scholarly journals The first complete mitochondrial genome sequence of Cynopterus brachyotis (Müller, 1838) from the Philippines

2021 ◽  
Author(s):  
Paul Lorenzo Gaite ◽  
Wilson Aala, Jr ◽  
Michael Bacus ◽  
Christian Labrador ◽  
April Mae Numeron ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Gc Content ◽  
Illumina Miseq ◽  
The Philippines ◽  
Sequence Length ◽  
Bootstrap Support ◽  
Gene Markers ◽  
Mitogenome Sequence ◽  
Cynopterus Brachyotis

The technical limitations of capillary sequencing in providing insights on phylogeny have been greatly aided in recent years by the implementation of next generation sequencing platforms which can generate whole mitochondrial genome (mitogenome) sequences. In this study, enriched mitochondrial DNA of Cynopterus brachyotis from Mindanao, Philippines was sequenced using the Illumina MiSeq platform. A total of 653,967 clean paired-end reads was assembled using a MIRA-MITObim pipeline, resulting to a consensus mitogenome sequence length of 17,382 bases and a GC content of 41.48%, which is consistent with other published mitogenomes in fruit bats. The assembled C. brachyotis mitogenome was annotated using the MITOS online server and was able to resolve all mitochondrial genes, except for one transfer RNA gene (trnT) which may be further resolved by additional capillary sequencing of the region. Sequence analysis showed that the Philippine C. brachyotis is only 90%-91% homologous with other Cynopterus spp. based on its full mitogenome sequence. Phylogenetic analysis of fruit bat mitogenomes deposited in online repositories revealed that the Philippine C. brachyotis in this study has diverged from Asian Cynopterus, namely Cynopterus brachyotis and Cynopterus sphinx from other parts of Asia (100% bootstrap support) with the latter two forming a separate clade. This divergence at the species level was consistent with phylogentic inference using cytochrome oxidase 1 (CO1) and cytochrome B (cytb) gene markers. Our results strengthen the previously reported hypothesis that the C. brachyotis in the Philippines is distinct from its Asian counterparts and should be therefore elevated to a new species.

scholarly journals The first mitochondrial genome of the genus Exhippolysmata (Decapoda: Caridea: Lysmatidae), with gene rearrangements and phylogenetic associations in Caridea

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ying-ying Ye ◽  
Jing Miao ◽  
Ya-hong Guo ◽  
Li Gong ◽  
Li-hua Jiang ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Gene Order ◽  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Bootstrap Support ◽  
Trna Genes ◽  
Gene Rearrangements ◽  
Phylogenetic Studies ◽  
Gc Skew ◽  
Strong Bootstrap Support

AbstractThe complete mitochondrial genome (mitogenome) of animals can provide useful information for evolutionary and phylogenetic analyses. The mitogenome of the genus Exhippolysmata (i.e., Exhippolysmata ensirostris) was sequenced and annotated for the first time, its phylogenetic relationship with selected members from the infraorder Caridea was investigated. The 16,350 bp mitogenome contains the entire set of 37 common genes. The mitogenome composition was highly A + T biased at 64.43% with positive AT skew (0.009) and negative GC skew (− 0.199). All tRNA genes in the E. ensirostris mitogenome had a typical cloverleaf secondary structure, except for trnS1 (AGN), which appeared to lack the dihydrouridine arm. The gene order in the E. ensirostris mitogenome was rearranged compared with those of ancestral decapod taxa, the gene order of trnL2-cox2 changed to cox2-trnL2. The tandem duplication-random loss model is the most likely mechanism for the observed gene rearrangement of E. ensirostris. The ML and BI phylogenetic analyses place all Caridea species into one group with strong bootstrap support. The family Lysmatidae is most closely related to Alpheidae and Palaemonidae. These results will help to better understand the gene rearrangements and evolutionary position of E. ensirostris and lay a foundation for further phylogenetic studies of Caridea.

scholarly journals Complete mitochondrial genome of Atergatis integerrimus (Decapoda, Xanthidae) from the Philippines

2018 ◽  
Vol 3 (1) ◽  
pp. 205-206 ◽  
Author(s):  
Mustafa Zafer Karagozlu ◽  
Michelle M. Barbon ◽  
Thinh Do Dinh ◽  
Cesar G. Demayo ◽  
Chang-Bae Kim
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
The Philippines

The mitochondrial genome and phylogenetic analysis of the tick Haemaphysalis qinghaiensis Teng, 1980 (Acari:Ixodidae)

