scholarly journals Insights into origins and function of the unexplored majority of the reductive dehalogenase gene family as a result of genome assembly and ortholog group classification

2020 ◽  
Vol 22 (3) ◽  
pp. 663-678
Author(s):  
Olivia Molenda ◽  
Luz A. Puentes Jácome ◽  
Xuan Cao ◽  
Camilla L. Nesbø ◽  
Shuiquan Tang ◽  
...  
Keyword(s):  
Gene Family ◽  
Genome Assembly ◽  
Group Classification ◽  
Conserved Synteny ◽  
Ortholog Group ◽  
Reductive Dehalogenase ◽  
Reductive Dehalogenase Genes ◽  
And Function ◽  
Dehalogenase Gene

Classifying all reductive dehalogenase genes from organohalide respiring bacteria, including nine newly closed genomes, predicts function and conserved synteny within species.

scholarly journals Phylogenetic Comparison and Splicing Analysis of the U1 snRNP-specific Protein U1C in Eukaryotes

2021 ◽  
Vol 8 ◽  
Author(s):  
Kai-Lu Zhang ◽  
Jian-Li Zhou ◽  
Jing-Fang Yang ◽  
Yu-Zhen Zhao ◽  
Debatosh Das ◽  
...  
Keyword(s):  
Gene Family ◽  
Cancer Progression ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Specific Protein ◽  
Comprehensive Overview ◽  
Small Nuclear Ribonucleoprotein ◽  
U1 Snrnp ◽  
Multiple Copies ◽  
And Function

As a pivotal regulator of 5’ splice site recognition, U1 small nuclear ribonucleoprotein (U1 snRNP)-specific protein C (U1C) regulates pre-mRNA splicing by interacting with other components of the U1 snRNP complex. Previous studies have shown that U1 snRNP and its components are linked to a variety of diseases, including cancer. However, the phylogenetic relationships and expression profiles of U1C have not been studied systematically. To this end, we identified a total of 110 animal U1C genes and compared them to homologues from yeast and plants. Bioinformatics analysis shows that the structure and function of U1C proteins is relatively conserved and is found in multiple copies in a few members of the U1C gene family. Furthermore, the expression patterns reveal that U1Cs have potential roles in cancer progression and human development. In summary, our study presents a comprehensive overview of the animal U1C gene family, which can provide fundamental data and potential cues for further research in deciphering the molecular function of this splicing regulator.

scholarly journals A Deep Dive into Genome Assemblies of Non-vertebrate Animals

2021 ◽  
Author(s):  
Nadège Guiglielmoni ◽  
Ramón Rivera-Vicéns ◽  
Romain Koszul ◽  
Jean-François Flot
Keyword(s):  
Genome Assembly ◽  
Current Knowledge ◽  
Genome Structure ◽  
Deep Dive ◽  
Sequencing Technologies ◽  
Current State ◽  
Animal Diversity ◽  
And Function ◽  
Genome Assemblies ◽  
Genome Projects

Non-vertebrate species represent about ~95% of known metazoan (animal) diversity. They remain to this day relatively unexplored genetically, but understanding their genome structure and function is pivotal for expanding our current knowledge of evolution, ecology and biodiversity. Following the continuous improvements and decreasing costs of sequencing technologies, many genome assembly tools have been released, leading to a significant amount of genome projects being completed in recent years. In this review, we examine the current state of genome projects of non-vertebrate animal species. We present an overview of available sequencing technologies, assembly approaches, as well as pre and post-processing steps, genome assembly evaluation methods, and their application to non-vertebrate animal genomes.

scholarly journals The BAHD Gene Family in Cacao (Theobroma cacao, Malvaceae): Genome-Wide Identification and Expression Analysis

2021 ◽  
Vol 9 ◽  
Author(s):  
Abdullah ◽  
Sahar Faraji ◽  
Parviz Heidari ◽  
Péter Poczai
Keyword(s):  
Gene Family ◽  
Theobroma Cacao ◽  
Critical Role ◽  
Divergence Time ◽  
Purifying Selection ◽  
Plant Metabolites ◽  
Corchorus Capsularis ◽  
Cell Stability ◽  
Duplication Events ◽  
And Function

