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The complete mitogenome of Diaporthe nobilis.

ABSTRACT: The complete mitogenome of Diaporthe nobilis NIE8444 (KCTC No. 56710) isolated from alpine conifer Abies nephrolepis is determined by the Illumina Hiseq4000 platform in this study. This mitogenome consists of 67,437 bp length with 31.45% G + C content. A total of 51 genes were predicted in this mitogenome: 21 protein-coding genes, 2 rRNAs and 28 tRNAs. Phylogenetic tree based on small subunit ribosomal RNA of mitochondria showed that D. nobilis was close to D. longicolla. This complete mitogenome of D. nobilis provides valuable information on the mitochondrial evolution of endophytic fungi.

SUBMITTER: Eo JK

PROVIDER: S-EPMC7801033 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Diaporthe nobilis

Project description:Diaporthe nobilis overview

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Diaporthe nobilis isolate:DJY16A5-1

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The complete mitogenome of Fusarium equiseti.

Project description:The complete mitochondrial genome of plant pathogenic fungus, Fusarium equiseti, was sequenced. The circular molecule is 53,411 bp long with a GC content of 32.81%. It contains 22 protein-coding genes, 4 ribosomal RNA (rRNA), and 24 transfer RNA (tRNA) genes. Phylogenetic reconstructions confirmed that it has the closest relationship with Fusarium equiseti. The mitogenome analysis of Fusarium equiseti provides a molecular basis for further studies on molecular systematics and evolutionary dynamics.

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The complete chloroplast genome of Fissidens nobilis Griff. (Fissidentaceae, Bryophyta).

Project description:We presented a complete chloroplast genome of Fissidens nobilis which is 124,962?bp long and has four subregions: 86,122?bp of large single-copy (LSC) and 18,708?bp of small single-copy (SSC) regions are separated by 10,066?bp of inverted repeat (IR) regions including 127 genes (82 protein-coding genes, 8 rRNAs, and 37 tRNAs). The overall GC content is 29.2% and those in the LSC, SSC, and IR regions are 26.6%, 26.0%, and 43.5%, respectively. Phylogenetic trees show that the phylogenetic position of F. nobilis is congruent with the previous phylogenetic study of moss species.

| S-EPMC7687450 | biostudies-literature

Complete Chloroplast Genome of the Wollemi Pine (Wollemia nobilis): Structure and Evolution.

Project description:The Wollemi pine (Wollemia nobilis) is a rare Southern conifer with striking morphological similarity to fossil pines. A small population of W. nobilis was discovered in 1994 in a remote canyon system in the Wollemi National Park (near Sydney, Australia). This population contains fewer than 100 individuals and is critically endangered. Previous genetic studies of the Wollemi pine have investigated its evolutionary relationship with other pines in the family Araucariaceae, and have suggested that the Wollemi pine genome contains little or no variation. However, these studies were performed prior to the widespread use of genome sequencing, and their conclusions were based on a limited fraction of the Wollemi pine genome. In this study, we address this problem by determining the entire sequence of the W. nobilis chloroplast genome. A detailed analysis of the structure of the genome is presented, and the evolution of the genome is inferred by comparison with the chloroplast sequences of other members of the Araucariaceae and the related family Podocarpaceae. Pairwise alignments of whole genome sequences, and the presence of unique pseudogenes, gene duplications and insertions in W. nobilis and Araucariaceae, indicate that the W. nobilis chloroplast genome is most similar to that of its sister taxon Agathis. However, the W. nobilis genome contains an unusually high number of repetitive sequences, and these could be used in future studies to investigate and conserve any remnant genetic diversity in the Wollemi pine.

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Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths.

