- phylogenetic implications of the subfamily Cobitinae. - A specific 3 bp insertion (GCA) in the atp8-atp6 overlap was identified as a unique feature of loaches, compared to other Cypriniformes fish. - The strict molecular clock predicted that Cobitinae might have split into northern and southern lineages in the late Eocene (42.11 Ma), furthermore, mtDNA introgression might occur (14.40 Ma) between ancestral species of Cobitis and ancestral species of Misgurnus.. - The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. - If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. - Full list of author information is available at the end of the article. - Many Cobitis populations are mixed diploid-polyploid, even bisexual and unisexual forms co-existing in the same niche [19–21]. - However, di- lapidation of the ecological environment has led to a decrease of benthic organisms [26, 27]. - On this account, the diversity of these benthic fishes have been used as a bioindicator to assess the quality of the ecological environment [29, 30]. - Al- though the monophyly of the groups were resolved, the relationships within the groups are discordant with current taxonomic status.. - macrostigma, the type species of the genus Cobitis [25], and compared it with other 41 species (57 individuals) to amplify de- tailed features of the Cobitinae mitogenomes. - In the Cobitinae mitogenomes, un- matched base pairs are widespread among tRNAs. - In the 425 base pairs of other 21 tRNAs, there are unmatched base pairs that contain 28 noncanonical matches of G-U and 15 other mismatches, including A-C (7), A-A (1), C-C (2), C-U (2), and U-U (3) (Fig. - Most of them are lo- cated in the acceptor, DHU and anticodon stems.. - Two long overlaps (atp8- atp6 and nd4l-nd4) and two long IGSs (O L and tRNA Asp -cox2) were found in Cobitinae mitogenomes.. - Highly conserved motifs “ATGCTAA” and “ATGGCAA- TAA” were found in the overlapped junctions between nd4l and nd4, and between atp8 and atp6, respectively (Fig. - Among the 31 bp of O L , the C-G base pairs on stems are highly con- served while the loops in the middle are variable (Fig.. - Another long IGS, between tRNA Asp and cox2, is also conserved in the 5′ and 3′ end, and highly variable in the middle.. - Degenerated codons are biased to use more A/T than G/C in the 3rd position of PCGs, which. - results in the content of A + T is higher than G + C in the 3rd position of Cobitinae PCGs. - AT-skew and their linear correlations of Cobitinae mitogenomes. - 1 Circular sketch map of the C. - Table 2 Annotation of the C. - 2nd <3rd in the three position of PCGs in all analyzed fishes. - The correlations of Cobitinae mitogenomes (y A1. - The first split of Cobitinae lineages was estimated to have oc- curred in the late Eocene (42.11 Ma, 95% HPD: 36.35–. - Cobitis-Iksookimia- Kichulchoia-Niwaella lineage diverged from the rest of northern clade lineage during the Oligocene (30.07 Ma, 95% HPD Ma), similar to the previous Table 2 Annotation of the C. - The mtDNA introgression between ancestral species of Cobitis and ancestral species of Misgurnus seems to have taken place in the Middle Miocene (14.40. - macrostigma ap- peared about 0.36 Ma (95% HPD Ma) in the Pleistocene. - southern lineages, Pangio was estimated to have oc- curred about Ma, and the divergence times of the four species analyzed in this study are congruent with the previous described dating [24].. - Similarly, the widespread unmatched base pairs among Cobitinae tRNAs is also a conserved feature in the eukaryote mitogenome [59–61]. - However, in comparison with the conserved motif (ATGATAA) in other Cypriniformes fishes, there is a specific 3 bp insertion (GCA) in the atp8-atp6 over- lap motif of Cobitinae and other loaches [67–69], indi- cating this insertion is a characteristic feature of loaches.. - 6 Base compositions and AT-skew in Cobitinae mitogenomes. - A + T content of different regions in Cobitinae mitogenomes. - AT-skew of different regions in Cobitinae mitogenomes. - The correlations between A + T% and AT-skew in 13 PCGs of Cobitinae mitogenomes. - The correlations between G + C% and GC-skew in 13 PCGs of Cobitinae mitogenomes. - In tele- ost, the skew inversion of CR was only found in the mitogenomes of Albula glossodonta and Bathygadus. - The phylogenetic analyses show the monophyly of the genus Pangio and Lepidocephalichthys, consistent with the previous study [35]. - However, Cobitis, the biggest genus of Cobitinae [15], is a complex and controversial Table 3 Base composition and skewness of the mitogenomes in C. - The same re- sults were observed in the trees based on the cyt b [80]. - The first split of Cobitinae lineages was estimated to have occurred in the late Eocene (42.11 Ma, 95% HPD:. - Ma), separating northern clade and south- ern lineages, consistent with reconstruction dates of the paleo-drainages of East Asia [35, 88]. - 7 Nonsynonymous/synonymous ratios ( ω = dN/dS) of the 13 PCGs of Cobitinae mitogenomes. - We observed distinct base compositions among different genus and identified a specific 3 bp insertion (GCA) in the atp8-atp6 overlap as a unique feature of loaches. - In addtion, Cobitinae might have split into northern and southern lineages in the late Eocene (42.11 Ma), and a mtDNA introgression between Cobitis and Misgurnus might have occured about 14.40 Ma. - It possesses 5–9 large and round spot in the midline of lateral body side [89]. - 8 Phylogenetic tree constructed by BI methods, based on 13 PCGs of 58 Cobitinae mitogenomes. - The silimlarity of the sequences was calculated in MEGA 7.0 [95] under p-distance and NCBI-BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi).. - The phylogenetic analysis was performed based on 13 PCGs of 58 Cobitinae mitogenomes. - Each of the 