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Kiwoung Yang, Ujjal Kumar Nath, Manosh Kumar Biswas, Md Abdul Kayum, Go-Eun Yi, Jonghoon Lee, Tae-Jin Yang, Ill-Sup Nou
Plant mitochondrial genomes (mtDNAs) vary in sequence structure. We assembled the Brassica oleracea var. capitata mtDNA using a mean coverage depth of 25X whole genome sequencing (WGS) and confirmed the presence of eight contigs/fragments by BLASTZ using the previously reported KJ820683 and AP012988 mtDNA as reference. Assembly of the mtDNA sequence reads resulted in a circular structure of 219,975 bp. Our assembled mtDNA, NCBI acc. no. KU831325, contained 34 protein-coding genes, 3 rRNA genes, and 19 tRNA genes with similarity to the KJ820683 and AP012988 reference mtDNA...
2018: PloS One
Mingsheng Yang, Lu Song, Jianhang Mao, Yuxia Shi, Changjing Wu, Yunxia Zhang, Li Huang, Weifeng Peng, Xiaomeng Liu
Complete mitochondrial genome (mitogenome) of the Omiodes indicata was sequenced and characterized. The circular mitogenome is 15,367 bp long, including 13 protein-coding genes (PCGs), two ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and an A + T-rich region. Nucleotide composition is highly biased toward A + T nucleotides (81.6%). All 13 PCGs initiate with canonical start codon (ATN), except for cox1 that initiates with CGA. All tRNAs have a typical clover-leaf structure, except for trnS1 (AGN) in which the base pairs of the dihydrouridine (DHU) arm are reduced...
March 11, 2018: International Journal of Biological Macromolecules
Qi-Lin Zhang, Xing-Zhuo Yang, Li Zhang, Run-Qiu Feng, Qian-Hua Zhu, Jun-Yuan Chen, Ming-Long Yuan
Given mitochondrion is the 'energy and oxygen usage factories', adaptive signatures of mitochondrial genes have been extensively investigated in vertebrates from different altitudes, but few studies focus on insects. Here, we sequenced the complete mitochondrial genome (mitogenome) of Dolycoris. baccarum living in the Tibetan Plateau (DBHC, ∼3200 m above sea level (asl)) and conducted a detailed comparative analysis with another D. baccarum mitogenome (DBQY) from relatively low altitude (∼1300 m asl)...
March 9, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Jing Yang, Hong-Xia Liu, Ya-Xiao Li, Zhao-Ming Wei
The complete sequence of the mitochondrial genome of Podagrion sp. (Hymenoptera: Torymidae) is described. The mitogenome was 15,845 bp in size, and contained typical sets of mitochondrial genes. The base composition of the Podagrion sp. mitogenome was also biased toward A + T bases (81.8%). The mitochondrial genome of Podagrion sp. has a weak AT skew (0.07) and a strong GC skew (-0.26). Podagrion sp. exhibits a novel rearrangement compared with the ancestral order, including six protein-coding genes (nad3, cox3, atp6, atp8, cox2 and cox1), which have inverted to the minor strand from the major strand...
March 2, 2018: Genomics
Jun Li, Yaoyao Zhang, Kunjie Hu, Yaqi Zhao, Ruirui Lin, Yan Li, Zhuoran Huang, Xu Zhang, Xuexia Geng, Jianhua Ding
In this study, complete mitogenomes of P. increta and M. stellatarum (Lepidoptera: Sphingidae) were sequenced and compared with other Sphingidae species. The mitogenomes containing 37 genes and a AT rich region are circular molecules with 15,252 and 15,290 base pairs in length respectively. Except cox1 all 13 protein-coding genes (PCGs) are initiated by ATN codons. Most of PCGs terminate with TAA except nad5 and cox1 in P. increta and nad5 and cox2 in M. stellatarum. Ile and Leu2 are the most frequently used codon families in both species and codons CGC, CCG, TCG and ACG are absent in P...
