scholarly journals Comparison of Envelope-Related Genes in Unicellular and Filamentous Cyanobacteria

2007 ◽  
Vol 2007 ◽  
pp. 1-10 ◽  
Author(s):  
Yu Yang ◽  
Song Qin ◽  
Fangqing Zhao ◽  
Xiaoyuan Chi ◽  
Xiaowen Zhang
Keyword(s):  
Comparative Genomics ◽  
Cell Envelope ◽  
Gene Families ◽  
Environmental Adaptation ◽  
Gene Content ◽  
Filamentous Cyanobacteria ◽  
Conserved Domains ◽  
Significant Variance ◽  
Glycosyl Transferase ◽  
Phylogenetic Profiles

To elucidate the evolution of cyanobacterial envelopes and the relation between gene content and environmental adaptation, cell envelope structures and components of unicellular and filamentous cyanobacteria were analyzed in comparative genomics. Hundreds of envelope biogenesis genes were divided into 5 major groups and annotated according to their conserved domains and phylogenetic profiles. Compared to unicellular species, the gene numbers of filamentous cyanobacteria expanded due to genome enlargement effect, but only few gene families amplified disproportionately, such as those encoding waaG and glycosyl transferase 2. Comparison of envelope genes among various species suggested that the significant variance of certain cyanobacterial envelope biogenesis genes should be the response to their environmental adaptation, which might be also related to the emergence of filamentous shapes with some new functions.

scholarly journals Genomic Characteristics and Comparative Genomics Analysis of Two Chinese Corynespora cassiicola Strains Causing Corynespora Leaf Fall (CLF) Disease

2021 ◽  
Vol 7 (6) ◽  
pp. 485
Author(s):  
Boxun Li ◽  
Yang Yang ◽  
Jimiao Cai ◽  
Xianbao Liu ◽  
Tao Shi ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Single Molecule ◽  
Rubber Tree ◽  
Gene Families ◽  
Gene Clusters ◽  
The Philippines ◽  
Tree Plantations ◽  
Comparative Genomic ◽  
Corynespora Cassiicola ◽  
Leaf Fall

Rubber tree Corynespora leaf fall (CLF) disease, caused by the fungus Corynespora cassiicola, is one of the most damaging diseases in rubber tree plantations in Asia and Africa, and this disease also threatens rubber nurseries and young rubber plantations in China. C. cassiicola isolates display high genetic diversity, and virulence profiles vary significantly depending on cultivar. Although one phytotoxin (cassicolin) has been identified, it cannot fully explain the diversity in pathogenicity between C. cassiicola species, and some virulent C. cassiicola strains do not contain the cassiicolin gene. In the present study, we report high-quality gapless genome sequences, obtained using short-read sequencing and single-molecule long-read sequencing, of two Chinese C. cassiicola virulent strains. Comparative genomics of gene families in these two stains and a virulent CPP strain from the Philippines showed that all three strains experienced different selective pressures, and metabolism-related gene families vary between the strains. Secreted protein analysis indicated that the quantities of secreted cell wall-degrading enzymes were correlated with pathogenesis, and the most aggressive CCP strain (cassiicolin toxin type 1) encoded 27.34% and 39.74% more secreted carbohydrate-active enzymes (CAZymes) than Chinese strains YN49 and CC01, respectively, both of which can only infect rubber tree saplings. The results of antiSMASH analysis showed that all three strains encode ~60 secondary metabolite biosynthesis gene clusters (SM BGCs). Phylogenomic and domain structure analyses of core synthesis genes, together with synteny analysis of polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS) gene clusters, revealed diversity in the distribution of SM BGCs between strains, as well as SM polymorphisms, which may play an important role in pathogenic progress. The results expand our understanding of the C. cassiicola genome. Further comparative genomic analysis indicates that secreted CAZymes and SMs may influence pathogenicity in rubber tree plantations. The findings facilitate future exploration of the molecular pathogenic mechanism of C. cassiicola.

Comparative genomics reveals environmental adaptation differences between Cronobacter species

2021 ◽  
pp. 110541
Author(s):  
Xue Qin ◽  
Hao Wang ◽  
Chao Miao ◽  
Xinyan Yang ◽  
Yanming Zhang ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Environmental Adaptation ◽  
Cronobacter Species

scholarly journals Gene family innovation, conservation and loss on the animal stem lineage

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Daniel J Richter ◽  
Parinaz Fozouni ◽  
Michael B Eisen ◽  
Nicole King
Keyword(s):  
Gene Family ◽  
Gene Families ◽  
Gene Content ◽  
Gene Repertoire ◽  
Toll Like Receptor ◽  
Stem Lineage ◽  
Gains And Losses ◽  
Core Features

Choanoflagellates, the closest living relatives of animals, can provide unique insights into the changes in gene content that preceded the origin of animals. However, only two choanoflagellate genomes are currently available, providing poor coverage of their diversity. We sequenced transcriptomes of 19 additional choanoflagellate species to produce a comprehensive reconstruction of the gains and losses that shaped the ancestral animal gene repertoire. We identified ~1944 gene families that originated on the animal stem lineage, of which only 39 are conserved across all animals in our study. In addition, ~372 gene families previously thought to be animal-specific, including Notch, Delta, and homologs of the animal Toll-like receptor genes, instead evolved prior to the animal-choanoflagellate divergence. Our findings contribute to an increasingly detailed portrait of the gene families that defined the biology of the Urmetazoan and that may underpin core features of extant animals.

