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.

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 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 Distribution of bacteriocin genes in the lineages of Lactiplantibacillus plantarum

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sungmi Choi ◽  
Min-gyung Baek ◽  
Myung-Jun Chung ◽  
Sanghyun Lim ◽  
Hana Yi
Keyword(s):  
Genetic Diversity ◽  
Comparative Genomic ◽  
Genome Sequences ◽  
Strain Diversity ◽  
Genomic Analyses ◽  
High Level ◽  
Encoding Genes ◽  
Probiotic Activity ◽  
Bacteriocin Genes ◽  
Ancestral Type

AbstractLactiplantibacillus plantarum, previously named “Lactobacillus plantarum,” is found in a wide variety of environments exhibiting a high level of intraspecies genetic diversity. To investigate the strain diversity, we performed comparative genomic analyses of the 54 complete genome sequences. The results revealed that L. plantarum subsp. plantarum was split into three lineages, A, B and C. Of the genes beneficial for probiotic activity, only those associated with the biosynthesis of plantaricin (Pln), an L. plantarum-specific bacteriocin, were found to be significantly different among the lineages. The genes related to the biosynthesis of plnE/F were conserved throughout the three lineages, whereas the outgroups did not possess any Pln-producing genes. In lineage C, the deepest and ancestral type branch, plnE/F genes, were well conserved. In lineage B, loss of gene function was observed due to mobile elements in the pln loci. In lineage A, most strains were predicted to produce more than one type of Pln by possessing diverse Pln-encoding genes. These results showed the presence of functional diversity arising from the trifurcating evolution in L. plantarum subsp. plantarum and demonstrated that Pln is an indicator for differentiating the three lineages.

scholarly journals Draft Genome Sequences of Elsinoë fawcettii and Elsinoë australis Causing Scab Diseases on Citrus

2020 ◽  
Vol 33 (2) ◽  
pp. 135-137 ◽  
Author(s):  
Gnanendra Shanmugam ◽  
Junhyun Jeon ◽  
Jae-Wook Hyun
Keyword(s):  
Ab Initio ◽  
Host Range ◽  
Draft Genome ◽  
Phytopathogenic Fungi ◽  
Comparative Genomic ◽  
Sequence Information ◽  
Genome Sequences ◽  
High Quality ◽  
Genomic Analyses ◽  
Genome Sequence Information

Elsinoë fawcettii and E. australis (phylum Ascomycota) are phytopathogenic fungi causing scab diseases on citrus plants. We report here the high-quality draft genome sequences and ab initio gene predictions of two E. fawcettii strains and one E. australis strain, which differ in their host range. This genome sequence information will provide valuable resources to underpin genomic attributes for determining host range through comparative genomic analyses of citrus scab fungi.

scholarly journals Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications

2011 ◽  
Vol 29 (5) ◽  
pp. 415-420 ◽  
Author(s):  
Pelin Yilmaz ◽  
Renzo Kottmann ◽  
Dawn Field ◽  
Rob Knight ◽  
James R Cole ◽  
...  
Keyword(s):  
Gene Sequence ◽  
Marker Gene ◽  
Minimum Information

scholarly journals Whole-genome sequencing highlights conservative genomic strategies of a stress-tolerant, long-lived scleractinian coral, Porites australiensis Vaughan, 1918

2021 ◽  
Author(s):  
Chuya Shinzato ◽  
Takeshi Takeuchi ◽  
Yuki Yoshioka ◽  
Ipputa Tada ◽  
Miyuki Kanda ◽  
...  
Keyword(s):  
Stress Tolerance ◽  
Matrix Protein ◽  
Proteome Analysis ◽  
Matrix Proteins ◽  
Comparative Genomic ◽  
Acropora Digitifera ◽  
A Genome ◽  
Genomic Analyses ◽  
Relative Stress ◽  
Comparable Quality

