scholarly journals In-Silico Identification of EST Based Microsatellite Markers and Snps, and Comparative Genomic Analysis of Ests in Barnyard Millet for their Omics Applications

2017 ◽  
Vol 5 (3) ◽  
pp. 279-287 ◽  
Author(s):  
B. Kalyana Babu ◽  
Rashmi Chauhan
Keyword(s):  
Microsatellite Markers ◽  
Rice Genome ◽  
Genomic Analysis ◽  
Repeat Motif ◽  
Waxy Gene ◽  
Comparative Genomic ◽  
Diabetic Patients ◽  
Genome Database ◽  
Barnyard Millet ◽  
Nucleotide Repeats

Barnyard millet belongs to the family poaceae, having good nutritional properties and is also effective for diabetic patients because of its ability to reduce the blood glucose levels. The research on genomics in barnyard millet lagging behind other millets and cereals, where there is a need of more focus towards identification of microsatellite markers. The availability of EST sequences given possibility to develop and explore the EST based SSRs and SNPs. Hence, the present study was conducted at ICAR-Vivekananda Parvateeya Krishi Anusanthan Sansthan, Almora, Uttarakhand in the year 2014-2015. In the present study, the barnyard millet EST sequences (41) were downloaded in FASTA format to find the microsatellite type, distribution, frequency and developed a total of 22 primer pairs from the ESTs. The most frequent SSR repeats found to be tetra- nucleotide repeats (50 percent) followed by the penta- and hexa- nucleotide repeats. Among the dimeric SSRs, GT was found to be the most common repeat motif, AGG was the most common repeat motif in trimeric repeat motifs. The most common tetra-, penta- and hexa nucleotide repeat motifs were AGA, CAAA, TGTTT, AGACGA respectively. The SNP mining of barnyard millet ESTs found to have 1 potential SNP and 1 reliable SNP and two haplotypes. Comparative analysis of barnyard millet EST sequences with the rice genome database showed that they were homology to the rice chromosomal regions of 2, 5, 6, 8, 9 and 12, however with maize genome showed homology with respect to Zea mays Waxy gene. Thus the identified twenty two microsatellite markers and SNPs can be effectively used for barnyard millet genomics applications to study diversity, and mapping aspects.

scholarly journals MoG+: a database of genomic variations across three mouse subspecies for biomedical research

2021 ◽  
Author(s):  
Toyoyuki Takada ◽  
Kentaro Fukuta ◽  
Daiki Usuda ◽  
Tatsuya Kushida ◽  
Shinji Kondo ◽  
...  
Keyword(s):  
Phenotypic Diversity ◽  
Laboratory Mouse ◽  
Genomic Analysis ◽  
Inbred Strains ◽  
Genetic Distances ◽  
Mouse Strains ◽  
Comparative Genomic ◽  
Genome Database ◽  
Data Resource ◽  
Genomic Variations

AbstractLaboratory mouse strains have mosaic genomes derived from at least three major subspecies that are distributed in Eurasia. Here, we describe genomic variations in ten inbred strains: Mus musculus musculus-derived BLG2/Ms, NJL/Ms, CHD/Ms, SWN/Ms, and KJR/Ms; M. m. domesticus-derived PGN2/Ms and BFM/Ms; M. m. castaneus-derived HMI/Ms; and JF1/Ms and MSM/Ms, which were derived from a hybrid between M. m. musculus and M. m. castaneus. These strains were established by Prof. Moriwaki in the 1980s and are collectively named the “Mishima Battery”. These strains show large phenotypic variations in body size and in many physiological traits. We resequenced the genomes of the Mishima Battery strains and performed a comparative genomic analysis with dbSNP data. More than 81 million nucleotide coordinates were identified as variant sites due to the large genetic distances among the mouse subspecies; 8,062,070 new SNP sites were detected in this study, and these may underlie the large phenotypic diversity observed in the Mishima Battery. The new information was collected in a reconstructed genome database, termed MoG+ that includes new application software and viewers. MoG+ intuitively visualizes nucleotide variants in genes and intergenic regions, and amino acid substitutions across the three mouse subspecies. We report statistical data from the resequencing and comparative genomic analyses and newly collected phenotype data of the Mishima Battery, and provide a brief description of the functions of MoG+, which provides a searchable and unique data resource of the numerous genomic variations across the three mouse subspecies. The data in MoG+ will be invaluable for research into phenotype-genotype links in diverse mouse strains.

scholarly journals A database for risk assessment and comparative genomic analysis of foodborne Vibrio parahaemolyticus in China

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Rui Pang ◽  
Yanping Li ◽  
Moutong Chen ◽  
Haiyan Zeng ◽  
Tao Lei ◽  
...  
Keyword(s):  
Risk Assessment ◽  
Foodborne Pathogens ◽  
Vibrio Parahaemolyticus ◽  
Foodborne Pathogen ◽  
Genomic Analysis ◽  
Food Samples ◽  
Comparative Genomic ◽  
Genome Database ◽  
Scientific Database ◽  
Need To Evaluate

