MyMedR

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 complete mitochondrial genome of Malayan Gaur (Bos gaurus hubbacki) from Peninsular Malaysia

Rosli N, Sitam FT, Rovie-Ryan JJ, Gan HM, Lee YP, Hartini Ithnin, et al.

Mitochondrial DNA B Resour, 2019 Jul 13;4(2):2535-2536.

PMID: 33365614 DOI: 10.1080/23802359.2019.1640085

Here, we present the first complete mitochondrial genome of Malayan Gaur (Bos gaurus hubbacki) inferred using next-generation sequencing. The mitogenome is 16,367 bp in length with the structural organization of a typical bovine mitochondrial arrangement comprising 13 protein-coding genes, 21 tRNAs, and 2 rRNAs. No internal stop codon was found in the protein-coding genes. Phylogenetic tree analysis revealed that Malayan gaur is more closely related to Burmese banteng instead of gaur.

Matched MeSH terms: Genome, Mitochondrial

The utility of the Laplace effect size prior distribution in Bayesian fine-mapping studies

Walters K, Cox A, Yaacob H

Genet Epidemiol, 2021 Jun;45(4):386-401.

PMID: 33410201 DOI: 10.1002/gepi.22375

The Gaussian distribution is usually the default causal single-nucleotide polymorphism (SNP) effect size prior in Bayesian population-based fine-mapping association studies, but a recent study showed that the heavier-tailed Laplace prior distribution provided a better fit to breast cancer top hits identified in genome-wide association studies. We investigate the utility of the Laplace prior as an effect size prior in univariate fine-mapping studies. We consider ranking SNPs using Bayes factors and other summaries of the effect size posterior distribution, the effect of prior choice on credible set size based on the posterior probability of causality, and on the noteworthiness of SNPs in univariate analyses. Across a wide range of fine-mapping scenarios the Laplace prior generally leads to larger 90% credible sets than the Gaussian prior. These larger credible sets for the Laplace prior are due to relatively high prior mass around zero which can yield many noncausal SNPs with relatively large Bayes factors. If using conventional credible sets, the Gaussian prior generally yields a better trade off between including the causal SNP with high probability and keeping the set size reasonable. Interestingly when using the less well utilised measure of noteworthiness, the Laplace prior performs well, leading to causal SNPs being declared noteworthy with high probability, whilst generally declaring fewer than 5% of noncausal SNPs as being noteworthy. In contrast, the Gaussian prior leads to the causal SNP being declared noteworthy with very low probability.

Matched MeSH terms: Genome-Wide Association Study

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

Fulltext The complete chloroplast genome of Aquilaria malaccensis Lam. (Thymelaeaceae), an important and threatened agarwood-producing tree species

Lee SY, Ng WL, Mohamed R, Terhem R

Mitochondrial DNA B Resour, 2018 Oct 29;3(2):1120-1121.

PMID: 33474439 DOI: 10.1080/23802359.2018.1519382

Known for its valuable agarwood, Aquilaria malaccensis Lam. is an evergreen tropical forest tree species endemic to the Indo-malesian region. Indiscriminate damaging and harvesting of the trees in the wild have resulted in it being listed in the CITES Appendix II for controlled trade and in the IUCN Red List as 'Vulnerable (VU)'. In this study, the complete chloroplast genome of A. malaccensis was assembled using data from high-throughput Illumina sequencing. The chloroplast genome was 174,832 bp in size, which included two inverted repeat regions of 42,091 bp each, separated by a large single copy region of 87,302 bp and a small single copy region of 3,348 bp. A total of 139 genes were predicted, including 39 tRNA, 8 rRNA, and 92 protein-coding genes. Phylogenetic analysis placed A. malaccensis within the family Thymelaeaceae. The chloroplast genome sequence of A. malaccensis offers a useful resource for future studies on the taxonomy and conservation of the threatened Aquilaria trees.