The benzyl alcohol O-acetyl transferase, anthocyanin O-hydroxycinnamoyl transferase, N-hydroxycinnamoyl anthranilate benzoyl transferase, and deacetylvindoline 4-O-acetyltransferase (BAHD) enzymes play a critical role in regulating plant metabolites and affecting cell stability. In the present study, members of the BAHD gene family were recognized in the genome of Theobroma cacao and characterized using various bioinformatics tools. We found 27 non-redundant putative tcBAHD genes in cacao for the first time. Our findings indicate that tcBAHD genes are diverse based on sequence structure, physiochemical properties, and function. When analyzed with BAHDs of Gossypium raimondii and Corchorus capsularis clustered into four main groups. According to phylogenetic analysis, BAHD genes probably evolved drastically after their divergence. The divergence time of duplication events with purifying selection pressure was predicted to range from 1.82 to 15.50 MYA. Pocket analysis revealed that serine amino acid is more common in the binding site than other residuals, reflecting its key role in regulating the activity of tcBAHDs. Furthermore, cis-acting elements related to the responsiveness of stress and hormone, particularly ABA and MeJA, were frequently observed in the promoter region of tcBAHD genes. RNA-seq analysis further illustrated that tcBAHD13 and tcBAHD26 are involved in response to Phytophthora megakarya fungi. In conclusion, it is likely that evolutionary processes, such as duplication events, have caused high diversity in the structure and function of tcBAHD genes.

scholarly journals Extrachromosomal circular elements targeted by CRISPR-Cas in Dehalococcoides mccartyi are linked to mobilization of reductive dehalogenase genes

2018 ◽  
Vol 13 (1) ◽  
pp. 24-38 ◽  
Author(s):  
Olivia Molenda ◽  
Shuiquan Tang ◽  
Line Lomheim ◽  
Vasu K. Gautam ◽  
Sofia Lemak ◽  
...  
Keyword(s):  
Reductive Dehalogenase ◽  
Dehalococcoides Mccartyi ◽  
Reductive Dehalogenase Genes

Genome-wide identification, phylogeny and function analysis of GRAS gene family in Dendrobium catenatum (Orchidaceae)

Gene ◽  
2019 ◽  
Vol 705 ◽  
pp. 5-15 ◽  
Author(s):  
Xu Zeng ◽  
Hong Ling ◽  
Xiaomei Chen ◽  
Shunxing Guo
Keyword(s):  
Gene Family ◽  
Function Analysis ◽  
Genome Wide ◽  
And Function ◽  
Gras Gene

scholarly journals Overview of organohalide-respiring bacteria and a proposal for a classification system for reductive dehalogenases

2013 ◽  
Vol 368 (1616) ◽  
pp. 20120322 ◽  
Author(s):  
Laura A. Hug ◽  
Farai Maphosa ◽  
David Leys ◽  
Frank E. Löffler ◽  
Hauke Smidt ◽  
...  
Keyword(s):  
Classification System ◽  
Sequence Similarity ◽  
Halogenated Hydrocarbons ◽  
Sequence Information ◽  
Sequencing Data ◽  
Functional Prediction ◽  
Groundwater Contaminants ◽  
Reductive Dehalogenase ◽  
Bacterial Phyla ◽  
Reductive Dehalogenase Genes

Organohalide respiration is an anaerobic bacterial respiratory process that uses halogenated hydrocarbons as terminal electron acceptors during electron transport-based energy conservation. This dechlorination process has triggered considerable interest for detoxification of anthropogenic groundwater contaminants. Organohalide-respiring bacteria have been identified from multiple bacterial phyla, and can be categorized as obligate and non-obligate organohalide respirers. The majority of the currently known organohalide-respiring bacteria carry multiple reductive dehalogenase genes. Analysis of a curated set of reductive dehalogenases reveals that sequence similarity and substrate specificity are generally not correlated, making functional prediction from sequence information difficult. In this article, an orthologue-based classification system for the reductive dehalogenases is proposed to aid integration of new sequencing data and to unify terminology.

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