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Shu Zhang, Xiu-Na Wang, Xiao-Ling Zhang, Xing-Zhong Liu, Yong-Jie Zhang
Endophytic fungi (EF) live within plants and have profound impacts on plant communities. They are astonishingly diverse but poorly studied at the genome level. Herein, we assembled the mitochondrial genome (mitogenome) of the EF Pestalotiopsis fici, annotated and compared it with those of other relatives to better understand the evolution of the EF lineage. Except for standard fungal mitochondrial genes, the 69,529-bp circular mitogenome of P. fici harbors 18 introns acquired possibly through lateral transfer from other fungi and nine free-standing open reading frames with some scarcely seen in fungal mitogenomes...
January 17, 2017: Applied Microbiology and Biotechnology
Martin Malmstrøm, Michael Matschiner, Ole K Tørresen, Kjetill S Jakobsen, Sissel Jentoft
Teleost fishes comprise more than half of all vertebrate species, yet genomic data are only available for 0.2% of their diversity. Here, we present whole genome sequencing data for 66 new species of teleosts, vastly expanding the availability of genomic data for this important vertebrate group. We report on de novo assemblies based on low-coverage (9-39×) sequencing and present detailed methodology for all analyses. To facilitate further utilization of this data set, we present statistical analyses of the gene space completeness and verify the expected phylogenetic position of the sequenced genomes in a large mitogenomic context...
January 17, 2017: Scientific Data
Alicia Grealy, Matthew Phillips, Gifford Miller, M Thomas P Gilbert, Jean-Marie Rouillard, David Lambert, Michael Bunce, James Haile
Palaeognaths, the sister group of all other living birds (neognaths), were once considered to be vicariant relics from the breakup of the Gondwanan supercontinent. However, recent molecular studies instead argue for dispersal of volant ancestors across marine barriers. Resolving this debate hinges upon accurately reconstructing their evolutionary relationships and dating their divergences, which often relies on phylogenetic information from extinct relatives and nuclear genomes. Mitogenomes from the extinct elephant birds of Madagascar have helped inform the palaeognath phylogeny; however, nuclear information has remained unavailable...
January 9, 2017: Molecular Phylogenetics and Evolution
Ning Wang, Peter A Hosner, Bin Liang, Edward L Braun, Rebecca T Kimball
The phylogeny of the Phasianidae (pheasants, partridges, and allies) has been studied extensively. However, these studies have largely ignored three enigmatic genera because of scarce DNA source material and limited overlapping phylogenetic data: blood pheasants (Ithaginis), snow partridges (Lerwa), and long-billed partridges (Rhizothera). Thus, phylogenetic positions of these three genera remain uncertain in what is otherwise a well-resolved phylogeny. Previous studies using different data types place Lerwa and Ithaginis in similar positions, but the absence of overlapping data means the relationship between them could not be inferred...
January 11, 2017: Molecular Phylogenetics and Evolution
Solene Janique, Wantana Sriratanasak, Kulchana Ketsuwan, Jirapong Jairin, Ekgachai Jeratthitikul
The Asian rice gall midge (RGM) Orseolia oryzae (Wood Mason) (Diptera: Cecidomyiidae) is a major pest of rice, leading to yield losses in Thailand and many Asian countries. Despite an increasing number of reported midge outbreaks and the presence of many susceptible rice varieties, only a few studies have focused on the genetic variation of the midges. Therefore, we analyzed the phylogeography among Thai RGM populations covering north, northeast and central Thailand. Two mitochondrial DNA genes, cytochrome C oxidase I (COI) and 12S, and a non-coding repeat region (RR) situated just before COI were amplified...
January 9, 2017: Genetica
Hai B Wen, Zhe M Cao, Dan Hua, Pao Xu, Xue Y Ma, Wu Jin, Xin H Yuan, Ruo B Gu
Doubly uniparental inheritance (DUI) of mitochondrial DNA, found only in some bivalve families and characterized by the existence of gender-associated mtDNA lineages that are inherited through males (M-type) or females (F-type), is one of the very few exceptions to the general rule of strict maternal mtDNA inheritance in animals. M-type sequences are often undetected and hence still underrepresented in the GenBank, which hinders the progress of the understanding of the DUI phenomenon. We have sequenced and analyzed the complete M and F mitogenomes of a freshwater mussel, Potamilus alatus...
2017: PloS One
A Pavlova, H M Gan, Y P Lee, C M Austin, D M Gilligan, M Lintermans, P Sunnucks
Genetic variation in mitochondrial genes could underlie metabolic adaptations because mitochondrially encoded proteins are directly involved in a pathway supplying energy to metabolism. Macquarie perch from river basins exposed to different climates differ in size and growth rate, suggesting potential presence of adaptive metabolic differences. We used complete mitochondrial genome sequences to build a phylogeny, estimate lineage divergence times and identify signatures of purifying and positive selection acting on mitochondrial genes for 25 Macquarie perch from three basins: Murray-Darling Basin (MDB), Hawkesbury-Nepean Basin (HNB) and Shoalhaven Basin (SB)...
