scholarly journals Evolutionary History of LTR Retrotransposon Chromodomains in Plants

2012 ◽  
Vol 2012 ◽  
pp. 1-17 ◽  
Author(s):  
Anton Novikov ◽  
Georgiy Smyshlyaev ◽  
Olga Novikova

Chromodomain-containing LTR retrotransposons are one of the most successful groups of mobile elements in plant genomes. Previously, we demonstrated that two types of chromodomains (CHDs) are carried by plant LTR retrotransposons. Chromodomains from group I (CHD_I) were detected only in Tcn1-like LTR retrotransposons from nonseed plants such as mosses (including the model moss species Physcomitrella) and lycophytes (the Selaginella species). LTR retrotransposon chromodomains from group II (CHD_II) have been described from a wide range of higher plants. In the present study, we performed computer-based mining of plant LTR retrotransposon CHDs from diverse plants with an emphasis on spike-moss Selaginella. Our extended comparative and phylogenetic analysis demonstrated that two types of CHDs are present only in the Selaginella genome, which puts this species in a unique position among plants. It appears that a transition from CHD_I to CHD_II and further diversification occurred in the evolutionary history of plant LTR retrotransposons at approximately 400 MYA and most probably was associated with the evolution of chromatin organization.

2020 ◽  
Author(s):  
Natasha Avila Bertocchi ◽  
Fabiano Pimentel Torres ◽  
Maríndia Deprá ◽  
Vera Lúcia da Silva Valente

AbstractLTR-retrotransposons are structurally similar to retroviruses, as they possess the enzymes reverse transcriptase, Ribonuclease H, integrase, proteinase, and the gag gene and are flanked by long terminal repeats (LTRs). The 412/mdg1 lineage, belonging to the Ty3/Gypsy group, consists of the TEs 412, mdg1, stalker, pilgrim, and blood. The 412/mdg1 lineage is distinguished from the others in the gypsy group in that it has small ORFs at the beginning of the TE and is highly similar to the pol ORF among the TEs that make up the lineage. In this study, our aim was to elucidate the evolutionary history of the 412/mdg1 lineage in the 127 dipteran genomes available to date, and the characteristics of the sequences in each genome. We used the canonical TE 412 probe described in Drosophila melanogaster as the query. We found sequences homologous to the 412/mdg1 lineage restricted to the suborder Brachycera. These sequences are widely distributed in drosophilids but are also present in other groups of flies. We note the presence of the 412/mg1 lineage in tsetse flies (Glossina). Furthermore, our results showed an elaborate evolutionary history for the pol ORF in the 412/mdg1 lineage of the LTR-Retrotransposon.


2021 ◽  
Author(s):  
Caitlin Cherryh ◽  
Bui Quang Minh ◽  
Rob Lanfear

AbstractMost phylogenetic analyses assume that the evolutionary history of an alignment (either that of a single locus, or of multiple concatenated loci) can be described by a single bifurcating tree, the so-called the treelikeness assumption. Treelikeness can be violated by biological events such as recombination, introgression, or incomplete lineage sorting, and by systematic errors in phylogenetic analyses. The incorrect assumption of treelikeness may then mislead phylogenetic inferences. To quantify and test for treelikeness in alignments, we develop a test statistic which we call the tree proportion. This statistic quantifies the proportion of the edge weights in a phylogenetic network that are represented in a bifurcating phylogenetic tree of the same alignment. We extend this statistic to a statistical test of treelikeness using a parametric bootstrap. We use extensive simulations to compare tree proportion to a range of related approaches. We show that tree proportion successfully identifies non-treelikeness in a wide range of simulation scenarios, and discuss its strengths and weaknesses compared to other approaches. The power of the tree-proportion test to reject non-treelike alignments can be lower than some other approaches, but these approaches tend to be limited in their scope and/or the ease with which they can be interpreted. Our recommendation is to test treelikeness of sequence alignments with both tree proportion and mosaic methods such as 3Seq. The scripts necessary to replicate this study are available at https://github.com/caitlinch/treelikeness


2020 ◽  
Vol 66 (3-4) ◽  
pp. 142-150
Author(s):  
Jessica Worthington Wilmer ◽  
Andrew P. Amey ◽  
Carmel McDougall ◽  
Melanie Venz ◽  
Stephen Peck ◽  
...  

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.


