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mitochondrial genome evolution

Zhichao Yan, Qi Fang, Yu Tian, Fang Wang, Xuexin Chen, John H Werren, Gongyin Ye
Chalcidoidea (chalcidoid wasps) are an abundant and megadiverse insect group with both ecological and economical importance. Here we report a complete mitochondrial genome in Chalcidoidea from Pteromalus puparum (Pteromalidae). Eight tandem repeats followed by 6 reversed repeats were detected in its 3308 bp control region. This long and complex control region may explain failures of amplifying and sequencing of complete mitochondrial genomes in some chalcidoids. In addition to 37 typical mitochondrial genes, an extra identical isoleucine tRNA (trnI) was detected...
October 10, 2018: International Journal of Biological Macromolecules
Qiang Li, Qiangfeng Wang, Xin Jin, Zuqin Chen, Chuan Xiong, Ping Li, Jian Zhao, Wenli Huang
Lyophyllum decastes and Lyophyllum shimeji are the two primary species within the L. decastes complex, and they differ considerably in their nutritional lifestyles and preferred growth environments. However, differences in their mitogenomes have not yet been investigated. In this study, the mitogenomes of the two species were sequenced by next-generation sequencing technology, successfully assembled, and compared. The two mitogenomes of L. decastes and L. shimeji comprised circular DNA molecules of sizes 50,643 bp and 73,678 bp, respectively...
October 11, 2018: International Journal of Biological Macromolecules
Huayun Guo, Hao Yang, Yitao Tao, Dan Tang, Qiong Wu, Zhengfei Wang, Boping Tang
Cave shrimps from the genera Typhlatya, Stygiocaris and Typhlopatsa (TST complex) comprises twenty cave-adapted taxa, which mainly occur in the anchialine environment. Anchialine habitats may undergo drastic environmental fluctuations, including spatial and temporal changes in salinity, temperature, and dissolved oxygen content. Previous studies of crustaceans from anchialine caves suggest that they have possessed morphological, behavioral, and physiological adaptations to cope with the extreme conditions, similar to other cave-dwelling crustaceans...
November 2018: Genes & Genomics
Ben J Mans, Jonathan Featherston, Marija Kvas, Kerry-Anne Pillay, Daniel G de Klerk, Ronel Pienaar, Minique H de Castro, Tom G Schwan, Job E Lopez, Pete Teel, Adalberto A Pérez de León, Daniel E Sonenshine, Noble I Egekwu, Deon K Bakkes, Heloise Heyne, Esther G Kanduma, Nkululeko Nyangiwe, Ali Bouattour, Abdalla A Latif
The systematics of the genera and subgenera within the soft tick family Argasidae is not adequately resolved. Different classification schemes, reflecting diverse schools of scientific thought that elevated or downgraded groups to genera or subgenera, have been proposed. In the most recent classification scheme, Argas and Ornithodoros are paraphyletic and the placement of various subgenera remains uncertain because molecular data are lacking. Thus, reclassification of the Argasidae is required. This will enable an understanding of soft tick systematics within an evolutionary context...
October 1, 2018: Ticks and Tick-borne Diseases
Qiang Li, Qiangfeng Wang, Xin Jin, Zuqin Chen, Chuan Xiong, Ping Li, Qiaofeng Liu, Wenli Huang
Lactarius is one of the most prominent genera of mushroom-forming fungi in the world. In the present study, complete mitochondrial genomes (mitogenomes) from six Lactarius species were sequenced and assembled. The six mitogenomes were all composed of circular DNA molecules, with total lengths ranging from 38,445 bp to 60,843 bp. The GC contents, GC skews, and AT skews of the mitogenomes varied among the six species. Mitogenomic synteny analysis revealed the presence of gene rearrangements among the mitogenomes...
October 9, 2018: International Journal of Biological Macromolecules
Timothy D O'Hara, Andrew F Hugall, Paula A Cisternas, Emilie Boissin, Guadalupe Bribiesca-Contreras, Javier Sellanes, Gustav Paulay, Maria Byrne
Brittle-stars in the family Ophiocomidae are large and colourful inhabitants of tropical shallow water habitats across the globe. Here we use targeted capture and next-generation sequencing to generate robust phylogenomic trees for 39 of the 43 species in order to test the monophyly of existing genera. The large genus Ophiocoma, as currently constituted, is paraphyletic on our trees and required revision. Four genera are recognised herein: an expanded Ophiomastix (now including Ophiocoma wendtii, O. occidentalis, O...
October 8, 2018: Molecular Phylogenetics and Evolution
Xiao-Chen Huang, Jin-Hui Su, Jie-Xiu Ouyang, Shan Ouyang, Chun-Hua Zhou, Xiao-Ping Wu
The Yangtze River Basin in China is one of the global hotspots of freshwater mussel (order Unionida) diversity with 68 nominal species. Few studies have tested the validity of these nominal species. Some taxa from the Yangtze unionid fauna have not been adequately examined using molecular data and well-positioned phylogenetically with respect to the global Unionida. We evaluated species boundaries of Chinese freshwater mussels, and disentangled their phylogenetic relationships within the context of the global freshwater mussels based on the multi-locus data and complete mitochondrial genomes...
