Development of soybean aphid genomic SSR markers using next generation sequencing

Simple sequence repeats (SSRs) or microsatellites are very useful molecular markers, owing to their locus-specific codominant and multiallelic nature, high abundance in the genome, and high rates of transferability across species. The soybean aphid ( Aphis glycines Matsumura) has become the most damaging insect pest of soybean ( Glycine max (L.) Merr.) in North America, since it was first found in the Midwest of the United States in 2000. Biotypes of the soybean aphid capable of colonizing newly developed aphid-resistant soybean cultivars have been recently discovered. Genetic resources, including molecular markers, to study soybean aphids are severely lacking. Recently developed next generation sequencing platforms offer opportunities for high-throughput and inexpensive genome sequencing and rapid marker development. The objectives of this study were (i) to develop and characterize genomic SSR markers from soybean aphid genomic sequences generated by next generation sequencing technology and (ii) to evaluate the utility of the SSRs for genetic diversity or relationship analyses. In total 128 SSR primer pairs were designed from sequences generated by Illumina GAII from a reduced representation library of A. glycines. Nearly 94% (120) of the primer pairs amplified SSR alleles of expected size and 24 SSR loci were polymorphic among three aphid samples from three populations. The polymorphic SSRs were successfully used to differentiate among 24 soybean aphids from Ohio and South Dakota. Sequencing of PCR products of two SSR markers from four aphid samples revealed that the allelic polymorphism was due to variation in the SSR repeats among the aphids. These markers should be particularly useful for genetic differentiation among aphids collected from soybean fields at different localities and regions. These SSR markers provide the soybean aphid research community with the first set of PCR-based codominant markers developed from the genomic sequences of A. glycines.

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Development of Saccharina japonica genomic SSR markers using next-generation sequencing

Journal of Applied Phycology ◽

10.1007/s10811-015-0643-0 ◽

2015 ◽

Vol 28 (2) ◽

pp. 1387-1390 ◽

Cited By ~ 10

Author(s):

Qiuying Li ◽

Jie Zhang ◽

Jianting Yao ◽

Xiuliang Wang ◽

Delin Duan

Keyword(s):

Next Generation Sequencing ◽

Ssr Markers ◽

Saccharina Japonica ◽

Next Generation ◽

Genomic Ssr ◽

Generation Sequencing

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Molecular marker information from de novo assembled transcriptomes of chilli pepper (Capsicum annuum L.) varieties based on next-generation sequencing technology

Plant Genetic Resources ◽

10.1017/s147926211400032x ◽

2014 ◽

Vol 12 (S1) ◽

pp. S83-S86 ◽

Cited By ~ 1

Author(s):

Yul-Kyun Ahn ◽

Swati Tripathi ◽

Young-Il Cho ◽

Jeong-Ho Kim ◽

Hye-Eun Lee ◽

...

Keyword(s):

Molecular Markers ◽

Next Generation Sequencing ◽

De Novo ◽

Transcriptome Assembly ◽

Sequence Variant ◽

Nucleotide Polymorphisms ◽

Next Generation ◽

Chilli Pepper ◽

Next Generation Sequencing Technology ◽

Generation Sequencing

Next-generation sequencing technique has been known as a useful tool for de novo transcriptome assembly, functional annotation of genes and identification of molecular markers. This study was carried out to mine molecular markers from de novo assembled transcriptomes of four chilli pepper varieties, the highly pungent ‘Saengryeg 211’ and non-pungent ‘Saengryeg 213’ and variably pigmented ‘Mandarin’ and ‘Blackcluster’. Pyrosequencing of the complementary DNA library resulted in 361,671, 274,269, 279,221, and 316,357 raw reads, which were assembled in 23,607, 19,894, 18,340 and 20,357 contigs, for the four varieties, respectively. Detailed sequence variant analysis identified numerous potential single-nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) for all the varieties for which the primers were designed. The transcriptome information and SNP/SSR markers generated in this study provide valuable resources for high-density molecular genetic mapping in chilli pepper and Quantitative trait loci analysis related to fruit qualities. These markers for pepper will be highly valuable for marker-assisted breeding and other genetic studies.

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Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants

Molecules ◽

10.3390/molecules23020399 ◽

2018 ◽

Vol 23 (2) ◽

pp. 399 ◽

Cited By ~ 41

Author(s):

Sima Taheri ◽

Thohirah Lee Abdullah ◽

Mohd Yusop ◽

Mohamed Hanafi ◽

Mahbod Sahebi ◽

...

Keyword(s):

Next Generation Sequencing ◽

Ssr Markers ◽

Next Generation ◽

Next Generation Sequencing Ngs ◽

Ngs Data ◽

Generation Sequencing

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Next Generation Sequencing-Based Molecular Marker Development: A Case Study in Betula Alnoides

Molecules ◽

10.3390/molecules23112963 ◽

2018 ◽

Vol 23 (11) ◽

pp. 2963 ◽

Cited By ~ 3

Author(s):

Jing Tan ◽

Jun-Jie Guo ◽

Ming-Yu Yin ◽

Huan Wang ◽

Wen-Pan Dong ◽

...