Matched MeSH terms: Genome, Chloroplast

Fulltext Complete mitochondrial genome of six Cheilinus undulatus (Napoleon Wrasse): an endangered marine fish species from Sabah, Malaysia

Matthew P, Manjaji-Matsumoto BM, Rodrigues KF

Mitochondrial DNA B Resour, 2018 Oct 12;3(2):943-944.

PMID: 33474374 DOI: 10.1080/23802359.2018.1473725

We report here the complete mitochondrial (mt) genomes of six individuals of Cheilinus undulatus (Napoleon Wrasse), an endangered marine fish species. The six mt DNA sequences had an average size of 17,000 kb and encoded 22 tRNA, two sRNA, 13 highly conserved protein coding genes and a control region. The polymorphic variation (control region) in these six individuals suggests their potential use as a specific marker for phylogeographic conservation. Moreover, the sequence polymorphism within the control region (D-loop) suggests that this locus can be applied for phylogenetic studies.

Matched MeSH terms: Genome, Mitochondrial

Fulltext Characterization of the complete mitochondrial genome of Xanthid crab, Atergatis integerrimus from China (Decapoda: Brachyura) and its phylogenetic analysis

Xie Z, Tan H, Lin F, Guan M, Waiho K, Fang S, et al.

Mitochondrial DNA B Resour, 2018 Mar 27;3(1):397-398.

PMID: 33474181 DOI: 10.1080/23802359.2018.1456374

The complete mitochondrial genome sequence of Atergatis integerrimus from China has been amplified and sequenced in this study. The mitogenome assembly was found to be 15,924 bp in length with base composition of A (32.88%), G (10.58%), C (20.87%), T (35.66%), A + T (68.54%), and G + C (31.46%). It contained 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes and a control region. The phylogenetic position was constructed and the A. integerrimus was closely clustered with Pseudocarcinus gigas and Leptodius sanguineus. The complete mitochondrial genome sequence would be useful for further understanding the evolution of A. integerrimus.

Matched MeSH terms: Genome, Mitochondrial

Fulltext The complete mitochondrial genome of Varuna yui (Decapoda: Brachyura: Varunidae) and its phylogeny

Lin F, Xie Z, Fazhan H, Baylon JC, Yang X, Tan H, et al.

Mitochondrial DNA B Resour, 2018 Feb 23;3(1):263-264.

PMID: 33474136 DOI: 10.1080/23802359.2018.1443043

The complete mitochondrial genome plays an important role in the research on phylogenetic relationship. Here, we reported the first complete mitochondrial genome sequence of Varuna yui Hwang & Takeda, 1986 (Varunidae). The complete mtDNA (15,915 bp in length) consisted of 13 protein-coding genes, 22 tRNAs, two rRNA genes, and a control region. The gene arrangement was identical to those observed in the Varunidae species. The phylogenetic analysis suggested that V. yui had close relationship with other Varunidae species (Helicetient sinensis, Eriocher sinesis, etc.). The newly described genome may facilitate further comparative mitogenomic analysis within Varunidae species.

Matched MeSH terms: Genome, Mitochondrial

Fulltext The complete chloroplast genome of Artocarpus heterophyllus (Moraceae)

Liu J, Niu YF, Ni SB, Liu ZY, Zheng C, Shi C

Mitochondrial DNA B Resour, 2017 Dec 12;3(1):13-14.

PMID: 33474051 DOI: 10.1080/23802359.2017.1413317

The Artocarpus heterophyllus, native to Western Ghats of India, Malaysia and south-eastern Asia, is a tree member of the mulberry family (Moraceae). Chloroplast genome sequences play a significant role in the development of molecular markers in plant phylogenetic and population genetic studies. In this study, we report the complete chloroplast genome sequence of A. heterophyllus for the first time. The chloroplast genome is 160,387 bp long and includes 113 genes. Its LSC, SSC and IR regions are 88,422, 18,869 and 26,548 bp long, respectively. Phylogenetic tree analysis exhibited that A. heterophyllus was clustered with other Moraceae species with high bootstrap values.

