Genome survey sequencing of Atractylodes lancea and identification of its SSR markers

Abstract Atractylodes lancea (Thunb.) DC. is a traditional Chinese medicine rich in sesquiterpenes that has been widely used in China and Japan for the treatment of viral infections. Despite its important pharmacological value, genomic information regarding A. lancea is currently unavailable. In the present study, the whole genome sequence of A. lancea was obtained using an Illumina sequencing platform. The results revealed an estimated genome size for A. lancea of 4,159.24 Mb, with 2.28% heterozygosity, and a repeat rate of 89.2%, all of which indicate a highly heterozygous genome. Based on the genomic data of A. lancea, 27,582 simple sequence repeat (SSR) markers were identified. The differences in representation among nucleotide repeat types were large, e.g., the mononucleotide repeat type was the most abundant (54.74%) while the pentanucleotide repeats were the least abundant (0.10%), and sequence motifs GA/TC (31.17%) and TTC/GAA (7.23%) were the most abundant among the dinucleotide and trinucleotide repeat motifs, respectively. A total of 93,434 genes matched known genes in common databases including 48,493 genes in the Gene Ontology (GO) database and 34,929 genes in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. This is the first report to sequence and characterize the whole genome of A. lancea and will provide a theoretical basis and reference for further genome-wide deep sequencing and SSR molecular marker development of A. lancea.

Download Full-text

Whole genome survey analysis and microsatellite motif identification of Sebastiscus marmoratus

Bioscience Reports ◽

10.1042/bsr20192252 ◽

2020 ◽

Vol 40 (2) ◽

Author(s):

Sheng-yong Xu ◽

Na Song ◽

Shi-jun Xiao ◽

Tian-xiang Gao

Keyword(s):

Microsatellite Markers ◽

Gc Content ◽

The Philippines ◽

Whole Genome Sequence ◽

Northwestern Pacific ◽

Whole Genome ◽

Survey Analysis ◽

Genome Survey ◽

Sebastiscus Marmoratus ◽

Wide Range

Abstract The marbled rockfish Sebastiscus marmoratus is an ecologically and economically important marine fish species distributed along the northwestern Pacific coast from Japan to the Philippines. Here, next-generation sequencing was used to generate a whole genome survey dataset to provide fundamental information of its genome and develop genome-wide microsatellite markers for S. marmoratus. The genome size of S. marmoratus was estimated as approximate 800 Mb by using K-mer analyses, and its heterozygosity ratio and repeat sequence ratio were 0.17% and 39.65%, respectively. The preliminary assembled genome was nearly 609 Mb with GC content of 41.3%, and the data were used to develop microsatellite markers. A total of 191,592 microsatellite motifs were identified. The most frequent repeat motif was dinucleotide with a frequency of 76.10%, followed by 19.63% trinucleotide, 3.91% tetranucleotide, and 0.36% pentanucleotide motifs. The AC, GAG, and ATAG repeats were the most abundant motifs of dinucleotide, trinucleotide, and tetranucleotide motifs, respectively. In summary, a wide range of candidate microsatellite markers were identified and characterized in the present study using genome survey analysis. High-quality whole genome sequence based on the “Illumina+PacBio+Hi-C” strategy is warranted for further comparative genomics and evolutionary biology studies in this species.

Download Full-text

Whole-genome sequencing data of Kazakh individuals

BMC Research Notes ◽

10.1186/s13104-021-05464-4 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Ulykbek Kairov ◽

Askhat Molkenov ◽

Saule Rakhimova ◽

Ulan Kozhamkulov ◽

Aigul Sharip ◽

...

Keyword(s):

Next Generation Sequencing ◽

Whole Genome Sequence ◽

Whole Genome ◽

Next Generation ◽

Sequencing Data ◽

Sequencing Platform ◽

Next Generation Sequencing Platform ◽

Central Asian ◽

Whole Genomes ◽

Generation Sequencing

Abstract Objectives Kazakhstan is a Central Asian crossroad of European and Asian populations situated along the way of the Great Silk Way. The territory of Kazakhstan has historically been inhabited by nomadic tribes and today is the multi-ethnic country with the dominant Kazakh ethnic group. We sequenced and analyzed the whole-genomes of five ethnic healthy Kazakh individuals with high coverage using next-generation sequencing platform. This whole-genome sequence data of healthy Kazakh individuals can be a valuable reference for biomedical studies investigating disease associations and population-wide genomic studies of ethnically diverse Central Asian region. Data description Blood samples have been collected from five ethnic healthy Kazakh individuals living in Kazakhstan. The genomic DNA was extracted from blood and sequenced. Sequencing was performed on Illumina HiSeq2000 next-generation sequencing platform. We sequenced and analyzed the whole-genomes of ethnic Kazakh individuals with the coverage ranging from 26 to 32X. Ranging from 98.85 to 99.58% base pairs were totally mapped and aligned on the human reference genome GRCh37 hg19. Het/Hom and Ts/Tv ratios for each whole genome ranged from 1.35 to 1.49 and from 2.07 to 2.08, respectively. Sequencing data are available in the National Center for Biotechnology Information SRA database under the accession number PRJNA374772.

