MyMedR

Characteristics of complete mitogenome of the lesser short-nosed fruit bat Cynopterus brachyotis (Chiroptera: Pteropodidae) in Malaysia

Yoon KB, Kim JY, Park YC

Mitochondrial DNA A DNA Mapp Seq Anal, 2016 05;27(3):2091-2.

PMID: 25418628 DOI: 10.3109/19401736.2014.982571

We describe the characteristics of complete mitogenome of C. brachyotis in this article. The complete mitogenome of C. brachyotis is 16,701 bp long with a total base composition of 32.4% A, 25.7% T, 27.7% C and 14.2% G. The mitogenome consists of 13 protein-coding genes (11,408 bp), (KM659865) two rRNA (12S rRNA and 16S rRNA) genes (2,539 bp), 22 tRNA genes (1518 bp) and one control region (1239 bp).

Matched MeSH terms: Base Composition/genetics

The complete mitogenome of the soldier crab Mictyris longicarpus (Latreille, 1806) (Crustacea: Decapoda: Mictyridae)

Tan MH, Gan HM, Lee YP, Austin CM

Mitochondrial DNA A DNA Mapp Seq Anal, 2016 05;27(3):2121-2.

PMID: 25423510 DOI: 10.3109/19401736.2014.982585

The Mictyris longicarpus (soldier crab) complete mitochondrial genome sequence is reported making it the first for the family Mictyridae and the second for the superfamily Ocypodoidea. The mitogenome is 15,548 base pairs made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a non-coding AT-rich region. The soldier crab mitogenome gene order is characteristic of brachyuran crabs with a base composition of 36.58% for T, 19.15% for C, 32.43% for A and 11.83% for G, with an AT bias of 69.01%.

Matched MeSH terms: Base Composition/genetics

The complete mitogenome of the river blackfish, Gadopsis marmoratus (Richardson, 1848) (Teleostei: Percichthyidae)

Gan HM, Tan MH, Lee YP, Austin CM

Mitochondrial DNA A DNA Mapp Seq Anal, 2016 05;27(3):2030-1.

PMID: 25329292 DOI: 10.3109/19401736.2014.974174

The mitogenome of the Australian freshwater blackfish, Gadopsis marmoratus was recovered coverage by genome skimming using the MiSeq sequencer (GenBank Accession Number: NC_024436). The blackfish mitogenome has 16,407 base pairs made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs, and a 819 bp non-coding AT-rich region. This is the 5th mitogenome sequence to be reported for the family Percichthyidae.

Matched MeSH terms: Base Composition/genetics

The complete mitogenome of the hermit crab Clibanarius infraspinatus (Hilgendorf, 1869), (Crustacea; Decapoda; Diogenidae) - a new gene order for the Decapoda

Gan HY, Gan HM, Tan MH, Lee YP, Austin CM

Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):4099-4100.

PMID: 25629489

The complete mitochondrial genome of the hermit crab Clibanarius infraspinatus was recovered by genome skimming using Next-Gen sequencing. The Clibanarius infraspinatus mitogenome has 16,504 base pairs (67.94% A + T content) made up of 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNAs and a putative 1500 bp non-coding AT-rich region. The Clibanarius infraspinatus mitogenome sequence is the first for the family Diogenidae and the second for the superfamily Paguroidea and exhibits a translocation of the ND3 gene not previously reported for the Decapoda.

Matched MeSH terms: Base Composition/genetics

Complete mitogenome of two moray eels of Gymnothorax formosus and Scuticaria tigrina (Anguilliformes: Muraenidae)

Loh KH, Shao KT, Chen CH, Chen HM, Then AY, Loo PL, et al.

Mitochondrial DNA A DNA Mapp Seq Anal, 2016 Jul;27(4):2651-2.