2022 ◽  
Author(s):  
Tianhong Wang ◽  
Zihao Wang ◽  
Ruwei Bai ◽  
Zhijun Yu ◽  
Jingze Liu
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Trna Genes ◽  
Illumina Hiseq ◽  
Protein Coding ◽  
Haemaphysalis Qinghaiensis ◽  
Mitogenome Sequence ◽  
Illumina Hiseq Platform

Haemaphysalis qinghaiensis is an endemic species and mainly inhabiting in the northwestern plateau of China, which can transmit many zoonotic pathogens and cause great harm to animals. In this study, the complete mitochondrial genome (mitogenome) of H. qinghaiensis was assembled through the Illumina HiSeq platform. The mitogenome was 14,533 bp in length, consisting of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes and 3 noncoding regions (NCRs). The bias towards a high A+T content with 77.65% in mitogenome of H. qinghaiensis. The rearrangement of mitochondrial genes in H. qinghaiensis was consistent with other hard ticks. The phylogenetic analysis based on the concatenation of 13 PCGs from 65 tick mitogenomes showed that the H. qinghaiensis was clustered into a well-supported clade within the Haemaphysalis genus. This is the first complete mitogenome sequence of H. qinghaiensis, which provides a useful reference for understanding of the taxonomic and genetics of ticks.

Complete mitochondrial genome of the Western Capercaillie Tetrao urogallus (Phasianidae, Tetraoninae)

Zootaxa ◽  
2019 ◽  
Vol 4550 (4) ◽  
pp. 585
Author(s):  
GAËL ALEIX-MATA ◽  
FRANCISCO J. RUIZ-RUANO ◽  
JESÚS M. PÉREZ ◽  
MATHIEU SARASA ◽  
ANTONIO SÁNCHEZ
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Sequence Data ◽  
Complete Mitochondrial Genome ◽  
Tetrao Urogallus ◽  
Protein Coding ◽  
Mitogenome Sequence ◽  
Putative Origin ◽  
Fragmented Population ◽  
Galliform Bird

The Western Capercaillie (Tetrao urogallus) is a galliform bird of boreal climax forests from Scandinavia to eastern Siberia, with a fragmented population in southwestern Europe. We extracted the DNA of T. urogallus aquitanicus and obtained the complete mitochondrial genome (mitogenome) sequence by combining Illumina and Sanger sequencing sequence data. The mitochondrial genome of T. urogallus is 16,683 bp long and is very similar to that of Lyrurus tetrix (16,677 bp). The T. urogallus mitogenome contains the normal 13 protein-coding genes (PCGs), 22 transfer RNAs, 2 ribosomal RNAs, and the control region. The number, order, and orientation of the mitochondrial genes are the same as in L. tetrix and in other species of the same and other bird families. The three domains of the control region contained conserved sequences (ETAS; CSBs), boxes (F, E, D, C, B, BS box), the putative origin of replication of the H-strand (OH) and bidirectional promoters of translation (LSP/HSP). 

scholarly journals The complete mitochondrial genome sequence of Scolopendra mutilans L. Koch, 1878 (Scolopendromorpha, Scolopendridae), with a comparative analysis of other centipede genomes

ZooKeys ◽  
2020 ◽  
Vol 925 ◽  
pp. 73-88
Author(s):  
Chaoyi Hu ◽  
Shuaibin Wang ◽  
Bisheng Huang ◽  
Hegang Liu ◽  
Lei Xu ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Gc Content ◽  
Sister Group ◽  
Rrna Genes ◽  
Sister Group Relationship ◽  
Trna Genes ◽  
Protein Coding ◽  
Generation Sequencing ◽  
Simple Sequence

Scolopendra mutilans L. Koch, 1878 is an important Chinese animal with thousands of years of medicinal history. However, the genomic information of this species is limited, which hinders its further application. Here, the complete mitochondrial genome (mitogenome) of S. mutilans was sequenced and assembled by next-generation sequencing. The genome is 15,011 bp in length, consisting of 13 protein-coding genes (PCGs), 14 tRNA genes, and two rRNA genes. Most PCGs start with the ATN initiation codon, and all PCGs have the conventional stop codons TAA and TAG. The S. mutilans mitogenome revealed nine simple sequence repeats (SSRs), and an obviously lower GC content compared with other seven centipede mitogenomes previously sequenced. After analysis of homologous regions between the eight centipede mitogenomes, the S. mutilans mitogenome further showed clear genomic rearrangements. The phylogenetic analysis of eight centipedes using 13 conserved PCG genes was finally performed. The phylogenetic reconstructions showed Scutigeromorpha as a separate group, and Scolopendromorpha in a sister-group relationship with Lithobiomorpha and Geophilomorpha. Collectively, the S. mutilans mitogenome provided new genomic resources, which will improve its medicinal research and applications in the future.

