scholarly journals Genome-Wide Identification, Evolutionary, and Expression Analyses of Histone H3 Variants in Plants

2015 ◽  
Vol 2015 ◽  
pp. 1-7 ◽  
Author(s):  
Jinteng Cui ◽  
Zhanlu Zhang ◽  
Yang Shao ◽  
Kezhong Zhang ◽  
Pingsheng Leng ◽  
...  
Keyword(s):  
Chromosome Segregation ◽  
Posttranslational Modifications ◽  
Evolutionary History ◽  
Histone H3 ◽  
Purifying Selection ◽  
Histone Variants ◽  
Nucleosome Structure ◽  
Genome Wide ◽  
Eukaryotic Species ◽  
History Of

Histone variants alter the nucleosome structure and play important roles in chromosome segregation, transcription, DNA repair, and sperm compaction. Histone H3 is encoded by many genes in most eukaryotic species and is the histone that contains the largest variety of posttranslational modifications. Compared with the metazoan H3 variants, little is known about the complex evolutionary history of H3 variants proteins in plants. Here, we study the identification, evolutionary, and expression analyses of histone H3 variants from genomes in major branches in the plant tree of life. Firstly we identified all the histone three related (HTR) genes from the examined genomes, then we classified the four groups variants: centromeric H3, H3.1, H3.3 and H3-like, by phylogenetic analysis, intron information, and alignment. We further demonstrated that the H3 variants have evolved under strong purifying selection, indicating the conservation of HTR proteins. Expression analysis revealed that the HTR has a wide expression profile in maize and rice development and plays important roles in development.

scholarly journals Evolutionary History of Mammalian Transposons Determined by Genome-wide Defragmentation

2005 ◽  
Vol preprint (2007) ◽  
pp. e137
Author(s):  
Joti Giordano ◽  
Yongchao Ge ◽  
Yevgeniy Gelfand ◽  
Gyorgy Abrusan ◽  
Gary Benson ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Genome Wide ◽  
History Of

scholarly journals Identification of Histone H3 (HH3) Genes in Gossypium hirsutum Revealed Diverse Expression During Ovule Development and Stress Responses

Genes ◽  
2019 ◽  
Vol 10 (5) ◽  
pp. 355
Author(s):  
Ghulam Qanmber ◽  
Faiza Ali ◽  
Lili Lu ◽  
Huijuan Mo ◽  
Shuya Ma ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Stress Responses ◽  
Functional Divergence ◽  
Histone H3 ◽  
Purifying Selection ◽  
Histone Variants ◽  
Biological Information ◽  
Amino Acid Residues ◽  
Sequence Logos ◽  
Indole 3 Acetic Acid

Histone acts as the core for nucleosomes and is a key protein component of chromatin. Among different histone variants, histone H3 (HH3) variants have been reported to play vital roles in plant development. However, biological information and evolutionary relationships of HH3 genes in cotton remain to be elucidated. The current study identified 34 HH3 genes in Gossypium hirsutum. Phylogenetic analysis classified HH3 genes of 19 plant species into eight distinct clades. Sequence logos analysis among Arabidopsis, rice, and G. hirsutum amino acid residues showed higher conservation in amino acids. Using collinearity analysis, we identified 81 orthologous/paralogous gene pairs among the four genomes (A, D, At, and Dt) of cotton. Further, orthologous/paralogous and the Ka/Ks ratio demonstrated that cotton HH3 genes experienced strong purifying selection pressure with restricted functional divergence resulting from segmental and whole genome duplication. Expression pattern analysis indicated that GhHH3 genes were preferentially expressed in cotton ovule tissues. Additionally, GhHH3 gene expression can be regulated by abiotic stresses (cold, heat, sodium chloride (NaCl), and polyethylene glycol (PEG)) and phytohormonal (brassinolide (BL), gibberellic acid (GA), indole-3-acetic acid (IAA), salicylic acid (SA), and methyl jasmonate (MeJA)) treatments, suggesting that GhHH3 genes might play roles in abiotic and hormone stress resistance. Taken together, this work provides important information to decipher complete molecular and physiological functions of HH3 genes in cotton.

scholarly journals Early diversification and permeable species boundaries in the Mediterranean firs

2019 ◽  
Vol 125 (3) ◽  
pp. 495-507 ◽  
Author(s):  
Francisco Balao ◽  
María Teresa Lorenzo ◽  
José Manuel Sánchez-Robles ◽  
Ovidiu Paun ◽  
Juan Luis García-Castaño ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Evolutionary History ◽  
Taxonomic Status ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Early Diversification ◽  
Genome Wide ◽  
History Of ◽  
The Mediterranean ◽  
Independent Species

