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mitochondrial genome evolution

Shanshan Dong, Chaoxian Zhao, Fei Chen, Yanhui Liu, Shouzhou Zhang, Hong Wu, Liangsheng Zhang, Yang Liu
BACKGROUND: Mitochondrial genomes of flowering plants (angiosperms) are highly dynamic in genome structure. The mitogenome of the earliest angiosperm Amborella is remarkable in carrying rampant foreign DNAs, in contrast to Liriodendron, the other only known early angiosperm mitogenome that is described as 'fossilized'. The distinctive features observed in the two early flowering plant mitogenomes add to the current confusions of what early flowering plants look like. Expanded sampling would provide more details in understanding the mitogenomic evolution of early angiosperms...
August 14, 2018: BMC Genomics
Xi Huang, Roland Hansson, Vaidas Palinauskas, Gediminas Valkiūnas, Olof Hellgren, Staffan Bensch
Genomic sequencing of avian haemosporidian parasites (Haemosporida) has been challenging due to excessive contamination from host DNA. In this study, we developed a cost-effective protocol to obtain parasite sequences from naturally infected birds, based on targeted sequence capture and next generation sequencing. With the genomic data of Haemoproteus tartakovskyi as a reference, we successfully sequenced up to 1,000 genes from each of the 15 selected samples belonging to nine different cytochrome b lineages, eight of which belong to Haemoproteus and one to Plasmodium...
August 11, 2018: International Journal for Parasitology
Mitsuaki Ogata, Max Lambert, Tariq Ezaz, Ikuo Miura
Sex-determining mechanisms change repeatedly throughout evolution and it is difficult to track this continual process. The Japanese soil-frog Glandirana rugosa is a remarkable evolutionary witness to the ongoing process of the evolution of sex-determining modes. The two geographic groups, designated XY and Neo-ZW, have homologous sex chromosomes, yet display opposite types of sex-chromosomes, XX-XY and ZZ-ZW, respectively. These two groups are sympatric at the edges of their respective ranges in Central Japan...
August 7, 2018: Molecular Ecology
Runsheng Li, Xiaoliang Ren, Yu Bi, Qiutao Ding, Vincy Wing Sze Ho, Zhongying Zhao
Mitochondrial genome (mtDNA) carries not only well-conserved protein coding, tRNA and rRNA genes, but also highly variable non-coding regions (NCRs). However, the NCRs show poor conservation across species, making their function and evolution elusive. Identification and functional characterization of NCRs across species would be critical for addressing these questions. To this end, we devised a computational pipeline and performed de novo assembly and annotation of mtDNA from 19 Caenorhabditis species using next-generation sequencing (NGS) data...
August 6, 2018: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
Qiang Li, Qiangfeng Wang, Cheng Chen, Xin Jin, Zuqin Chen, Chuan Xiong, Ping Li, Jian Zhao, Wenli Huang
In this study, the mitochondrial genomes of six Russula species were sequenced using next generation sequencing. The six mitogenomes were all composed of circular DNA molecules, with lengths ranging from 40,961 bp to 69,423 bp. The length and number of protein coding genes (PCGs), GC content, AT skew, and GC skew varied among the six mitogenomes. The increased number and total size of introns likely contributed to the size expansion of mitogenomes in some Russula species. Gene synteny analysis revealed some gene rearrangements among the six mitochondrial genomes...
August 1, 2018: International Journal of Biological Macromolecules
Lichun Jiang, Zhangqiang You, Peng Yu, Qiping Ruan, Wei Chen
Members of the Nanorana genus (family Dicroglossidae) are often referred to as excellent model species with which to study amphibian adaptations to extreme environments and also as excellent keystone taxa for providing insights into the evolution of the Dicroglossidae. However, a complete mitochondrial genome is currently only available for Nanorana pleskei . Thus, we analyzed the complete mitochondrial genomes of Nanorana parkeri and Nanorana ventripunctata to investigate their evolutionary relationships within Nanorana and their phylogenetic position in the family Dicroglossidae...
July 2018: Ecology and Evolution
Michael Veith, Sergé Bogaerts, Frank Pasmans, Sarah Kieren
The phylogenetic relationships among members of the family Salamandridae have been repeatedly investigated over the last 90 years, with changing character and taxon sampling. We review the changing composition and the phylogenetic position of salamandrid genera and species groups and add a new phylogeny based exclusively on sequences of nuclear genes. Salamandrina often changed its position depending on the characters used. It was included several times in a clade together with the primitive newts (Echinotriton, Pleurodeles, Tylototriton) due to their seemingly ancestral morphology...