scholarly journals The complete mitochondrial genome sequence of Oryctes rhinoceros (Coleoptera: Scarabaeidae) based on long-read nanopore sequencing

2020 ◽  
Author(s):  
Igor Filipović ◽  
James P. Hereward ◽  
Gordana Rašić ◽  
Gregor J. Devine ◽  
Michael J. Furlong ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Invasive Pest ◽  
Long Control Region ◽  
Trna Genes ◽  
Oryctes Rhinoceros ◽  
Mitogenome Sequence ◽  
Long Read

AbstractThe coconut rhinoceros beetle (CRB, Oryctes rhinoceros) is a severe and invasive pest of coconut and other palms throughout Asia and the Pacific. The biocontrol agent, Oryctes rhinoceros nudivirus (OrNV), has successfully suppressed O. rhinoceros populations for decades but new CRB invasions started appearing after 2007. A single-SNP variant within the mitochondrial cox1 gene is used to distinguish the recently-invading CRB-G lineage from other haplotypes, but the lack of mitogenome sequence for this species hinders further development of a molecular toolset for biosecurity and management programmes against CRB. Here we report the complete circular sequence and annotation for CRB mitogenome, generated to support such efforts.Sequencing data were generated using long-read Nanopore technology from genomic DNA isolated from a CRB-G female. The mitochondrial genome was assembled with Flye v.2.5, using the short-read Illumina sequences to remove homopolymers with Pilon, and annotated with MITOS. Independently-generated transcriptome data were used to assess the O. rhinoceros mitogenome annotation and transcription. The aligned sequences of 13 protein-coding genes (PCGs) (with degenerate third codon position) from O. rhinoceros, 13 other Scarabaeidae taxa and two outgroup taxa were used for the phylogenetic reconstruction with the Maximum likelihood (ML) approach in IQ-TREE and Bayesian (BI) approach in MrBayes.The complete circular mitochondrial genome of O. rhinoceros is 20,898 bp-long, with a gene content canonical for insects (13 PCGs, 2 rRNA genes, and 22 tRNA genes), as well as one structural variation (rearrangement of trnQ and trnI) and a long control region (6,204 bp). Transcription was detected across all 37 genes, and interestingly, within three domains in the control region. ML and BI phylogenies had the same topology, correctly grouping O. rhinoceros with one other Dynastinae taxon, and recovering the previously reported relationship among lineages in the Scarabaeidae. In silico PCR-RFLP analysis recovered the correct fragment set that is diagnostic for the CRB-G haplogroup. These results validate the high-quality of the CRB mitogenome sequence and annotation.

Complete mitochondrial genome of the endangered Mary River turtle (Elusor macrurus) and low mtDNA variation across the species' range

2016 ◽  
Vol 64 (2) ◽  
pp. 117 ◽  
Author(s):  
Daniel J. Schmidt ◽  
Brittany Brockett ◽  
Thomas Espinoza ◽  
Marilyn Connell ◽  
Jane M. Hughes
Keyword(s):  
Mitochondrial Genome ◽  
Control Region ◽  
Tandem Repeats ◽  
Complete Mitochondrial Genome ◽  
Illumina Miseq ◽  
Base Pairs ◽  
Pet Trade ◽  
Nucleotide Variability ◽  
Natural Range ◽  
Miseq Platform

Elusor macrurus is an endangered short-necked turtle restricted to the Mary River catchment in south-eastern Queensland. Shotgun sequencing of genomic DNA was used to generate a complete mitochondrial genome sequence for E. macrurus using the Illumina MiSeq platform. The mitogenome is 16 499 base pairs (bp) long with 37 genes arranged in the typical vertebrate order and a relatively short 918-bp control region, which does not feature extensive tandem repeats as observed in some turtles. Primers were designed to amplify a 1270-bp region that includes 81% of the typically hypervariable control region. Two haplotypes were detected in a sample of 22 wild-caught individuals from eight sites across its natural range. The Mary River turtle is a species with low mtDNA nucleotide variability relative to other Chelidae. The combination of a very restricted distribution and dramatic reduction in population size due to exploitation for the pet trade are the conditions likely to have led to very low mtDNA variability in this endangered species.

scholarly journals Population dynamics in the Japanese Archipelago since the Pleistocene revealed by the complete mitochondrial genome sequences

