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Characterisation of the mitochondrial genome and phylogenetic analysis of Toxocara apodemi (Nematoda: Ascarididae)

Gao Y, Hu Y, Xu S, Liang H, Lin H, Yin TH, et al.

J Helminthol, 2024 Apr 15;98:e33.
PMID: 38618902 DOI: 10.1017/S0022149X24000221

We first sequenced and characterised the complete mitochondrial genome of Toxocara apodeme, then studied the evolutionary relationship of the species within Toxocaridae. The complete mitochondrial genome was amplified using PCR with 14 specific primers. The mitogenome length was 14303 bp in size, including 12 PCGs (encoding 3,423 amino acids), 22 tRNAs, 2 rRNAs, and 2 NCRs, with 68.38% A+T contents. The mt genomes of T. apodemi had relatively compact structures with 11 intergenic spacers and 5 overlaps. Comparative analyses of the nucleotide sequences of complete mt genomes showed that T. apodemi had higher identities with T. canis than other congeners. A sliding window analysis of 12 PCGs among 5 Toxocara species indicated that nad4 had the highest sequence divergence, and cox1 was the least variable gene. Relative synonymous codon usage showed that UUG, ACU, CCU, CGU, and UCU most frequently occurred in the complete genomes of T. apodemi. The Ka/Ks ratio showed that all Toxocara mt genes were subject to purification selection. The largest genetic distance between T. apodemi and the other 4 congeneric species was found in nad2, and the smallest was found in cox2. Phylogenetic analyses based on the concatenated amino acid sequences of 12 PCGs demonstrated that T. apodemi formed a distinct branch and was always a sister taxon to other congeneric species. The present study determined the complete mt genome sequences of T. apodemi, which provide novel genetic markers for further studies of the taxonomy, population genetics, and systematics of the Toxocaridae nematodes.

Matched MeSH terms: Genome, Mitochondrial*
Fulltext Variants in the mitochondrial genome sequence of Oryctes rhinoceros (Coleoptera: Scarabaeidae) infected with Oryctes rhinoceros nudivirus in oil palm and coconut plantations

Anggraini E, Vadamalai G, Kong LL, Mat M, Lau WH

Sci Rep, 2023 Oct 06;13(1):16850.
PMID: 37803044 DOI: 10.1038/s41598-023-43691-w

The CRB (coconut rhinoceros beetle) haplotype was classified into CRB-S and CRB-G, based on the presence of single nucleotide polymorphisms (SNPs) in the mitochondrial cox1 gene. Mitochondrial genomes (mitogenomes) are the most widely used genetic resources for molecular evolution, phylogenetics, and population genetics in relation to insects. This study presents the mitogenome CRB-G and CRB-S which were collected in Johor, Malaysia. The mitogenome of CRB-G collected from oil palm plantations in 2020 and 2021, and wild coconut palms in 2021 was 15,315 bp, 15,475 bp, and 17,275 bp, respectively. The CRB-S was discovered in coconut and oil palms in 2021, and its mitogenome was 15,484 bp and 17,142 bp, respectively. All the mitogenomes have 37 genes with more than 99% nucleotide sequence homology, except the CRB-G haplotype collected from oil palm in 2021 with 89.24% nucleotide sequence homology. The mitogenome of Johor CRBs was variable in the natural population due to its elevated mutation rate. Substitutions and indels in cox1, cox2, nad2 and atp6 genes were able to distinguish the Johor CRBs into two haplotypes. The mitogenome data generated in the present study may provide baseline information to study the infection and relationship between the two haplotypes of Johor CRB and OrNV in the field. This study is the first report on the mitogenomes of mixed haplotypes of CRB in the field.

