scholarly journals Current Progress in Evolutionary Comparative Genomics of Great Apes

2021 ◽  
Vol 12 ◽  
Author(s):  
Aisha Yousaf ◽  
Junfeng Liu ◽  
Sicheng Ye ◽  
Hua Chen
Keyword(s):  
Evolutionary History ◽  
Comparative Genomic ◽  
Great Ape ◽  
Structural Variations ◽  
Genome Sequences ◽  
New Genes ◽  
Genomic Analyses ◽  
Genomic Studies ◽  
High Quality Genome ◽  
Human Specific

The availability of high-quality genome sequences of great ape species provides unprecedented opportunities for genomic analyses. Herein, we reviewed the recent progress in evolutionary comparative genomic studies of the existing great ape species, including human, chimpanzee, bonobo, gorilla, and orangutan. We elaborate discovery on evolutionary history, natural selection, structural variations, and new genes of these species, which is informative for understanding the origin of human-specific phenotypes.

scholarly journals High-Quality Genome Assembly of Peronospora destructor, the Causal Agent of Onion Downy Mildew

2020 ◽  
Vol 33 (5) ◽  
pp. 718-720
Author(s):  
Karthi Natesan ◽  
Ji Yeon Park ◽  
Cheol-Woo Kim ◽  
Dong Suk Park ◽  
Young-Seok Kwon ◽  
...  
Keyword(s):  
Downy Mildew ◽  
De Novo ◽  
Gc Content ◽  
Comparative Genomic ◽  
High Quality ◽  
Sequencing Platform ◽  
Peronospora Destructor ◽  
Genomic Studies ◽  
Genome Assemblies ◽  
High Quality Genome

Peronospora destructor is an obligate biotrophic oomycete that causes downy mildew on onion (Allium cepa). Onion is an important crop worldwide, but its production is affected by this pathogen. We sequenced the genome of P. destructor using the PacBio sequencing platform, and de novo assembly resulted in 74 contigs with a total contig size of 29.3 Mb and 48.48% GC content. Here, we report the first high-quality genome sequence of P. destructor and its comparison with the genome assemblies of other oomycetes. The genome is a very useful resource to serve as a reference for analysis of P. destructor isolates and for comparative genomic studies of the biotrophic oomycetes.

scholarly journals Genome Sequence Resource for Elsinoë ampelina, the Causal Organism of Grapevine Anthracnose

2020 ◽  
Vol 33 (4) ◽  
pp. 576-579 ◽  
Author(s):  
Zhi Li ◽  
Yanchun Fan ◽  
Pingping Chang ◽  
Linlin Gao ◽  
Xiping Wang
Keyword(s):  
Genome Sequence ◽  
Management Strategies ◽  
Comparative Genomic ◽  
Causal Organism ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Elsinoe Ampelina ◽  
Genomic Studies ◽  
High Quality Genome ◽  
Ascomycetous Fungus

Elsinoë ampelina is an ascomycetous fungus that causes grape anthracnose, a potentially devastating disease worldwide. Here, we report a 28.29 Mb high-quality genome sequence of E. ampelina YL-1 that encodes 8,057 predicted protein-coding genes and represents the first sequenced genome assembly of E. ampelina. This study adds to the current genomic resources for the genus Elsinoë and paves the way for research on comparative genomic studies, E. ampelina–grape interactions, and improvement of management strategies.

Complete plastid genome sequences of three tropical Alseodaphne trees in the family Lauraceae

Holzforschung ◽  
2018 ◽  
Vol 72 (4) ◽  
pp. 337-345 ◽  
Author(s):  
Yu Song ◽  
Xin Yao ◽  
Bing Liu ◽  
Yunhong Tan ◽  
Richard T. Corlett
Keyword(s):  
Type Species ◽  
Phylogenetic Analyses ◽  
Comparative Genomic ◽  
Inverted Repeats ◽  
Genome Sequences ◽  
Complete Chloroplast Genome ◽  
Tropical Asia ◽  
Length Difference ◽  
The Family ◽  
Genomic Analyses