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Fuzuki Mizuno ◽  
Jun Gojobori ◽  
Masahiko Kumagai ◽  
Hisao Baba ◽  
Yasuhiro Taniguchi ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Demographic History ◽  
Complete Mitochondrial Genome ◽  
Cultural Transition ◽  
Rice Agriculture ◽  
Japanese Archipelago ◽  
Mitogenome Sequence ◽  
Basal Group ◽  
History Of ◽  
The Japanese Archipelago

AbstractThe Japanese Archipelago is widely covered with acidic soil made of volcanic ash, an environment which is detrimental to the preservation of ancient biomolecules. More than 10,000 Palaeolithic and Neolithic sites have been discovered nationwide, but few skeletal remains exist and preservation of DNA is poor. Despite these challenging circumstances, we succeeded in obtaining a complete mitogenome (mitochondrial genome) sequence from Palaeolithic human remains. We also obtained those of Neolithic (the hunting-gathering Jomon and the farming Yayoi cultures) remains, and over 2,000 present-day Japanese. The Palaeolithic mitogenome sequence was not found to be a direct ancestor of any of Jomon, Yayoi, and present-day Japanese people. However, it was an ancestral type of haplogroup M, a basal group of the haplogroup M. Therefore, our results indicate continuity in the maternal gene pool from the Palaeolithic to present-day Japanese. We also found that a vast increase of population size happened and has continued since the Yayoi period, characterized with paddy rice farming. It means that the cultural transition, i.e. rice agriculture, had significant impact on the demographic history of Japanese population.

scholarly journals Complete mitochondrial genome of Indian tent turtle, Pangshura tentoria and comparative mitochondriomics

2018 ◽  
Author(s):  
Shantanu Kundu ◽  
Vikas Kumar ◽  
Kaomud Tyagi ◽  
Rajasree Chakraborty ◽  
Iftikar Rahaman ◽  
...  
Keyword(s):  
Mitochondrial Genome ◽  
Nadh Dehydrogenase ◽  
Tandem Repeats ◽  
Synonymous Codon ◽  
Complete Mitochondrial Genome ◽  
Mitochondrial Gene ◽  
Gene Arrangement ◽  
Bootstrap Support ◽  
Nadh Dehydrogenase Subunit ◽  
Strong Negative Selection

Complete mitochondrial genomes of Indian tent turtle, Pangshura tentoria was sequenced and annotated as 16,657 bp in length. This first assembly was encoded by 37 genes: 13 protein coding genes (PCGs), 22 transfer RNA (tRNAs), two ribosomal RNA (rRNAs) as similar to the typical vertebrate mitochondrial gene arrangement. The complete mitogenome has a base composition of A (33.30%), G (13.54%), C (27%), and T (26.13%). Most of the genes were encoded on major strand, except for the eight tRNAs and one PCG (nad6). Almost all PCGs were starting with an ATG initiation codon, except for cytochrome oxidase subunit 1 (cox1) with ‘GTG’ and NADH dehydrogenase subunit 5 (nad5) with ‘ATA’. The typical termination codons, ‘TAA’ and ‘AGA’ has been observed in NADH dehydrogenase subunit 4l (nad4l) and NADH dehydrogenase subunit 6 (nad6) respectively; and others were used incomplete stop codons. The Relative Synonymous Codon Usage (RSCU) analysis revealed the maximum abundance of Alanine, Isoleucine, Leucine, and Threonine in P. tentoria. Codon distribution per thousand codon (CDsPT) values for all the amino acids showed the maximum values were present for Leucine in all geoemydid turtles. Further, the PCGs showed non-synonymous (Ka)/synonymous (Ks) values were <1 that indicated a strong negative selection among the studied species. The tRNAs were folded into classic clover-leaf secondary structures, except for trnS (GCT), lacking of the conventional DHU arm or stem. Further, the 10 tRNAs showed G-T mismatches and forming weak bonds. In the control region (CR) of P. tentoria, a single tandem repeat of eight base pairs (TTCTCTTT) was resulted with two copy numbers. The comparative study of CR with other geoemydid turtles revealed the numbers of tandem repeats were frequent in the 3´ end and structural characteristic were species-specific. The Maximum Likelihood (ML) phylogeny showed 32 geoemydid turtles were clustered distinctly with high bootstrap support and congruent with the previous phylogenetic hypothesis. Further, the representative mitogenome sequences of other family/suborder were depicted discrete clades in the ML tree. The study argued the complete mitochondrial genome sequence of P. tentoria and comparative mitochondriomics of geoemydid turtles would be useful for further phylogenetic reconciliation and evolutionary research.

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