Paleobiology ◽  
1992 ◽  
Vol 18 (1) ◽  
pp. 50-79 ◽  
Author(s):  
Benjamin J. Greenstein

The class Echinoidea apparently originated during the Ordovician Period and diversified slowly through the Paleozoic Era. The clade then mushroomed in diversity beginning in Late Triassic time and continued expanding into the present. Although this evolutionary history is generally accepted, the taphonomic overprint affecting it has not been explored. To gain a more accurate perception of the evolutionary history of the group, I have compared the diversity history of the family Cidaridae (Echinodermata: Echinoidea) with the preservational style of fossil type species using literature-derived data. The Cidaridae apparently originated in Middle Triassic time and diversified slowly through the Neocomian (Early Cretaceous). Diversity was maintained through the remainder of the Cretaceous and Tertiary Periods, reflecting the diversity history of the subclass. Characterization of the preservational style of type fossil material for the family revealed the following breakdown of preservational states: 60% of species were described on the basis of disarticulated skeletal material, primarily spines; 20% based on intact coronas denuded of spines, apical system, Aristotle's lantern and peristomial plates; 10% based on large coronal fragments; and 10% based on other skeletal elements. This distribution may represent the effect of a disarticulation threshold on the condition of echinoid carcasses before final burial and suggests that preservation of intact specimens may be very unlikely. For cidaroids, previous work has suggested that this threshold is likely to be reached after 7 days of decay.Comparison of the diversity history of the Cidaridae with the preservation data reveals that characteristic patterns of taphonomic overprint have affected the group since its origination in Middle Triassic time, and the nature of that overprint has changed over time: the early diversity history of the group is characterized by occurrences of fragmented fossil material, with spines predominant; further radiation of the group in mid-Jurassic time coincided with an increase in modes of preservation, ranging between exceptionally well-preserved material and disarticulated skeletal elements. Finally, type material is more rarely described from younger stratigraphic intervals (Miocene–Pleistocene) and consists predominantly of disarticulated skeletal elements and coronal fragments larger than an interambulacrum in size. Intact, denuded coronas are noticeably lacking.The number of type species of Cidaridae described in each stratigraphic interval has not been consistent during post-Paleozoic time. Middle Triassic, Malm (Upper Jurassic), Senonian (Upper Cretaceous) and Eocene series yielded significantly (α = .05) higher numbers of type specimens per million years, while the Lias (Lower Jurassic), Dogger (Mid-Jurassic), Lower Cretaceous and Paleocene yielded significantly (α = .05) lower numbers of type specimens per million years. This may be the result of a combination of taxonomic, sampling, and geographical biases.


Author(s):  
Chao Zhang ◽  
Leilei Zhang ◽  
Dongdong Wang ◽  
Haoli Ma ◽  
Bailin Liu ◽  
...  

Glycoside Hydrolase 3 (GH3) is a phytohormone-responsive family of genes that has been found in many plant species. It is implicated in the biological activity of indolacetic (IAA) and jasmonic acids (JA), and also affects plant growth and developmental processes and some stresses. In this study, GH3 genes were identified in 48 plants, which belong to algae, moss, fern, gymnosperm and angiosperm. No GH3 representative gene has been found in algae, and our research identified 4 genes in mosses, 19 in ferns, 7 in gymnosperms, and numerous in Angiosperms. The results showed that GH3 genes mainly occur in seed plants. Phylogenetic analysis of all GH3 genes showed three separate clades. Group I was related to JA adenylation, group II was related to IAA adenylation, and group III was separated from group II but the function was not clear. The structure of GH3 protein indicated highly conserved sequence in the plant kingdom. The analysis of JA-adenylation related to gene expression of GH3 in potato (Solanum tuberosum) showed that StGH3.12 highly responded to Methyl Jasmonate (MeJA) treatment. Expression levels of StGH3.1, StGH3.11, and StGH3.12 were high in flower and StGH3.11 expression was also high in stolon. Our research revealed the evolution of the GH3 family, which is useful for studying the precise function about JA-adenylation GH3 genes in S. tuberosum under development and biotic stresses.


