The complete mitochondrial DNA genome of Eremias brenchleyi (Reptilia: Lacertidae) and its phylogeny position within squamata reptiles

AbstractSquamata is the most diversified reptilian order that has been traditionally classified into three suborders – Lacertilia, Serpentes and Amphisbaenia in which Lacertilia have about 16-19 families. But the phylogenetic relationships among major groups of Lacertilia remain controversial. In this paper, the complete mitochondrial DNA sequence of Eremias brenchleyi was determined by using long-and-accurate PCR (LA-PCR). The mtDNA sequence is 19 542 bp, making it the longest mitochondrial genome in squamates species reported so far. It shows the typical vertebrate arrangement of genes. The control region of E. brenchleyi was characterized by two conspicuous 65 bp and 56 bp tandem repeats at its 5′ and 3′ terminus respectively. In order to study the higher level relationships of squamates, the phylogenetic study including all currently available squamates mitochondrial sequences was carried out. We obtained a relationship of 16 families of lizards (Lacertidae, Scincidae, Iguanidae, Chameleonidae, Agamidae, Trogonophidae, Bipedidae, Shinisauridae, Helodermatidae, Amphisbaenidae, Gekkonidae, Varanidae, Anguidae, Xantusiidae, Rhineuridae, Cordylidae) and 8 families of Serpentes. The internal relationships within this group yielded high bootstrap support and were more congruent with morphological analyses.

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Mitochondrial DNA Sequence Phylogeny of Daucus

Systematic Botany ◽

10.1600/036364420x15862837791311 ◽

2020 ◽

Vol 45 (2) ◽

pp. 403-408 ◽

Cited By ~ 1

Author(s):

David M. Spooner ◽

Holly Ruess ◽

Philipp Simon ◽

Douglas Senalik

Keyword(s):

Mitochondrial Dna ◽

Dna Sequences ◽

Phylogenetic Trees ◽

Plastid Dna ◽

Nuclear Data ◽

Bootstrap Support ◽

Illumina Hiseq ◽

Data Set ◽

Closely Related Species ◽

Mitochondrial Sequences

Abstract—We explored the phylogenetic utility of mitochondrial DNA sequences in Daucus and compared the results with prior phylogenetic results using the same 36 accessions of Daucus (and two additional outgroups) with plastid DNA sequences and with other nuclear results. As in the plastid study we used Illumina HiSeq sequencer to obtain resequencing data of the same accessions of Daucus and outgroups, and analyzed the data with maximum parsimony and maximum likelihood. We obtained data from 47 of 71 total mitochondrial genes but only 17 of these 47 genes recovered major clades that were common in prior plastid and nuclear studies. Our phylogenetic trees of the concatenated data set of 47 genes were moderately resolved, with 100% bootstrap support for most of the external and many of the internal clades, except for the clade of D. carota and its most closely related species D. syrticus. There are areas of hard incongruence with phylogenies using plastid and nuclear data. In agreement with other studies, we conclude that mitochondrial sequences are generally poor phylogenetic markers, at least at the genus level, despite their utility in some other studies.

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Molecular phylogenetic reconstruction of the endemic Asian salamander family Hynobiidae (Amphibia, Caudata)

Zootaxa ◽

10.11646/zootaxa.3626.1.3 ◽

2013 ◽

Vol 3626 (1) ◽

pp. 77-93 ◽

Cited By ~ 10

Author(s):

DAVID W. WEISROCK ◽

J. ROBERT MACEY ◽

MASAFUMI MATSUI ◽

DANIEL G. MULCAHY

Keyword(s):