13 gene sequences was separately aligned using Muscle v and concatenated into a sequence matrix by PhyloSuite v1.2.2 [97]. - The convergence of the BI ana- lyses was investigated using Tracer v1.7.1 software. - The analyses were simultaneously run for generations, with parameters sampled every 1000, then the first 25% of the trees were discarded as burn-in.. - Start and stop codons of 13 PCGs in Cobitinae mitogenomes.. - Codon distribution (A) and relative synonymous codon usage (B) of PCGs in the 58 Cobitinae mitogenomes.. - mitogenome: Mitochondrial genome. - This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB31000000) and the China Agriculture Research System (CARS-45-07).. - macrostigma analyzed in this study was caught from the Yangtze River in Yibin City, Sichuan Province, China and reared in the National Aquatic Biological Resource Center (NABRC). - The acquisition of experimental fish complies with the laws of Fishery Administration of the Ministry of Agriculture and Rural Affairs of the People ’ s Republic of China. - question, key design features, and analysis plan, was provided to the Animal Care and Use Committee of Institute of Hydrobiology, Chinese Academy of Sciences before the study, and all procedures in this research performed with the approval of the Committee. - Structure and variation of the mitochondrial genome of fishes. - Mitochondrial DNA clonality in the dock: can surveillance swing the case? Trends Genet. - The complete mitochondrial genome of Leptobotia taeniaps (Cypriniformes: Cobitidae). - Mechanisms of gene rearrangement in 13 bothids based on comparison with a newly completed mitogenome of the threespot flounder, Grammatobothus polyophthalmus (Pleuronectiformes:. - Mitochondrial genomes of the early land plant lineage liverworts (Marchantiophyta):. - Diploid clone produces unreduced diploid gametes but tetraploid clone generates reduced diploid gametes in the Misgurnus loach. - Ice age cloning--comparison of the quaternary evolutionary histories of sexual and clonal forms of spiny loaches (Cobitis. - Phylogeny of the southeast Asian freshwater fish genus Pangio (Cypriniformes. - Microplastics in sediments of the Changjiang estuary, China. - High levels of microplastic pollution in the sediments and benthic organisms of the South Yellow Sea, China. - Different histories, different DestiniesImpact of evolutionary history and population genetic structure on extinction risk of the Adriatic Spined loaches (genus Cobitis;. - Role of living environments in the accumulation characteristics of heavy metals in fishes and crabs in the Yangtze River estuary, China. - Cryptic clonal lineages and genetic diversity in the loach Misgurnus anguillicaudatus (Teleostei: Cobitidae) inferred from nuclear and mitochondrial DNA analyses. - Molecular phylogeny of the freshwater fish family Cobitidae (Cypriniformes: Teleostei): delimitation of genera, mitochondrial introgression and evolution of sexual dimorphism. - Evolution and phylogenetic application of the MC1R gene in the Cobitoidea (Teleostei: Cypriniformes). - Molecular evidence for multiple origins of the European Spined loaches (Teleostei, Cobitidae). - Mitogenomic evolution and interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): the first evidence toward resolution of higher- level relationships of the world's largest freshwater fish clade based on 59 whole mitogenome sequences. - The complete mitochondrial genome of natural Cobitis elongatoides (Cypriniformes:. - The complete mitochondrial genome of Cobitis granoei (Cyprinformes: Cobitidae). - Mitochondrial genome of the natural tetraploid loach Misgurnus anguillicaudatus. - Complete mitochondrial genome of the natural hexaploid loach, Misgurnus anguillicaudatus (Teleostei:. - Molecular characteristics of mitochondrial DNA and phylogenetic analysis of the loach (Misgurnus anguillicaudatus) from the Poyang Lake. - Phylogenetic position of the enigmatic genus Psilorhynchus (Ostariophysi: Cypriniformes):. - evidence from the mitochondrial genome. - The complete mitochondrial genome of natural Misgurnus bipartitus (Cypriniformes:. - Complete mitochondrial genome of the Amur weatherfish, Misgurnus mohoity (Teleostei:. - The complete mitochondrial genome of the Rhodeus shitaiensis (Teleostei, Cypriniformes, Acheilognathidae).. - Evolutionary patterns of the mitochondrial genome in Metazoa: exploring the role of mutation and selection in mitochondrial protein coding genes. - Complete mitochondrial genome of dinorhynchus dybowskyi (hemiptera:. - A novel type of RNA editing occurs in the mitochondrial tRNAs of the centipede Lithobius forficatus. - The complete sequence of the zebrafish (Danio rerio) mitochondrial genome and evolutionary patterns in vertebrate mitochondrial DNA. - Complete sequence and characterization of the paradise fish Macropodus erythropterus (Perciformes:. - Macropodusinae) mitochondrial genome. - Complete mitochondrial genome sequence of the Tyrolean iceman. - The complete mitochondrial genome of Sinibotia robusta (Cypriniformes: Cobitidae). - The mitochondrial genome of the leaf-cutter ant Atta laevigata: a mitogenome with a large number of intergenic spacers. - Phylogenetic and biogeographic implications inferred by mitochondrial intergenic region analyses and ITS1 – 5.8S-ITS2 of the entomopathogenic fungi Beauveria bassiana and B.. - Origin of the two major distinct mtDNA clades of the Japanese population of the oriental weather loach Misgurnus anguillicaudatus (Teleostei: Cobitidae). - Genetics of the loach, Misgurnus anguillicaudatus: recent progress and perspective. - First record of the natural occurrence of hexaploid loach Misgurnus anguillicaudatus in Hubei Province, China
Xem thử không khả dụng, vui lòng xem tại trang nguồn hoặc xem
Tóm tắt