scholarly journals Comparative Genomics of Cell Envelope Components in Mycobacteria

PLoS ONE ◽  
2011 ◽  
Vol 6 (5) ◽  
pp. e19280 ◽  
Author(s):  
Ruma Banerjee ◽  
Pankaj Vats ◽  
Sonal Dahale ◽  
Sunitha Manjari Kasibhatla ◽  
Rajendra Joshi
Keyword(s):  
Comparative Genomics ◽  
Cell Envelope

Comparative Genomics of the Major Chemosensory Gene Families in Arthropods

2011 ◽  
Author(s):  
Alejandro Sánchez-Gracia ◽  
Filipe G Vieira ◽  
Francisca C Almeida ◽  
Julio Rozas
Keyword(s):  
Comparative Genomics ◽  
Gene Families ◽  
Chemosensory Gene

scholarly journals BUSCO applications from quality assessments to gene prediction and phylogenomics

2017 ◽  
Author(s):  
Robert M. Waterhouse ◽  
Mathieu Seppey ◽  
Felipe A. Simão ◽  
Mosè Manni ◽  
Panagiotis Ioannidis ◽  
...  
Keyword(s):  
Quality Control ◽  
Comparative Genomics ◽  
Gene Prediction ◽  
Single Copy ◽  
Quality Metrics ◽  
Gene Content ◽  
Link Type ◽  
Gene Predictor ◽  
Sequencing Quality ◽  
Quality Assessments

ABSTRACTGenomics promises comprehensive surveying of genomes and metagenomes, but rapidly changing technologies and expanding data volumes make evaluation of completeness a challenging task. Technical sequencing quality metrics can be complemented by quantifying completeness in terms of the expected gene content of Benchmarking Universal Single-Copy Orthologs (BUSCO, http://busco.ezlab.org). Now in its third release, BUSCO utilities extend beyond quality control to applications in comparative genomics, gene predictor training, metagenomics, and phylogenomics.

scholarly journals Assembly and Annotation of an Ashkenazi Human Reference Genome

2020 ◽  
Author(s):  
Alaina Shumate ◽  
Aleksey V. Zimin ◽  
Rachel M. Sherman ◽  
Daniela Puiu ◽  
Justin M. Wagner ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Reference Genome ◽  
Gene Families ◽  
Gene Content ◽  
Specific Reference ◽  
Protein Coding ◽  
Human Reference Genome ◽  
Protein Coding Genes ◽  
Reference Genomes ◽  
Similar Gene

AbstractHere we describe the assembly and annotation of the genome of an Ashkenazi individual and the creation of a new, population-specific human reference genome. This genome is more contiguous and more complete than GRCh38, the latest version of the human reference genome, and is annotated with highly similar gene content. The Ashkenazi reference genome, Ash1, contains 2,973,118,650 nucleotides as compared to 2,937,639,212 in GRCh38. Annotation identified 20,157 protein-coding genes, of which 19,563 are >99% identical to their counterparts on GRCh38. Most of the remaining genes have small differences. 40 of the protein-coding genes in GRCh38 are missing from Ash1; however, all of these genes are members of multi-gene families for which Ash1 contains other copies. 11 genes appear on different chromosomes from their homologs in GRCh38. Alignment of DNA sequences from an unrelated Ashkenazi individual to Ash1 identified ~1 million fewer homozygous SNPs than alignment of those same sequences to the more-distant GRCh38 genome, illustrating one of the benefits of population-specific reference genomes.

scholarly journals Genus-Wide Comparative Genomics Analysis ofNeisseriato Identify New Genes Associated with Pathogenicity and Niche Adaptation ofNeisseriaPathogens

2019 ◽  
Vol 2019 ◽  
pp. 1-19 ◽  
Author(s):  
Qun-Feng Lu ◽  
De-Min Cao ◽  
Li-Li Su ◽  
Song-Bo Li ◽  
Guang-Bin Ye ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Phase Variation ◽  
Gene Families ◽  
Human Pathogens ◽  
Gene Set ◽  
Unique Gene ◽  
New Genes ◽  
Niche Adaptation ◽  
Comparative Genomics Analysis ◽  
Conserved Gene

N. gonorrhoeaeandN. meningitidis, the only two human pathogens ofNeisseria, are closely related species. But the niches they survived in and their pathogenic characteristics are distinctly different. However, the genetic basis of these differences has not yet been fully elucidated. In this study, comparative genomics analysis was performed based on 15N. gonorrhoeae, 75N. meningitidis, and 7 nonpathogenicNeisseriagenomes. Core-pangenome analysis found 1111 conserved gene families among them, and each of these species groups had opening pangenome. We found that 452, 78, and 319 gene families were unique inN. gonorrhoeae,N. meningitidis, and both of them, respectively. Those unique gene families were regarded as candidates that related to their pathogenicity and niche adaptation. The relationships among them have been partly verified by functional annotation analysis. But at least one-third genes for each gene set have not found the certain functional information. Simple sequence repeat (SSR), the basis of gene phase variation, was found abundant in the membrane or related genes of each unique gene set, which may facilitate their adaptation to variable host environments. Protein-protein interaction (PPI) analysis found at least five distinct PPI clusters inN. gonorrhoeaeand four inN. meningitides, and 167 and 52 proteins with unknown function were contained within them, respectively.

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