Mitochondrial Dna ◽

Phylogenetic Trees ◽

Sequence Data ◽

Bootstrap Support ◽

Phylogenetic Study ◽

Taxon Sampling ◽

12S Rrna ◽

Sister Relationship ◽

Data Set ◽

History Of

The salamander family Hynobiidae contains over 50 species and has been the subject of a number of molecular phylo-genetic investigations aimed at reconstructing branches across the entire family. In general, studies using the greatest amount of sequence data have used reduced taxon sampling, while the study with the greatest taxon sampling has used a limited sequence data set. Here, we provide insights into the phylogenetic history of the Hynobiidae using both dense taxon sampling and a large mitochondrial DNA sequence data set. We report exclusive new mitochondrial DNA data of 2566 aligned bases (with 151 excluded sites, of included sites 1157 are variable with 957 parsimony informative). This is sampled from two genic regions encoding a 12S–16S region (the 3’ end of 12S rRNA, tRNAVAl, and the 5’ end of 16S rRNA), and a ND2–COI region (ND2, tRNATrp, tRNAAla, tRNAAsn, the origin for light strand replication—OL, tRNACys, tRNATyr, and the 5’ end of COI). Analyses using parsimony, Bayesian, and maximum likelihood optimality criteria produce similar phylogenetic trees, with discordant branches generally receiving low levels of branch support. Monophyly of the Hynobiidae is strongly supported across all analyses, as is the sister relationship and deep divergence between the genus Onychodactylus with all remaining hynobiids. Within this latter grouping our phylogenetic results identify six clades that are relatively divergent from one another, but for which there is minimal support for their phy-logenetic placement. This includes the genus Batrachuperus, the genus Hynobius, the genus Pachyhynobius, the genus Salamandrella, a clade containing the genera Ranodon and Paradactylodon, and a clade containing the genera Liua and Pseudohynobius. This latter clade receives low bootstrap support in the parsimony analysis, but is consistent across all three analytical methods. Our results also clarify a number of well-supported relationships within the larger Batrachu-perus and Hynobius clades. While the relationships identified in this study do much to clarify the phylogenetic history of the Hynobiidae, the poor resolution among major hynobiid clades, and the contrast of mtDNA-derived relationships with recent phylogenetic results from a small number of nuclear genes, highlights the need for continued phylogenetic study with larger numbers of nuclear loci.

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Characterization of the mitochondrial genome and phylogeny of the black arowana (Osteoglossum ferreirai)

Biologia ◽

10.2478/s11756-014-0426-0 ◽

2014 ◽

Vol 69 (9) ◽

Author(s):

Xidong Mu ◽

Yi Liu ◽

Xuejie Wang ◽

Chao Liu ◽

Hongmei Song ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Nucleotide Composition ◽

Gene Arrangement ◽

Bootstrap Support ◽

Radiation Process ◽

Molecular Approaches ◽

The Family ◽

High Bootstrap ◽

Relationship Of

AbstractIn this study, we sequenced and assembled the mitochondrial (mt) genome of Osteoglossum ferreirai to re-assess the phylogenetic relationship of the family Osteoglossidae. We determined that the mitogenome of O. ferreirai contains the entire set of 37 mt genes, and the nucleotide composition and gene arrangement were similar to those of other bonytongues. Our phylogenetic analyses exhibited monophyly of the family Osteoglossidae with high bootstrap support, which is in agreement with the currently accepted phylogenetic viewpoint that is based on both morphological and molecular approaches. These findings provide additional informative data for the further study of phylogenetic relationships and help to elucidate a key component of the species radiation process within the family Osteoglossidae.

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Latitudinal distribution and mitochondrial DNA (COI) variability of Stereotydeus spp. (Acari: Prostigmata) in Victoria Land and the central Transantarctic Mountains

Antarctic Science ◽

10.1017/s0954102010000659 ◽

2010 ◽

Vol 22 (6) ◽

pp. 749-756 ◽

Cited By ~ 12

Author(s):

Nicholas J. Demetras ◽

Ian D. Hogg ◽

Jonathan C. Banks ◽

Byron J. Adams

Keyword(s):