2019 ◽  
Vol 36 (11) ◽  
pp. 2604-2619 ◽  
Author(s):  
Elodie Laine ◽  
Yasaman Karami ◽  
Alessandra Carbone

Abstract The systematic and accurate description of protein mutational landscapes is a question of utmost importance in biology, bioengineering, and medicine. Recent progress has been achieved by leveraging on the increasing wealth of genomic data and by modeling intersite dependencies within biological sequences. However, state-of-the-art methods remain time consuming. Here, we present Global Epistatic Model for predicting Mutational Effects (GEMME) (www.lcqb.upmc.fr/GEMME), an original and fast method that predicts mutational outcomes by explicitly modeling the evolutionary history of natural sequences. This allows accounting for all positions in a sequence when estimating the effect of a given mutation. GEMME uses only a few biologically meaningful and interpretable parameters. Assessed against 50 high- and low-throughput mutational experiments, it overall performs similarly or better than existing methods. It accurately predicts the mutational landscapes of a wide range of protein families, including viral ones and, more generally, of much conserved families. Given an input alignment, it generates the full mutational landscape of a protein in a matter of minutes. It is freely available as a package and a webserver at www.lcqb.upmc.fr/GEMME/.


GigaScience ◽  
2021 ◽  
Vol 10 (5) ◽  
Author(s):  
Mengni Liu ◽  
Jianyu Chen ◽  
Xin Wang ◽  
Chengwei Wang ◽  
Xiaolong Zhang ◽  
...  

Abstract Background Multi-region sequencing (MRS) has been widely used to analyze intra-tumor heterogeneity (ITH) and cancer evolution. However, comprehensive analysis of mutational data from MRS is still challenging, necessitating complicated integration of a plethora of computational and statistical approaches. Findings Here, we present MesKit, an R/Bioconductor package that can assist in characterizing genetic ITH and tracing the evolutionary history of tumors based on somatic alterations detected by MRS. MesKit provides a wide range of analysis and visualization modules, including ITH evaluation, metastatic route inference, and mutational signature identification. In addition, MesKit implements an auto-layout algorithm to generate phylogenetic trees based on somatic mutations. The application of MesKit for 2 reported MRS datasets of hepatocellular carcinoma and colorectal cancer identified known heterogeneous features and evolutionary patterns, together with potential driver events during cancer evolution. Conclusions In summary, MesKit is useful for interpreting ITH and tracing evolutionary trajectory based on MRS data. MesKit is implemented in R and available at https://bioconductor.org/packages/MesKit under the GPL v3 license.


2020 ◽  
Vol 42 (4) ◽  
pp. 14-18
Author(s):  
Hiroaki Adachi ◽  
Aleksandra Białas ◽  
Sophien Kamoun

Plants can get sick too. In fact, they get infected by all types of microbes and little critters. But plants have evolved an effective immune system to fight off pathogen invasion. Amazingly, nearly every single plant cell is able to protect itself and its neighbours against infections. The plant immune system gets switched on when one of its many immune receptors matches a ligand in the pathogen. As a consequence of a long evolutionary history of fighting off pathogens, immune receptors are now encoded by hundreds of genes that populate the majority of plant genomes. Understanding how the plant immune system functions and how it has evolved can give invaluable insights that would benefit modern agriculture and help breeding disease-resistant crops.


2021 ◽  
Author(s):  
Dhanushya Ramachandran ◽  
Cynthia D Huebner ◽  
Mark Daly ◽  
Jasmine Haimovitz ◽  
Thomas Swale ◽  
...  

The invasive Japanese stiltgrass (Microstegium vimineum) affects a wide range of ecosystems and threatens biodiversity across the eastern USA. However, the mechanisms underlying rapid adaptation, plasticity, and epigenetics in the invasive range are largely unknown. We present a chromosome-level assembly for M. vimineum to investigate genome dynamics, evolution, adaptation, and the genomics of phenotypic plasticity. We generated a 1.12 Gb genome with scaffold N50 length of 53.44 Mb respectively, taking a de novo assembly approach that combined PacBio and Dovetail Genomics Omni-C sequencing. The assembly contains 23 pseudochromosomes, representing 99.96% of the genome. BUSCO assessment indicated that 80.3% of Poales gene groups are present in the assembly. The genome is predicted to contain 39,604 protein-coding genes, of which 26,288 are functionally annotated. Furthermore, 66.68% of the genome is repetitive, of which unclassified (35.63%) and long terminal repeat (LTR) retrotransposons (26.90%) are predominant. Similar to other grasses, Gypsy (41.07%) and Copia (32%) are the most abundant LTR-retrotransposon families. The majority of LTR-retrotransposons are derived from a significant expansion in the past 1-2 million years, suggesting the presence of relatively young LTR-retrotransposon lineages. We find corroborating evidence from Ks plots for a stiltgrass-specific duplication event, distinct from the more ancient grass-specific duplication event. The assembly and annotation of M. vimineum will serve as an essential genomic resource facilitating studies of the invasion process, the history and consequences of polyploidy in grasses, and provides a crucial tool for natural resource managers.


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