Matched MeSH terms: Genome, Chloroplast

Fulltext The complete mitochondrial genome of the cavity-nesting honeybee, Apis cerana (Insecta: Hymenoptera: Apidae) from Borneo

Okuyama H, Tingek S, Takahashi JI

Mitochondrial DNA B Resour, 2017 Jul 31;2(2):475-476.

PMID: 33473869 DOI: 10.1080/23802359.2017.1361344

The complete mitochondrial genome of the cavity-nesting honeybee Apis cerana from Sabah on Borneo Island was analyzed using next-generation sequencing. The mitochondrial genome of A. cerana was a circular molecule of 15,884 bp and was similar to that of the other cavity-nesting honeybee species. The average AT content in the A. cerana mitochondrial genome was 84.4%. It was predicted to contain 13 protein-coding, 22 tRNA, and two rRNA genes, along with one A + T-rich control region.

Matched MeSH terms: Genome, Mitochondrial

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

Fulltext The complete chloroplast genome of tropical and sub-tropical fruit tree Lucuma nervosa (Sapotaceae)

Niu YF, Ni SB, Liu ZY, Zheng C, Mao CL, Shi C, et al.

Mitochondrial DNA B Resour, 2018 Apr 03;3(1):440-441.

PMID: 33490512 DOI: 10.1080/23802359.2018.1457995

The Lucuma nervosa, native to Western Ghats of India, Malaysia and south-eastern Asia, is a tree member of the mulberry family (Sapotaceae). Chloroplast genome sequences play an significant role in the development of molecular markers in plant phylogenetic and population genetic studies. In this study, we report the complete chloroplast genome sequence of L. nervosa for the first time. The chloroplast genome is 157,920 bp long and includes 113 genes. Its LSC, SSC, and IR regions are 88,123, 18,861, and 25,468 bp long, respectively. Phylogenetic tree analysis exhibited that L. nervosa was clustered with other Sapotaceae species with high bootstrap values.

Matched MeSH terms: Genome, Chloroplast

Fulltext The whole mitochondrial genome of the mangrove crab, Metopograpsus frontalis (Miers, 1880) (Decapoda, Grapsidae) and its phylogenetic relationship

Guan M, Liu X, Lin F, Xie Z, Fazhan H, Ikhwanuddin M, et al.

Mitochondrial DNA B Resour, 2018 Mar 14;3(1):368-369.

PMID: 33490509 DOI: 10.1080/23802359.2018.1450685

In this study, we sequenced and analyzed the whole mitochondrial genome of Metopograpsus frontalis Miers, 1880 (Decapoda, Grapsidae). The circular genome is 15,587 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, as well as a control region. Both atp8/atp6 and nad4L/nad4 share 7 nucleotides in their adjacent overlapping region, which is identical to those observed in other Grapsidae crabs. The genome composition and gene order follow a classic crab-type arrangement regulation. The phylogenetic analysis suggested that Grapsidae crabs formed a solid monophyletic group. The newly described mitochondrial genome may provide genetic marker for studies on phylogeny of the grapsid crabs.

Matched MeSH terms: Genome, Mitochondrial

Fulltext PlantFuncSSR: Integrating First and Next Generation Transcriptomics for Mining of SSR-Functional Domains Markers

Sablok G, Pérez-Pulido AJ, Do T, Seong TY, Casimiro-Soriguer CS, La Porta N, et al.

Front Plant Sci, 2016;7:878.