2018: PloS One
Fernando A Seixas, Pierre Boursot, José Melo-Ferreira
BACKGROUND: The extent to which selection determines interspecific patterns of genetic exchange enlightens the role of adaptation in evolution and speciation. Often reported extensive interspecific introgression could be selection-driven, but also result from demographic processes, especially in cases of invasive species replacements, which can promote introgression at their invasion front. Because invasion and selective sweeps similarly mold variation, population genetics evidence for selection can only be gathered in an explicit demographic framework...
July 30, 2018: Genome Biology
Yongle Xu, Rui Zhang, Nannan Wang, Lanlan Cai, Yigang Tong, Qiang Sun, Feng Chen, Nianzhi Jiao
Cyanophages are thought to affect the community structure, population dynamics, metabolic activity, and evolution of picocyanobacteria and to impact the biogeochemical cycling in aquatic ecosystems. Here, we report an estuarine Synechococcus phage, S-CBWM1, which represents a novel viral lineage and exhibits interesting genetic features related to phage-host interactions and evolution. S-CBWM1 encapsidates four virion-associated proteins related to cellular metabolic regulation. Several novel auxiliary metabolic genes related to multidrug efflux, cell wall and capsule synthesis or modification were also identified...
July 26, 2018: Environmental Microbiology
Lucas Torres, Andreanna J Welch, Catherine Zanchetta, R Terry Chesser, Maxime Manno, Cécile Donnadieu, Vincent Bretagnolle, Eric Pante
Mitochondrial genetic markers have been extensively used to study the phylogenetics and phylogeography of many birds, including seabirds of the order Procellariiformes. Evidence suggests that part of the mitochondrial genome of Procellariiformes, especially albatrosses, is duplicated, but no DNA fragment covering the entire duplication has been sequenced. We sequenced the complete mitochondrial genome of a non-albatross species of Procellariiformes, Puffinus lherminieri (Audubon's shearwater) using the long-read MinION (ONT) technology...
July 25, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Diego Bogarín, Oscar Alejandro Pérez-Escobar, Dick Groenenberg, Sean D Holland, Adam P Karremans, Emily Moriarty Lemmon, Alan R Lemmon, Franco Pupulin, Erik Smets, Barbara Gravendeel
Phylogenetic relationships in species complexes and lineages derived from rapid diversifications are often challenging to resolve using morphology or standard DNA barcoding markers. The hyper-diverse genus Lepanthes from Neotropical cloud forest includes over 1200 species and many recent, explosive diversifications that have resulted in poorly supported nodes and morphological convergence across clades. Here, we assess the performance of 446 nuclear-plastid-mitochondrial markers derived from an anchored hybrid enrichment approach (AHE) coupled with coalescence- and species network-based inferences to resolve phylogenetic relationships and improve species recognition in the Lepanthes horrida species group...
July 21, 2018: Molecular Phylogenetics and Evolution
Mateus Ferreira, Alexandre M Fernandes, Alexandre Aleixo, Alexandre Antonelli, Urban Olsson, John M Bates, Joel Cracraft, Camila C Ribas
Jacamar species occur throughout Amazonia, with most species occupying forested habitats. One species-complex, Galbula leucogastra / chalcothorax, is associated to white sand ecosystems (WSE). Previous studies of WSE bird species recovered shallow genetic structure in mtDNA coupled with signs of gene flow among WSE patches. Here, we characterize diversification of the G. leucogastra/chalcothorax species-complex with dense sampling across its distribution using mitochondrial and genomic (Ultraconserved Elements, UCEs) DNA sequences...
July 16, 2018: Molecular Phylogenetics and Evolution
Shirley A Lang, Daniel H Shain
The glacier ice worm, Mesenchytraeus solifugus , is among a few animals that reside permanently in glacier ice. Their adaptation to cold temperature has been linked to relatively high intracellular adenosine triphosphate (ATP) levels, which compensate for reductions in molecular motion at low physiological temperatures. Here, we show that ATP6-the critical regulatory subunit of the F1Fo-ATP synthase and primary target of mitochondrial disease-acquired an unprecedented histidine-rich, 18-amino acid carboxy-terminal extension, which counters the strong evolutionary trend of mitochondrial genome compaction...