PMID: 26029876 DOI: 10.3109/19401736.2015.1043530

In this study, the complete mitogenome sequence of two moray eels of Gymnothorax formosus and Scuticaria tigrina (Anguilliformes: Muraenidae) has been sequenced by the next-generation sequencing method. The assembled mitogenome, with the length of 16,558 bp for G. formosus and 16,521 bp for S. tigrina, shows 78% identity to each other. Both mitogenomes follow the typical vertebrate arrangement, including 13 protein coding genes, 22 transfer RNAs, two ribosomal RNAs genes, and a non-coding control region of D-loop. The length of D-loop is 927 bp (G. formosus) and 850 bp (S. tigrina), which is located between tRNA-Pro and tRNA-Phe. The overall GC content is 45.5% for G. formosus and 47.9% for S. tigrina. Complete mitogenomes of G. formosus and S. tigrina provide essential and important DNA molecular data for further phylogenetic and evolutionary analysis for moray eel.

Matched MeSH terms: Base Composition/genetics

Next generation sequencing yields the complete mitochondrial genome of the Zebra moray, Gymnomuraena zebra (Anguilliformes: Muraenidae)

Loh KH, Shao KT, Chen HM, Chen CH, Chong VC, Loo PL, et al.

Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):4230-4231.

PMID: 26000942

In this study, the complete mitogenome sequence of the Zebra moray, Gymnomuraena zebra (Anguilliformes: Muraenidae) has been sequenced by the next-generation sequencing method. The assembled mitogenome consisting of 16,576 bp includes 13 protein coding genes, 22 transfer RNAs, and two ribosomal RNAs genes. The overall base composition of Zebra moray is 30.2% for A, 26.8% for C, 17.2% for G, and 25.8% for T and show 80% identities to Kidako moray, Gymnothorax kidako. The complete mitogenome of the Zebra moray provides an essential and important DNA molecular data for further phylogeography and evolutionary analysis for moray eel phylogeny.

Matched MeSH terms: Base Composition/genetics

Thaumasiovibrio occultus gen. nov. sp. nov. and Thaumasiovibrio subtropicus sp. nov. within the family Vibrionaceae, isolated from coral reef seawater off Ishigaki Island, Japan

Amin AKMR, Tanaka M, Al-Saari N, Feng G, Mino S, Ogura Y, et al.

Syst Appl Microbiol, 2017 Jul;40(5):290-296.

PMID: 28648725 DOI: 10.1016/j.syapm.2017.04.003

Two phylogenetically distinct Vibrionaceae strains C4II189Tand C4V358Tisolated from reef seawater off Ishigaki Island, Japan, in 2014 were studied with advanced genome-based taxonomy approaches. All aspects of phylogenetic (16S rRNA phylogeny, MLSA), phenotypic and genetic (ANI, DDH, AAI, and the number of core genes) cohesions between the two identified species were high enough to propose them as members of a new genus within the family Vibrionaceae. Consequently, an eighth genus Thaumasiovibrio gen. nov. is proposed that contains two new species Thaumasiovibrio occultus sp. nov. strain C4II189T(=DSM 101554T=JCM 31629T) (type species) and Thaumasiovibrio subtropicus sp. nov. strain C4V358T(=DSM 101555T=JCM 31630T). Thaumasiovibrio species were phylogenetically distinct from the other Vibrionaceae species based on pyrH gene sequences. The combination of catalase negative, sensitivity to vibriostatic agent O/129, and green colony formation on TCBS for the phylogenetically affiliated strains was the diagnostic features for the current tentative identification of this genus.

Matched MeSH terms: Base Composition/genetics

Fulltext Complete mitochondrial genome of Dacus vijaysegarani and phylogenetic relationships with congeners and other tephritid fruit flies (Insecta: Diptera)

Yong HS, Chua KO, Song SL, Liew YJ, Eamsobhana P, Chan KG

Mol Biol Rep, 2021 Aug;48(8):6047-6056.

PMID: 34357549 DOI: 10.1007/s11033-021-06608-2

BACKGROUND: Tephritid fruit flies of the genus Dacus are members of the tribe Dacini, subfamily Dacinae. There are some 274 species worldwide, distributed in Africa and the Asia-Pacific. To date, only five complete mitochondrial genomes (mitogenomes) of Dacus fruit flies have been published and are available in the GenBank.