Download Full-text

Whole-Genome Sequence of Salmonella enterica Serovar Enteritidis Phage Type 4, Isolated from a Brazilian Poultry Farm

Genome Announcements ◽

10.1128/genomea.00340-16 ◽

2016 ◽

Vol 4 (3) ◽

Cited By ~ 2

Author(s):

Guilherme Paier Milanez ◽

Leandro Costa Nascimento ◽

Adriane Holtz Tirabassi ◽

Marcelo Zuanaze ◽

Dália Prazeres Rodrigues ◽

...

Keyword(s):

Salmonella Enterica ◽

Phage Type ◽

Draft Genome ◽

Whole Genome Sequence ◽

Whole Genome ◽

Poultry Farm ◽

Salmonella Enterica Serovar Enteritidis ◽

Sequencing Platform ◽

Paulo State ◽

Illumina Sequencing Platform

The draft genome of Salmonella enterica serovar Enteritidis phage type 4 (PT4) strain IOC4647/2004, isolated from a poultry farm in São Paulo state, was obtained with high-throughput Illumina sequencing platform, generating 4,173,826 paired-end reads with 251 bp. The assembly of 4,804,382 bp in 27 scaffolds shows strong similarity to other S . Enteritidis strains.

Download Full-text

Whole-Genome Sequence of Staphylococcus hominis Strain J31 Isolated from Healthy Human Skin

Genome Announcements ◽

10.1128/genomea.01548-16 ◽

2017 ◽

Vol 5 (15) ◽

Cited By ~ 1

Author(s):

Rosanna Coates-Brown ◽

Malcolm J. Horsburgh

Keyword(s):

Human Skin ◽

Genome Sequence ◽

Whole Genome Sequence ◽

Whole Genome ◽

Healthy Human ◽

Content Type ◽

Sequencing Platform ◽

Long Read ◽

Staphylococcus Hominis

ABSTRACT We report here the first whole-genome sequence of a skin-associated strain of Staphylococcus hominis determined using the PacBio long-read sequencing platform. S. hominis is a major commensal of the skin microflora. This genome sequence adds to our understanding of this species and will aid studies of gene traffic between staphylococci.

Download Full-text

Genome-wide simple sequence repeats (SSR) markers discovered from whole-genome sequence comparisons of multiple spinach accessions

Scientific Reports ◽

10.1038/s41598-021-89473-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Gehendra Bhattarai ◽

Ainong Shi ◽

Devi R. Kandel ◽

Nora Solís-Gracia ◽

Jorge Alberto da Silva ◽

...

Keyword(s):

Ssr Markers ◽

Genome Sequence ◽

Reference Genome ◽

Whole Genome Sequence ◽

Large Set ◽

Whole Genome ◽

Genome Sequences ◽

Sequence Comparisons ◽

Ssr Loci ◽

Simple Sequence

AbstractThe availability of well-assembled genome sequences and reduced sequencing costs have enabled the resequencing of many additional accessions in several crops, thus facilitating the rapid discovery and development of simple sequence repeat (SSR) markers. Although the genome sequence of inbred spinach line Sp75 is available, previous efforts have resulted in a limited number of useful SSR markers. Identification of additional polymorphic SSR markers will support genetics and breeding research in spinach. This study aimed to use the available genomic resources to mine and catalog a large number of polymorphic SSR markers. A search for SSR loci on six chromosome sequences of spinach line Sp75 using GMATA identified a total of 42,155 loci with repeat motifs of two to six nucleotides in the Sp75 reference genome. Whole-genome sequences (30x) of additional 21 accessions were aligned against the chromosome sequences of the reference genome and in silico genotyped using the HipSTR program by comparing and counting repeat numbers variation across the SSR loci among the accessions. The HipSTR program generated SSR genotype data were filtered for monomorphic and high missing loci, and a final set of the 5986 polymorphic SSR loci were identified. The polymorphic SSR loci were present at a density of 12.9 SSRs/Mb and were physically mapped. Out of 36 randomly selected SSR loci for validation, two failed to amplify, while the remaining were all polymorphic in a set of 48 spinach accessions from 34 countries. Genetic diversity analysis performed using the SSRs allele score data on the 48 spinach accessions showed three main population groups. This strategy to mine and develop polymorphic SSR markers by a comparative analysis of the genome sequences of multiple accessions and computational genotyping of the candidate SSR loci eliminates the need for laborious experimental screening. Our approach increased the efficiency of discovering a large set of novel polymorphic SSR markers, as demonstrated in this report.

