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mitochondrial genome evolution

Shuaibin Wang, Dawei Li, Xiaohong Yao, Qingwei Song, Zupeng Wang, Qiong Zhang, Caihong Zhong, Yifei Liu, Hongwen Huang
Angiosperm mitochondrial genomes (mitogenomes) are notable for their extreme diversity in both size and structure. However, our current understanding of this diversity is limited, and the underlying mechanism contributing to this diversity remains unclear. Here, we completely assembled and compared the mitogenomes of three kiwifruit (Actinidia) species, which represent an early divergent lineage in asterids. We found conserved gene content and fewer genomic repeats, particularly large repeats (>1 kb), in the three mitogenomes...
March 21, 2019: Genome Biology and Evolution
Kevin Correia, Shi M Yu, Radhakrishnan Mahadevan
Budding yeasts inhabit a range of environments by exploiting various metabolic traits. The genetic bases for these traits are mostly unknown, preventing their addition or removal in a chassis organism for metabolic engineering. Insight into the evolution of orthologs, paralogs and xenologs in the yeast pan-genome can help bridge these genotypes; however, existing phylogenomic databases do not span diverse yeasts, and sometimes cannot distinguish between these homologs. To help understand the molecular evolution of these traits in yeasts, we created Analyzing Yeasts by Reconstructing Ancestry of Homologs (AYbRAH), an open-source database of predicted and manually curated ortholog groups for 33 diverse fungi and yeasts in Dikarya, spanning 600 million years of evolution...
January 1, 2019: Database: the Journal of Biological Databases and Curation
Yuki Nishimura, Takashi Shiratori, Ken-Ichiro Ishida, Tetsuo Hashimoto, Moriya Ohkuma, Yuji Inagaki
Mitochondrial genomes exhibit diverse features among eukaryotes in the aspect of gene content, genome structure, and the mobile genetic elements such as introns and plasmids. Although the number of published mitochondrial genomes is increasing at tremendous speed, those of several lineages remain unexplored. Here, we sequenced the complete mitochondrial genome of a unicellular heterotrophic eukaryote, Marophrys sp. SRT127 belonging to the Centroheliozoa, as the first report on this lineage. The circular-mapped mitochondrial genome, which is 113,062 bp in length, encodes 69 genes typically found in mitochondrial genomes...
March 19, 2019: Scientific Reports
Anna Klucnika, Hansong Ma
The mitochondrial genome is an evolutionarily persistent and cooperative component of metazoan cells that contributes to energy production and many other cellular processes. Despite sharing the same host as the nuclear genome, the multi-copy mitochondrial DNA (mtDNA) follows very different rules of replication and transmission, which translate into differences in the patterns of selection. On one hand, mtDNA is dependent on the host for its transmission, so selections would favour genomes that boost organismal fitness...
March 29, 2019: Open Biology
Charikleia Karageorgiou, Víctor Gámez-Visairas, Rosa Tarrío, Francisco Rodríguez-Trelles
BACKGROUND: Drosophila subobscura has long been a central model in evolutionary genetics. Presently, its use is hindered by the lack of a reference genome. To bridge this gap, here we used PacBio long-read technology, together with the available wealth of genetic marker information, to assemble and annotate a high-quality nuclear and complete mitochondrial genome for the species. With the obtained assembly, we performed the first synteny analysis of genome structure evolution in the subobscura subgroup...
March 18, 2019: BMC Genomics
Jie Luo, Piyush Padhi, Huajun Jin, Vellareddy Anantharam, Gary Zenitsky, Qian Wang, Auriel A Willette, Arthi Kanthasamy, Anumantha G Kanthasamy
Chronic and debilitating neurodegenerative diseases, such as Parkinson's disease (PD), impose an immense medical, emotional, and economic burden on patients and society. Due to a complex interaction between genetic and environmental risk factors, the etiology of PD remains elusive. However, the cumulative evidence emerging from clinical and experimental research over the last several decades has identified mitochondrial dysfunction, oxidative stress, neuroinflammation, and dysregulated protein degradation as the main drivers of PD neurodegeneration...
March 16, 2019: Journal of Neuroimmune Pharmacology: the Official Journal of the Society on NeuroImmune Pharmacology
Annika Mae Lamb, Anders Gonçalves da Silva, Leo Joseph, Paul Sunnucks, Alexandra Pavlova
Understanding how environmental change has shaped species evolution can inform predictions of how future climate change might continue to do so. Research of widespread biological systems spanning multiple climates that have been subject to environmental change can yield generalizable inferences about the neutral and adaptive processes driving lineage divergence during periods of environmental change. We contribute to the growing body of multi-locus phylogeographic studies investigating the effect of Pleistocene climate change on species evolution by focusing on a widespread Australo-Papuan songbird with several mitochondrial lineages that diverged during the Pleistocene, the grey shrike-thrush (Colluricincla harmonica)...