AbstractAlseodaphneis a genus of timber trees (ca. 40 spp.) belonging to thePerseagroup of the Lauraceae. It is widely distributed in tropical Asia, but is often confused withDehaasiaandNothaphoebe, and the systematics of the genus is unclear. Here, the complete chloroplast genome sequences ofA. semecarpifoliawill be reported, the type species ofAlseodaphne, and two China-endemic species,A. gracilisandA. huanglianshanensis. The three plastomes were 153 051 bp, 153 099 bp and 153 070 bp, respectively. Comparative genomic analyses indicate that the threeAlseodaphneplastomes have similar genome size and those are very different with previously published plastomes of Lauraceae in length. The length difference is directly caused by inverted repeats expansion/contraction. Four highly variable loci includingpsbD-trnM,ndhF-rpl32,rpl32-trnLandycf1among the threeAlseodaphnespecies were identified as useful plastid candidate barcodes forAlseodaphneand Lauraceae species. Phylogenetic analyses based on 12 complete plastomes of Lauraceae species confirm a monophyleticPerseagroup comprising species ofAlseodaphne,Phoebe,PerseaandMachilus.

scholarly journals The genome of the camphor tree and the genetic and climatic relevance of the top-geoherbalism in this medicinal plant

2021 ◽  
Author(s):  
Rihong Jiang ◽  
Xianlian Chen ◽  
Xuezhu Liao ◽  
Dan Peng ◽  
Xiaoxu Han ◽  
...  
Keyword(s):  
Evolutionary History ◽  
Three Dimensional ◽  
Sister Group ◽  
Cold Season ◽  
Comparative Genomic ◽  
Climate Data ◽  
Volatile Oils ◽  
Expression Of Genes ◽  
Genomic Analyses ◽  
Camphor Tree

Camphor tree (Cinnamomum camphora (L.) J. Presl), a species in the magnoliid family Lauraceae, is known for its rich volatile oils and is used as a medical cardiotonic and as a scent in many perfumed hygiene products. Here, we present a high-quality chromosome-scale genome of C. camphora with a scaffold N50 of 64.34 Mb and an assembled genome size of 755.41 Mb. Phylogenetic inference revealed that the magnoliids are a sister group to the clade of eudicots and monocots. Comparative genomic analyses identified two rounds of ancient whole-genome duplication (WGD). Tandem duplicated genes exhibited a higher evolutionary rate, a more recent evolutionary history and a more clustered distribution on chromosomes, contributing to the production of secondary metabolites, especially monoterpenes and sesquiterpenes, which are the principal essential oil components. Three-dimensional analyses of the volatile metabolites, gene expression and climate data of samples with the same genotype grown in different locations showed that low temperature and low precipitation during the cold season modulate the expression of genes in the terpenoid biosynthesis pathways, especially TPS genes, which facilitates the accumulation of volatile compounds. Our study lays a theoretical foundation for policy-making regarding the agroforestry applications of camphor tree.

scholarly journals Comparative genomic analysis of the secondary flagellar (flag-2) system in the order Enterobacterales

2019 ◽  
Author(s):  
Pieter De Maayer ◽  
Talia Pillay ◽  
Teresa A Coutinho
Keyword(s):  
Evolutionary History ◽  
Potential Role ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Flagellar Biosynthesis ◽  
Genomic Analyses ◽  
Variable Feature ◽  
Locomotory Organ ◽  
Protein Number ◽  
Horizontal Acquisition

Abstract Background The order Enterobacterales encompasses a broad range of metabolically and ecologically versatile bacterial taxa, most of which are motile by means of peritrichous flagella. Flagellar biosynthesis has been linked to a primary flagella locus, flag -1, encompassing ~ 50 genes. A discrete locus, flag -2, encoding a distinct flagellar system, has been observed in a limited number of enterobacterial taxa, but its function remains largely uncharacterized.Results and Discussion Comparative genomic analyses showed that orthologous flag -2 loci are present in 592/4,028 taxa belonging to 5/8 and 31/76 families and genera, respectively, in the order Enterobacterales. Furthermore, the presence of the outermost flag- 2 genes only in many taxa suggest that this locus was far more prevalent and has subsequently been lost through gene deletion events. The flag -2 loci range in size from ~3.4 to 81.1 kilobases and code for between five and 102 distinct proteins. The discrepancy in size and protein number can be attributed to the presence of cargo gene islands within the loci. Evolutionary analyses revealed a complex evolutionary history for the flag -2 loci, representing ancestral elements in some taxa, while showing evidence of recent horizontal acquisition in other enterobacteria.Conclusions The flag -2 flagellar system is a relatively common, but highly variable feature among members of the Enterobacterales. Given the energetic burden of flagellar biosynthesis and functioning, the prevalence of a second flagellar system suggests it plays important biological roles in the enterobacteria and we postulate on its potential role as locomotory organ or as secretion system.