Matched MeSH terms: Genome, Mitochondrial*
Rediscovery of Bipalium admarginatum de Beauchamp, 1933 (Platyhelminthes, Tricladida, Geoplanidae) in Malaysia, with molecular characterisation including the mitogenome

Soo OYM, Gastineau R, Verdon G, Winsor L, Justine JL

Zootaxa, 2023 May 03;5277(3):585-599.
PMID: 37518300 DOI: 10.11646/zootaxa.5277.3.11

We present here the first observation of Bipalium admarginatum de Beauchamp, 1933 since its original description 90 years ago. Three specimens were found on Perhentian Kecil Island, off Terengganu State, Malaysia and photographed in the field, and two were collected. This report thus includes the first colour photographs published for this species, from a locality close to the type-locality, Tioman Island (which is ca. 200 km south of the locality in this study, on the east coast of Peninsula Malaysia). We describe the external morphology and colour pattern of the species, which correspond well to the original description, itself based only on two preserved specimens. We performed an in-depth molecular characterisation of the species, including its complete mitochondrial genome, the 18S sequence and elongation 1-alpha (EF1-α) sequence. In addition, EF1-α sequences were also retrieved for 5 additional geoplanid species. No tRNA-Thr could be detected in the mitogenome of B. admarginatum, a lack already reported in several species of geoplanids, but we found a 13 bp sequence that contains the anticodon loop and seems to be conserved among geoplanids and might thus possibly represent a non-canonical undetected tRNA. We discuss the difficulties encountered in trying to reconstruct the cluster of nuclear ribosomal genes, a problem already mentioned for other Triclads. Three phylogenies, based respectively on all mitochondrial proteins, 18S, and EF1-α, were computed; the position of B. admarginatum within the Bipaliinae was confirmed in each tree, as sister-group to various bipaliine species according to the sequences available for each tree. In the mitochondrial proteins tree, which had high support, B. admarginatum was sister to Bipalium kewense and Diversibipalium multilineatum.

Matched MeSH terms: Genome, Mitochondrial*
Another piece for the syllid puzzle: A new species from Japan and its mitochondrial genome reveal the enigmatic Clavisyllis (Phyllodocida: Syllidae) as a member of Eusyllinae

Cejp B, Jimi N, Aguado MT

Zootaxa, 2023 Feb 21;5244(4):341-360.
PMID: 37044457 DOI: 10.11646/zootaxa.5244.4.2

The phylogenetic relationships of Syllidae have been analyzed in several studies during the last decades, resulting in highly congruent topologies. Most of the subfamilies were found to be monophyletic, while other groups (Eusyllinae and several genera) have been reorganized attending their phylogenetic relationships. However, there are still several enigmatic genera, which could not be assigned to any of the established subgroups. These enigmatic genera usually show a combination of characters indicating relationships with several different groups, and some show morphological traits unique to Syllidae. One of the most intriguing genera, still unclassified within Syllidae is Clavisyllis Knox. Herein, we provide a complete description of a new species Clavisyllis tenjini n. sp. from Japan. We sequence the complete mitochondrial genome, compare with the available data from other syllids, and perform a phylogenetic analysis of three genes (18S, 16S, COI), traditionally used in previous studies. Clavisyllis shows a unique combination of characters within Syllidae, such as nuchal lappets and large ovoid dorsal cirri. The new species has additional anterior appendages that have not been found in any other syllid. Our results show the genus is a member of Eusyllinae, closely related to Pionosyllis Malmgren. The mitochondrial gene order agrees with the considered plesiomorphic gene order in Annelida, which is present in all members of Eusyllinae investigated so far. Clavisyllis reproduces by epigamy, the reproductive mode of members of Eusyllinae. The present study contributes to the systematics of Syllidae, a complex group with a large number of species and striking reproductive modes.

Matched MeSH terms: Genome, Mitochondrial*
Somatic mitochondrial DNA mutations in different grades of glioma

Soon BH, Abu N, Abdul Murad NA, Then SM, Abu Bakar A, Fadzil F, et al.