Abstract Background and Aims Inferring the evolutionary relationships of species and their boundaries is critical in order to understand patterns of diversification and their historical drivers. Despite Abies (Pinaceae) being the second most diverse group of conifers, the evolutionary history of Circum-Mediterranean firs (CMFs) remains under debate. Methods We used restriction site-associated DNA sequencing (RAD-seq) on all proposed CMF taxa to investigate their phylogenetic relationships and taxonomic status. Key Results Based on thousands of genome-wide single nucleotide polymorphisms (SNPs), we present here the first formal test of species delimitation, and the first fully resolved, complete species tree for CMFs. We discovered that all previously recognized taxa in the Mediterranean should be treated as independent species, with the exception of Abies tazaotana and Abies marocana. An unexpectedly early pulse of speciation in the Oligocene–Miocene boundary is here documented for the group, pre-dating previous hypotheses by millions of years, revealing a complex evolutionary history encompassing both ancient and recent gene flow between distant lineages. Conclusions Our phylogenomic results contribute to shed light on conifers’ diversification. Our efforts to resolve the CMF phylogenetic relationships help refine their taxonomy and our knowledge of their evolution.

scholarly journals Phylogenomic Reconstruction of the Neotropical Poison Frogs (Dendrobatidae) and Their Conservation

Diversity ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 126 ◽  
Author(s):  
Wilson X. Guillory ◽  
Morgan R. Muell ◽  
Kyle Summers ◽  
Jason L. Brown
Keyword(s):  
Bayesian Methods ◽  
Evolutionary History ◽  
Conservation Status ◽  
Nuclear Data ◽  
Nuclear Markers ◽  
Poison Frog ◽  
Sequence Capture ◽  
Genome Wide ◽  
Frog Species ◽  
History Of

The evolutionary history of the Dendrobatidae, the charismatic Neotropical poison frog family, remains in flux, even after a half-century of intensive research. Understanding the evolutionary relationships between dendrobatid genera and the larger-order groups within Dendrobatidae is critical for making accurate assessments of all aspects of their biology and evolution. In this study, we provide the first phylogenomic reconstruction of Dendrobatidae with genome-wide nuclear markers known as ultraconserved elements. We performed sequence capture on 61 samples representing 33 species across 13 of the 16 dendrobatid genera, aiming for a broadly representative taxon sample. We compare topologies generated using maximum likelihood and coalescent methods and estimate divergence times using Bayesian methods. We find most of our dendrobatid tree to be consistent with previously published results based on mitochondrial and low-count nuclear data, with notable exceptions regarding the placement of Hyloxalinae and certain genera within Dendrobatinae. We also characterize how the evolutionary history and geographic distributions of the 285 poison frog species impact their conservation status. We hope that our phylogeny will serve as a backbone for future evolutionary studies and that our characterizations of conservation status inform conservation practices while highlighting taxa in need of further study.

scholarly journals Papio cynocephalus Endogenous Retrovirus among Old World Monkeys: Evidence for Coevolution and Ancient Cross-Species Transmissions

2000 ◽  
Vol 74 (3) ◽  
pp. 1578-1586 ◽  
Author(s):  
Rui Mang ◽  
Jolanda Maas ◽  
Antoinette C. van der Kuyl ◽  
Jaap Goudsmit
Keyword(s):  
Evolutionary History ◽  
Germ Line ◽  
Purifying Selection ◽  
Endogenous Retrovirus ◽  
New World Monkeys ◽  
Papio Cynocephalus ◽  
Genetic Characteristics ◽  
Old World ◽  
Colobus Badius ◽  
History Of

ABSTRACT To study the evolutionary history of Papio cynocephalus endogenous retrovirus (PcEV), we analyzed the distribution and genetic characteristics of PcEV among 17 different species of primates. The viral pol-env and long terminal repeat and untranslated region (LTR-UTR) sequences could be recovered from all Old World species of the papionin tribe, which includes baboons, macaques, geladas, and mangabeys, but not from the New World monkeys and hominoids we tested. The Old World genera Cercopithecus andMiopithecus hosted either a PcEV variant with an incomplete genome or a virus with substantial mismatches in the LTR-UTR. A complete PcEV was found in the genome of Colobus guereza—but not in Colobus badius—with a copy number of 44 to 61 per diploid genome, comparable to that seen in papionins, and with a sequence most closely related to a virus of the papionin tribe. Analysis of evolutionary distances among PcEV sequences for synonymous and nonsynonymous sites indicated that purifying selection was operational during PcEV evolution. Phylogenetic analysis suggested that possibly two subtypes of PcEV entered the germ line of a common ancestor of the papionins and subsequently coevolved with their hosts. One strain of PcEV was apparently transmitted from a papionin ancestor to an ancestor of the central African lowland C. guereza.