2018: Evolutionary Bioinformatics Online
Astrid Schuster, Sergio Vargas, Ingrid S Knapp, Shirley A Pomponi, Robert J Toonen, Dirk Erpenbeck, Gert Wörheide
BACKGROUND: Approximately 80% of all described extant sponge species belong to the class Demospongiae. Yet, despite their diversity and importance, accurate divergence times are still unknown for most demosponge clades. The estimation of demosponge divergence time is key to answering fundamental questions on the origin of Demospongiae, their diversification and historical biogeography. Molecular sequence data alone is not informative on an absolute time scale, and therefore needs to be "calibrated" with additional data such as fossils...
July 18, 2018: BMC Evolutionary Biology
Gerda Fourie, Nicolaas A Van der Merwe, Brenda D Wingfield, Mesfin Bogale, Michael J Wingfield, Emma T Steenkamp
The Fusarium fujikuroi species complex (FFSC) is an economically important monophyletic lineage in the genus Fusarium. Incongruence observed among mitochondrial gene trees, as well as the multiple non-orthologous copies of the internal transcribed spacer region of the ribosomal RNA genes, suggests that the origin and history of this complex likely involved interspecies gene flow. Based on this hypothesis, the mitochondrial genomes of non-conspecific species should harbour signatures of introgression or introgressive hybridization...
June 2018: IMA Fungus
Daniel B Sloan, Jessica M Warren, Alissa M Williams, Zhiqiang Wu, Salah E Abdel-Ghany, Adam J Chicco, Justin C Havird
The partitioning of genetic material between the nucleus and cytoplasmic (mitochondrial and plastid) genomes within eukaryotic cells necessitates coordinated integration between these genomic compartments, with important evolutionary and biomedical implications. Classic questions persist about the pervasive reduction of cytoplasmic genomes via a combination of gene loss, transfer and functional replacement - and yet why they are almost always retained in some minimal form. One striking consequence of cytonuclear integration is the existence of 'chimeric' enzyme complexes composed of subunits encoded in two different genomes...
July 17, 2018: Nature Reviews. Genetics
Olga Klebanov-Akopyan, Amartya Mishra, Galina Glousker, Yehuda Tzfati, Joseph Shlomai
Universal minicircle sequence binding proteins (UMSBPs) are CCHC-type zinc-finger proteins that bind a single-stranded G-rich sequence, UMS, conserved at the replication origins of the mitochondrial (kinetoplast) DNA of trypanosomatids. Here, we report that Trypanosoma brucei TbUMSBP2, which has been previously proposed to function in the replication and segregation of the mitochondrial DNA, colocalizes with telomeres at the nucleus and is essential for their structure, protection and function. Knockdown of TbUMSBP2 resulted in telomere clustering in one or few foci, phosphorylation of histone H2A at the vicinity of the telomeres, impaired nuclear division, endoreduplication and cell growth arrest...
July 11, 2018: Nucleic Acids Research
Sergei V Turanov, Youn-Ho Lee, Yuri Ph Kartavtsev
Control region (CR) is a major non-coding domain of mitochondrial DNA in vertebrates which contains the promoters for replication and transcription of mitochondrial genome along with the binding sites for metabolic machinery and, hence, is a vital element for the integrity of mitochondrial genome as a biological replicator. The origin and diversity of structural elements within CR have been intensively studied in recent years with the involvement of new diverse taxa. In this paper, we provide new data on the nucleotide and structural patterns of CR evolution and phylogenetic suitability among eelpouts (Cottoidei: Zoarcales)...
July 10, 2018: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
Cintia Iha, Christopher J Grassa, Goia de M Lyra, Charles C Davis, Heroen Verbruggen, Mariana C Oliveira
Gracilariaceae has a worldwide distribution including numerous economically important species. We applied high-throughput sequencing to obtain organellar genomes (mitochondria and chloroplast) from ten species of Gracilariaceae and, combined with published genomes, to infer phylogenies and compare genome architecture among species representing main lineages. We obtained similar topologies between chloroplast and mitochondrial genomes phylogenies. However, the chloroplast phylogeny was better resolved with full support...
July 10, 2018: Journal of Phycology
Hernán E Morales, Alexandra Pavlova, Nevil Amos, Richard Major, Andrzej Kilian, Chris Greening, Paul Sunnucks
Metabolic processes in eukaryotic cells depend on interactions between mitochondrial and nuclear gene products (mitonuclear interactions). These interactions could have a direct role in population divergence. Here, we study mitonuclear co-evolution in a widespread bird that experienced population divergence followed by bidirectional mitochondrial introgression into different nuclear backgrounds. Using >60,000 single nucleotide polymorphisms, we quantify patterns of nuclear genetic differentiation between populations that occupy areas with different climates and harbour deeply divergent mitochondrial lineages despite ongoing nuclear gene flow...
August 2018: Nature Ecology & Evolution
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