The Mitochondrial Genome of Nematodontous Moss Polytrichum commune and Analysis of Intergenic Repeats Distribution Among Bryophyta

An early-branched moss Polytrichum commune is a widely accepted model object for ecological, environmental, physiological, and genetic studies. Its mitochondrial genome has been sequenced and annotated. The genome contains 67 genes in total and has a length equal to 114,831 bp, which exceeds the length of most known mitochondrial genomes for mosses. A phylogenetic tree based on 33 coding sequences of mitochondrial genome was constructed, and the pairwise identity of whole mitogenome sequences was estimated for 44 Bryophyta species. Based on the analysis of pairwise identity, it was shown that mitogenomes of Tetraphis pellucida and Buxbaumia aphylla sufficiently differ from those of other Bryophyta species. The first known Bryophyta mitogenome rearrangement was identified in Pogonatum inflexum within Polytrichopsida. Based on the intergenic repeats occurrence in 44 bryophyte mitochondrial genomes and available data on repetitive elements content in other Viridiplantae groups, it was noted for the first time that greater stability of the moss’s mitogenomes is probably associated mainly with the absence of long (>1 kb) repeats. The phenomenon of absence of the intergenic repetitive elements in the terminal clades species was discovered.

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The analysis of the canid mitochondrial genome studied in Morocco shows that it is neither wolf (Canis lupus) nor Eurasian jackal (Canis aureus)

10.7287/peerj.preprints.1763 ◽

2016 ◽

Author(s):

Vicente Urios Moliner ◽

Maria P Donat-Torres ◽

Carlos A Ramírez Castillo ◽

Octavio Monroy-Vilchis ◽

Hamid Rguibi Idrissi

Keyword(s):

Mitochondrial Genome ◽

Canis Lupus ◽

Mitochondrial Genomes ◽

Golden Jackal ◽

Accession Number ◽

Canis Aureus ◽

And Control ◽

First Time ◽

Scientific Name ◽

Complete Mitochondrial Genomes

The mitochondrial genome of three Moroccan canids has been analysed. Two of them complete and one partial. The sequences are included in GenBank with the accession number KT378605 (16721 bp), KT378606 (16734bp) and KT378607 (27809bp) Theses results have been compared with the results currently available in GenBank. In the phylogenetic analysis of the of cytochrome b regions and control region the three are grouped together with Canis lupus lupaster and the Senegalese golden jackal Canis aureus and separate from the wolf Canis lupus and the Eurasian golden jackal Canis aureus. The comparison of the complete mitochondrial genomes with Canis lupus confirms the distance between the two groups. We conclude that they belong to a different species to the wolf Canis lupus and the Eurasian golden jackal. We propose in agreement with (Koepfli et al., 2015) that it´s scientific name be Canis anthus by merit of being the name by which it was classified and published for the first time as a different species by Cuvier in 1824. The preprint is a translation of a Spanish document published in Altorero journal on the 15th August 2015.

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The analysis of the canid mitochondrial genome studied in Morocco shows that it is neither wolf (Canis lupus) nor Eurasian jackal (Canis aureus)

10.7287/peerj.preprints.1763v1 ◽

2016 ◽

Author(s):

Vicente Urios Moliner ◽

Maria P Donat-Torres ◽

Carlos A Ramírez Castillo ◽

Octavio Monroy-Vilchis ◽

Hamid Rguibi Idrissi

Keyword(s):

Mitochondrial Genome ◽

Canis Lupus ◽

Mitochondrial Genomes ◽

Golden Jackal ◽

Accession Number ◽

Canis Aureus ◽

And Control ◽

First Time ◽

Scientific Name ◽

Complete Mitochondrial Genomes

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Description of the female, nymph and larva and mitochondrial genome, and redescription of the male, of Ixodes barkeri Barker, 2019 (Acari: Ixodidae) from the short-beaked echidna, Tachyglossus aculeatus, with a consideration of the most suitable subgenus for this tick

10.21203/rs.3.rs-1097590/v1 ◽

2021 ◽

Author(s):

Dayana Barker ◽

Samuel Kelava ◽

Renfu Shao ◽

Owen D. Seeman ◽

Malcolm K. Jones ◽

...