February 28, 2018: International Journal of Biological Macromolecules
Ying Wang, Jin-Jun Cao, Wei-Hai Li
Stoneflies comprise an ancient group of insects, but the phylogenetic position of Plecoptera and phylogenetic relations within Plecoptera have long been controversial, and more molecular data is required to reconstruct precise phylogeny. Herein, we present the complete mitogenome of a stonefly, Suwallia teleckojensis , which is 16146 bp in length and consists of 13 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and a control region (CR). Most PCGs initiate with the standard start codon ATN...
February 28, 2018: International Journal of Molecular Sciences
Jia-Yong Zhang, Le-Ping Zhang, Dan-Na Yu, Kenneth B Storey, Rong-Quan Zheng
BACKGROUND: Complete mitochondrial (mt) genomes have been used extensively to test hypotheses about microevolution and to study population structure, phylogeography, and phylogenetic relationships of Anura at various taxonomic levels. Large-scale mt genomic reorganizations have been observed among many fork-tongued frogs (family Dicroglossidae). The relationships among Dicroglossidae and validation of the genus Feirana are still problematic. Hence, we sequenced the complete mt genomes of Nanorana taihangnica (=F...
February 27, 2018: BMC Evolutionary Biology
Daniela Strobbe, Leonardo Caporali, Luisa Iommarini, Alessandra Maresca, Monica Montopoli, Andrea Martinuzzi, Alessandro Achilli, Anna Olivieri, Antonio Torroni, Valerio Carelli, Anna Ghelli
There is growing evidence that the sequence variation of mitochondrial DNA (mtDNA), which clusters in population- and/or geographic-specific haplogroups, may result in functional effects that, in turn, become relevant in disease predisposition or protection, interaction with environmental factors and ultimately in modulating longevity. To unravel functional differences between mtDNA haplogroups we here employed transmitochondrial cytoplasmic hybrid cells (cybrids) grown in galactose medium, culture condition that force oxidative phosphorylation, and in the presence of rotenone, the classic inhibitor of respiratory Complex I...
February 24, 2018: Neurobiology of Disease
Li Qian, Wang Xiaoxi, Chen Xuexin, Han Baoyu
The complete mitochondrial genome (mitogenome) of the Ectropis obliqua (Lepidoptera: Geometridae) was sequenced and compared with other species of Geometridae. The mitochondrial genome of E. obliqua is 15,475 bp long and contains 37 genes including 13 protein coding genes (PCGs), 22 transfer RNA genes, 2 ribosomal RNA genes and an A + T-rich region. Gene cluster trnI-trnQ-trnM rearranged to trnM-trnI-trnQ comparing with the ancestral mitogenome of insects. All tRNA genes have typical cloverleaf secondary structure except for trnS (AGN)...
February 20, 2018: International Journal of Biological Macromolecules
Nan Zheng, Yu-Xuan Sun, Liang-Li Yang, Liang Wu, Muhammad Nadeem Abbas, Chen Chen, Jin Gao, Xiao-Kun Li, Chao-Liang Liu, Li-Shang Dai
The complete mitochondrial genome (mitogenome) of Biston marginata (Lepidoptera: Geometridae) was determined and annotated. The circular genome is 15,470 bp long and it contains the entire set of 37 genes usually present in lepidopteran mitogenomes. The nucleotide composition of the genome is highly A + T biased, accounting for 81.20%, with a slightly positive AT skewness (0.028), indicating the occurrence of more As than Ts, as found in other Geometridae species. Except for cox1 gene starts with non-canonical initial codon CGA, all protein-coding genes start with ATN codon...
February 17, 2018: International Journal of Biological Macromolecules
Yuanqiu Dong, Bo Li, Lizhi Zhou
Dusky thrush complex comprises of two sister species breeding in SC Siberia, which is the member of thrush Turdus from Turdidae. The phylogenetic resolution of Dusky thrush complex remains controversial, and a detailed research is still necessary. In this research, we determined the complete mtDNAs of both species, and estimated phylogenetic trees based on the mtDNA alignment of these and 21 other Turdidae species, to clarify the taxa status of the Dusky thrush complex. The squenced lengths of these three mitochondrial genomes were 16,737, 16,788 and 16,750 bp...