Mitochondrial Dna ◽

Phylogenetic Trees ◽

Bootstrap Support ◽

Latitudinal Distribution ◽

Monophyletic Clade ◽

The North ◽

Victoria Land ◽

High Bootstrap ◽

Transantarctic Mountains ◽

Coi Sequences

AbstractWe examined mitochondrial DNA (COI) variability and distribution of Stereotydeus spp. in Victoria Land and the Transantarctic Mountains, and constructed Neighbour Joining (NJ) and Maximum Likelihood (ML) phylogenetic trees using all publicly available COI sequences for the three Stereotydeus species present (S. belli, S. mollis and S. shoupi). We also included new COI sequences from Miers, Marshall and Garwood valleys in southern Victoria Land (78°S), as well as from the Darwin (79°S) and Beardmore Glacier (83°S) regions. Both NJ and ML methods produced trees which were similar in topology differing only in the placement of the single available S. belli sequence from Cape Hallett (72°S) and a S. mollis haplotype from Miers Valley. Pairwise sequence divergences among species ranged from 9.5–18.1%. NJ and ML grouped S. shoupi from the Beardmore Glacier region as sister to those from the Darwin with pairwise divergences of 8%. These individuals formed a monophyletic clade with high bootstrap support basal to S. mollis and S. belli. Based on these new data, we suggest that the distributional range of S. shoupi extends northward to Darwin Glacier and that a barrier to dispersal for Stereotydeus, and possibly other arthropods, exists immediately to the north of this area.

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The Chloroplast Phylogenomics and Systematics of Zoysia (Poaceae)

Plants ◽

10.3390/plants10081517 ◽

2021 ◽

Vol 10 (8) ◽

pp. 1517

Author(s):

Se-Hwan Cheon ◽

Min-Ah Woo ◽

Sangjin Jo ◽

Young-Kee Kim ◽

Ki-Joong Kim

Keyword(s):

Northeast Asia ◽

Single Copy ◽

Rrna Genes ◽

Bootstrap Support ◽

Trna Genes ◽

Protein Coding ◽

Tropical Regions ◽

Relationship Of ◽

The Relationship ◽

Simple Sequence

The genus Zoysia Willd. (Chloridoideae) is widely distributed from the temperate regions of Northeast Asia—including China, Japan, and Korea—to the tropical regions of Southeast Asia. Among these, four species—Zoysia japonica Steud., Zoysia sinica Hance, Zoysia tenuifolia Thiele, and Zoysia macrostachya Franch. & Sav.—are naturally distributed in the Korean Peninsula. In this study, we report the complete plastome sequences of these Korean Zoysia species (NCBI acc. nos. MF953592, MF967579~MF967581). The length of Zoysia plastomes ranges from 135,854 to 135,904 bp, and the plastomes have a typical quadripartite structure, which consists of a pair of inverted repeat regions (20,962~20,966 bp) separated by a large (81,348~81,392 bp) and a small (12,582~12,586 bp) single-copy region. In terms of gene order and structure, Zoysia plastomes are similar to the typical plastomes of Poaceae. The plastomes encode 110 genes, of which 76 are protein-coding genes, 30 are tRNA genes, and four are rRNA genes. Fourteen genes contain single introns and one gene has two introns. Three evolutionary hotspot spacer regions—atpB~rbcL, rps16~rps3, and rpl32~trnL-UAG—were recognized among six analyzed Zoysia species. The high divergences in the atpB~rbcL spacer and rpl16~rpl3 region are primarily due to the differences in base substitutions and indels. In contrast, the high divergence between rpl32~trnL-UAG spacers is due to a small inversion with a pair of 22 bp stem and an 11 bp loop. Simple sequence repeats (SSRs) were identified in 59 different locations in Z. japonica, 63 in Z. sinica, 62 in Z. macrostachya, and 63 in Z. tenuifolia plastomes. Phylogenetic analysis showed that the Zoysia (Zoysiinae) forms a monophyletic group, which is sister to Sporobolus (Sporobolinae), with 100% bootstrap support. Within the Zoysia clade, the relationship of (Z. sinica, Z japonica), (Z. tenuifolia, Z. matrella), (Z. macrostachya, Z. macrantha) was suggested.

