Dataset Information

Characterization of the Complete Mitochondrial Genome of Basidiomycete Yeast Hannaella oryzae: Intron Evolution, Gene Rearrangement, and Its Phylogeny.

ABSTRACT: In this study, the mitogenome of Hannaella oryzae was sequenced by next-generation sequencing (NGS) and successfully assembled. The H. oryzae mitogenome comprised circular DNA molecules with a total size of 26,444 bp. We found that the mitogenome of H. oryzae partially deleted the tRNA gene transferring cysteine. Comparative mitogenomic analyses showed that intronic regions were the main factors contributing to the size variations of mitogenomes in Tremellales. Introns of the cox1 gene in Tremellales species were found to have undergone intron loss/gain events, and introns of the H. oryzae cox1 gene may have different origins. Gene arrangement analysis revealed that H. oryzae contained a unique gene order different from other Tremellales species. Phylogenetic analysis based on a combined mitochondrial gene set resulted in identical and well-supported topologies, wherein H. oryzae was closely related to Tremella fuciformis. This study represents the first report of mitogenome for the Hannaella genus, which will allow further study of the population genetics, taxonomy, and evolutionary biology of this important phylloplane yeast and other related species.

SUBMITTER: Li Q

PROVIDER: S-EPMC8193148 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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Publications

Characterization of the Complete Mitochondrial Genome of Basidiomycete Yeast Hannaella oryzae: Intron Evolution, Gene Rearrangement, and Its Phylogeny.

Li Qiang Q Li Lijiao L Feng Huiyu H Tu Wenying W Bao Zhijie Z Xiong Chuan C Wang Xu X Qing Yuan Y Huang Wenli W

Frontiers in microbiology 20210528

In this study, the mitogenome of Hannaella oryzae was sequenced by next-generation sequencing (NGS) and successfully assembled. The H. oryzae mitogenome comprised circular DNA molecules with a total size of 26,444 bp. We found that the mitogenome of H. oryzae partially deleted the tRNA gene transferring cysteine. Comparative mitogenomic analyses showed that intronic regions were the main factors contributing to the size variations of mitogenomes in Tremellales. Introns of th ...[more]

PMID: 34122362

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Project description:BackgroundEchinolaelaps fukienensis is the dominant mite species parasitic on the body surface of the genus Niviventer. The mitochondrial genome (mitogenome) has its own independent genetic material and genetic system, and is now widely used in population genetics, genealogical biogeography, phylogeny and molecular evolution studies. Species diversity of the superfamily Dermanyssoidea is very rich, but its mitogenomes AT content is high, and it is difficult to amplify the complete mitogenome by routine PCR. To date, we have only obtained the mitogenomes of 6 species, scarcity on sequence data has greatly impeded the studies in the superfamily Dermanyssoidea.MethodsEchinolaelaps fukienensis were collected in 2019 from the body surface of Niviventer confucianus (Rodentia, Muridae) in Yunnan Province. The E. fukienensis mitogenome was determined and analyzed for the first time using the Illumina Novoseq 6000 platform. Phylogenetic analyses of the superfamily Dermanyssoidea were conducted based on the entire mitogenome sequences.ResultsThe E. fukienensis mitogenome was 14,402 bp, which is known the smallest genome of the superfamily Dermanyssoidea, encoding a total of 37 genes, including 13 PCGs, 22 tRNAs, 2 rRNAs and 1 control region. Most protein-coding genes use ATN as the start codon and TAN as the stop codon. AT and GC skew of atp8 genes in E. fukienensis were both 0. The average length of 22 tRNA genes of E. fukienensis was 64 bp, and secondary structures of tRNAs showed base mismatches and missing D-arms in many places. Compared with gene arrangement pattern of the hypothetical ancestor of arthropods, the E. fukienensis mitogenome shows a novel arrangement pattern. Phylogenetic tree supported the monophyly of the superfamily Dermanyssoidea. Echinolaelaps fukienensis being the least genetic distant (0.2762) and most closely related to Varroa destructor.ConclusionsThis study analyzed comprehensive the structure and evolution of the E. fukienensis mitogenome for the first time, enriches molecular data of the genus Echinolaelaps, which will contribute to further understand phylogeny and rearrangement patterns of the superfamily Dermanyssoidea.

Project description:BackgroundThe evolutionary history and relationships of the mud shrimps (Crustacea: Decapoda: Gebiidea and Axiidea) are contentious, with previous attempts revealing mixed results. The mud shrimps were once classified in the infraorder Thalassinidea. Recent molecular phylogenetic analyses, however, suggest separation of the group into two individual infraorders, Gebiidea and Axiidea. Mitochondrial (mt) genome sequence and structure can be especially powerful in resolving higher systematic relationships that may offer new insights into the phylogeny of the mud shrimps and the other decapod infraorders, and test the hypothesis of dividing the mud shrimps into two infraorders.ResultsWe present the complete mitochondrial genome sequences of five mud shrimps, Austinogebia edulis, Upogebia major, Thalassina kelanang (Gebiidea), Nihonotrypaea thermophilus and Neaxius glyptocercus (Axiidea). All five genomes encode a standard set of 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes and a putative control region. Except for T. kelanang, mud shrimp mitochondrial genomes exhibited rearrangements and novel patterns compared to the pancrustacean ground pattern. Each of the two Gebiidea species (A. edulis and U. major) and two Axiidea species (N. glyptocercus and N. thermophiles) share unique gene order specific to their infraorders and analyses further suggest these two derived gene orders have evolved independently. Phylogenetic analyses based on the concatenated nucleotide and amino acid sequences of 13 protein-coding genes indicate the possible polyphyly of mud shrimps, supporting the division of the group into two infraorders. However, the infraordinal relationships among the Gebiidea and Axiidea, and other reptants are poorly resolved. The inclusion of mt genome from more taxa, in particular the reptant infraorders Polychelida and Glypheidea is required in further analysis.ConclusionsPhylogenetic analyses on the mt genome sequences and the distinct gene orders provide further evidences for the divergence between the two mud shrimp infraorders, Gebiidea and Axiidea, corroborating previous molecular phylogeny and justifying their infraordinal status. Mitochondrial genome sequences appear to be promising markers for resolving phylogenetic issues concerning decapod crustaceans that warrant further investigations and our present study has also provided further information concerning the mt genome evolution of the Decapoda.

Dataset Information

Characterization of the Complete Mitochondrial Genome of Basidiomycete Yeast Hannaella oryzae: Intron Evolution, Gene Rearrangement, and Its Phylogeny.

Publications

Characterization of the Complete Mitochondrial Genome of Basidiomycete Yeast <i>Hannaella oryzae</i>: Intron Evolution, Gene Rearrangement, and Its Phylogeny.

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