METHODS AND RESULTS: In view of the lack of study on their mitogenome, we sequenced (by next generation sequencing) and annotated the complete mitogenome of D. vijaysegarani from Malaysia to determine its features and phylogenetic relationship. The whole mitogenome of D. vijaysegarani has identical gene order with the published mitogenomes of the genus Dacus, with 13 protein-coding genes, two rRNA genes, 22 tRNAs, a non-coding A + T rich control region, and intergenic spacer and overlap sequences. Phylogenetic analysis based on 15 mitochondrial genes (13 PCGs and two rRNA genes), reveals Dacus, Zeugodacus and Bactrocera forming a distinct clade. The genus Dacus forms a monophyletic group in the subclade containing also the Zeugodacus group; this Dacus-Zeugodacus subclade is distinct from the Bactrocera subclade. D. (Mellesis) vijaysegarani forms a lineage with D. (Mellesis) trimacula in the subcluster containing also the lineage of D. (Mellesis) conopsoides and D. (Callantra) longicornis. D. (Dacus) bivittatus and D. (Didacus) ciliatus form a distinct subcluster. Based on cox1 sequences, the Malaysia and Vietnam taxa of D. vijaysegarani may not be conspecific.

CONCLUSIONS: Overall, the mitochondrial genome of D. vijaysegarani provided essential molecular data that could be useful for further studies for species diagnosis, evolution and phylogeny research of other tephritid fruit flies in the future.

Matched MeSH terms: Base Composition/genetics

The complete mitochondrial genome of the Blue-face angelfish, Pomacanthus xanthometapon (Perciformes: Pomacanthidae)

Shen KN, Loh KH, Chen CH, Hsiao CD

Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):4122-4123.

PMID: 25585497

In this study, the complete mitogenome sequence of the Blue-face angelfish, Pomacanthus xanthometapon (Perciformes: Pomacanthidae) has been sequenced by the next-generation sequencing method. The assembled mitogenome consisting of 16,533 bp includes 13 protein coding genes, 22 transfer RNAs, and two ribosomal RNAs genes. The overall base composition of Blue-face angelfish is 28.7% for A, 28.9% for C, 15.9% for G, 26.6% for T and show 84% identities to flame angelfish Centropyge loriculus. The complete mitogenome of the Blue-face angelfish provides essential and important DNA molecular data for further phylogeography and evolutionary analysis for marine angelfish phylogeny.

Matched MeSH terms: Base Composition/genetics

Fulltext Comparison of eight complete chloroplast genomes of the endangered Aquilaria tree species (Thymelaeaceae) and their phylogenetic relationships

Hishamuddin MS, Lee SY, Ng WL, Ramlee SI, Lamasudin DU, Mohamed R

Sci Rep, 2020 Aug 03;10(1):13034.

PMID: 32747724 DOI: 10.1038/s41598-020-70030-0

Aquilaria tree species are naturally distributed in the Indomalesian region and are protected against over-exploitation. They produce a fragrant non-timber product of high economic value, agarwood. Ambiguous species delimitation and limited genetic information within Aquilaria are among the impediments to conservation efforts. In this study, we conducted comparative analysis on eight Aquilaria species complete chloroplast (cp) genomes, of which seven were newly sequenced using Illumina HiSeq X Ten platform followed by de novo assembly. Aquilaria cp genomes possess a typical quadripartite structure including gene order and genomic structure. The length of each of the cp genome is about 174 kbp and encoded between 89 and 92 proteins, 38 tRNAs, and 8 rRNAs, with 27 duplicated in the IR (inverted repeat) region. Besides, 832 repeats (forward, reverse, palindrome and complement repeats) and nine highly variable regions were also identified. The phylogenetic analysis suggests that the topology structure of Aquilaria cp genomes were well presented with strong support values based on the cp genomes data set and matches their geographic distribution pattern. In summary, the complete cp genomes will facilitate development of species-specific molecular tools to discriminate Aquilaria species and resolve the evolutionary relationships of members of the Thymelaeaceae family.