October 8, 2018: Molecular Phylogenetics and Evolution
Gertraud Burger, Matus Valach
Mitochondria are the sandbox of evolution as exemplified most particularly by the diplonemids, a group of marine microeukaryotes. These protists are uniquely characterized by their highly multipartite mitochondrial genome and systematically fragmented genes whose pieces are spread out over several dozens of chromosomes. The type species Diplonema papillatum was the first member of this group in which the expression of fragmented mitochondrial genes was investigated experimentally. We now know that gene expression involves separate transcription of gene pieces (modules), RNA editing of module transcripts, and module joining to mature mRNAs and rRNAs...
October 10, 2018: IUBMB Life
Adam Dawid Urantowka, Aleksandra Kroczak, Tony Silva, Rafael Zamora Padrón, Nuhacet Fernández Gallardo, Julie Blanch, Barry Blanch, Pawel Mackiewicz
Mitochondrial genomes of vertebrates are generally thought to evolve under strong selection for size reduction and gene order conservation. Therefore, a growing number of mitogenomes with duplicated regions changes our view on the genome evolution. Among Aves, order Psittaciformes (parrots) is especially noteworthy because of its large morphological, ecological and taxonomical diversity, which offers an opportunity to study genome evolution in various aspects. Former analyses showed that tandem duplications comprising the control region with adjacent genes are restricted to several lineages in which the duplication occurred independently...
October 10, 2018: Molecular Biology and Evolution
S L van Esveld, M A Huynen
Most eukaryotic cells contain mitochondria with a genome that evolved from their α-proteobacterial ancestor. In the course of eukaryotic evolution, the mitochondrial genome underwent a dramatic reduction in size, caused by the loss and translocation of genes. This required adjustments in mitochondrial gene expression mechanisms and resulted in a complex collaborative system of mitochondrially encoded transfer RNAs and ribosomal RNAs with nuclear encoded proteins to express the mitochondrial encoded oxidative phosphorylation (OXPHOS) proteins...
October 3, 2018: IUBMB Life
Marco Severgnini, Barbara Lazzari, Emanuele Capra, Stefania Chessa, Mario Luini, Roberta Bordoni, Bianca Castiglioni, Matteo Ricchi, Paola Cremonesi
Prototheca zopfii (P. zopfii, class Trebouxiophyceae, order Chlorellales, family Chlorellaceae), a non-photosynthetic predominantly free-living unicellular alga, is one of the few pathogens belonging to the plant kingdom. This alga can affect many vertebrate hosts, sustaining systemic infections and diseases such as mastitis in cows. The aim of our work was to sequence and assemble the P. zopfii genotype 1 and genotype 2 mitochondrial and plastid genomes. Remarkably, the P. zopfii mitochondrial (38 Kb) and plastid (28 Kb) genomes are models of compaction and the smallest known in the Trebouxiophyceae...
October 2, 2018: Scientific Reports
Adam Herman, Yaniv Brandvain, James Weagley, William R Jeffery, Alex C Keene, Thomas J Y Kono, Helena Bilandžija, Richard Borowsky, Luis Espinasa, Kelly O'Quin, Claudia P Ornelas-García, Masato Yoshizawa, Brian Carlson, Ernesto Maldonado, Joshua B Gross, Reed A Cartwright, Nicolas Rohner, Wesley C Warren, Suzanne E McGaugh
Understanding the molecular basis of repeatedly evolved phenotypes can yield key insights into the evolutionary process. Quantifying gene flow between populations is especially important in interpreting mechanisms of repeated phenotypic evolution, and genomic analyses have revealed that admixture occurs more frequently between diverging lineages than previously thought. In this study, we resequenced 47 whole genomes of the Mexican tetra from three cave populations, two surface populations and outgroup samples...
September 25, 2018: Molecular Ecology
Youjin Deng, Tom Hsiang, Shuxian Li, Longji Lin, Qingfu Wang, Qinghe Chen, Baogui Xie, Ray Ming
Mitochondrial DNA (mtDNA) is a core non-nuclear genetic material found in all eukaryotic organisms, the size of which varies extensively in the eumycota, even within species. In this study, mitochondrial genomes of six isolates of Annulohypoxylon stygium (Lév.) were assembled from raw reads from PacBio and Illumina sequencing. The diversity of genomic structures, conserved genes, intergenic regions and introns were analyzed and compared. Genome sizes ranged from 132 to 147 kb and contained the same sets of conserved protein-coding, tRNA and rRNA genes and shared the same gene arrangements and orientation...
