Integrated evolutionary analysis of human miRNA gene clusters and families implicates evolutionary relationships

R2R3-MYB transcription factors (TFs) have been shown to play important roles in plants, including in development and in various stress conditions. Phylogenetic analysis showed the presence of 249 R2R3-MYB TFs in Brassica napus, called BnaR2R3-MYB TFs, clustered into 38 clades. BnaR2R3-MYB TFs were distributed on 19 chromosomes of B. napus. Sixteen gene clusters were identified. BnaR2R3-MYB TFs were characterized by motif prediction, gene structure analysis, and gene ontology. Evolutionary analysis revealed that BnaR2R3-MYB TFs are mainly formed as a result of whole-genome duplication. Orthologs and paralogs of BnaR2R3-MYB TFs were identified in B. napus, B. rapa, B. oleracea, and Arabidopsis thaliana using synteny-based methods. Purifying selection was pervasive within R2R3-MYB TFs. Kn/Ks values lower than 0.3 indicated that BnaR2R3-MYB TFs are being functionally converged. The role of gene conversion in the formation of BnaR2R3-MYB TFs was significant. Cis-regulatory elements in the upstream regions of BnaR2R3-MYB genes, miRNA targeting BnaR2R3MYB TFs, and post translational modifications were identified. Digital expression data revealed that BnaR2R3-MYB genes were highly expressed in the roots and under high salinity treatment after 24 h. BnaMYB21, BnaMYB141, and BnaMYB148 have been suggested for improving salt-tolerant B. napus. BnaR2R3-MYB genes were mostly up regulated on the 14th day post inoculation with Leptosphaeria biglobosa and L. maculan. BnaMYB150 is a candidate for increased tolerance to Leptospheria in B. napus.

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Revealing Mammalian Evolutionary Relationships by Comparative Analysis of Gene Clusters

Genome Biology and Evolution ◽

10.1093/gbe/evs032 ◽

2012 ◽

Vol 4 (4) ◽

pp. 586-601 ◽

Cited By ~ 7

Author(s):

Giltae Song ◽

Cathy Riemer ◽

Benjamin Dickins ◽

Hie Lim Kim ◽

Louxin Zhang ◽

...

Keyword(s):

Comparative Analysis ◽

Gene Clusters ◽

Evolutionary Relationships

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Recent Molecular Evolution of Human Metapneumovirus (HMPV): Subdivision of HMPV A2b Strains

Microorganisms ◽

10.3390/microorganisms8091280 ◽

2020 ◽

Vol 8 (9) ◽

pp. 1280

Author(s):

Naganori Nao ◽

Miwako Saikusa ◽

Ko Sato ◽

Tsuyoshi Sekizuka ◽

Shuzo Usuku ◽

...

Keyword(s):

Respiratory Infections ◽

Epidemiological Studies ◽

Human Metapneumovirus ◽

Evolutionary Relationships ◽

Acute Respiratory Infections ◽

Evolutionary Analysis ◽

The Novel ◽

Genome Wide ◽

A Genome

Human metapneumovirus (HMPV) is a major etiological agent of acute respiratory infections in humans. HMPV has been circulating worldwide for more than six decades and is currently divided into five agreed-upon subtypes: A1, A2a, A2b, B1, and B2. Recently, the novel HMPV subtypes A2c, A2b1, and A2b2 have been proposed. However, the phylogenetic and evolutionary relationships between these recently proposed HMPV subtypes are unclear. Here, we report a genome-wide phylogenetic and evolutionary analysis of 161 HMPV strains, including unique HMPV subtype A2b strains with a 180- or 111-nucleotide duplication in the G gene (nt-dup). Our data demonstrate that the HMPV A2b subtype contains two distinct subtypes, A2b1 and A2b2, and that the HMPV subtypes A2c and A2b2 may be different names for the same subtype. HMPV A2b strains with a nt-dup also belong to subtype A2b2. Molecular evolutionary analyses indicate that subtypes A2b1 and A2b2 diverged from subtype A2b around a decade after the subtype A2 was divided into the subtypes A2a and A2b. These data support the A2b1 and A2b2 subtypes proposed in 2012 and are essential for the unified classification of HMPV subtype A2 strains, which is important for future HMPV surveillance and epidemiological studies.