PMID: 27446111 DOI: 10.3389/fpls.2016.00878

Analysis of repetitive DNA sequence content and divergence among the repetitive functional classes is a well-accepted approach for estimation of inter- and intra-generic differences in plant genomes. Among these elements, microsatellites, or Simple Sequence Repeats (SSRs), have been widely demonstrated as powerful genetic markers for species and varieties discrimination. We present PlantFuncSSRs platform having more than 364 plant species with more than 2 million functional SSRs. They are provided with detailed annotations for easy functional browsing of SSRs and with information on primer pairs and associated functional domains. PlantFuncSSRs can be leveraged to identify functional-based genic variability among the species of interest, which might be of particular interest in developing functional markers in plants. This comprehensive on-line portal unifies mining of SSRs from first and next generation sequencing datasets, corresponding primer pairs and associated in-depth functional annotation such as gene ontology annotation, gene interactions and its identification from reference protein databases. PlantFuncSSRs is freely accessible at: http://www.bioinfocabd.upo.es/plantssr.

Matched MeSH terms: Genome, Plant

Fulltext Data set of phylogenetic analysis inferred based on the complete genomes of the family Nodaviridae

Low CF, Bunawan H

Data Brief, 2016 Sep;8:1454-61.

PMID: 27617282 DOI: 10.1016/j.dib.2016.08.025

In this article, nine complete genomes of viruses from the genus Alphanodavirus and Betanodavirus (Family Nodaviridae) were comparatively analyzed and the data of their evolutionary origins and relatedness are reported. The nucleotide sequence alignment of the complete genomes from all species and their deduced evolutionary relationships are presented. High sequence similarity within the genus Betanodavirus compared to the genus Alphanodavirus was revealed in multiple sequence alignment of the Nodaviridae genomes. The amino acid sequence similarity for both RNA1 and RNA2 ORF is more conserved in Betanodavirus, compared to Alphanodavirus. The conserved and variable regions within the virus genome that were defined based on the multiple sequence alignments are presented in this dataset.

Matched MeSH terms: Genome, Viral

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

Fulltext The complete chloroplast genome and phylogenetic analysis of Nephelium lappaceum (rambutan)

Liu J, Zheng C, Liu ZY, Niu YF

Mitochondrial DNA B Resour, 2021 Feb 09;6(2):485-487.

PMID: 33628898 DOI: 10.1080/23802359.2021.1872449

Nephelium lappaceum is a popular tropical fruit belonging to the Sapindaceae family. The plant originated in Malaysia and Indonesia and is commonly called rambutan. Because of its refreshing flavor and exotic appearance, rambutan is widely accepted in the World. Due to its significant medicinal properties, the fruit has also been employed in traditional medicine for centuries. The chloroplast genome of rambutan was sequenced, assembled, and annotated in the present study. The chloroplast genome length was 161,356 bp and contained 132 genes, including 87 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. It possessed the typical quadripartite circle structure with a large single-copy region (86,009 bp), a small single-copy region (18,153 bp), and two inverted repeat regions (28,597 bp). A total of 35 SSR markers were found in the chloroplast genome of Nephelium lappaceum, of which 33 were monomer, 1 was dimer and 1 was tetramer. Phylogenetic analysis based on the complete chloroplast genome sequences of 21 plant species showed that rambutan was closely related to Pometia tomentosa. These results provide a foundation for further phylogenetic and evolutionary studies of the Sapindaceae family.

Matched MeSH terms: Genome, Chloroplast

Fulltext Genetic Connections and Convergent Evolution of Tropical Indigenous Peoples in Asia

Deng L, Pan Y, Wang Y, Chen H, Yuan K, Chen S, et al.

Mol Biol Evol, 2022 Feb 03;39(2).