2018: Frontiers in Microbiology
Nathanaëlle Saclier, Clémentine M François, Lara Konecny-Dupré, Nicolas Lartillot, Laurent Guéguen, Laurent Duret, Florian Malard, Christophe J Douady, Tristan Lefébure
The rate of molecular evolution varies widely among species. Life history traits have been proposed as a major driver of these variations. However, the relative contribution of each trait is poorly understood. Here, we test the influence of metabolic rate, longevity and generation time on the nuclear and mitochondrial synonymous substitution rates using a group of isopod species that have made multiple independent transitions to subterranean environments. Subterranean species have repeatedly evolved a lower metabolic rate, a longer lifespan and a longer generation time...
September 24, 2018: Molecular Biology and Evolution
Rui Li, Gang Wang, Zheng-Yong Wen, Yuan-Chao Zou, Chuan-Jie Qin, Yu Luo, Jun Wang, Gui-Hong Chen
The snakehead fish, Channa siamensis, belongs to the genus of Channa (perciformes: Channidae) and was first reported by Günther in 1861. Despite it has been described approximately for 15 decades, the genetic information is limited and the taxon status of this kind of fish is still unclear. The primary objective of this study is to get more genomic data and calculate the taxon location of this kind of fish. The next generation sequencing method was used to obtain the whole mitochondrial DNA information, and bioinformatic analysis was performed to investigate the evolutionary status and taxon location of C...
September 21, 2018: Genes & Genomics
Yan Huang, Yu Liu, Xiao-Yu Zhu, Zhao-Zhe Xin, Hua-Bin Zhang, Dai-Zhen Zhang, Jia-Lian Wang, Bo-Ping Tang, Chun-Lin Zhou, Qiu-Ning Liu, Li-Shang Dai
The mitochondrial genome (mitogenome) plays an important role in revealing molecular evolution. In this study, the complete mitogenome of Grammodes geometrica (G. geometrica) (Lepidoptera: Erebidae) was sequenced and characterized. The nucleotide composition of the genome is highly A + T biased, accounting for 80.49%. Most protein-coding genes (PCGs) are initiated by ATN codons except for the cytochrome oxidase subunit 1 (cox1) gene, which was initiated by CGA. The order and orientation of genes with the order trnM-trnI-trnQ-nad2 is a typical rearrangement compared with those ancestral insects in which trnM is located between trnQ and nad2...
September 19, 2018: International Journal of Biological Macromolecules
Yanjie Shang, Lipin Ren, Wei Chen, Lagabaiyila Zha, Jifeng Cai, Jianan Dong, Yadong Guo
The flesh flies (Diptera: Sarcophagidae) are significant in forensic investigations. The mitochondrial genome (mitogeome) has been widely used as genetic markers for phylogenetic analysis and species identification. To further understand the mitogenome-level features in Sarcophagidae, the complete mitogenome of Sarcophaga formosensis (Kirneret Lopes, 1961) (Diptera: Sarcophagidae) and Sarcophaga misera (Walker, 1849) (Diptera: Sarcophagidae) was firstly sequenced, annotated, and compared with other 13 Sarcophagidae species...
September 20, 2018: Journal of Medical Entomology
Adam C Schneider, Harold Chun, Saša Stefanović, Bruce G Baldwin
Foundational studies of chloroplast genome (plastome) evolution in parasitic plants have focused on broad trends across large clades, particularly among the Orobanchaceae, a species-rich and ecologically diverse family of root parasites. However, the extent to which such patterns and processes of plastome evolution, such as stepwise gene loss following the complete loss of photosynthesis (shift to holoparasitism), are detectable at shallow evolutionary time scale is largely unknown. We used genome skimming to assemble eight chloroplast genomes representing complete taxonomic sampling of Aphyllon sect...
September 19, 2018: Proceedings. Biological Sciences
Joshua M Wang, Richard J Bennett, Matthew Z Anderson
The opportunistic fungal pathogen Candida albicans lacks a conventional sexual program and is thought to evolve, at least primarily, through the clonal acquisition of genetic changes. Here, we performed an analysis of heterozygous diploid genomes from 21 clinical isolates to determine the natural evolutionary processes acting on the C. albicans genome. Mutation and recombination shaped the genomic landscape among the C. albicans isolates. Strain-specific single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) clustered across the genome...
September 18, 2018: MBio
Qiang Li, Qiangfeng Wang, Xin Jin, Zuqin Chen, Chuan Xiong, Ping Li, Jian Zhao, Wenli Huang
Hygrophorus russula (Schaeff.) Kauffman is an edible ectomycorrhizal fungus that is widely distributed in the world. In this study, the mitogenome of H. russula was sequenced and assembled. The mitogenome of H. russula is composed of circular DNA molecules, with a total size of 55,769 bp. Further analysis indicated that the frequent use of A and T in codons contributes to the high AT content (80.87%) in the H. russula mitogenome. Comparative analysis indicated that the length and base composition of the core protein-encoding genes, and the number of tRNA genes in the H...
September 15, 2018: International Journal of Biological Macromolecules
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