Genetic diversity and evolutionary history of four closely relatedAquilegiaspecies revealed by 10 nuclear gene fragments

2018 ◽  
Vol 56 (2) ◽  
pp. 129-138 ◽  
Author(s):  
Lei Huang ◽  
Fang-Dong Geng ◽  
Jing-Jing Fan ◽  
Cheng Xue ◽  
Xiao-Yan Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Evolutionary History ◽  
Nuclear Gene ◽  
History Of

scholarly journals Genetic Diversity of Rice stripe necrosis virus and New Insights into Evolution of the Genus Benyvirus

Viruses ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 737
Author(s):  
Issiaka Bagayoko ◽  
Marcos Giovanni Celli ◽  
Gustavo Romay ◽  
Nils Poulicard ◽  
Agnès Pinel-Galzi ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Sierra Leone ◽  
Evolutionary History ◽  
Molecular Diversity ◽  
Genomic Data ◽  
Gene Recombination ◽  
Necrosis Virus ◽  
History Of ◽  
Complex Evolutionary History

The rice stripe necrosis virus (RSNV) has been reported to infect rice in several countries in Africa and South America, but limited genomic data are currently publicly available. Here, eleven RSNV genomes were entirely sequenced, including the first corpus of RSNV genomes of African isolates. The genetic variability was differently distributed along the two genomic segments. The segment RNA1, within which clusters of polymorphisms were identified, showed a higher nucleotidic variability than did the beet necrotic yellow vein virus (BNYVV) RNA1 segment. The diversity patterns of both viruses were similar in the RNA2 segment, except for an in-frame insertion of 243 nucleotides located in the RSNV tgbp1 gene. Recombination events were detected into RNA1 and RNA2 segments, in particular in the two most divergent RSNV isolates from Colombia and Sierra Leone. In contrast to BNYVV, the RSNV molecular diversity had a geographical structure with two main RSNV lineages distributed in America and in Africa. Our data on the genetic diversity of RSNV revealed unexpected differences with BNYVV suggesting a complex evolutionary history of the genus Benyvirus.

Molecular phylogeny of diploid Hordeum species and incongruence between chloroplast and nuclear datasets

Genome ◽  
2011 ◽  
Vol 54 (12) ◽  
pp. 986-992 ◽  
Author(s):  
Huan Wang ◽  
Dongfa Sun ◽  
Genlou Sun
Keyword(s):  
Evolutionary History ◽  
Nuclear Gene ◽  
Intergenic Spacer ◽  
Molecular Data ◽  
Genome Species ◽  
Different Types ◽  
History Of ◽  
Morphological And Molecular Data ◽  
Hordeum Species ◽  
Eurasian Species

The phylogeny of diploid Hordeum species has been studied using both chloroplast and nuclear gene sequences. However, the studies of different nuclear datasets of Hordeum species often arrived at similar conclusions, whereas the studies of different chloroplast DNA data generally resulted in inconsistent conclusions. Although the monophyly of the genus is well supported by both morphological and molecular data, the intrageneric phylogeny is still a matter of controversy. To better understand the evolutionary history of Hordeum species, two chloroplast gene loci (trnD-trnT intergenic spacer and rps16 gene) and one nuclear marker (thioreoxin-like gene (HTL)) were used to explore the phylogeny of Hordeum species. Two obviously different types of trnD-trnT sequences were observed, with an approximately 210 base pair difference between these two types: one for American species, another for Eurasian species. The trnD-trnT data generally separated the diploid Hordeum species into Eurasian and American clades, with the exception of Hordeum marinum subsp. gussoneanum. The rps16 data also grouped most American species together and suggested that Hordeum flexuosum has a different plastid type from the remaining American species. The nuclear gene HTL data clearly divided Hordeum species into two clades: the Xu + H genome clade and the Xa + I genome clade. Within clades, H genome species were well separated from the Xu species, and the I genome species were well separated from the Xa genome species. The incongruence between chloroplast and nuclear datasets was found and discussed.

scholarly journals SARS-Like Coronaviruses in Horseshoe Bats (Rhinolophus spp.) in Russia, 2020

Viruses ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 113
Author(s):  
Sergey Alkhovsky ◽  
Sergey Lenshin ◽  
Alexey Romashin ◽  
Tatyana Vishnevskaya ◽  
Oleg Vyshemirsky ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Evolutionary History ◽  
Structural Proteins ◽  
Rt Pcr ◽  
Phylogenetic Lineage ◽  
History Of ◽  
Horseshoe Bats ◽  
Regions Of Russia ◽  
Nonstructural Genes

We found and genetically described two novel SARS-like coronaviruses in feces and oral swabs of the greater (R. ferrumequinum) and the lesser (R. hipposideros) horseshoe bats in southern regions of Russia. The viruses, named Khosta-1 and Khosta-2, together with related viruses from Bulgaria and Kenya, form a separate phylogenetic lineage. We found evidence of recombination events in the evolutionary history of Khosta-1, which involved the acquisition of the structural proteins S, E, and M, as well as the nonstructural genes ORF3, ORF6, ORF7a, and ORF7b, from a virus that is related to the Kenyan isolate BtKY72. The examination of bats by RT-PCR revealed that 62.5% of the greater horseshoe bats in one of the caves were positive for Khosta-1 virus, while its overall prevalence was 14%. The prevalence of Khosta-2 was 1.75%. Our results show that SARS-like coronaviruses circulate in horseshoe bats in the region, and we provide new data on their genetic diversity.