scholarly journals The complex evolution of the HSP70 gene family

2020 ◽  
Author(s):  
Er-meng Yu ◽  
Tatsuki Yoshinaga ◽  
Frank L. Jalufka ◽  
Hashimul Ehsan ◽  
David B. Mark Welch ◽  
...  
Keyword(s):  
Heat Shock ◽  
Evolutionary History ◽  
Brachionus Plicatilis ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Evolutionary Genetics ◽  
Purifying Selection ◽  
Hsp70 Family ◽  
History Of ◽  
Species Specific

AbstractThe 70-kDa heat shock protein (HSP70) family contains several isoforms localized in different subcellular compartments. The cytosolic isoforms have been classified into stress-inducible HSP70s and constitutive heat shock cognates (HSC70s), but occasional reports of “constitutive HSP70s” and the lack of cross-phylum comparisons have been a source of confusion in the evolution of the metazoan HSP70 family. Here we provide novel insights into the evolutionary history of this important molecular chaperone. We first cloned two HSP70 genes from the rotifer Brachionus plicatilis, an emerging model in evolutionary genetics, and confirmed their stress inducibility. Subsequent phylogenetic analyses of 100 full-length HSP70 family member genes revealed an ancient duplication that gave rise to two lineages from which all metazoan cytosolic HSP70s descend. One lineage contains a relatively small number of Lophotrochozoan and Ecdysozoan genes, none of which have been shown to be constitutively expressed. The second included both inducible and constitutive genes from diverse phyla. Species-specific duplications are present in both lineages, and in the second there are well-supported phylum-specific clades for Rotifera, Nematoda, and Chordata. Some genes in this lineage have likely independently acquired stress inducibility, which may explain the sporadic distribution of genes designated as “HSP70” or “HSC70” in previous analyses. Consistent with the history of diversification within each group, stress-inducible members of the second lineage show lower purifying selection pressure compared to constitutive members. These results illustrate the evolutionary history of the HSP70 family independent from their expression patterns, encouraging the development of new nomenclature based on evolutionary history.

scholarly journals Killer whale genomes reveal a complex history of recurrent admixture and vicariance

2019 ◽  
Author(s):  
Andrew D. Foote ◽  
Michael D. Martin ◽  
Marie Louis ◽  
George Pacheco ◽  
Kelly M. Robertson ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Killer Whale ◽  
Natural Populations ◽  
Major Axis ◽  
Glacial Cycle ◽  
Genome Wide ◽  
Complex Population ◽  
Genome Wide Data ◽  
History Of ◽  
Global Population

AbstractReconstruction of the demographic and evolutionary history of populations assuming a consensus tree-like relationship can mask more complex scenarios, which are prevalent in nature. An emerging genomic toolset, which has been most comprehensively harnessed in the reconstruction of human evolutionary history, enables molecular ecologists to elucidate complex population histories. Killer whales have limited extrinsic barriers to dispersal and have radiated globally, and are therefore a good candidate model for the application of such tools. Here, we analyse a global dataset of killer whale genomes in a rare attempt to elucidate global population structure in a non-human species. We identify a pattern of genetic homogenisation at lower latitudes and the greatest differentiation at high latitudes, even between currently sympatric lineages. The processes underlying the major axis of structure include high drift at the edge of species’ range, likely associated with founder effects and allelic surfing during post-glacial range expansion. Divergence between Antarctic and non-Antarctic lineages is further driven by ancestry segments with up to four-fold older coalescence time than the genome-wide average; relicts of a previous vicariance during an earlier glacial cycle. Our study further underpins that episodic gene flow is ubiquitous in natural populations, and can occur across great distances and after substantial periods of isolation between populations. Thus, understanding the evolutionary history of a species requires comprehensive geographic sampling and genome-wide data to sample the variation in ancestry within individuals.