March 15, 2019: Heredity
Haishuo Ji, Xiaofeng Xu, Xiufeng Jin, Hong Yin, Jianxun Luo, Guangyuan Liu, Qiang Zhao, Ze Chen, Wenjun Bu, Shan Gao
In this study, we used a small RNA sequencing (sRNA-seq) based method to annotate the mitochondrial genome of the insect Erthesina fullo Thunberg at 1 bp resolution. The high-resolution annotations cover both entire strands of the mitochondrial genome without any gaps or overlaps. Most of the new annotations were consistent with the previous annotations which had been obtained using PacBio full-length transcripts. Two important findings were that animals transcribe both entire strands of mitochondrial genomes and the tandem repeats in the control region of the E...
March 14, 2019: RNA Biology
Yuka Sekigami, Takuya Kobayashi, Ai Omi, Koki Nishitsuji, Tetsuro Ikuta, Asao Fujiyama, Noriyuki Satoh, Hidetoshi Saiga
Background: In the previous paper published in 2017, we described the structure of Hox gene cluster of the ascidian, Halocynthia roretzi , and discussed the scenario for the disintegration of Hox gene clusters during evolution of ascidians. The description about the Hox gene cluster structure still represents the latest information, hence it has been left unchanged. In contrast, some points in Discussion, the description on the phylogenetic relationships among tunicates and the theoretical scenario for the disintegration of Hox gene cluster during evolution of ascidians, should be changed because the phylogenetic relationships among tunicates have recently been updated...
2019: Zoological Letters
Guang-Long Xie, Frank Köhler, Xiao-Chen Huang, Rui-Wen Wu, Chun-Hua Zhou, Shan Ouyang, Xiao-Ping Wu
Stylommatophora is a main clade of Gastropoda that encompasses approximately 112 gastropod families and may exceed a total of 30,000 species. Twenty-four complete stylommatophoran mitogenomes have been sequenced to date, yet our understanding of mitochondrial evolution in stylommatophorans is still in its infancy. To further expand the set of available mitogenomes, we sequenced the mitogenome of Meghimatium bilineatum (Arionoidea: Philomycidae), a widespread land slug in East Asia. This is the first report on a mitogenome of the superfamily Arionoidea, and indeed on a terrestrial slug...
March 8, 2019: Molecular Phylogenetics and Evolution
L Marandel, D J Kostyniuk, C Best, J L I Forbes, J Liu, S Panserat, J A Mennigen
Rainbow trout have, as salmonid fish species, undergone sequential genome duplication events in their evolutionary history. In addition to a teleost-specific whole genome duplication approximately 320-350 million years ago, rainbow trout and salmonids in general underwent an additional salmonid lineage-specific genome duplication event approximately 80 million years ago. Through the recent sequencing of salmonid genome sequences, including the rainbow trout, the identification and study of duplicated genes has become available...
March 5, 2019: Gene
N Bondarenko, A Bondarenko, V Starunov, G Slyusarev
Among invertebrates, only a few groups still have uncertain phylogenetic position, Orthonectida, a small group of rare multi-cellular parasites of marine invertebrates, being one of them. Recent molecular and morphological findings suggest that orthonectids belong to Lophotrochozoa and are close to Annelida. Nevertheless, phylogenetic relationships between orthonectids and annelids are unclear, and the phylogeny within the group itself has never been studied. Sequencing of mitochondrial genomes is used here to clarify this issue...
March 8, 2019: Molecular Genetics and Genomics: MGG
Tiezhu Yang, Guolyu Xu, Bingning Gu, Yanmei Shi, Hellen Lucas Mzuka, Heding Shen
The mitochondrial genome (mitogenome) can provide information for phylogenetic analyses and evolutionary biology. We first sequenced, annotated, and characterized the mitogenome of Philomycus bilineatus in this study. The complete mitogenome was 14,347 bp in length, containing 13 protein-coding genes (PCGs), 23 transfer RNA genes, two ribosomal RNA genes, and two non-coding regions (A + T-rich region). There were 15 overlap locations and 18 intergenic spacer regions found throughout the mitogenome of P. bilineatus ...