Per Med, 2022 01;19(1):25-39.
PMID: 34873928 DOI: 10.2217/pme-2021-0033

Aim: Mitochondrial DNA (mtDNA) alterations play an important role in the multistep processes of cancer development. Gliomas are among the most diagnosed brain cancer. The relationship between mtDNA alterations and different grades of gliomas are still elusive. This study aimed to elucidate the profile of somatic mtDNA mutations in different grades of gliomas and correlate it with clinical phenotype. Materials & methods: Forty histopathologically confirmed glioma tissue samples and their matched blood were collected and subjected for mtDNA sequencing. Results & conclusion: About 75% of the gliomas harbored at least one somatic mutation in the mtDNA gene, and 45% of these mutations were pathogenic. Mutations were scattered across the mtDNA genome, and the commonest nonsynonymous mutations were located at complex I and IV of the mitochondrial respiratory chain. These findings may have implication for future research to determine the mitochondrial energetics and its downstream metabolomics on gliomas.

Matched MeSH terms: Genome, Mitochondrial*
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: Genome, Mitochondrial/genetics*
Improving the phylogenetic resolution of Malaysian and Javan mahseer (Cyprinidae), Tor tambroides and Tor tambra: Whole mitogenomes sequencing, phylogeny and potential mitogenome markers

Lim LWK, Chung HH, Lau MML, Aziz F, Gan HM

Gene, 2021 Jul 30;791:145708.
PMID: 33984441 DOI: 10.1016/j.gene.2021.145708

The true mahseer (Tor spp.) is one of the highest valued fish in the world due to its high nutritional value and great unique taste. Nevertheless, its morphological characterization and single mitochondrial gene phylogeny in the past had yet to resolve the ambiguity in its taxonomical classification. In this study, we sequenced and assembled 11 complete mahseer mitogenomes collected from Java of Indonesia, Pahang and Terengganu of Peninsular Malaysia as well as Sarawak of East Malaysia. The mitogenome evolutionary relationships among closely related Tor spp. samples were investigated based on maximum likelihood phylogenetic tree construction. Compared to the commonly used COX1 gene fragment, the complete COX1, Cytb, ND2, ND4 and ND5 genes appear to be better phylogenetic markers for genetic differentiation at the population level. In addition, a total of six population-specific mitolineage haplotypes were identified among the mahseer samples analyzed, which this offers hints towards its taxonomical landscape.

Matched MeSH terms: Genome, Mitochondrial/genetics*
Fulltext Complete mitochondrial genomes and phylogenetic relationships of the genera Nephila and Trichonephila (Araneae, Araneoidea)

Yong HS, Song SL, Chua KO, Wayan Suana I, Eamsobhana P, Tan J, et al.

Sci Rep, 2021 May 21;11(1):10680.
PMID: 34021208 DOI: 10.1038/s41598-021-90162-1

Spiders of the genera Nephila and Trichonephila are large orb-weaving spiders. In view of the lack of study on the mitogenome of these genera, and the conflicting systematic status, we sequenced (by next generation sequencing) and annotated the complete mitogenomes of N. pilipes, T. antipodiana and T. vitiana (previously N. vitiana) to determine their features and phylogenetic relationship. Most of the tRNAs have aberrant clover-leaf secondary structure. Based on 13 protein-coding genes (PCGs) and 15 mitochondrial genes (13 PCGs and two rRNA genes), Nephila and Trichonephila form a clade distinctly separated from the other araneid subfamilies/genera. T. antipodiana forms a lineage with T. vitiana in the subclade containing also T. clavata, while N. pilipes forms a sister clade to Trichonephila. The taxon vitiana is therefore a member of the genus Trichonephila and not Nephila as currently recognized. Studies on the mitogenomes of other Nephila and Trichonephila species and related taxa are needed to provide a potentially more robust phylogeny and systematics.