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Comparative evolutionary analysis of olfactory receptor gene clusters between humans and mice

Gene ◽

10.1016/j.gene.2004.09.025 ◽

2005 ◽

Vol 346 ◽

pp. 13-21 ◽

Cited By ~ 65

Author(s):

Yoshihito Niimura ◽

Masatoshi Nei

Keyword(s):

Olfactory Receptor ◽

Receptor Gene ◽

Gene Clusters ◽

Evolutionary Analysis ◽

Olfactory Receptor Gene

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A phylogenetic and evolutionary analysis of antimycin biosynthesis

10.1101/164145 ◽

2017 ◽

Author(s):

Rebecca Joynt ◽

Ryan F. Seipke

Keyword(s):

Gene Clusters ◽

Evolutionary Analysis ◽

Biosynthetic Pathways ◽

Mitochondrial Cytochrome ◽

Biosynthetic Gene ◽

Phosphopantetheinyl Transferase ◽

Genome Sequences ◽

Biosynthetic Gene Clusters ◽

Biogeographical Distribution ◽

Cancerous Cells

AbstractStreptomyces species and other Actinobacteria are ubiquitous in diverse environments worldwide and are the source of, or inspiration for, the majority of pharmaceuticals. The genomic era has enhanced biosynthetic understanding of these valuable chemical entities and has also provided a window into the diversity and distribution of natural product biosynthetic gene clusters. Antimycin is an inhibitor of mitochondrial cytochrome c reductase and more recently was shown to inhibit Bcl-2/Bcl-XLsrelated anti-apoptotic proteins commonly overproduced by cancerous cells. Here we identify 65 putative antimycin biosynthetic gene clusters (BGCs) in publicly available genome sequences of Actinobacteria and classify them based on the presence or absence of cluster-situated genes antP and antQ, which encode a kynureninase and phosphopantetheinyl transferase (PPTase), respectively. The majority of BGCs possess either both antP and antQ (L-form) or neither (S-form), while a minority of them lack either antP or antQ (IQ or IPform, respectively). We also evaluate the biogeographical distribution and phylogenetic relationships of antimycin producers and BGCs. We show that antimycin BGCs occur on five of the seven continents and are frequently isolated from plants and other higher organisms. We also provide evidence for two distinct phylogenetic clades of antimycin producers and gene clusters, which delineate S-form from L- and I-form BGCs. Finally, our findings suggest that the ancestral antimycin producer harboured an L-form gene cluster which was primarily propagated by vertical transmission and subsequently diversified into S-, IQ and IPform biosynthetic pathways.

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Evolutionary clustering annotation of ortho-paralogous gene in a multi species using Venn diagram visualization

International Journal of Engineering & Technology ◽

10.14419/ijet.v7i1.9.9755 ◽

2018 ◽

Vol 7 (1.9) ◽

pp. 162

Author(s):

Bipin Nair B J ◽

Sarath M S

Keyword(s):