Project description:BACKGROUND:Late Pleistocene North America hosted at least two divergent and ecologically distinct species of mammoth: the periglacial woolly mammoth (Mammuthus primigenius) and the subglacial Columbian mammoth (Mammuthus columbi). To date, mammoth genetic research has been entirely restricted to woolly mammoths, rendering their genetic evolution difficult to contextualize within broader Pleistocene paleoecology and biogeography. Here, we take an interspecific approach to clarifying mammoth phylogeny by targeting Columbian mammoth remains for mitogenomic sequencing. RESULTS:We sequenced the first complete mitochondrial genome of a classic Columbian mammoth, as well as the first complete mitochondrial genome of a North American woolly mammoth. Somewhat contrary to conventional paleontological models, which posit that the two species were highly divergent, the M. columbi mitogenome we obtained falls securely within a subclade of endemic North American M. primigenius. CONCLUSIONS:Though limited, our data suggest that the two species interbred at some point in their evolutionary histories. One potential explanation is that woolly mammoth haplotypes entered Columbian mammoth populations via introgression at subglacial ecotones, a scenario with compelling parallels in extant elephants and consistent with certain regional paleontological observations. This highlights the need for multi-genomic data to sufficiently characterize mammoth evolutionary history. Our results demonstrate that the use of next-generation sequencing technologies holds promise in obtaining such data, even from non-cave, non-permafrost Pleistocene depositional contexts.

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Project description:In this study, combining the gonad transcripts of the both sexes by RNA-Seq with the DNA sequences by conventional PCRs, we have determined the complete mitogenome of Gobiopterus lacustris collected from the mangrove waters of the Leizhou Peninsula in tropical South China. This mitochondrial genome is 16593?bp in length and consists of 37 genes in the typical vertebrate mitochondrial gene arrangement. This study will contribute on the phylogenetics of genus Gobiopterus and the other genera of Gobiidae.

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Complete mitogenome of Nemacheilus subfusca (Cypriniformes: Cobitidae).

Project description:The Nemacheilus subfusca (N. subfusca) is a species of the Noemacheilinae in the Cobitidae family, which has been few reported. The first complete mitochondrion of the N. subfusca is 16 585 bp in length, containing 13 protein-coding genes, two rRNA genes (12S and 16S rRNA), 22 tRNA genes and a control region (D-loop region). The longest protein-coding gene of this mitochondrion was ND5 (1839 bp), and the 22 tRNA genes were range from 66 (tRNACys ) to 76 (tRNALys ) in length. The 12S rRNA (957 bp) and 16S rRNA (1677 bp) were separated by TrnaVal , and the D-loop region located between tRNAPro and tRNAPhe genes. The phylogenetic indicates that the N. subfusca was independent from other species of distinct genus in the Noemacheilinae, which provided the valuable evidence on phylogenetic relationship of the N. subfusca at the molecular level.

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Complete mitochondrial genome sequence of the northern red-shouldered macaw (Diopsittaca nobilis).

Project description:The northern red-shouldered macaw, Diopsittaca nobilis, is listed in the Convention on International Trade in Endangered Species of Wild Fauna and Flora Appendix II. Here, we report for the first time the complete mitochondrial genome of D. nobilis. This new sequence is 16,992 base pairs (bp) in length and includes 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and a single non-coding control region. The overall nucleotide composition of this sequence consists of 30.40% A, 14.00% G, 23.60% T, and 32.00% C. The phylogenetic relationships suggested that the mitogenome of D. nobilis is close to that of three other macaw species. Our results provide useful mitogenomic information to support further studies on the phylogeny and taxonomy of Psittaciformes.

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Complete mitogenome of the entomopathogenic fungus Akanthomyces lecanii.

Project description:In this study, the complete mitogenome of an entomopathogenic fungus Akanthomyces lecanii is assembled and annotated. This circular mitogenome is 24,643 bp in length and consists of 2 rRNA genes (rnl and rns), 26 tRNA genes and 14 standard protein-coding genes of the oxidative phosphorylation system. Only one intron (group IA) is identified, which invades rnl and carries an ORF coding for ribosomal protein S3. Phylogenetic analysis based on concatenated mitochondrial nucleotide sequences confirms A. lecanii in Cordycipitaceae, and A. lecanii clusters together with Akanthomyces muscarius.

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