Keyword(s):

Mitochondrial Genome ◽

Mitochondrial Genomes ◽

Far North ◽

The Core ◽

Wet Tropics ◽

Palpal Segment ◽

Subgenus Classification ◽

First Time ◽

Tachyglossus Aculeatus

Abstract Background Ixodes barkeri, a tick with a distinctive ventrolateral horn-like projection on palpal segment 1, was described in 2019 from two male ticks from the Wet Tropics of Far North Queensland, Australia. However, females lie at the core of the taxonomy and subgenus classification of Ixodes, hence we sought specimens of female ticks, successfully recovering females, plus nymphs and larvae. Mitochondrial genomes are also desirable additions to the descriptions of species of ticks particularly with regard to subgenus systematics. So, we sequenced the mt genomes of I. barkeri Barker, 2019 and the possible relatives of I. barkeri that were available to us (I. australiensis Neumann, 1904, I. fecialis Warburton & Nuttall, 1909, and I. woyliei Ash et al. 2017) with a view to discovering which if any of the subgenera of Ixodes would be most suitable for I. barkeri Barker, 2019. Results The female, nymph, larva, and mitochondrial genome of Ixodes barkeri Barker, 2019 are described for the first time and the male of I. barkeri is redescribed in greater detail than previously. So far, I. barkeri is known only from a monotreme, the short-beaked echidna, Tachyglossus aculeatus (Shaw, 1792), from the highland-rainforests of Far North Queensland, Australia. Conclusions Our phylogeny from entire mitochondrial genomes indicated that I. barkeri, and indeed I. woyliei Ash et al. 2017, another tick that was described recently, are best placed in the subgenus Endopalpiger Schulze, 1935.

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СИСТЕМА И КОНСПЕКТ ВИДОВ РОДА PEDICULARIS (OROBANCHACEAE) АЛТАЙСКОЙ ГОРНОЙ СТРАНЫ И ТЯНЬ-ШАНЯ

Biological Bulletin of Bogdan Chmelnitskiy Melitopol State Pedagogical University ◽

10.15421/201607 ◽

2016 ◽

Vol 6 (01) ◽

pp. 115-166

Author(s):

P. A. Kosachev

Keyword(s):

Phylogenetic Tree ◽

Molecular Genetic ◽

Tien Shan ◽

Genetic Studies ◽

Weak Support ◽

The Moment ◽

First Time ◽

Taxonomic Categories

The system and conspectus of the genus Pedicularis L. (Orobanchaceae) of Altai and Tien Shan is presented. The system is based of molecular genetic studies of the genus (Ree, 2005; Tkach et al., 2014; own data) and is represented by series that are grouped into sections. The building of the higher taxonomic categories is not possible at the moment due to the para- or polyphyletic origin genus of weak support for clads in the phylogenetic tree. Conspectus includes 61 species of the 32 series and 7 sections. 16 species and 1 subspecies of endemic for the territory of the Altai and Tien Shan. For the first time described in one section and 10 series. Three sections published of the lectotypes: Schizocalyx Li, Botryantha Li, Rhizophyllum Li. Clarified the amount and distribution of species, series, sections. Displaying Altai and Tien Shan origin some series (ser. Abrotanifoliae, Amoenae, Achilleifolia, Uliginosae, Physocalyces, Macrochilae, Platyrhynchae), the Tien-Shan (Semenowianae, Pycnanthae, Maximowiczianae, Pubiflorae), Altai (Brachystaches, Elatae).

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The Insights into Mitochondrial Genomes of Sunflowers

Plants ◽

10.3390/plants10091774 ◽

2021 ◽

Vol 10 (9) ◽

pp. 1774

Author(s):

Maksim S. Makarenko ◽

Denis O. Omelchenko ◽

Alexander V. Usatov ◽

Vera A. Gavrilova

Keyword(s):

Mitochondrial Genome ◽

Mitochondrial Gene ◽

Nuclear Genome ◽

Jerusalem Artichoke ◽

Mitochondrial Genomes ◽

Trna Genes ◽

Genetic Studies ◽

Protein Coding ◽

Significant Difference ◽

Complete Mitochondrial Genomes

The significant difference in the mtDNA size and structure with simultaneous slow evolving genes makes the mitochondrial genome paradoxical among all three DNA carriers in the plant cell. Such features make mitochondrial genome investigations of particular interest. The genus Helianthus is a diverse taxonomic group, including at least two economically valuable species—common sunflower (H. annuus) and Jerusalem artichoke (H. tuberosus). The successful investigation of the sunflower nuclear genome provided insights into some genomics aspects and significantly intensified sunflower genetic studies. However, the investigations of organelles’ genetic information in Helianthus, especially devoted to mitochondrial genomics, are presented by limited studies. Using NGS sequencing, we assembled the complete mitochondrial genomes for H. occidentalis (281,175 bp) and H. tuberosus (281,287 bp) in the current investigation. Besides the master circle chromosome, in the case of H. tuberosus, the 1361 bp circular plasmid was identified. The mitochondrial gene content was found to be identical for both sunflower species, counting 32 protein-coding genes, 3 rRNA, 23 tRNA genes, and 18 ORFs. The comparative analysis between perennial sunflowers revealed common and polymorphic SSR and SNPs. Comparison of perennial sunflowers with H. annuus allowed us to establish similar rearrangements in mitogenomes, which have possibly been inherited from a common ancestor after the divergence of annual and perennial sunflower species. It is notable that H. occidentalis and H. tuberosus mitogenomes are much more similar to H. strumosus than H. grosseserratus.