Matched MeSH terms: Genome, Mitochondrial*
Enhancing mitogenomic phylogeny and resolving the relationships of extinct megafaunal placental mammals

Phillips MJ, Shazwani Zakaria S

Mol Phylogenet Evol, 2021 05;158:107082.
PMID: 33482383 DOI: 10.1016/j.ympev.2021.107082

Mitochondrial genomes provided the first widely used sequences that were sufficiently informative to resolve relationships among animals across a wide taxonomic domain, from within species to between phyla. However, mitogenome studies supported several anomalous relationships and fell partly out of favour as sequencing multiple, independent nuclear loci proved to be highly effective. A tendency to blame mitochondrial DNA (mtDNA) has overshadowed efforts to understand and ameliorate underlying model misspecification. Here we find that influential assessments of the infidelity of mitogenome phylogenies have often been overstated, but nevertheless, substitution saturation and compositional non-stationarity substantially mislead reconstruction. We show that RY coding the mtDNA, excluding protein-coding 3rd codon sites, partitioning models based on amino acid hydrophobicity and enhanced taxon sampling improve the accuracy of mitogenomic phylogeny reconstruction for placental mammals, almost to the level of multi-gene nuclear datasets. Indeed, combined analysis of mtDNA with 3-fold longer nuclear sequence data either maintained or improved upon the nuclear support for all generally accepted clades, even those that mtDNA alone did not favour, thus indicating "hidden support". Confident mtDNA phylogeny reconstruction is especially important for understanding the evolutionary dynamics of mitochondria themselves, and for merging extinct taxa into the tree of life, with ancient DNA often only accessible as mtDNA. Our ancient mtDNA analyses lend confidence to the relationships of three extinct megafaunal taxa: glyptodonts are nested within armadillos, the South American ungulate, Macrauchenia is sister to horses and rhinoceroses, and sabre-toothed and scimitar cats are the monophyletic sister-group of modern cats.

Matched MeSH terms: Genome, Mitochondrial
Fulltext Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

Formenti G, Rhie A, Balacco J, Haase B, Mountcastle J, Fedrigo O, et al.

Genome Biol, 2021 04 29;22(1):120.
PMID: 33910595 DOI: 10.1186/s13059-021-02336-9

BACKGROUND: Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly.
RESULTS: As part of the Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (> 10 kbp, PacBio or Nanopore) and short (100-300 bp, Illumina) reads. Our pipeline leads to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We observe that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we identify errors, missing sequences, and incomplete genes in those references, particularly in repetitive regions. Our assemblies also identify novel gene region duplications. The presence of repeats and duplications in over half of the species herein assembled indicates that their occurrence is a principle of mitochondrial structure rather than an exception, shedding new light on mitochondrial genome evolution and organization.
CONCLUSIONS: Our results indicate that even in the "simple" case of vertebrate mitogenomes the completeness of many currently available reference sequences can be further improved, and caution should be exercised before claiming the complete assembly of a mitogenome, particularly from short reads alone.

Matched MeSH terms: Genome, Mitochondrial*
Fulltext Towards complete and error-free genome assemblies of all vertebrate species

Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, et al.

Nature, 2021 Apr;592(7856):737-746.
PMID: 33911273 DOI: 10.1038/s41586-021-03451-0

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.

Matched MeSH terms: Genome, Mitochondrial
Fulltext Molecular Systematics of the Firefly Genus Luciola (Coleoptera: Lampyridae: Luciolinae) with the Description of a New Species from Singapore

Jusoh WFA, Ballantyne L, Chan SH, Wong TW, Yeo D, Nada B, et al.