January 4, 2017: Heredity
Xue-Juan Li, Li-Liang Lin, Ai-Ming Cui, Jie Bai, Xiao-Yang Wang, Chao Xin, Zhen Zhang, Chao Yang, Rui-Rui Gao, Yuan Huang, Fu-Min Lei
The data in this paper are related to the research article entitled "Taxonomic status and phylogenetic relationship of tits based on mitogenomes and nuclear segments" (X.J. Li et al., 2016) [1]. The mitochondrial genomes and nuclear segments of tits were sequenced to analyze mitochondrial characteristics and phylogeny. In the data, the analyzed results are presented. The data holds the resulting files of mitochondrial characteristics, heterogeneity, best schemes, and trees.
February 2017: Data in Brief
Victor Corrêa Seixas, Claudia Augusta Moraes Russo, Paulo Cesar Paiva
Here we describe, for the first time, the mitochondrial genome of Spirobranchus giganteus (Annelida: Serpulidae) and compare it with all available annelid mitogenomes. The entire mitogenome has 22,058bp in length and bears 12 protein-coding genes (the ATP8 gene is missing), two rRNA, and 24 tRNA genes. The nucleotide composition and GC-skew are surprisingly different from those reported for other annelids. In addition, the pairwise genetic distances between the mitogenomes of S. giganteus and other annelids are higher than the distances for all annelid taxa analyzed...
December 26, 2016: Gene
Pierre-Henri Fabre, Nathan S Upham, Louise H Emmons, Fabienne Justy, Yuri L R Leite, Ana Carolina Loss, Ludovic Orlando, Marie-Ka Tilak, Bruce D Patterson, Emmanuel J P Douzery
Echimyidae is one of the most speciose and ecologically diverse rodent families in the world, occupying a wide range of habitats in the Neotropics. However, a resolved phylogeny at the genus-level is still lacking for these 22 genera of South American spiny rats, including the coypu (Myocastorinae), and 5 genera of West Indian hutias (Capromyidae) relatives. Here we used Illumina shotgun sequencing to assemble 38 new complete mitogenomes, establishing Echimyidae, and Capromyidae as the first major rodent families to be completely sequenced at the genus-level for their mitochondrial DNA...
December 25, 2016: Molecular Biology and Evolution
Zhiwen Chen, Hushuai Nie, Corrinne E Grover, Yumei Wang, Pengbo Li, Meiyan Wang, Haili Pei, Yanpeng Zhao, Shuangshuang Li, Jonathan F Wendel, Jinping Hua
Cotton (Gossypium spp.) is commonly grouped into eight diploid genomic groups, designated A-G and K, and an allotetraploid genomic group, AD. Gossypium raimondii (D5 ) and Gossypium arboreum (A2 ) are the putative contributors to the progenitor of G. hirsutum (AD1 ), the economically important fiber-producing cotton species. Mitochondrial DNA from week-old etiolated seedlings was extracted from isolated organelles using discontinuous sucrose density gradient method. Mitochondrial genomes were sequenced, assembled, annotated and analyzed orderly...
December 23, 2016: Plant Biology
Ricardo López-Wilchis, Miguel Ángel Del Río-Portilla, Luis Manuel Guevara-Chumacero
We described the complete mitochondrial genome (mitogenome) of the Wagner's mustached bat, Pteronotus personatus, a species belonging to the family Mormoopidae, and compared it with other published mitogenomes of bats (Chiroptera). The mitogenome of P. personatus was 16,570 bp long and contained a typically conserved structure including 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region (D-loop). Most of the genes were encoded on the H-strand, except for eight tRNA and the ND6 genes...
December 19, 2016: Genetica
Siqi Yuan, Yun Xia, Yuchi Zheng, Xiaomao Zeng
Recent improvements in next-generation sequencing (NGS) technologies can facilitate the obtainment of mitochondrial genomes. However, it is not clear whether NGS could be effectively used to reconstruct the mitogenome with high gene rearrangement. These high rearrangements would cause amplification failure, and/or assembly and alignment errors. Here, we choose two frogs with rearranged gene order, Amolops chunganensis and Quasipaa boulengeri, to test whether gene rearrangements affect the mitogenome assembly and alignment by using NGS...
2016: PeerJ
A Pavan-Kumar, Sudhanshu Raman, Prakash G Koringa, Namrata Patel, Tejas Shah, Rajeev K Singh, Gopal Krishna, C G Joshi, P Gireesh-Babu, Aparna Chaudhari
The mahseers (Tor, Neolissochilus and Naziritor) are an important group of fishes endemic to Asia with the conservation status of most species evaluated as threatened. Conservation plans to revive these declining wild populations are hindered by unstable taxonomy. Molecular phylogeny studies with mitochondrial genome have been successfully used to reconstruct the phylogenetic tree and to resolve taxonomic ambiguity. In the present study, complete mitochondrial genome of Tor tor has been sequenced using ion torrent next-generation sequencing platform with coverage of more than 1000 x...