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The complete mitochondrial genome of the freshwater crab Longpotamon kenliense (Decapoda, Brachyura, Potamidae) with phylogenetic consideration

Crustaceana ◽

10.1163/15685403-bja10085 ◽

2020 ◽

Vol 93 (11-12) ◽

pp. 1277-1293

Author(s):

Yi-Fan Wang ◽

Shu-Xin Xu ◽

Chun-Chao Zhu ◽

Xin-Nan Jia ◽

Xian-Min Zhou ◽

...

Keyword(s):

Mitochondrial Genome ◽

Complete Mitochondrial Genome ◽

Divergence Time ◽

Complete Sequence ◽

Divergence Times ◽

Mitochondrial Genomes ◽

Freshwater Crab ◽

Protein Coding ◽

Protein Coding Genes ◽

First Time

Abstract The authors herein report for the first time the complete sequence of the mitochondrial genome of Longpotamon kenliense. The results showed that the mitochondrial genome of L. kenliense is 18,499 bp in length, shares 37 genes and 1 control region with the typical metazoan mitochondrial genome, and has a strong A + T bias (74.48%), i.e., a characteristic of the metazoan mitochondrial genome. In addition, the authors used the 13 protein-coding genes from the mitochondrial genomes of L. kenliense and 67 other species of Brachyura available from the NCBI to estimate divergence times. The divergence time of L. kenliense was 14.39 Ma, which is close to the divergence times of L. xiushuiense and L. yangtsekiense, but later than that of Sinopotamon yaanense. The results indicate that the genera Sinopotamon and Longpotamon are closely related and that the genus Sinopotamon has a longer history, which may have been caused by geological events.

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Bayesian inference of cetacean phylogeny based on mitochondrial genomes

Biologia ◽

10.2478/s11756-009-0121-8 ◽

2009 ◽

Vol 64 (4) ◽

Cited By ~ 7

Author(s):

Xiao-Guang Yang

Keyword(s):

Bayesian Inference ◽

Mitochondrial Genome ◽

Phylogenetic Relationships ◽

Mitochondrial Genomes ◽

Bayesian Analyses ◽

Baleen Whales ◽

Phylogenetic Methods ◽

Representative Species ◽

First Time

AbstractThe phylogeny of Cetacea (whales, dolphins, porpoises) has long attracted the interests of biologists and has been investigated by many researchers based on different datasets. However, some phylogenetic relationships within Cetacea still remain controversial. In this study, Bayesian analyses were performed to infer the phylogeny of 25 representative species within Cetacea based on their mitochondrial genomes for the first time. The analyses recovered the clades resolved by the previous studies and strongly supported most of the current cetacean classifications, such as the monophyly of Odontoceti (toothed whales) and Mysticeti (baleen whales). The analyses provided a reliable and comprehensive phylogeny of Cetacea which can provide a foundation for further exploration of cetacean ecology, conservation and biology. The results also showed that: (i) the mitochondrial genomes were very informative for inferring phylogeny of Cetacea; and (ii) the Bayesian analyses outperformed other phylogenetic methods on inferring mitochondrial genome-based phylogeny of Cetacea.

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Mitochondrial genome evolution in pelagophyte algae

Genome Biology and Evolution ◽

10.1093/gbe/evab018 ◽

2021 ◽

Author(s):

Shannon J Sibbald ◽

Maggie Lawton ◽

John M Archibald

Keyword(s):