Animals (Basel), 2021 Mar 04;11(3).
PMID: 33806564 DOI: 10.3390/ani11030687

The firefly genus Luciola sensu McDermott contains 282 species that are distributed across major parts of Asia, Europe, Africa, Australia, and the Pacific islands. Due to phenotypic similarities, species identification using external morphological characters can be unreliable for this group. Consequently, decades of piecemeal taxonomic treatments have resulted in numerous erroneous and contentious classifications. Furthermore, our understanding of the group's evolutionary history is limited due to the lack of a robust phylogenetic framework that has also impeded efforts to stabilize its taxonomy. Here, we constructed molecular phylogenies of Luciola and its allies based on combined mitogenomes and Cytochrome c oxidase subunit 1 (COX1) sequences including a newly sequenced mitogenome of an unidentified taxon from Singapore. Our results showed that this taxon represents a distinct and hitherto undescribed evolutionary lineage that forms a clade with L. filiformis from Japan and L. curtithorax from China. Additionally, the Singaporean lineage can be differentiated from other congeners through several external and internal diagnostic morphological characters, and is thus described herein as a new species. Our phylogeny also strongly supported the paraphyly of Luciola with regard to L. cruciata and L. owadai, which were inferred to be more closely related to the genus Aquatica as opposed to other members of Luciola sensu stricto. The genus Hotaria was inferred as a derived clade within Luciola (sister to L. italica), supporting its status as a subgenus of Luciola instead of a distinct genus. This is the first time since 1909 that a new species of luminous firefly has been discovered in Singapore, highlighting the need for continued biodiversity research, even in small, well-studied and highly developed countries, such as Singapore.

Matched MeSH terms: Genome, Mitochondrial
Fulltext Characterization of the mitogenomes of long-tailed giant rat, Leopoldamys sabanus and a comparative analysis with other Leopoldamys species

Jahari PNS, Mohd Azman S, Munian K, Ahmad Ruzman NH, Shamsir MS, Richter SR, et al.

Mitochondrial DNA B Resour, 2021 Feb 11;6(2):502-504.
PMID: 33628904 DOI: 10.1080/23802359.2021.1872433

Two mitogenomes of long-tailed giant rat, Leopoldamys sabanus (Thomas, 1887), which belongs to the family Muridae were sequenced and assembled in this study. Both mitogenomes have a length of 15,973 bp and encode 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes and one control region. The circular molecule of L. sabanus has a typical vertebrate gene arrangement. Phylogenetic and BLASTn analysis using 10 Leopoldamys species mitogenomes revealed sequence variation occurred within species from different time zones. Along with the taxonomic issues, this suggests a landscape change might influence genetic connectivity.

Matched MeSH terms: Genome, Mitochondrial
The nearly complete mitogenome of the Southeast Asian firefly Pteroptyx tener (Coleoptera: Lampyridae)

Cheng S, Mat-Isa MN, Sapian IS, Ishak SF

Mol Biol Rep, 2021 Feb;48(2):1281-1290.
PMID: 33582950 DOI: 10.1007/s11033-021-06189-0

The estuarine firefly, Pteroptyx tener, aggregates in the thousands in mangrove trees lining tidal rivers in Southeast Asia where they engage one another in a nocturnal, pre-mating ritual of synchronised courtship flashes. Unfortunately, populations of the species by virtue of being restricted to isolated estuarine rivers systems in the region, are at risk of genetic isolation. Because of this concern we undertook the task of sequencing and characterising the mitochondrial DNA genome of P. tener, as the first step towards helping us to characterise and better understand their genetic diversity. We sequenced and assembled the mitochondrial DNA genome of P. tener from two male and female specimens from the district of Kuala Selangor in Peninsular Malaysia and announce the molecules in this publication. We also reconstructed the phylogenetic trees of all available lampyrids mitogenomes and suggest the need to re-examine our current understanding of their classification which have largely been based on morphological data and the cox1 gene. Separately, our analysis of codon usage patterns among lampyrid mitogenomes showed that the codon usage in a majority of the protein-coding genes were non-neutral. Codon usage patterns between mitogenome sequences of P. tener were, however, largely neutral. Our findings demonstrate the usefulness of mitochondrial genes/mitogenomes for analysing both inter- and intra- specific variation in the Lampyridae to aid in species discovery in this highly variable genus; and elucidate the phylogenetic relationships of Pteroptyx spp. from the region.