Structural Similarity ◽

Gene Clusters ◽

Single Copy ◽

Venn Diagram ◽

Specific Gene ◽

Evolutionary Analysis ◽

Paralogous Gene ◽

Gene Sequences ◽

Wide Range ◽

Diagram Representation

The evolutionary analysis of the genome of the immediate cluster is an important part of comparative genomics research. Identifying the overlap between immediate homologous clusters allows us to elucidate the function and evolution of proteins between species. Here, we report a network platform called Ortho-paralogous Venn-diagram representation that can be used to compare and visualize a wide range of ortho-paralogous clustering of genomes. In our work Ortho-paralogous Venn-diagram results show a functional summary of interactive Venn diagrams, summary counts, and interspecies shared cluster separations and intersections. Ortho-paralogous Venn-diagram also uses a variety of sequence analysis tools to gain an in-depth understanding of the cluster. In addition, Ortho-paralogous Venn identifies direct homologous clusters of single copy genes and allows custom search of specific gene clusters. It enables us in wide analysis of the genes and protein by comparing the genes using Venn diagram .Here the user can upload our own gene sequences into the application ,using three clustering approach to check the best clustering approches like SOM,K-means and advanced clustering after that we are using the Venn diagram repersentator to evolutionary cluster the genes having similar functionality and structural similarity from the uploaded data.Here we are using a venn diagram representation as an application which used to cluster the orthologous and paralogous gene on basics of their evolution and functional aspects.it enables us in wide analysis of the genes and protein bycomparing the genes using venn diagram representation.here the user can upload our own gene sequences into the application where the venn diagram representatorclusters.the genes having similar functionality and structural similarity from the uploaded data.

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Phylogenomic Synteny Network Analysis Reveals an Ancient MADS-Box Transcription Factor Tandem Duplication and Lineage-Specific Transpositions

10.1101/100990 ◽

2017 ◽

Author(s):

Tao Zhao ◽

Rens Holmer ◽

Suzanne de Bruijn ◽

Harrold A. van den Burg ◽

M. Eric Schranz

Keyword(s):

Transcription Factor ◽

Gene Clusters ◽

Specific Gene ◽

Evolutionary Analysis ◽

Mads Box ◽

Genomic Context ◽

Phylogenetic Groups ◽

Tandem Gene Duplication ◽

Plant Genomes ◽

Gene Synteny

ABSTRACTConserved genomic context (or synteny) provides critical information for comparative evolutionary analysis, such as the inference of ancient polyploidy events, recurrent genomic rearrangements across species and gene ancestry. With the increase of sequenced and assembled plant genomes, we now have the opportunity to use synteny to analyze the dynamics of gene family expansion and contraction across broad phylogenetic groups. Here we present an integrated approach to organize plant kingdom-wide gene synteny networks using k-clique percolation. As an example, we analyzed the gene synteny network of the MADS-box transcription factor family based on fifty-one completed plant genomes. We conclude from two massive gene clusters that one of the two Type II MADS-box gene clades evolved from an ancient tandem gene duplication likely predating the radiation of seed plants, which then expanded by polyploidy events and sub-functionalization. This gene clade now contains key regulators of major phenotypes of angiosperms including flower development. Moreover, we find lineage-specific gene clusters derived from transposition events. For example, lineage-specific clusters in the Brassicales containing genes that are well-known for their function in controlling flower morphology (AP3 and PI). Our phylogenomic synteny network approach can be applied to any group of species to gain new insights into the evolution and dynamics of any set of genes.

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Molecular evolutionary relationships of Vietnamese and global pulmonary Paragonimus species in the family paragonimidae and suborder xiphidiata (Platyhelminthes: Trematoda)

Vietnam Journal of Biotechnology ◽

10.15625/1811-4989/18/4/15673 ◽

2021 ◽

Vol 18 (4) ◽

pp. 653-662

Author(s):

Nguyen Thi Khue ◽

Pham Thi Khanh Linh ◽

Do Thi Roan ◽

Doan Thi Thanh Huong ◽

Pham Ngoc Doanh ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Phylogenetic Analyses ◽

