrial DNA,26(5):761-762,doi:10.3109/19401736.2013.855739
Wares J P.2015.Mitochondrial evolution across lineages of the vampire barnacle Notochthamalus scabrosus.Mitochondrial DNA26(1):7-10,doi:10.3109/19401736.2013.825791
Zhang Wenqi,Zhang Minghao.2012.Phylogeny and evolution of Cervidae based on complete mitochondrial genomes.Genetics and Molecular Research,11(1):628-635,doi:10.4238/2012.March.14.6
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