scholarly journals The complex evolution of the metazoan HSP70 gene family

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Er-meng Yu ◽  
Tatsuki Yoshinaga ◽  
Frank L. Jalufka ◽  
Hashimul Ehsan ◽  
David B. Mark Welch ◽  
...  
Keyword(s):  
Heat Shock ◽  
Molecular Chaperones ◽  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Evolutionary Relationship ◽  
Purifying Selection ◽  
Hsp70 Family ◽  
Number Of Genes ◽  
History Of ◽  
Species Specific

AbstractThe metazoan 70-kDa heat shock protein (HSP70) family contains several members localized in different subcellular compartments. The cytosolic members have been classified into inducible HSP70s and constitutive heat shock cognates (HSC70s), but their distinction and evolutionary relationship remain unclear because of occasional reports of “constitutive HSP70s” and the lack of cross-phylum comparisons. Here we provide novel insights into the evolution of these important molecular chaperones. Phylogenetic analyses of 125 full-length HSP70s from a broad range of phyla revealed an ancient duplication that gave rise to two lineages from which all metazoan cytosolic HSP70s descend. One lineage (A) contains a relatively small number of genes from many invertebrate phyla, none of which have been shown to be constitutively expressed (i.e., either inducible or unknown). The other lineage (B) included both inducible and constitutive genes from diverse phyla. Species-specific duplications are present in both lineages, and Lineage B contains well-supported phylum-specific clades for Platyhelminthes, Rotifera, Nematoda, Porifera/Cnidaria, and Chordata. Some genes in Lineage B have likely independently acquired inducibility, which may explain the sporadic distribution of “HSP70” or “HSC70” in previous phylogenetic analyses. Consistent with the diversification history within each group, inducible members show lower purifying selection pressure compared to constitutive members. These results illustrate the evolutionary history of the HSP70 family, encouraging us to propose a new nomenclature: “HSP70 + subcellular localization + linage + copy number in the organism + inducible or constitutive, if known.” e.g., HSP70cA1i for cytosolic Lineage A, copy 1, inducible.

scholarly journals The First Co-Opted Endogenous Foamy Viruses and the Evolutionary History of Reptilian Foamy Viruses

Viruses ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 641 ◽  
Author(s):  
Pakorn Aiewsakun ◽  
Peter Simmonds ◽  
Aris Katzourakis
Keyword(s):  
Evolutionary History ◽  
Phylogenetic Analyses ◽  
Foamy Virus ◽  
Purifying Selection ◽  
The Other ◽  
Cellular Functions ◽  
Foamy Viruses ◽  
History Of ◽  
Flanking Sequences ◽  
Reading Frames

A recent study reported the discovery of an endogenous reptilian foamy virus (FV), termed ERV-Spuma-Spu, found in the genome of tuatara. Here, we report two novel reptilian foamy viruses also identified as endogenous FVs (EFVs) in the genomes of panther gecko (ERV-Spuma-Ppi) and Schlegel’s Japanese gecko (ERV-Spuma-Gja). Their presence indicates that FVs are capable of infecting reptiles in addition to mammals, amphibians, and fish. Numerous copies of full length ERV-Spuma-Spu elements were found in the tuatara genome littered with in-frame stop codons and transposable elements, suggesting that they are indeed endogenous and are not functional. ERV-Spuma-Ppi and ERV-Spuma-Gja, on the other hand, consist solely of a foamy virus-like env gene. Examination of host flanking sequences revealed that they are orthologous, and despite being more than 96 million years old, their env reading frames are fully coding competent with evidence for strong purifying selection to maintain expression and for them likely being transcriptionally active. These make them the oldest EFVs discovered thus far and the first documented EFVs that may have been co-opted for potential cellular functions. Phylogenetic analyses revealed a complex virus–host co-evolutionary history and cross-species transmission routes of ancient FVs.

scholarly journals A genome‐wide linkage map for the house sparrow ( Passer domesticus ) provides insights into the evolutionary history of the avian genome

2020 ◽  
Vol 20 (2) ◽  
pp. 544-559 ◽  
Author(s):  
Ingerid J. Hagen ◽  
Sigbjørn Lien ◽  
Anna M. Billing ◽  
Tore O. Elgvin ◽  
Cassandra Trier ◽  
...  
Keyword(s):  
Linkage Map ◽  
Evolutionary History ◽  
House Sparrow ◽  
Passer Domesticus ◽  
Genome Wide ◽  
A Genome ◽  
Avian Genome ◽  
History Of
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