Matched MeSH terms: Genome, Mitochondrial/genetics*
Fulltext The first mitochondrial genome data of an old world fruit bat, Cynopterus sphinx from Malaysia

Jahari PNS, Mohd Azman S, Munian K, Zakaria NA, Omar MSS, Richter SR, et al.

Mitochondrial DNA B Resour, 2021 Jan 12;6(1):53-55.
PMID: 33521264 DOI: 10.1080/23802359.2020.1846472

We assembled the complete mitogenome of Cynopterus sphinx (Vahl, 1797) of the family Pteropodidae originating from Malaysia. The total mitogenome size was 16,710bp which consists of 37 genes (13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and one control region). A phylogenetic and BLASTn result showed the mitogenome sequence in this study varies by nearly 7% (93.48% similarity) from the same species in Cambodia. The next closest match of BLASTn was at 92% similarity to the C. brachyotis. This suggests the species-complex in Cynopterus sp. has given rise to the genetic variability.

Matched MeSH terms: Genome, Mitochondrial
Sequencing and characterisation of complete mitogenome DNA for Rasbora sarawakensis (Cypriniformes: Cyprinidae: Rasbora) with phylogenetic consideration

Lim LWK, Kamar CKA, Roja JS, Chung HH, Liao Y, Lam TT, et al.

Comput Biol Chem, 2020 Dec;89:107403.
PMID: 33120127 DOI: 10.1016/j.compbiolchem.2020.107403

The Blueline Rasbora (Rasbora sarawakensis) is a small ray-finned fish categorized under the genus Rasbora in the Cyprinidae family. In this study, the complete mitogenome sequence of R. sarawakensis was sequenced using four primers targeting overlapping regions. The mitogenome is 16,709 bp in size, accommodating 22 transfer RNA genes, 13 protein-coding genes, two ribosomal RNA genes and a putative control region. Identical gene organisation was detected between this species and other genus counterparts. The heavy strand houses 28 genes while the light strand stores the other nine genes. Most protein-coding genes employ ATG as start codon, excluding COI gene, which utilizes GTG instead. The central conserved sequence blocks (CSB-F, CSB-E and CSB-D), variable sequence blocks (CSB-3, CSB-2 and CSB-1) as well as the terminal associated sequence (TAS) are conserved in the control region. The maximum likelihood phylogenetic tree revealed the divergence of R. sarawakensis from the basal region of the Rasbora clade, where its evolutionary relationships with R. maculatus and R. pauciperforata are poorly resolved as indicated by the low bootstrap values. This work acts as steppingstone towards further molecular evolution and population genetics studies of Rasbora genus in future.

Matched MeSH terms: Genome, Mitochondrial*
Fulltext The complete mitochondrial genome of Amyda cartilaginea (Testudines: Trionychidae)

Cui L, Rao D, Zhang M

Mitochondrial DNA B Resour, 2020 Nov 03;5(3):3670-3672.
PMID: 33367054 DOI: 10.1080/23802359.2020.1832595

The Asiatic softshell turtle, also known as the black-rayed softshell turtle (Amyda cartilaginea; Accession no: MT039230), is found in northeastern India (Mizoram), Brunei Darussalam, Indonesia, Malaysia, Singapore, Myanmar, Laos, Vietnam, Cambodia, and Thailand. This turtle is thought to have been introduced into the Sunda Islands, Sulawesi, and Yunnan, China, through the Malay Peninsula to Sumatra, Java, and Borneo. Herein, we determined the complete mitochondrial genome of A. cartilaginea for the first time using next-generation sequencing (NGS). The assembled mitogenome was 16,763 bp in length and encoded 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA genes (12S rRNA and 16S rRNA), and one control region (CR). The PCGs based maximum-likelihood phylogeny discriminated A. cartilaginea from other Testudines and clusters within family Trionychidae with the sister taxa of Nilssonia nigricans.

