A genome assembly-integrated dog 1 Mb BAC microarray: a cytogenetic resource for canine cancer studies and comparative genomic analysis

Cultivated soybean (Glycine max) is an important source for protein and oil. Many elite cultivars with different traits have been developed for different conditions. Each soybean strain has its own genetic diversity, and the availability of more high-quality soybean genomes can enhance comparative genomic analysis for identifying genetic underpinnings for its unique traits. In this study, we constructed a high-quality de novo assembly of an elite soybean cultivar Jidou 17 (JD17) with chromsome contiguity and high accuracy. We annotated 52,840 gene models and reconstructed 74,054 high-quality full-length transcripts. We performed a genome-wide comparative analysis based on the reference genome of JD17 with three published soybeans (WM82, ZH13 and W05) , which identified five large inversions and two large translocations specific to JD17, 20,984 - 46,912 PAVs spanning 13.1 - 46.9 Mb in size, and 5 - 53 large PAV clusters larger than 500kb. 1,695,741 - 3,664,629 SNPs and 446,689 - 800,489 Indels were identified and annotated between JD17 and them. Symbiotic nitrogen fixation (SNF) genes were identified and the effects from these variants were further evaluated. It was found that the coding sequences of 9 nitrogen fixation-related genes were greatly affected. The high-quality genome assembly of JD17 can serve as a valuable reference for soybean functional genomics research.

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A genome-annotated bacterial collection of the barley rhizosphere microbiota

10.1101/2021.03.10.434690 ◽

2021 ◽

Author(s):

Senga Robertson-Albertyn ◽

Federico Concas ◽

Lynn H Brown ◽

Jamie N Orr ◽

James C Abbott ◽

...

Keyword(s):

Plant Growth ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

Strain Specificity ◽

Bacterial Microbiota ◽

A Genome ◽

Plant Growth Promoting ◽

Plant Microbiota ◽

Growth Promoting

ABSTRACTWe generated a bacterial collection from the rhizosphere of cultivated barley (Hordeum vulgare L. ssp. vulgare) to assess taxonomic distribution of culturable members of the barley microbiota and their plant growth-promoting potential. From this we retrieved strains belonging to the dominant phyla of the plant microbiota— Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria—and gathered evidence they code for functional genes implicated in nitrogen fixation, hydrogen cyanide channels and phosphate solubilisation. Here we present an initial comparative genomic analysis of the collection revealing that plant growth-promoting potential of the culturable barley bacterial microbiota appears to have a relatively broad phylogenetic base while retaining some strain-specificity.

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De novo phased assembly of the Vitis riparia grape genome

10.1101/640565 ◽

2019 ◽

Author(s):

Nabil Girollet ◽

Bernadette Rubio ◽

Pierre-François Bert

Keyword(s):

Genome Assembly ◽

De Novo ◽

Genomic Analysis ◽

Comparative Genomic ◽

Protein Coding ◽

Important Species ◽

Vitis Riparia ◽

Fruit Species ◽

Long Reads ◽

A Genome

AbstractGrapevine is one of the most important fruit species in the world. In order to better understand genetic basis of traits variation and facilitate the breeding of new genotypes, we sequenced, assembled, and annotated the genome of the American native Vitis riparia, one of the main species used worldwide for rootstock and scion breeding. A total of 164 Gb raw DNA reads were obtained from Vitis riparia resulting in a 225X depth of coverage. We generated a genome assembly of the V. riparia grape de novo using the PacBio long-reads that was phased with the 10x Genomics Chromium linked-reads. At the chromosome level, a 500 Mb genome was generated with a scaffold N50 size of 1 Mb. More than 34% of the whole genome were identified as repeat sequences, and 37,207 protein-coding genes were predicted. This genome assembly sets the stage for comparative genomic analysis of the diversification and adaptation of grapevine and will provide a solid resource for further genetic analysis and breeding of this economically important species.

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Genomic analysis based on chromosome-level genome assembly reveals an expansion of terpene biosynthesis of Azadirachta indica

10.1101/2021.11.11.468207 ◽

2021 ◽

Author(s):

Yuhui Du ◽

Wei Song ◽

Zhiqiu Yin ◽

shengbo wu ◽

jiaheng liu ◽

...

Keyword(s):

Azadirachta Indica ◽

Genome Assembly ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Genomic Research ◽

Comparative Genomic ◽

Terpene Biosynthesis ◽

Chromosome 13 ◽

Duplication Events ◽

Chromosome Level

Azadirachta indica (neem), an evergreen tree of the Meliaceae family, is a source of the potent biopesticide azadirachtin. The lack of a chromosome-level assembly impedes the understanding of in-depth genomic architecture and the comparative genomic analysis of A. indica. Here, a high-quality genome assembly of A. indica was constructed using a combination of data from Illumina, PacBio, and Hi-C technology, which is the first chromosome-scale genome assembly of A. indica. The genome size of A. indica is 281 Mb anchored to 14 chromosomes (contig N50=6 Mb and scaffold N50=19 Mb). The genome assembly contained 115 Mb repetitive elements and 25,767 protein-coding genes. Evolutional analysis revealed that A. indica did not experience any whole-genome duplication (WGD) event after the core eudicot γ event, but some genes and genome segment might undergo recent duplications. The secondary metabolite clusters, TPS genes, and CYP genes were also identified. Comparative genomic analysis revealed that most of the A. indica-specific TPS genes and CYP genes were located on the terpene-related clusters on chromosome 13. It is suggested that chromosome 13 may play an important role in the specific terpene biosynthesis of A. indica. And the gene duplication events may be responsible for the terpene biosynthesis expansion in A. indica. This will shed light on terpene biosynthesis in A. indica and facilitate comparative genomic research of the family Meliaceae.

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Comparative genomic analysis of Staphylococcus aureus CC80 strains. (c2015)

10.26756/th.2015.34 ◽

2015 ◽

Author(s):

Melhem E. Bilen

Keyword(s):

Staphylococcus Aureus ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Comparative Genomic

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Faculty Opinions recommendation of Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1108969.575120 ◽

2008 ◽

Author(s):

David Alpers

Keyword(s):

Pure Culture ◽

Bifidobacterium Longum ◽

Genomic Analysis ◽

Comparative Genomic Analysis ◽

Comparative Genomic ◽

Culture Growth

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

Microorganisms ◽

10.3390/microorganisms9020348 ◽

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.

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