Abstract Vibrio parahaemolyticus is a major foodborne pathogen worldwide. The increasing number of cases of V. parahaemolyticus infections in China indicates an urgent need to evaluate the prevalence and genetic diversity of this pathogenic bacterium. In this paper, we introduce the Foodborne Vibrio parahaemolyticus genome database (FVPGD), the first scientific database of foodborne V. parahaemolyticus distribution and genomic data in China, based on our previous investigations of V. parahaemolyticus contamination in different kinds of food samples across China from 2011 to 2016. The dataset includes records of 2,499 food samples and 643 V. parahaemolyticus strains from supermarkets and marketplaces distributed over 39 cities in China; 268 whole-genome sequences have been deposited in this database. A spatial view on the risk situations of V. parahaemolyticus contamination in different food types is provided. Additionally, the database provides a functional interface of sequence BLAST, core genome multilocus sequence typing, and phylogenetic analysis. The database will become a powerful tool for risk assessment and outbreak investigations of foodborne pathogens in China.

Divergent evolution of the myosin heavy chain gene family in fish and tetrapods: evidence from comparative genomic analysis

2007 ◽  
Vol 32 (1) ◽  
pp. 1-15 ◽  
Author(s):  
Daisuke Ikeda ◽  
Yosuke Ono ◽  
Phil Snell ◽  
Yvonne J. K. Edwards ◽  
Greg Elgar ◽  
...  
Keyword(s):  
Myosin Heavy Chain ◽  
Heavy Chain ◽  
Genomic Analysis ◽  
Divergent Evolution ◽  
Comparative Genomic ◽  
Chain Gene ◽  
Takifugu Rubripes ◽  
Genome Database ◽  
Genomic Regions ◽  
Syntenic Analysis

Myosin heavy chain genes ( MYHs) are the most important functional domains of myosins, which are highly conserved throughout evolution. The human genome contains 15 MYHs, whereas the corresponding number in teleost appears to be much higher. Although teleosts comprise more than one-half of all vertebrate species, our knowledge of MYHs in teleosts is rather limited. A comprehensive analysis of the torafugu ( Takifugu rubripes) genome database enabled us to detect at least 28 MYHs, almost twice as many as in humans. RT-PCR revealed that at least 16 torafugu MYH representatives (5 fast skeletal, 3 cardiac, 2 slow skeletal, 1 superfast, 2 smooth, and 3 nonmuscle types) are actually transcribed. Among these, MYH M743-2 and MYH M5 of fast and slow skeletal types, respectively, are expressed during development of torafugu embryos. Syntenic analysis reveals that torafugu fast skeletal MYHs are distributed across five genomic regions, three of which form clusters. Interestingly, while human fast skeletal MYHs form one cluster, its syntenic region in torafugu is duplicated, although each locus contains just a single MYH in torafugu. The results of the syntenic analysis were further confirmed by corresponding analysis of MYHs based on databases from Tetraodon, zebrafish, and medaka genomes. Phylogenetic analysis suggests that fast skeletal MYHs evolved independently in teleosts and tetrapods after fast skeletal MYHs had diverged from four ancestral MYHs.

scholarly journals Phylogenomic analysis of the genus Pseudomonas and reclassification of P. humi, P. zeshuii, P. psychrotolerans, P. nitritireducens, P. pharmacofabricae and P. panacis are later heterotypic synonym of P. citronellolis Lang 2007, P. luteola, P. oryzihabitans, P. nitroreducens Lang 2007, P. fluvialis and P. marginalis (Brown 1918) Stevens 1925 (Approved Lists 1980), respectively

2021 ◽  
Author(s):  
Ritu Rani Kujur ◽  
Sushanta Deb ◽  
Subrata K Das
Keyword(s):  
Dna Hybridization ◽  
Type Species ◽  
Genomic Analysis ◽  
Amino Acid Identity ◽  
Comparative Genomic ◽  
Phylogenomic Analysis ◽  
Taxonomic Assignment ◽  
Genome Database ◽  
Average Amino Acid Identity ◽  
Genome Comparisons

The present study described the comparative genomic analysis of the validly named species of the genus Pseudomonas to define the taxonomic assignment. Genomic information for 208 type strains was available in the NCBI genome database at the time of conducting this analysis. The ANI, AAI and in silico DNA DNA hybridization (isDDH) data were higher than the threshold values for the twelve strains with their closely related type species. Whole genome comparisons shared 97 - 99 % average nucleotide identity, 97.85 to 99.19 % average amino acid identity and 72.80 to 90.40 % digital DNA DNA hybridization values. Further, the phylogenomic analysis based on the core genome confirmed that P. humi CCA1 and P. citronellolis LMG 18378, P. zeshuii KACC 15471 and P. luteola NBRC 103146, P. oryzihabitans DSM 6835 and P. psychrotolerans DSM 15758, P. nitroreducens DSM 14399 and P. nitritireducens WZBFD3-5A2, P. fluvialis CCM 8778 and P. pharmacofabricae ZYSR67-Z, P. panacis DSM 18529 and P. marginalis DSM 13124 formed a monophyletic clade. Thus, we proposed six type species viz., P. humi CCA1, P. zeshuii KACC 15471, P. psychrotolerans DSM 15758, P. nitritireducens WZBFD3 5A2, P. pharmacofabricae ZYSR67 Z and P. panacis DSM 18529 are the later heterotypic synonym of P. citronellolis Lang 2007, P. luteola, P. oryzihabitans, P. nitroreducens Lang 2007, P. fluvialis and P. marginalis (Brown 1918) Stevens 1925 (Approved Lists 1980), respectively considering the priority date of publication.