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The Complete DNA Sequence of the Mitochondrial Genome of a “Living Fossil,” the Coelacanth (Latimeria chalumnae)

Genetics ◽

10.1093/genetics/146.3.995 ◽

1997 ◽

Vol 146 (3) ◽

pp. 995-1010 ◽

Cited By ~ 1

Author(s):

Rafael Zardoya ◽

Axel Meyer

Keyword(s):

Mitochondrial Genome ◽

Tandem Repeats ◽

Phylogenetic Analyses ◽

Large Data ◽

Molecular Data ◽

Phylogenetic Position ◽

Data Set ◽

Living Fossil ◽

Latimeria Chalumnae ◽

Relationship Of

The complete nucleotide sequence of the 16,407-bp mitochondrial genome of the coelacanth (Latimeria chalumnae) was determined. The coelacanth mitochondrial genome order is identical to the consensus vertebrate gene order which is also found in all ray-finned fishes, the lungfish, and most tetrapods. Base composition and codon usage also conform to typical vertebrate patterns. The entire mitochondrial genome was PCR-amplified with 24 sets of primers that are expected to amplify homologous regions in other related vertebrate species. Analyses of the control region of the coelacanth mitochondrial genome revealed the existence of four 22-bp tandem repeats close to its 3′ end. The phylogenetic analyses of a large data set combining genes coding for rRNAs, tRNA, and proteins (16,140 characters) confirmed the phylogenetic position of the coelacanth as a lobe-finned fish; it is more closely related to tetrapods than to ray-finned fishes. However, different phylogenetic methods applied to this largest available molecular data set were unable to resolve unambiguously the relationship of the coelacanth to the two other groups of extant lobe-finned fishes, the lungfishes and the tetrapods. Maximum parsimony favored a lungfish/coelacanth or a lungfish/tetrapod sistergroup relationship depending on which transversion:transition weighting is assumed. Neighbor-joining and maximum likelihood supported a lungfish/tetrapod sistergroup relationship.

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Complete mitochondrial DNA and phylogenetic study of qionglai native black chicken

MATEC Web of Conferences ◽

10.1051/matecconf/20166203004 ◽

2016 ◽

Vol 62 ◽

pp. 03004

Author(s):

Yaodong Hu ◽

Yun Zhu ◽

Huizhong Pang ◽

Dan Lan

Keyword(s):

Mitochondrial Dna ◽

Phylogenetic Study

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Models of mitochondrial DNA transmission genetics and evolution in higher eucaryotes

Genetics Research ◽

10.1017/s0016672300018899 ◽

1982 ◽

Vol 40 (1) ◽

pp. 41-57 ◽

Cited By ~ 34

Author(s):

Robert W. Chapman ◽

J. Claiborne Stephens ◽

Robert A. Lansman ◽

John C. Avise

Keyword(s):

Mitochondrial Dna ◽

Population Biology ◽

Sequence Information ◽

Random Allocation ◽

Cell Lineages ◽

Daughter Cells ◽

Mtdna Sequence ◽

Population Sizes ◽

Future Value ◽

Mtdna Evolution

SUMMARYThe future value of mitochondrial DNA (mtDNA) sequence information to studies in population biology will depend in part on understanding of mtDNA transmission genetics both within cell lineages and between animal generations. A series of stochastic models has been constructed here based on various possibilities concerning this transmission. Several of the models generate predictions inconsistent with available data and, hence, their assumptions are provisionally rejected. Other models cannot yet be falsified. These latter models include assumptions that (1) mtDNA's are sorted through cellular lineages by random allocation to daughter cells in germ cell lineages; (2) the effective intracellular population sizes (nM's) of mtDNA's are small; and (3) sperm may (or may not) provide a low level ‘gene-flow’ bridge between otherwise isolated female lineages. It is hoped that the models have helped to identify and will stimulate further empirical study of various parameters likely to strongly influence mtDNA evolution. In particular, critical experiments or measurements are needed to determine the effective sizes of mtDNA populations in germ (and somatic) cells and to examine possible paternal contributions to zygote mtDNA composition.