Abstract Massive corals of the genus Porites, common, keystone reef builders in the Indo-Pacific Ocean, are distinguished by their relative stress tolerance and longevity. In order to identify genetic bases of these attributes, we sequenced the complete genome of a massive coral, Porites australiensis. We developed a genome assembly and gene models of comparable quality to those of other coral genomes. Proteome analysis identified sixty Porites skeletal matrix protein genes, all of which show significant similarities to genes from other corals and even to those from a sea anemone, which has no skeleton. Nonetheless, 30% of its skeletal matrix proteins were unique to Porites, and were not present in the skeletons of other corals. Comparative genomic analyses showed that genes widely conserved among other organisms are selectively expanded in Porites. Specifically, comparisons of transcriptomic responses of P. australiensis and Acropora digitifera, a stress-sensitive coral, reveal significant differences in regard to genes that respond to increased water temperature, and some of the genes expanded exclusively in Porites may account for the different thermal tolerances of these corals. Taken together, widely shared genes may have given rise to unique biological characteristics of Porites, massive skeletons and stress tolerance.

scholarly journals Bacillus niabensis sp. nov., isolated from cotton-waste composts for mushroom cultivation

2007 ◽  
Vol 57 (8) ◽  
pp. 1909-1913 ◽  
Author(s):  
Soon-Wo Kwon ◽  
Seon-Young Lee ◽  
Byung-Yong Kim ◽  
Hang-Yeon Weon ◽  
Jung-Bong Kim ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Comparative Genomic ◽  
Rrna Gene ◽  
Mushroom Cultivation ◽  
Rrna Gene Sequence ◽  
Sequence Analyses ◽  
Genomic Analyses ◽  
Cotton Waste

A group of five bacilli, designated strains 4T12, 4T19T, 5M45, 5M53 and 5T52, isolated from cotton-waste composts for mushroom cultivation, were examined. These strains were Gram-positive, aerobic, motile, spore-forming rods. 16S rRNA gene sequence analyses revealed that the isolates belonged to the genus Bacillus, showing the highest levels of similarity (approx. 96.6–96.9 %) with respect to Bacillus herbersteinensis DSM 16534T. The values for DNA–DNA hybridization (approx. 85–96 %) among these five strains revealed that they belong to the same species. The major menaquinone present was MK-7 and the predominant cellular fatty acids were anteiso-C15 : 0 (approx. 24.5–33.9 %) and C16 : 0 (approx. 15.1–34.1 %). The DNA G+C contents were 37.7–40.9 mol%. On the basis of physiological, biochemical, chemotaxonomic and comparative genomic analyses, the five isolates represent a novel species of the genus Bacillus, for which the name Bacillus niabensis sp. nov. is proposed. The type strain is 4T19T (=KACC 11279T =DSM 17723T).

scholarly journals Complete Genome Sequences of Mycobacteriophages Clautastrophe, Kingsolomon, Krypton555, and Nicholas

2017 ◽  
Vol 5 (45) ◽  
Author(s):  
Hui-Min Chung ◽  
Tom D’Elia ◽  
Joseph F. Ross ◽  
Samuel M. Alvarado ◽  
Molly-Catherine Brantley ◽  
...  
Keyword(s):  
Mycobacterium Smegmatis ◽  
Complete Genome ◽  
Soil Samples ◽  
Comparative Genomic ◽  
Gene Conservation ◽  
Genome Sequences ◽  
Content Type ◽  
Genomic Analyses

ABSTRACT We report here the complete genome sequences of four subcluster L3 mycobacteriophages newly isolated from soil samples, using Mycobacterium smegmatis mc2155 as the host. Comparative genomic analyses with four previously described subcluster L3 phages reveal strong nucleotide similarity and gene conservation, with several large insertions/deletions near their right genome ends.

scholarly journals Pathogenic Determinants of the Mycobacterium kansasii Complex: An Unsuspected Role for Distributive Conjugal Transfer

2021 ◽  
Vol 9 (2) ◽  
pp. 348
Author(s):  
Florian Tagini ◽  
Trestan Pillonel ◽  
Claire Bertelli ◽  
Katia Jaton ◽  
Gilbert Greub
Keyword(s):  
Genomic Analysis ◽  
Comparative Genomic ◽  
Mycobacterium Kansasii ◽  
Type Vii Secretion ◽  
A Genome ◽  
Genes Encoding ◽  
Associated Proteins ◽  
Immunosuppressed Patients ◽  
Type Vii Secretion System ◽  
Clinical Records