Download Full-text

Use of a Whole Genome Approach To Identify Vaccine Molecules Affording Protection against Streptococcus pneumoniae Infection

Infection and Immunity ◽

10.1128/iai.69.3.1593-1598.2001 ◽

2001 ◽

Vol 69 (3) ◽

pp. 1593-1598 ◽

Cited By ~ 233

Author(s):

Theresa M. Wizemann ◽

Jon H. Heinrichs ◽

John E. Adamou ◽

Alice L. Erwin ◽

Charles Kunsch ◽

...

Keyword(s):

Streptococcus Pneumoniae ◽

Bacterial Pathogen ◽

Human Infection ◽

Open Reading Frames ◽

Whole Genome Sequence ◽

Whole Genome ◽

Sequence Motifs ◽

Surface Binding ◽

Protective Antigens ◽

Surface Localization

ABSTRACT Microbial targets for protective humoral immunity are typically surface-localized proteins and contain common sequence motifs related to their secretion or surface binding. Exploiting the whole genome sequence of the human bacterial pathogen Streptococcus pneumoniae, we identified 130 open reading frames encoding proteins with secretion motifs or similarity to predicted virulence factors. Mice were immunized with 108 of these proteins, and 6 conferred protection against disseminated S. pneumoniaeinfection. Flow cytometry confirmed the surface localization of several of these targets. Each of the six protective antigens showed broad strain distribution and immunogenicity during human infection. Our results validate the use of a genomic approach for the identification of novel microbial targets that elicit a protective immune response. These new antigens may play a role in the development of improved vaccines against S. pneumoniae.

Download Full-text

Development of Whole Genome Sequence-based Novel SSR Markers in Astragalus membranaceus (Fisch.)

Korean Journal of Medicinal Crop Science ◽

10.7783/kjmcs.2021.29.6.418 ◽

2021 ◽

Vol 29 (6) ◽

pp. 418-424

Author(s):

Mok Hur ◽

Yurry Um ◽

Yi Lee ◽

Yoon Jeong Lee ◽

Sung Cheol Koo ◽

...

Keyword(s):

Ssr Markers ◽

Genome Sequence ◽

Whole Genome Sequence ◽

Astragalus Membranaceus ◽

Whole Genome

Download Full-text

Development of Genome-wide Simple Sequence Repeat Markers from Whole-genome Sequence of Mungbean (Vigna radiata)

Legume Research - An International Journal ◽

10.18805/lr-4444 ◽

2021 ◽

Author(s):

Kanimoli Mathivathana Mayalagu ◽

Karthikeyan Adhimoolam ◽

Jagadeeshselvam Nallathambi ◽

Veera Ranjani Rajagopalan ◽

Madhumitha Balasubramanian ◽

...

Keyword(s):

Ssr Markers ◽

Genome Sequence ◽

Genomic Sequence ◽

Model Organism ◽

Cost Effective ◽

Whole Genome Sequence ◽

Human Consumption ◽

Whole Genome ◽

Ssr Primers ◽

Simple Sequence

Background: Mungbean is an important pulse crop and it is mainly cultivated in Asia for human consumption. Its small genome and diploid nature make it a well-suited model organism among legume crops. Thus, cost-effective, reliable and highly polymorphic molecular markers distributing the whole genome are needed for diversity, mapping and functional genomics studies in this model species. Methods: The whole-genome sequence of mungbean was obtained and used as a source of identification of simple sequence repeats (SSR). The sequence reads were aligned and SSRs detection was performed using the Phobos plugin tandem repeat finder in the Geneious software program. A total of 12 mungbean genotypes were selected to validate the newly developed SSR markers. Result: In the present study, a total of 12, 49,774 and 11, 86, 386 perfect and imperfect SSR repeats were identified from the mungbean genome. The tri-repeats were the most abundant (26.10%), followed by hexa (20.82%), penta (20.45%), tetra (17.65%) and di-repeats (14.95%). We designed 1330 SSR primers based on the genomic sequence of flanking perfect SSRs (Di and tri-repeats). Among them, 50 SSR primers uniformly distributed across the 11 mungbean chromosomes were selected and used to validate 12 mungbean genotypes. The newly developed genomic SSR markers generated in the present study are a valuable genomic resource for the mungbean breeding programs.

Download Full-text