scholarly journals Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

2017 ◽  
Vol 35 (8) ◽  
pp. 725-731 ◽  
Author(s):  
Robert M Bowers ◽  
◽  
Nikos C Kyrpides ◽  
Ramunas Stepanauskas ◽  
Miranda Harmon-Smith ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Marker Gene ◽  
Comparative Genomic ◽  
Archaeal Diversity ◽  
Genome Sequences ◽  
Assembly Quality ◽  
Metagenomic Sequence ◽  
Minimum Information ◽  
A Genome ◽  
Genomic Analyses

AbstractWe present two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences. Both are extensions of the Minimum Information about Any (x) Sequence (MIxS). The standards are the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum Information about a Metagenome-Assembled Genome (MIMAG), including, but not limited to, assembly quality, and estimates of genome completeness and contamination. These standards can be used in combination with other GSC checklists, including the Minimum Information about a Genome Sequence (MIGS), Minimum Information about a Metagenomic Sequence (MIMS), and Minimum Information about a Marker Gene Sequence (MIMARKS). Community-wide adoption of MISAG and MIMAG will facilitate more robust comparative genomic analyses of bacterial and archaeal diversity.

scholarly journals Oomycete Gene Table: an online database for comparative genomic analyses of the oomycete microorganisms

Database ◽  
2019 ◽  
Vol 2019 ◽  
Author(s):  
Thidarat Rujirawat ◽  
Preecha Patumcharoenpol ◽  
Weerayuth Kittichotirat ◽  
Theerapong Krajaejun
Keyword(s):  
Economic Loss ◽  
Comparative Genomic ◽  
Online Database ◽  
Eukaryotic Microorganisms ◽  
Pathogenesis Related ◽  
Genomic Analyses ◽  
Bioinformatic Tool ◽  
Genomic Studies ◽  
User Friendly ◽  
Gene Table

Abstract Oomycetes form a unique group of the fungal-like, aquatic, eukaryotic microorganisms. Lifestyle and pathogenicity of the oomycetes are diverse. Many pathogenic oomycetes affect a broad range of plants and cause enormous economic loss annually. Some pathogenic oomycetes cause destructive and deadly diseases in a variety of animals, including humans. No effective antimicrobial agent against the oomycetes is available. Genomic data of many oomycetes are currently available. Comparative analyses of the oomycete genomes must be performed to better understand the oomycete biology and virulence, as well as to identify conserved and biologically important proteins that are potential diagnostic and therapeutic targets of these organisms. However, a tool that facilitates comparative genomic studies of the oomycetes is lacking. Here, we described in detail the Oomycete Gene Table, which is an online user-friendly bioinformatic tool, designed to search, analyze, compare and visualize gene contents of 20 oomycetes in a customizable table. Genomic contents of other oomycete species, when available, can be added to the existing database. Some of the applications of the Oomycete Gene Table include investigations of phylogenomic relationships, as well as identifications of biologically important and pathogenesis-related genes of oomycetes. In summary, the Oomycete Gene Table is a simple and useful tool for comparative genomic analyses of oomycetes.

scholarly journals A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes

2021 ◽  
Author(s):  
Guangwei Li ◽  
Lijian Wang ◽  
Jianping Yang ◽  
Hang He ◽  
Huaibing Jin ◽  
...  
Keyword(s):  
Cereal Crops ◽  
Comparative Genomic ◽  
Gene Duplications ◽  
Forage Crop ◽  
Genome Wide ◽  
Genomic Studies ◽  
Physical Organization ◽  
Prolamin Loci ◽  
High Quality Genome ◽  
Strong Expansion

AbstractRye is a valuable food and forage crop, an important genetic resource for wheat and triticale improvement and an indispensable material for efficient comparative genomic studies in grasses. Here, we sequenced the genome of Weining rye, an elite Chinese rye variety. The assembled contigs (7.74 Gb) accounted for 98.47% of the estimated genome size (7.86 Gb), with 93.67% of the contigs (7.25 Gb) assigned to seven chromosomes. Repetitive elements constituted 90.31% of the assembled genome. Compared to previously sequenced Triticeae genomes, Daniela, Sumaya and Sumana retrotransposons showed strong expansion in rye. Further analyses of the Weining assembly shed new light on genome-wide gene duplications and their impact on starch biosynthesis genes, physical organization of complex prolamin loci, gene expression features underlying early heading trait and putative domestication-associated chromosomal regions and loci in rye. This genome sequence promises to accelerate genomic and breeding studies in rye and related cereal crops.