The Philippines ◽

28S Rdna ◽

Evolutionary Relationships ◽

Evolutionary Analysis ◽

North West ◽

Rdna Sequences ◽

The Family ◽

28S Rdna Sequences

Paragonimiasis, caused by Paragonimus species belonging to the family Paragonimidae of the suborder Xiphidiata (Platyhelminthes: Trematoda), often occurs in poor, upland, ethnic minorities, in Vietnam and the world. Asian Paragonimus species are distributed from Japan, South Korea, along with North and Southeast China, North-West and Central Vietnam, the Philippines, Thailand, Bangladesh, India, and Sri Lanka. There are various genetic variants, strains, and genotypes forming different complexes and evolutionary lineages. The 18S, 28S rDNA sequences and the intergenic transcribed spacer regions (ITS-1, ITS-2) of nuclear ribosomal transcription units are commonly used as molecular markers in genetic studies and phylogenetic analyses. We obtained a portion of 28S rDNA (domains D1–D3) of Paragonimus spp. including P. heterotremus (from Vietnam), P. ohirai (Japan), P. iloktsuenensis (Japan), and P. westermani (India and Vietnam) and conducted phylogenetic analysis for molecular evolutionary studies. The results showed that the family Paragonimidae formed the biggest cluster in a phylogenetic tree, which comprises of 46 sequences of 11 species belonging to 11 subgroups, among which the P. westermani complex of strains originating from China, Korea, Japan, India, Philippines, Malaysia, and Vietnam is present. P. westermani complex is arranged in a position of "sister" (sister group) with the subgroup P. siamensis. The P. heterotremus and P. ohirai complexes, and the P. miyazakii, P. harinasutai, P. mexicanus, P. kellicotti, and P. macrorchis complexes are clustered in a common population. P. westermani of Vietnam is in close proximity to the East Asian strains, as of which has been previously reported. P. ohirai and P. iloktsuenensis are considered “sibling” species, sharing the same clade. Phylogenetic analysis using the 28S rDNA sequences directly presented species position and their molecular evolutionary relationships in the families Paragonimidae, Troglotrematidae, Nanophyetidae, and Collyriclidae. Evolutionary analysis has also clarified a number of complex delineation problems and made a clear nomenclature for Paragonimus sp. of Vietnam, in particular, which has scientific grounds merited to recognize as that it is really the P. westermani species.

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Determination of Evolutionary Relationships of Outbreak-Associated Listeria monocytogenes Strains of Serotypes 1/2a and 1/2b by Whole-Genome Sequencing

Applied and Environmental Microbiology ◽

10.1128/aem.02440-15 ◽

2015 ◽

Vol 82 (3) ◽

pp. 928-938 ◽

Cited By ~ 30

Author(s):

Teresa M. Bergholz ◽

Henk C. den Bakker ◽

Lee S. Katz ◽

Benjamin J. Silk ◽

Kelly A. Jackson ◽

...

Keyword(s):

Genetic Variation ◽

Listeria Monocytogenes ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Evolutionary Relationships ◽

Whole Genome ◽

Evolutionary Analysis ◽

Production Chain ◽

Content Type ◽

Accessory Genome

ABSTRACTWe used whole-genome sequencing to determine evolutionary relationships among 20 outbreak-associated clinical isolates ofListeria monocytogenesserotypes 1/2a and 1/2b. Isolates from 6 of 11 outbreaks fell outside the clonal groups or “epidemic clones” that have been previously associated with outbreaks, suggesting that epidemic potential may be widespread inL. monocytogenesand is not limited to the recognized epidemic clones. Pairwise comparisons between epidemiologically related isolates within clonal complexes showed that genome-level variation differed by 2 orders of magnitude between different comparisons, and the distribution of point mutations (core versus accessory genome) also varied. In addition, genetic divergence between one closely related pair of isolates from a single outbreak was driven primarily by changes in phage regions. The evolutionary analysis showed that the changes could be attributed to horizontal gene transfer; members of the diverse bacterial community found in the production facility could have served as the source of novel genetic material at some point in the production chain. The results raise the question of how to best utilize information contained within the accessory genome in outbreak investigations. The full magnitude and complexity of genetic changes revealed by genome sequencing could not be discerned from traditional subtyping methods, and the results demonstrate the challenges of interpreting genetic variation among isolates recovered from a single outbreak. Epidemiological information remains critical for proper interpretation of nucleotide and structural diversity among isolates recovered during outbreaks and will remain so until we understand more about how various population histories influence genetic variation.

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