Mitochondrial Genome ◽

Harmful Algal Blooms ◽

Algal Blooms ◽

23S Rrna ◽

Mitochondrial Genomes ◽

Trna Genes ◽

Unique Region ◽

Long Read ◽

Genomic Studies ◽

Aureoumbra Lagunensis

Abstract The Pelagophyceae are marine stramenopile algae that include Aureoumbra lagunensis and Aureococcus anophagefferens, two microbial species notorious for causing harmful algal blooms. Despite their ecological significance, relatively few genomic studies of pelagophytes have been carried out. To improve understanding of the biology and evolution of pelagophyte algae, we sequenced complete mitochondrial genomes for A. lagunensis (CCMP1510), Pelagomonas calceolata (CCMP1756) and five strains of A. anophagefferens (CCMP1707, CCMP1708, CCMP1850, CCMP1984 and CCMP3368) using Nanopore long-read sequencing. All pelagophyte mitochondrial genomes assembled into single, circular mapping contigs between 39,376 base-pairs (bp) (P. calceolata) and 55,968 bp (A. lagunensis) in size. Mitochondrial genomes for the five A. anophagefferens strains varied slightly in length (42,401 bp—42,621 bp) and were 99.4%-100.0% identical. Gene content and order was highly conserved between the A. anophagefferens and P. calceolata genomes, with the only major difference being a unique region in A. anophagefferens containing DNA adenine and cytosine methyltransferase (dam/dcm) genes that appear to be the product of lateral gene transfer from a prokaryotic or viral donor. While the A. lagunensis mitochondrial genome shares seven distinct syntenic blocks with the other pelagophyte genomes, it has a tandem repeat expansion comprising ∼40% of its length, and lacks identifiable rps19 and glycine tRNA genes. Laterally acquired self-splicing introns were also found in the 23S rRNA (rnl) gene of P. calceolata and the coxI gene of the five A. anophagefferens genomes. Overall, these data provide baseline knowledge about the genetic diversity of bloom-forming pelagophytes relative to non-bloom-forming species.

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Survey of the Bradysia odoriphaga Transcriptome Using PacBio Single-Molecule Long-Read Sequencing

Genes ◽

10.3390/genes10060481 ◽

2019 ◽

Vol 10 (6) ◽

pp. 481 ◽

Cited By ~ 1

Author(s):

Chen ◽

Lin ◽

Xie ◽

Zhong ◽

Zhang ◽

...

Keyword(s):

Insecticide Resistance ◽

Single Molecule ◽

Functional Categories ◽

Genetic Studies ◽

Sequencing Technologies ◽

Clusters Of Orthologous Groups ◽

Long Read ◽

Main Gene ◽

First Time ◽

Main Factor

The damage caused by Bradysia odoriphaga is the main factor threatening the production of vegetables in the Liliaceae family. However, few genetic studies of B. odoriphaga have been conducted because of a lack of genomic resources. Many long-read sequencing technologies have been developed in the last decade; therefore, in this study, the transcriptome including all development stages of B. odoriphaga was sequenced for the first time by Pacific single-molecule long-read sequencing. Here, 39,129 isoforms were generated, and 35,645 were found to have annotation results when checked against sequences available in different databases. Overall, 18,473 isoforms were distributed in 25 various Clusters of Orthologous Groups, and 11,880 isoforms were categorized into 60 functional groups that belonged to the three main Gene Ontology classifications. Moreover, 30,610 isoforms were assigned into 44 functional categories belonging to six main Kyoto Encyclopedia of Genes and Genomes functional categories. Coding DNA sequence (CDS) prediction showed that 36,419 out of 39,129 isoforms were predicted to have CDS, and 4319 simple sequence repeats were detected in total. Finally, 266 insecticide resistance and metabolism-related isoforms were identified as candidate genes for further investigation of insecticide resistance and metabolism in B. odoriphaga.

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The mitochondrial genome organization of a maize fertile cmsT revertant line is generated through recombination between two sets of repeats.

Genetics ◽

10.1093/genetics/124.2.423 ◽

1990 ◽

Vol 124 (2) ◽

pp. 423-428 ◽

Cited By ~ 1

Author(s):

C M Fauron ◽

M Havlik ◽

R I Brettell

Keyword(s):

Mitochondrial Genome ◽

Genome Organization ◽

Callus Tissue ◽

Mitochondrial Genomes ◽

Normal Type ◽

Male Sterile ◽

Sequence Complexity ◽

Mtdna Organization ◽

Callus Tissue Culture ◽

Fertile Revertant

Abstract The mitochondrial genome (mtDNA) organization from a fertile revertant line (V3) derived from the maize cytoplasmic male sterile type T (cmsT) callus tissue culture has been determined. We report that the sequence complexity can be mapped on to a circular "master chromosome" of 705 kb which includes a duplication of 165 kb of DNA when compared to its male sterile progenitor. Associated with this event is also a 0.423-kb deletion, which removed the cmsT-associated urf13 gene. As found for the maize normal type (N) and cmsT mitochondrial genomes, the V3 master chromosome also exists as a multipartite structure generated by recombination through repeated sequences.

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