Comparative mitochondrial phylogeography of two legless lizards (Pygopodidae) from Queensland’s fragmented woodlands

2020 ◽  
Vol 66 (3-4) ◽  
pp. 142-150
Author(s):  
Jessica Worthington Wilmer ◽  
Andrew P. Amey ◽  
Carmel McDougall ◽  
Melanie Venz ◽  
Stephen Peck ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Evolutionary History ◽  
The West ◽  
European Settlement ◽  
Low Genetic Diversity ◽  
Eastern Australia ◽  
Wide Range ◽  
History Of ◽  
Open Forests ◽  
Fossorial Species

Sclerophyll woodlands and open forests once covered vast areas of eastern Australia, but have been greatly fragmented and reduced in extent since European settlement. The biogeographic and evolutionary history of the biota of eastern Australia’s woodlands also remains poorly known, especially when compared to rainforests to the east, or the arid biome to the west. Here we present an analysis of patterns of mitochondrial genetic diversity in two species of Pygopodid geckos with distributions centred on the Brigalow Belt Bioregion of eastern Queensland. One moderately large and semi-arboreal species, Paradelma orientalis, shows low genetic diversity and no clear geographic structuring across its wide range. In contrast a small and semi-fossorial species, Delma torquata, consists of two moderately divergent clades, one from the ranges and upland of coastal areas of south-east Queensland, and other centred in upland areas further inland. These data point to varying histories of geneflow and refugial persistance in eastern Australia’s vast but now fragmented open woodlands. The Carnarvon Ranges of central Queensland are also highlighted as a zone of persistence for cool and/or wet-adapted taxa, however the evolutionary history and divergence of most outlying populations in these mountains remains unstudied.

Study of molecular genetic diversity and evolutionary history of medicinally important endangered genus Chlorophytum using DNA barcodes

2016 ◽  
Vol 65 ◽  
pp. 245-252 ◽  
Author(s):  
Swapnil M. Patil ◽  
Niraj R. Rane ◽  
Avinash A. Adsul ◽  
Avinash R. Gholave ◽  
Shrirang R. Yadav ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Evolutionary History ◽  
Molecular Genetic ◽  
Dna Barcodes ◽  
Molecular Genetic Diversity ◽  
History Of

scholarly journals Sequence Diversity in the Tetraploid Zea perennis and the Closely Related Diploid Z. diploperennis: Insights From Four Nuclear Loci

Genetics ◽  
2001 ◽  
Vol 158 (1) ◽  
pp. 401-412 ◽  
Author(s):  
Peter Tiffin ◽  
Brandon S Gaut
Keyword(s):  
Genetic Diversity ◽  
Evolutionary History ◽  
Molecular Data ◽  
Sequence Diversity ◽  
Common Phenomenon ◽  
Factors Associated ◽  
History Of ◽  
Recent Origin ◽  
Nuclear Loci ◽  
Few Data

Abstract Polyploidy has been an extremely common phenomenon in the evolutionary history of angiosperms. Despite this there are few data available to evaluate the effects of polyploidy on genetic diversity and to compare the relative effects of drift and selection in polyploids and related diploids. We investigated DNA sequence diversity at four nuclear loci (adh1, glb1, c1, and waxy) from the tetraploid Zea perennis and the closely related diploid Z. diploperennis. Contrary to expectations, we detected no strong evidence for greater genetic diversity in the tetraploid, or for consistent differences in the effects of either drift or selection between the tetraploid and the diploid. Our failure to find greater genetic diversity in Z. perennis may result from its relatively recent origin or demographic factors associated with its origin. In addition to comparing genetic diversity in the two species, we constructed genealogies to infer the evolutionary origin of Z. perennis. Although these genealogies are equivocal regarding the mode of origin, several aspects of these genealogies support an autotetraploid origin. Consistent with previous molecular data the genealogies do not, however, support the division of Zea into two sections, the section Zea and the section Luxuriantes.

scholarly journals SARS-like coronaviruses in horseshoe bats (Rhinolophus spp.) in Russia, 2020.