PMID: 34940850 DOI: 10.1093/molbev/msab361

Tropical indigenous peoples in Asia (TIA) attract much attention for their unique appearance, whereas their genetic history and adaptive evolution remain mysteries. We conducted a comprehensive study to characterize the genetic distinction and connection of broad geographical TIAs. Despite the diverse genetic makeup and large interarea genetic differentiation between the TIA groups, we identified a basal Asian ancestry (bASN) specifically shared by these populations. The bASN ancestry was relatively enriched in ancient Asian human genomes dated as early as ∼50,000 years before the present and diminished in more recent history. Notably, the bASN ancestry is unlikely to be derived from archaic hominins. Instead, we suggest it may be better modeled as a survived lineage of the initial peopling of Asia. Shared adaptations inherited from the ancient Asian ancestry were detected among the TIA groups (e.g., LIMS1 for hair morphology, and COL24A1 for bone formation), and they are enriched in neurological functions either at an identical locus (e.g., NKAIN3), or different loci in an identical gene (e.g., TENM4). The bASN ancestry could also have formed the substrate of the genetic architecture of the dark pigmentation observed in the TIA peoples. We hypothesize that phenotypic convergence of the dark pigmentation in TIAs could have resulted from parallel (e.g., DDB1/DAK) or genetic convergence driven by admixture (e.g., MTHFD1 and RAD18), new mutations (e.g., STK11), or notably purifying selection (e.g., MC1R). Our results provide new insights into the initial peopling of Asia and an advanced understanding of the phenotypic convergence of the TIA peoples.

Matched MeSH terms: Genome, Human

Fulltext Global research alliance in infectious disease: a collaborative effort to combat infectious diseases through dissemination of portable sequencing

Runtuwene LR, Sathirapongsasuti N, Srisawat R, Komalamisra N, Tuda JSB, Mongan AE, et al.

BMC Res Notes, 2022 Feb 12;15(1):44.

PMID: 35151353 DOI: 10.1186/s13104-022-05927-2

OBJECTIVE: To disseminate the portable sequencer MinION in developing countries for the main purpose of battling infectious diseases, we found a consortium called Global Research Alliance in Infectious Diseases (GRAID). By holding and inviting researchers both from developed and developing countries, we aim to train the participants with MinION's operations and foster a collaboration in infectious diseases researches. As a real-life example in which resources are limited, we describe here a result from a training course, a metagenomics analysis from two blood samples collected from a routine cattle surveillance in Kulan Progo District, Yogyakarta Province, Indonesia in 2019.

RESULTS: One of the samples was successfully sequenced with enough sequencing yield for further analysis. After depleting the reads mapped to host DNA, the remaining reads were shown to map to Theileria orientalis using BLAST and OneCodex. Although the reads were also mapped to Clostridium botulinum, those were found to be artifacts derived from the cow genome. An effort to construct a consensus sequence was successful using a reference-based approach with Pomoxis. Hence, we concluded that the asymptomatic cow might be infected with T. orientalis and showed the usefulness of sequencing technology, specifically the MinION platform, in a developing country.

Matched MeSH terms: Genome

Genome characterization of a breeding line derived from a cross between Oryza sativa and Oryza rufipogon

Keong BP, Harikrishna JA

Biochem Genet, 2012 Feb;50(1-2):135-45.

PMID: 22089543 DOI: 10.1007/s10528-011-9479-8

A preliminary screening was conducted on BC3F1 and BC4F1 backcross families developed from crossing Oryza sativa (MR219) and O. rufipogon (IRGC105491). Despite earlier results showing that O. rufipogon alleles (wild introgression) contributed to both number of panicles (qPPL-2) and tillers (qTPL-2) at loci RM250, RM208, and RM48 in line A20 of the BC2F2 population, we observed that wild introgression was lost at loci RM250 and RM208 but retained at locus RM48 in BC3F1 and BC4F1. Progeny tests conducted utilizing genotype and phenotype data on both BC4F1 and a reference population, BC2F7 (A20 line), did not show significant differences between groups having the MR219 allele and wild introgression at locus RM48. This suggests that there is no additive and transgressive effect of wild introgression in the BC3F1 and BC4F1 generated. The presence of wild introgression was largely due to gene contamination by cross-pollination during field breeding practices.

Matched MeSH terms: Genome, Plant

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