The Mycobacterium kansasii species comprises six subtypes that were recently classified into six closely related species; Mycobacterium kansasii (formerly M. kansasii subtype 1), Mycobacterium persicum (subtype 2), Mycobacterium pseudokansasii (subtype 3), Mycobacterium ostraviense (subtype 4), Mycobacterium innocens (subtype 5) and Mycobacterium attenuatum (subtype 6). Together with Mycobacterium gastri, they form the M. kansasii complex. M. kansasii is the most frequent and most pathogenic species of the complex. M. persicum is classically associated with diseases in immunosuppressed patients, and the other species are mostly colonizers, and are only very rarely reported in ill patients. Comparative genomics was used to assess the genetic determinants leading to the pathogenicity of members of the M. kansasii complex. The genomes of 51 isolates collected from patients with and without disease were sequenced and compared with 24 publicly available genomes. The pathogenicity of each isolate was determined based on the clinical records or public metadata. A comparative genomic analysis showed that all M. persicum, M. ostraviense, M innocens and M. gastri isolates lacked the ESX-1-associated EspACD locus that is thought to play a crucial role in the pathogenicity of M. tuberculosis and other non-tuberculous mycobacteria. Furthermore, M. kansasii was the only species exhibiting a 25-Kb-large genomic island encoding for 17 type-VII secretion system-associated proteins. Finally, a genome-wide association analysis revealed that two consecutive genes encoding a hemerythrin-like protein and a nitroreductase-like protein were significantly associated with pathogenicity. These two genes may be involved in the resistance to reactive oxygen and nitrogen species, a required mechanism for the intracellular survival of bacteria. Three non-pathogenic M. kansasii lacked these genes likely due to two distinct distributive conjugal transfers (DCTs) between M. attenuatum and M. kansasii, and one DCT between M. persicum and M. kansasii. To our knowledge, this is the first study linking DCT to reduced pathogenicity.

scholarly journals The domestication of Cucurbita argyrosperma as revealed by the genome of its wild relative

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Josué Barrera-Redondo ◽  
Guillermo Sánchez-de la Vega ◽  
Jonás A. Aguirre-Liguori ◽  
Gabriela Castellanos-Morales ◽  
Yocelyn T. Gutiérrez-Guerrero ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Population Level ◽  
Growth Hormones ◽  
Comparative Genomic ◽  
Structural Variants ◽  
Closely Related Species ◽  
Level Data ◽  
Genomic Analyses ◽  
Genotype By Sequencing ◽  
Regulation Of Growth

AbstractDespite their economic importance and well-characterized domestication syndrome, the genomic impact of domestication and the identification of variants underlying the domestication traits in Cucurbita species (pumpkins and squashes) is currently lacking. Cucurbita argyrosperma, also known as cushaw pumpkin or silver-seed gourd, is a Mexican crop consumed primarily for its seeds rather than fruit flesh. This makes it a good model to study Cucurbita domestication, as seeds were an essential component of early Mesoamerican diet and likely the first targets of human-guided selection in pumpkins and squashes. We obtained population-level data using tunable Genotype by Sequencing libraries for 192 individuals of the wild and domesticated subspecies of C. argyrosperma across Mexico. We also assembled the first high-quality wild Cucurbita genome. Comparative genomic analyses revealed several structural variants and presence/absence of genes related to domestication. Our results indicate a monophyletic origin of this domesticated crop in the lowlands of Jalisco. We found evidence of gene flow between the domesticated and wild subspecies, which likely alleviated the effects of the domestication bottleneck. We uncovered candidate domestication genes that are involved in the regulation of growth hormones, plant defense mechanisms, seed development, and germination. The presence of shared selected alleles with the closely related species Cucurbita moschata suggests domestication-related introgression between both taxa.

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