February 18, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Renato Caparroz, Amanda V Rocha, Gustavo S Cabanne, Pablo Tubaro, Alexandre Aleixo, Emily M Lemmon, Alan R Lemmon
At least four mitogenome arrangements occur in Passeriformes and differences among them are derived from an initial tandem duplication involving a segment containing the control region (CR), followed by loss or reduction of some parts of this segment. However, it is still unclear how often duplication events have occurred in this bird order. In this study, the mitogenomes from two species of Neotropical passerines (Sicalis olivascens and Lepidocolaptes angustirostris) with different gene arrangements were first determined...
February 17, 2018: Molecular Biology Reports
Leonardo Caporali, Luisa Iommarini, Chiara La Morgia, Anna Olivieri, Alessandro Achilli, Alessandra Maresca, Maria Lucia Valentino, Mariantonietta Capristo, Francesca Tagliavini, Valentina Del Dotto, Claudia Zanna, Rocco Liguori, Piero Barboni, Michele Carbonelli, Veronica Cocetta, Monica Montopoli, Andrea Martinuzzi, Giovanna Cenacchi, Giuseppe De Michele, Francesco Testa, Anna Nesti, Francesca Simonelli, Anna Maria Porcelli, Antonio Torroni, Valerio Carelli
We here report on the existence of Leber's hereditary optic neuropathy (LHON) associated with peculiar combinations of individually non-pathogenic missense mitochondrial DNA (mtDNA) variants, affecting the MT-ND4, MT-ND4L and MT-ND6 subunit genes of Complex I. The pathogenic potential of these mtDNA haplotypes is supported by multiple evidences: first, the LHON phenotype is strictly inherited along the maternal line in one very large family; second, the combinations of mtDNA variants are unique to the two maternal lineages that are characterized by recurrence of LHON; third, the Complex I-dependent respiratory and oxidative phosphorylation defect is co-transferred from the proband's fibroblasts into the cybrid cell model...
February 14, 2018: PLoS Genetics
Renata F Martins, Anke Schmidt, Dorina Lenz, Andreas Wilting, Joerns Fickel
In this study we compared the phylogeographic patterns of two Rusa species, Rusa unicolor and Rusa timorensis, in order to understand what drove and maintained differentiation between these two geographically and genetically close species and investigated the route of introduction of individuals to the islands outside of the Sunda Shelf. We analyzed full mitogenomes from 56 archival samples from the distribution areas of the two species and 18 microsatellite loci in a subset of 16 individuals to generate the phylogeographic patterns of both species...
February 2018: Ecology and Evolution
Rama K Sarvani, Drashti R Parmar, Wajeeda Tabasum, Neelima Thota, Ara Sreenivas, Ajay Gaur
The mitochondrial genome of Indian mouse deer (Moschiola indica) was sequenced, assembled and characterized for the first time using 22 pairs of polymerase chain reaction (PCR) primers. The mitogenome of M. indica which is 16,444 bp in size was found very similar to most vertebrates in organisation that harbours 13 protein-coding genes, 22 transfer RNA, 2 ribosomal RNA and 1A + T-rich region. Its comparison with over 52 mitogenomes of the order Artiodactyla, showed a conserved nature of gene organisation, codon usage, gene orientation and evolutionary rates of proteins except that M...
February 9, 2018: Scientific Reports
Denis V Goruynov, Svetlana V Goryunova, Oxana I Kuznetsova, Maria D Logacheva, Irina A Milyutina, Alina V Fedorova, Michael S Ignatov, Aleksey V Troitsky
The mitochondrial genome of moss Mielichhoferia elongata has been sequenced and assembled with Spades genome assembler. It consists of 100,342 base pairs and has practically the same gene set and order as in other known bryophyte chondriomes. The genome contains 66 genes including three rRNAs, 24 tRNAs, and 40 conserved mitochondrial proteins genes. Unlike the majority of previously sequenced bryophyte mitogenomes, it lacks the functional nad7 gene. The phylogenetic reconstruction and scrutiny analysis of the primary structure of nad7 gene carried out in this study suggest its independent pseudogenization in different bryophyte lineages...