Matched MeSH terms: Base Composition/genetics

The complete mitochondrial genome of Bactrocera diaphora (Diptera: Tephtitidae)

Zhang KJ, Liu L, Rong X, Zhang GH, Liu H, Liu YH

Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):4314-4315.

PMID: 26462416

We sequenced and annotated the complete mitochondrial genome (mitogenome) of Bactrocera diaphora (Diptera: Tephtitidae), which is an economically important pest in the southwest area of China, India, Sri Lanka, Vietnam and Malaysia. This mitogenome is 15 890 bp in length with an A + T content of 74.103%, and contains 37 typical animal mitochondrial genes that are arranged in the same order as that of the inferred ancestral insects. All protein-coding genes (PCGs) start with a typical ATN codon, except cox1 that begins with TCG. Ten PCGs stop with termination codon TAA or TAG, whereas cox1, nad1 and nad5 have single T-- as the incomplete stop codon. All of the transfer RNA genes present the typical clover leaf secondary structure except trnS1 (AGN) with a looping D-arm. The A + T-rich region is located between rrnS and trnI with a length of 946 bp, and contains a 20 bp poly-T stretch and 22 bp poly-A stretch. Except the control region, the longest intergenic spacer is located between trnR and trnN that is 94 bp long with an excessive high A + T content (95.74%) and a microsatellite-like region (TA)13.

Matched MeSH terms: Base Composition/genetics

Pseudomonas versuta sp. nov., isolated from Antarctic soil

See-Too WS, Salazar S, Ee R, Convey P, Chan KG, Peix Á

Syst Appl Microbiol, 2017 Jun;40(4):191-198.

PMID: 28501448 DOI: 10.1016/j.syapm.2017.03.002

In this study we analysed three bacterial strains coded L10.10T, A4R1.5 and A4R1.12, isolated in the course of a study of quorum-quenching bacteria occurring in Antarctic soil. The 16S rRNA gene sequence was identical in the three strains and showed 99.7% pairwise similarity with respect to the closest related species Pseudomonas weihenstephanensis WS4993T. Therefore, the three strains were classified within the genus Pseudomonas. Analysis of housekeeping genes (rpoB, rpoD and gyrB) sequences showed similarities of 84-95% with respect to the closest related species of Pseudomonas, confirming its phylogenetic affiliation. The ANI values were less than 86% to the closest related species type strains. The respiratory quinone is Q9. The major fatty acids are C16:0, C16:1 ω7c/ C16:1 ω6c in summed feature 3 and C18:1 ω7c / C18:1 ω6c in summed feature 8. The strains are oxidase- and catalase-positive. Growth occurs at 4-30°C, and at pH 4.0-10. The DNA G+C content is 58.2-58.3mol %. The combined genotypic, phenotypic and chemotaxonomic data support the classification of strains L10.10T, A4R1.5 and A4R1.12 into a novel species of Pseudomonas, for which the name P. versuta sp. nov. is proposed. The type strain is L10.10T (LMG 29628T, DSM 101070T).

Matched MeSH terms: Base Composition/genetics

Next generation sequencing yields the complete mitochondrial genome of the Clarion angelfish, Holacanthus clarionensis (Perciformes: Pomacanthidae)

Shen KN, Chang CW, Loh KH, Chen CH, Hsiao CD

Mitochondrial DNA A DNA Mapp Seq Anal, 2016 11;27(6):4118-4119.

PMID: 25600747

In this study, the complete mitogenome sequence of the Clarion angelfish, Holacanthus clarionensis (Perciformes: Pomacanthidae) has been sequenced by next-generation sequencing method. The length of the assembled mitogenome is 16,615 bp, including 13 protein coding genes, 22 transfer RNAs, and two ribosomal RNAs genes. The overall base composition of Clarion angelfish is 28.3% for A, 29.3% for C, 16.5% for G, 25.9% for T and show 85% identities to flame angelfish Centropyge loriculus. The complete mitogenome of the Clarion angelfish provides essential and important DNA molecular data for further phylogeography and evolutionary analysis for marine angelfish phylogeny.

Matched MeSH terms: Base Composition/genetics

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