scholarly journals High-quality genome assembly of Cinnamomum burmami (chvar. Borneol) provides insights into the natural borneol biosynthesis

2021 ◽  
Author(s):  
Fangping Li ◽  
Shilin Huang ◽  
Yu Mei ◽  
Bingqi Wu ◽  
Zhuangwei Hou ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genome Assembly ◽  
Herbal Medicines ◽  
Genomic Analysis ◽  
Biological Tissues ◽  
Industrial Plant ◽  
Size Difference ◽  
Comparative Genomic ◽  
High Quality ◽  
Genome Database

Cinnamomum burmami (chvar. Borneol) is a well-known medicinal and industrial plant cultivated in the Lingnan region of China. It is the key source from organism of natural borneol (D-borneol), one of the precious and widely used Chinese herbal medicines with a variety of medicinal effects. Here, we report a high-quality chromosome-scale genome assembly of C. burmami (chvar. Borneol) using Pacbio single-molecule sequencing and Hi-C technology. The assembled genome size was 1.14 GB with a scaffold N50 of 94.30 Mb, while 98.77% of the assembled sequences were anchored on 12 pseudochromosomes including 41549 protein-coding genes. Genomic evolution analysis revealed C. burmami and C. micranthum shared two Lauraceae unique ancestral whole-genome duplication (WGD) events. Likewise, comparative genomic analysis showed strong collinearity between these two species. Besides, the analysis for Long Terminal Repeat Retrotransposons (LTR-RTs) indicated the outbreak of LTR-RTs insertion made a great contribution to the size difference of genomes between C. burmami and C. micranthum. Furthermore, the candidate genes in pathway associated with natural borneol synthesis were identified on the genome and their differential expressions were analyzed in various biological tissues. We considered that several of genes in Mevalonate (MVA) Methylerythritol Phosphate (MEP) pathways or in downstream pathway have the potential to be the key factors in the biosynthesis of D-borneol. We also constructed the genome database (CAMD; http://www.cinnamomumdatabase.com/) of Cinnamomum species for a better data utilization in the future. All these results will enrich the genomic data of Lauraceae plants and facilitate genetic improvement of this commercially important plant.

scholarly journals Comparative Genomic Analysis of 450 Strains of Salmonella enterica Isolated from Diseased Animals

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1025
Author(s):  
Shaohua Zhao ◽  
Cong Li ◽  
Chih-Hao Hsu ◽  
Gregory H. Tyson ◽  
Errol Strain ◽  
...  
Keyword(s):  
Resistance Genes ◽  
Bacterial Infections ◽  
Genomic Analysis ◽  
Heavy Metal Resistance ◽  
Metal Resistance ◽  
Comparative Genomic ◽  
Salmonella Infections ◽  
Antimicrobial Resistance Genes ◽  
Salmonella Pathogenicity Islands ◽  
Shed Light

Salmonella is a leading cause of bacterial infections in animals and humans. We sequenced a collection of 450 Salmonella strains from diseased animals to better understand the genetic makeup of their virulence and resistance features. The presence of Salmonella pathogenicity islands (SPIs) varied by serotype. S. Enteritidis carried the most SPIs (n = 15), while S. Mbandaka, S. Cerro, S. Meleagridis, and S. Havana carried the least (n = 10). S. Typhimurium, S. Choleraesuis, S. I 4,5,12:i:-, and S. Enteritidis each contained the spv operon on IncFII or IncFII-IncFIB hybrid plasmids. Two S. IIIa carried a spv operon with spvD deletion on the chromosome. Twelve plasmid types including 24 hybrid plasmids were identified. IncA/C was frequently associated with S. Newport (83%) and S. Agona (100%) from bovine, whereas IncFII (100%), IncFIB (100%), and IncQ1 (94%) were seen in S. Choleraesuis from swine. IncX (100%) was detected in all S. Kentucky from chicken. A total of 60 antimicrobial resistance genes (ARGs), four disinfectant resistances genes (DRGs) and 33 heavy metal resistance genes (HMRGs) were identified. The Salmonella strains from sick animals contained various SPIs, resistance genes and plasmid types based on the serotype and source of the isolates. Such complicated genomic structures shed light on the strain characteristics contributing to the severity of disease and treatment failures in Salmonella infections, including those causing illnesses in animals.

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.

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