2018: PeerJ
Michelle A Peck, Kimberly Sturk-Andreaggi, Jacqueline T Thomas, Robert S Oliver, Suzanne Barritt-Ross, Charla Marshall
Generating mitochondrial genome (mitogenome) data from reference samples in a rapid and efficient manner is critical to harnessing the greater power of discrimination of the entire mitochondrial DNA (mtDNA) marker. The method of long-range target enrichment, Nextera XT library preparation, and Illumina sequencing on the MiSeq is a well-established technique for generating mitogenome data from high-quality samples. To this end, a validation was conducted for this mitogenome method processing up to 24 samples simultaneously along with analysis in the CLC Genomics Workbench and utilizing the AQME (AFDIL-QIAGEN mtDNA Expert) tool to generate forensic profiles...
January 16, 2018: Forensic Science International. Genetics
Ming-Long Yuan, Qi-Lin Zhang, Li Zhang, Cheng-Lin Jia, Xiao-Peng Li, Xing-Zhuo Yang, Run-Qiu Feng
Grassland caterpillars (Lepidoptera: Lymantriinae: Gynaephora) are the most important pests in alpine meadows of the Tibetan Plateau (TP) and have well adapted to high-altitude environments. To further understand the evolutionary history and their adaptation to the TP, we newly determined seven complete TP Gynaephora mitogenomes. Compared to single genes, whole mitogenomes provided the best phylogenetic signals and obtained robust results, supporting the monophyly of the TP Gynaephora species and a phylogeny of Arctiinae + (Aganainae + Lymantriinae)...
February 2, 2018: Molecular Phylogenetics and Evolution
Priscila T Rodrigues, Hugo O Valdivia, Thais C de Oliveira, João Marcelo P Alves, Ana Maria R C Duarte, Crispim Cerutti-Junior, Julyana C Buery, Cristiana F A Brito, Júlio César de Souza, Zelinda M B Hirano, Marina G Bueno, José Luiz Catão-Dias, Rosely S Malafronte, Simone Ladeia-Andrade, Toshihiro Mita, Ana Maria Santamaria, José E Calzada, Indah S Tantular, Fumihiko Kawamoto, Leonie R J Raijmakers, Ivo Mueller, M Andreina Pacheco, Ananias A Escalante, Ingrid Felger, Marcelo U Ferreira
We examined the mitogenomes of a large global collection of human malaria parasites to explore how and when Plasmodium falciparum and P. vivax entered the Americas. We found evidence of a significant contribution of African and South Asian lineages to present-day New World malaria parasites with additional P. vivax lineages appearing to originate from Melanesia that were putatively carried by the Australasian peoples who contributed genes to Native Americans. Importantly, mitochondrial lineages of the P. vivax-like species P...
January 31, 2018: Scientific Reports
Rubi N Meza-Lázaro, Chantal Poteaux, Natalia J Bayona-Vásquez, Michael G Branstetter, Alejandro Zaldívar-Riverón
We assembled mitogenomes from 21 ant workers assigned to four morphospecies (E. ruidum spp. 1-4) and putative hybrids of the Ectatomma ruidum complex (E. ruidum spp. 2x3), and to E. tuberculatum using NGS data. Mitogenomes from specimens of E. ruidum spp. 3, 4 and 2 × 3 had a high proportion of polymorphic sites. We investigated whether polymorphisms in mitogenomes are due to nuclear mt paralogues (numts) or due to the presence of more than one mitogenome within an individual (heteroplasmy). We did not find loss of function signals in polymorphic protein-coding genes, and observed strong evidence for purifying selection in two haplotype-phased genes, which indicate the presence of two functional mitochondrial genomes coexisting within individuals instead of numts...
January 31, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
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