2021 ◽  
Author(s):  
Sergey V Alkhovsky ◽  
Sergey V Lenshin ◽  
Alexey V Romashin ◽  
Tatyana V Vishnevskaya ◽  
Oleg I Vyshemirsky ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Evolutionary History ◽  
Southern Region ◽  
Structural Proteins ◽  
Rt Pcr ◽  
Phylogenetic Lineage ◽  
History Of ◽  
Horseshoe Bats ◽  
Nonstructural Genes

We found and genetically described two novel SARS-like coronaviruses in feces and oral swabs of the great (R. ferrumequinum) and the lesser (R. hipposideros) horseshoe bats in southern region of Russia. The viruses, named Khosta-1 and Khosta-2, together with related viruses from Bulgaria and Kenya, form a separate phylogenetic lineage. We found an evidence of recombination events in evolutionary history of Khosta-1, which involved the acquisition of structural proteins S, E, and M as well as nonstructural genes ORF3, ORF6, ORF7a, and ORF7b from a virus that is closely related to Kenyan isolate BtKY72. Examination of bats by RT-PCR revealed that 62,5% of great horseshoe bats in one of the caves were positive for Khosta-1 virus while its overall prevalence was 14%. The prevalence of Khosta-2 was 1,75%. Our results show that SARS-like coronaviruses circulate in horseshoe bats in the region and provide a new data on their genetic diversity.

scholarly journals Most Compositae (Asteraceae) are descendants of a paleohexaploid and all share a paleotetraploid ancestor with the Calyceraceae

2016 ◽  
Author(s):  
Michael S. Barker ◽  
Zheng Li ◽  
Thomas I. Kidder ◽  
Chris R. Reardon ◽  
Zhao Lai ◽  
...  
Keyword(s):  
Gene Family ◽  
Linkage Map ◽  
Evolutionary History ◽  
Genome Duplication ◽  
Nuclear Gene ◽  
Flowering Plants ◽  
The Family ◽  
History Of ◽  
Phylogenomic Analyses

AbstractPremise of the studyLike many other flowering plants, members of the Compositae (Asteraceae) have a polyploid ancestry. Previous analyses found evidence for an ancient duplication or possibly triplication in the early evolutionary history of the family. We sought to better place this paleopolyploidy in the phylogeny and assess its nature.MethodsWe sequenced new transcriptomes for Barnadesia, the lineage sister to all other Compositae, and four representatives of closely related families. Using a recently developed algorithm, MAPS, we analyzed nuclear gene family phylogenies for evidence of paleopolyploidy.Key resultsWe found that the previously recognized Compositae paleopolyploidy is also in the ancestry of the Calyceraceae. Our phylogenomic analyses uncovered evidence for a successive second round of genome duplication among all sampled Compositae except Barnadesia.ConclusionsOur analyses of new samples with new tools provide a revised view of paleopolyploidy in the Compositae. Together with results from a high density Lactuca linkage map, our results suggest that the Compositae and Calyceraceae have a common paleotetraploid ancestor and most Compositae are descendants of a paleohexaploid. Although paleohexaploids have been previously identified, this is the first example where the paleotetraploid and paleohexaploid lineages have survived over tens of millions of years. The complex polyploidy in the ancestry of the Compositae and Calyceraceae represents a unique opportunity to study the long-term evolutionary fates and consequences of different ploidal levels.

scholarly journals Genetic diversity and evolutionary history of Korean isolates of severe fever with thrombocytopenia syndrome virus from 2013–2016

2020 ◽  
Vol 165 (11) ◽  
pp. 2599-2603
Author(s):  
Mi-ran Yun ◽  
Jungsang Ryou ◽  
Wooyoung Choi ◽  
Joo-Yeon Lee ◽  
Sun-Whan Park ◽  
...  
Keyword(s):  
Infectious Disease ◽  
Genetic Diversity ◽  
Amino Acid ◽  
Evolutionary History ◽  
Public Database ◽  
Korean Strain ◽  
Future Studies ◽  
History Of ◽  
Phylogeny And Evolution ◽  
Severe Fever

AbstractSevere fever with thrombocytopenia syndrome (SFTS) is caused by SFTS virus (SFTSV). Although SFTS originated in China, it is an emerging infectious disease with prevalence confirmed in Japan, Korea, and Vietnam. The full-length genomes of 51 Korean SFTSV isolates from 2013 to 2016 were sequenced, and the sequences were deposited into a public database (GenBank) and analyzed to elucidate the phylogeny and evolution of the virus. Although most of the Korean SFTSV isolates were closely related to previously reported Japanese isolates, some were closely related to previously reported Chinese isolates. We identified one Korean strain that appears to have resulted from multiple inter-lineage reassortments. Several nucleotide and amino acid variations specific to the Korean isolates were identified. Future studies should focus on how these variations affect virus pathogenicity and evolution.

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