December 2016: Journal of Genetics
I Stöger, K M Kocot, A J Poustka, N G Wilson, D Ivanov, K M Halanych, M Schrödl
BACKGROUND: Although recent studies have greatly advanced understanding of deep molluscan phylogeny, placement of some taxa remains uncertain as different datasets support competing class-relationships. Traditionally, morphologists have placed Monoplacophora, a group of morphologically simple, limpet-like molluscs as sister group to all other conchiferans (shelled molluscs other than Polyplacophora), a grouping that is supported by the latest large-scale phylogenomic study that includes Laevipilina...
December 16, 2016: BMC Evolutionary Biology
Yu-Xuan Sun, Lei Wang, Guo-Qing Wei, Cen Qian, Li-Shang Dai, Yu Sun, Muhammad Nadeem Abbas, Bao-Jian Zhu, Chao-Liang Liu
The complete mitochondrial genome (mitogenome) of Leucoma salicis (Lepidoptera: Lymantriidae) was sequenced and annotated. It is a circular molecule of 15,334 bp, containing the 37 genes usually present in insect mitogenomes. All protein-coding genes (PCGs) are initiated by ATN codons, other than cox1, which is initiated by CGA. Three of the 13 PCGs had an incomplete termination codon, T or TA, while the others terminated with TAA. The relative synonymous codon usage of the 13 protein-coding genes (PCGs) was consistent with those of published lepidopteran sequences...
December 15, 2016: Scientific Reports
Y Cao, J S Hao, X Y Sun, B Zheng, Q Yang
Pieridae is a butterfly family whose evolutionary history is poorly understood. Due to the difficulties in identifying morphological synapomorphies within the group and the scarcity of the fossil records, only a few studies on higher phylogeny of Pieridae have been reported to date. In this study, we describe the complete mitochondrial genomes of four pierid butterfly species (Aporia martineti, Aporia hippia, Aporia bieti, and Mesapia peloria), in order to better characterize the pierid butterfly mitogenomes and perform the phylogenetic analyses using all available mitogenomic sequence data (13PCGs, rRNAs, and tRNAs) from the 18 pierid butterfly species comprising the three main subfamilies (Dismorphiinae, Coliadinae and Pierinae)...
December 2, 2016: Genetics and Molecular Research: GMR
Zhi-Juan Nie, Ruo-Bo Gu, Fu-Kuan Du, Nai-Lin Shao, Pao Xu, Gang-Chun Xu
In contrast to the highly conserved mitogenomic structure and organisation in most animals (including rotifers), the two previously sequenced monogonont rotifer mitogenomes were fragmented into two chromosomes similar in size, each of which possessed one major non-coding region (mNCR) of about 4-5 Kbp. To further explore this phenomenon, we have sequenced and analysed the mitogenome of one of the most studied monogonont rotifers, Brachionus calyciflorus. It is also composed of two circular chromosomes, but the chromosome-I is extremely large (27 535 bp; 3 mNCRs), whereas the chromosome-II is relatively small (9 833 bp; 1 mNCR)...
2016: PloS One
Artur Burzyński, Marianna Soroka, Monika Mioduchowska, Agnieszka Kaczmarczyk, Jerzy Sell
The availability of a rapidly growing number of complete mitochondrial genome sequences provokes high confidence dating approaches. However, even if the congruence between mitochondrial and nuclear markers is reasonable, the resulting topologies are frequently questionable. The unique opportunity to study the evolutionary history of two independent mitochondrial genomes in one phylogenetic context exists in the freshwater mussels family Unionidae. The two lineages function under doubly uniparental inheritance since well before the emergence of the family...
December 9, 2016: Molecular Phylogenetics and Evolution
Philippe Gaubert, Riddhi Patel, Géraldine Veron, Steven M Goodman, Maraike Willsch, Raquel Vasconcelos, André Lourenço, Marie Sigaud, Fabienne Justy, Bheem Dutt Joshi, Jörns Fickel, Andreas Wilting
The biogeographic dynamics affecting the Indian subcontinent, East and Southeast Asia during the Plio-Pleistocene has generated complex biodiversity patterns. We assessed the molecular biogeography of the small Indian civet (Viverricula indica) through mitogenome and cytochrome b + control region sequencing of 89 historical and modern samples to (i) establish a time-calibrated phylogeography across the species' native range and (ii) test introduction scenarios to western Indian Ocean islands. Bayesian phylogenetic analyses identified three geographic lineages (East Asia, sister-group to Southeast Asia and the Indian subcontinent + northern Indochina) diverging 3...
December 11, 2016: Journal of Heredity
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