March 5, 2019: Genes
Thi Thuy Hang Tran, Duc Hinh Nguyen, Van Khanh Tran, Quy Linh Nguyen, Hong Anh Trinh, Long Hoang Luong, Van Anh Tran, Le Anh Tuan Pham, Thu Thuy Nguyen, Van Bang Nguyen, Thinh Huy Tran, Thanh Van Ta
BACKGROUND: The sequence polymorphism of mitochondrial DNA (mtDNA) hypervariable segment 1 (HV1) and hypervariable segment 2 (HV2) is studied and applied to genetic diversity and human evolution assessment, forensic genetics, consanguinity determination, and mitochondrial disease diagnosis. METHODS: The study identified the variations of HV1 and HV2 of 517 unrelated Vietnamese individuals in Kinh, Muong, Cham, and Khmer ethnic. We performed sequencing of two hypervariable segments of mitochondrial DNA: HV1 and HV2...
March 6, 2019: Advances in Experimental Medicine and Biology
Dong-Bin Chen, Ru-Song Zhang, Hai-Xu Bian, Qun Li, Run-Xi Xia, Yu-Ping Li, Yan-Qun Liu, Cheng Lu
The domestication of domestic silkworm Bombyx mori, the only truly domesticated insect, is a distinctive event in agricultural history. The domestication and origin of domestic silkworm remains unclear, although it has connected with human for ~5500 years. In the present study, we would like to highlight our evidence from whole mitochondrial genome for the presence of two genetically distinctive subtypes in Chinese B. mandarina populations, corresponding to northern Chinese B. mandarina and southern Chinese B...
March 2, 2019: International Journal of Biological Macromolecules
Lidia Skuza, Izabela Szućko, Ewa Filip, Tomasz Strzała
The genus Secale is small but very diverse. Despite the high economic importance, phylogenetic relationships of rye species have not been fully determined, and they are extremely important for the process of breeding of new cultivars that can be enriched with functional traits derived from wild rye species. The study analyzed the degree of relationship of 35 accessions of the genus Secale, representing 13 most often distinguished species and subspecies, originating from various seed collections in the world, based on the analysis of non-coding regions of the chloroplast (cpDNA) and mitochondrial genome (mtDNA), widely used in phylogenetic and population plant studies, because of a higher rate of evolution than the coding regions...
2019: PloS One
Claire L Riggs, Rosey Le, Dietmar Kültz, Daniel Zajic, Amanda Summers, Luz Alvarez, Jason E Podrabsky
Most animal cells rely on aerobic metabolism for survival and are damaged or die within minutes without oxygen. Embryos of the annual killifish Austrofundulus limnaeus, however, survive months without oxygen. Determining how their cells survive without oxygen has the potential to revolutionize our understanding of the cellular mechanisms supporting vertebrate anoxia tolerance and the evolution of such tolerance. Therefore, we aimed to establish and characterize an anoxia-tolerant cell line from A. limnaeus for investigating mechanisms of vertebrate anoxia tolerance...
February 22, 2019: Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology
Sarah Ehl, Miguel Vences, Michael Veith
Reconstructing reliable timescales for species evolution is an important and indispensable goal of modern biogeography. However, many factors influence the estimation of divergence times, and uncertainty in the inferred time trees remains a major issue that is often insufficiently acknowledged. We here focus on a fundamental problem of time tree analysis: the combination of slow-evolving (nuclear DNA) and fast-evolving (mitochondrial DNA) markers in a single time tree. Both markers differ in their suitability to infer divergences at different time scales (the 'genome-timescale-dilemma')...
February 21, 2019: Molecular Phylogenetics and Evolution
Zhichao Yan, Gongyin Ye, John H Werren
The mitochondrion is a pivotal organelle for energy production, and includes components encoded by both the mitochondrial and nuclear genomes. Functional and evolutionary interactions are expected between the nuclear and mitochondrial encoded components. The topic is of broad interest in biology, with implications to genetics, evolution, and medicine. Here we compare the evolutionary rates of mitochondrial proteins and ribosomal RNAs to rates of mitochondria-associated nuclear-encoded proteins, across the major orders of holometabolous insects...
February 20, 2019: Molecular Biology and Evolution
W P T James, R J Johnson, J R Speakman, D C Wallace, G Frühbeck, P O Iverson, P J Stover
Our understanding of human evolution has improved rapidly over recent decades, facilitated by large-scale cataloguing of genomic variability amongst both modern and archaic humans. It seems clear that the evolution of the ancestors of chimpanzees and hominins separated 7-9 million years ago with some migration out of Africa by the earlier hominins; Homo sapiens slowly emerged as climate change resulted in drier, less forested African conditions. The African populations expanded and evolved in many different conditions with slow mutation and selection rates in the human genome, but with much more rapid mutation occurring in mitochondrial DNA...
February 17, 2019: Journal of Internal Medicine
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