scholarly journals Comparative genomic analysis of the secondary flagellar (flag-2) system in the order Enterobacterales

2020 ◽  
Author(s):  
Pieter De Maayer ◽  
Talia Pillay ◽  
Teresa A Coutinho
Keyword(s):  
Evolutionary History ◽  
Potential Role ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Flagellar Biosynthesis ◽  
Genomic Analyses ◽  
Variable Feature ◽  
Locomotory Organ ◽  
Protein Number ◽  
Horizontal Acquisition

Abstract Background The order Enterobacterales encompasses a broad range of metabolically and ecologically versatile bacterial taxa, most of which are motile by means of peritrichous flagella. Flagellar biosynthesis has been linked to a primary flagella locus, flag -1, encompassing ~ 50 genes. A discrete locus, flag -2, encoding a distinct flagellar system, has been observed in a limited number of enterobacterial taxa, but its function remains largely uncharacterized. Results and Discussion Comparative genomic analyses showed that orthologous flag -2 loci are present in 592/4,028 taxa belonging to 5/8 and 31/76 families and genera, respectively, in the order Enterobacterales. Furthermore, the presence of only the outermost flag- 2 genes in many taxa suggests that this locus was far more prevalent and has subsequently been lost through gene deletion events. The flag -2 loci range in size from ~3.4 to 81.1 kilobases and code for between five and 102 distinct proteins. The discrepancy in size and protein number can be attributed to the presence of cargo gene islands within the loci. Evolutionary analyses revealed a complex evolutionary history for the flag -2 loci, representing ancestral elements in some taxa, while showing evidence of recent horizontal acquisition in other enterobacteria. Conclusions The flag -2 flagellar system is a fairly common, but highly variable feature among members of the Enterobacterales. Given the energetic burden of flagellar biosynthesis and functioning, the prevalence of a second flagellar system suggests it plays important biological roles in the enterobacteria and we postulate on its potential role as locomotory organ or as secretion system.

scholarly journals Comparative cytogenomics reveals genome reshuffling and centromere repositioning in the legume tribe Phaseoleae

2021 ◽  
Author(s):  
Claudio Montenegro ◽  
Livia Martins ◽  
Fernanda de Oliveira Bustamante ◽  
Ana Christina Brasileiro-Vidal ◽  
Andrea Pedrosa-Harand
Keyword(s):  
Genomic Analysis ◽  
In Silico Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Orthologous Genes ◽  
Genomic Analyses ◽  
Genomic Studies ◽  
Macroptilium Atropurpureum ◽  
Evolutionary New Centromeres ◽  
Silico Analysis

The tribe Phaseoleae (Leguminosae; Papilionoideae) includes several legume crops with assembled genomes. Comparative genomic studies indicated the preservation of large genomic blocks in legumes. However, the chromosome dynamics along its evolution was not investigated in the tribe. We conducted a comparative genomic analysis using CoGe Synmap platform to define a useful genomic block (GB) system and to reconstruct the ancestral Phaseoleae karyotype (APK). We defined the GBs based on orthologous genes between Phaseolus vulgaris and Vigna unguiculata genomes (n = 11), then searched for these GBs in different genome species belonging to the Phaseolinae (P. lunatus, n = 11) and Glycininae (Amphicarpaea edgeworthii, n = 11 and Spatholobus suberectus, n = 9) subtribes, and in the outgroup (Medicago truncaluta, n = 8). To support our in silico analysis, we used oligo-FISH probes of P. vulgaris chromosomes 2 and 3 to paint the orthologous chromosomes of the non-sequenced Phaseolinae species (Macroptilium atropurpureum and Lablab purpureusi, n = 11). We inferred the APK with n = 11, 22 GBs (A to V) and 60 sub-GBs. We hypothesized that the main rearrangements within Phaseolinae involved nine APK chromosomes, with extensive centromere repositioning resulting from evolutionary new centromeres (ENC) in the Phaseolus lineage. We demonstrated that the A. edgeworthii genome is more reshuffled than the dysploid S. suberectus genome, in which we could reconstructed the main events responsible for the chromosome number reduction. The development of the GB system and the proposed APK provide useful tools for future comparative genomic analyses of legume species.

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