Matched MeSH terms: Genome, Mitochondrial
Fulltext Complete mitochondrial genome of the black-winged fly, Felderimyia fuscipennis (Diptera: Tephritidae) and its phylogenetic relationship within family Tephritidae

Yang MJ, Liu JH, Wan XS, Zhang QL, Fu DY, Wang XB, et al.

Mitochondrial DNA B Resour, 2020 Oct 27;5(3):3638-3639.
PMID: 33367040 DOI: 10.1080/23802359.2020.1831984

The black-winged fly, Felderimyia fuscipennis (Diptera: Tephritidae), is an insect pest of bamboo shoot, mainly distributed in Thailand, Malaysia and Yunnan Province and Guangxi Autonomous Region, China. The complete sequence of the mitogenome of F. fuscipennis has been determined in this study. The whole mitogenome sequence is 16,536 bp in length, which totally contains 13 protein-coding genes (PCGs), 2 rRNA genes, 22 tRNA genes, and a non-coding region (putative control region, CR). The phylogeny indicates that F. fuscipennis of subfamily Trypetinae was monophyletic and clearly separated from both Dacinae and Tephritinae with high bootstrap value supported.

Matched MeSH terms: Genome, Mitochondrial
Fulltext The first complete mitochondrial genome data of Geoffroy's rousette, Rousettus amplexicaudatus originating from Malaysia

Jahari PNS, Mohd Azman S, Munian K, M Fauzi NF, Shamsir MS, Richter SR, et al.

Mitochondrial DNA B Resour, 2020 Sep 01;5(3):3262-3264.
PMID: 33458132 DOI: 10.1080/23802359.2020.1812449

The increasing interest in understanding the evolutionary relationship between members of the Pteropodidae family has been greatly aided by genomic data from the Old World fruit bats. Here we present the complete mitogenome of Geoffroy's rousette, Rousettus amplexicaudatus found in Peninsular Malaysia . The mitogenome constructed is 16,511bp in length containing 37 genes; 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, and a D-loop region. The overall base composition is estimated to be 32.28% for A, 25.64% for T, 14.09% for G and 27.98% for C, indicating a slightly AT rich feature (57.93%). A phylogenetic and BLASTn analysis against other available mitogenomes showed Malaysian R. amplexicaudatus matched 98% similarity to the same species in Cambodia and Vietnam. However, it differed considerably (92.53% similarity) with the same species in the Philippines. This suggests flexibility in Rousettus sp. with regards to adapting to mesic and dry habitats, ability for long-distance dispersal and remarkably precise lingual echolocation thus supporting its wide-range distribution and colonization. Further taxonomical and mitogenomic comparatives are required in resolving the evolutionary relationship between Rousettus spp.

Matched MeSH terms: Genome, Mitochondrial
Fulltext Molecular identification and phylogenetic analysis of a Callosciurus notatus complete mitogenome from Peninsular Malaysia

Jahari PNS, Mohd Azman S, Munian K, Ahmad Ruzman NH, Shamsir MS, Richter SR, et al.

Mitochondrial DNA B Resour, 2020 Aug 26;5(3):3004-3006.
PMID: 33458034 DOI: 10.1080/23802359.2020.1797583

The mitogenome of a plantain squirrel, Callosciurus notatus, collected from Bukit Tarek Forest Reserve (Extension), Selangor, Malaysia was sequenced using BGISEQ-500RS technology. The 16,582 bp mitogenome consists of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region. A phylogenetic and BLASTn analysis against other available datasets showed that the mitogenome matched with 99.49% similarity to a previously published C. notatus mitogenome from Peninsular Malaysia. However, it also diverged by nearly 8% (92.24% match) from a second previously published mitogenome for the same species, sampled in East Kalimantan, Indonesia. This suggests a difference in landscape features between both localities might affect its genetic connectivity.

Matched MeSH terms: Genome, Mitochondrial

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