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Species in section Peltidea (aphthosa group) of the genus Peltigera remain cryptic after molecular phylogenetic revision

Plant and Fungal Systematics ◽

10.2478/pfs-2018-0007 ◽

2018 ◽

Vol 63 (2) ◽

pp. 45-64 ◽

Cited By ~ 2

Author(s):

Jolanta Miadlikowska ◽

Nicolas Magain ◽

Carlos J. Pardo-De la Hoz ◽

Dongling Niu ◽

Trevor Goward ◽

...

Keyword(s):

High Specificity ◽

Molecular Data ◽

Fungal Species ◽

Bootstrap Support ◽

Phenotypic Traits ◽

Phylogenetic Structure ◽

Putative Species ◽

Molecular Phylogenetic ◽

High Bootstrap ◽

Phylogenetic Revision

AbstractClosely related lichen-forming fungal species circumscribed using phenotypic traits (morphospecies) do not always align well with phylogenetic inferences based on molecular data. Using multilocus data obtained from a worldwide sampling, we inferred phylogenetic relationships among five currently accepted morphospecies of Peltigera section Peltidea (P. aphthosa group). Monophyletic circumscription of all currently recognized morphospecies (P. britannica, P. chionophila, P. frippii and P. malacea) except P. aphthosa, which contained P. britannica, was confirmed with high bootstrap support. Following their re-delimitation using bGMYC and Structurama, BPP validated 14 putative species including nine previously unrecognized potential species (five within P. malacea, five within P. aphthosa, and two within P. britannica). Because none of the undescribed potential species are corroborated morphologically, chemically, geographically or ecologically, we concluded that these monophyletic entities represent intraspecific phylogenetic structure, and, therefore, should not be recognized as new species. Cyanobionts associated with Peltidea mycobionts (51 individuals) represented 22 unique rbcLX haplotypes from five phylogroups in Clade II subclades 2 and 3. With rare exceptions, Nostoc taxa involved in trimembered and bimembered associations are phylogenetically closely related (subclade 2) or identical, suggesting a mostly shared cyanobiont pool with infrequent switches. Based on a broad geographical sampling, we confirm a high specificity of Nostoc subclade 2 with their mycobionts, including a mutualistically exclusive association between phylogroup III and specific lineages of P. malacea.

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The male sterility-associated pcf gene and the normal atp9-1 gene in Petunia are located on different mitochondrial DNA molecules.

Genetics ◽

10.1093/genetics/129.3.885 ◽

1991 ◽

Vol 129 (3) ◽

pp. 885-895

Author(s):

O Folkerts ◽

M R Hanson

Keyword(s):

Mitochondrial Dna ◽

Male Sterility ◽

Nadh Dehydrogenase ◽

Ribosomal Subunit ◽

Cms Line ◽

Ribosomal Subunit Protein ◽

Mtdna Organization ◽

Relationship Of ◽

The Relationship ◽

Functional Copy

Abstract A mitochondrial DNA (mtDNA) region termed the S-pcf locus has previously been correlated with cytoplasmic male sterility (CMS) in Petunia. In order to understand the relationship of the S-pcf locus to homologous sequences found elsewhere in mtDNAs of both CMS and fertile lines, the structure of the mitochondrial genome of CMS Petunia line 3688 was determined by cosmid walking. The S-pcf locus, which includes the only copies of genes for NADH dehydrogenase subunit 3 (nad3) and small ribosomal subunit protein 12 (rps12) was found to be located on a circular map of 396 kb, while a second almost identical circular map of 407 kb carries the only copies of the genes for 18S and 5S rRNA (rrn18 and rrn5), the only copy of a conserved unidentified gene (orf25), and the only known functional copy of atp9. Three different copies of a recombination repeat were found in six genomic environments, predicting sub-genomic circles of 277, 266 and 130 kb. The ratio of atp9 to S-pcf mtDNA sequences was approximately 1.5 to 1, indicating that sub-genomic molecules carrying these genes differ in abundance. Comparison of the mtDNA organization of the CMS line with that of the master circle of fertile Petunia line 3704 reveals numerous changes in order and orientation of ten different sectors.

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