Keyword(s):

Next Generation Sequencing ◽

Molecular Marker ◽

Ssr Markers ◽

Southern China ◽

Diversity Index ◽

Next Generation ◽

Wiener Diversity Index ◽

Nucleotide Repeats ◽

Betula Alnoides ◽

Generation Sequencing

Betula alnoides is a fast-growing valuable indigenous tree species with multiple uses in the tropical and warm subtropical regions in South-East Asia and southern China. It has been proved to be tetraploid in most parts of its distribution in China. In the present study, next generation sequencing (NGS) technology was applied to develop numerous SSR markers for B. alnoides, and 64,376 contig sequences of 106,452 clean reads containing 164,357 candidate SSR loci were obtained. Among the derived SSR repeats, mono-nucleotide was the main type (77.05%), followed by di- (10.18%), tetra- (6.12%), tri- (3.56%), penta- (2.14%) and hexa-nucleotide (0.95%). The short nucleotide sequence repeats accounted for 90.79%. Among the 291 repeat motifs, AG/CT (46.33%) and AT/AT (44.15%) were the most common di-nucleotide repeats, while AAT/ATT (48.98%) was the most common tri-nucleotide repeats. A total of 2549 primer sets were designed from the identified putative SSR regions of which 900 were randomly selected for evaluation of amplification successfulness and detection of polymorphism if amplified successfully. Three hundred and ten polymorphic markers were obtained through testing with 24 individuals from B. alnoides natural forest in Jingxi County, Guangxi, China. The number of alleles (NA) of each marker ranged from 2 to 19 with a mean of 5.14. The observed (HO) and expected (HE) heterozygosities varied from 0.04 to 1.00 and 0.04 to 0.92 with their means being 0.64 and 0.57, respectively. Shannon-Wiener diversity index (I) ranged from 0.10 to 2.68 with a mean of 1.12. Cross-species transferability was further examined for 96 pairs of SSR primers randomly selected, and it was found that 48.96–84.38% of the primer pairs could successfully amplify each of six related Betula species. The obtained SSR markers can be used to study population genetics and molecular marker assisted breeding, particularly genome-wide association study of these species in the future.

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Development of Genome-Wide SSR Markers from Angelica gigas Nakai Using Next Generation Sequencing

Genes ◽

10.3390/genes8100238 ◽

2017 ◽

Vol 8 (10) ◽

pp. 238 ◽

Cited By ~ 5

Author(s):

Jinsu Gil ◽

Yurry Um ◽

Serim Kim ◽

Ok Kim ◽

Sung Koo ◽

...

Keyword(s):

Next Generation Sequencing ◽

Ssr Markers ◽

Next Generation ◽

Angelica Gigas ◽

Angelica Gigas Nakai ◽

Genome Wide ◽

Generation Sequencing

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Next-Generation Sequencing and Bioinformatics Protocol for Malaria Drug Resistance Marker Surveillance

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02474-17 ◽

2018 ◽

Vol 62 (4) ◽

pp. e02474-17 ◽

Cited By ~ 20

Author(s):

Eldin Talundzic ◽

Shashidhar Ravishankar ◽

Julia Kelley ◽

Dhruviben Patel ◽

Mateusz Plucinski ◽

...

Keyword(s):

Drug Resistance ◽

Next Generation Sequencing ◽

Deep Sequencing ◽

Artemisinin Resistance ◽

The United States ◽

Imported Malaria ◽

Chloroquine Resistance ◽

Next Generation ◽

Content Type ◽

Generation Sequencing

ABSTRACT The recent advances in next-generation sequencing technologies provide a new and effective way of tracking malaria drug-resistant parasites. To take advantage of this technology, an end-to-end Illumina targeted amplicon deep sequencing (TADS) and bioinformatics pipeline for molecular surveillance of drug resistance in P. falciparum, called malaria resistance surveillance (MaRS), was developed. TADS relies on PCR enriching genomic regions, specifically target genes of interest, prior to deep sequencing. MaRS enables researchers to simultaneously collect data on allele frequencies of multiple full-length P. falciparum drug resistance genes (crt, mdr1, k13, dhfr, dhps, and the cytochrome b gene), as well as the mitochondrial genome. Information is captured at the individual patient level for both known and potential new single nucleotide polymorphisms associated with drug resistance. The MaRS pipeline was validated using 245 imported malaria cases that were reported to the Centers for Disease Control and Prevention (CDC). The chloroquine resistance crt CVIET genotype (mutations underlined) was observed in 42% of samples, the highly pyrimethamine-resistant dhps IRN triple mutant in 92% of samples, and the sulfadoxine resistance dhps mutation SGEAA in 26% of samples. The mdr1 NFSND genotype was found in 40% of samples. With the exception of two cases imported from Cambodia, no artemisinin resistance k13 alleles were identified, and 99% of patients carried parasites susceptible to atovaquone-proguanil. Our goal is to implement MaRS at the CDC for routine surveillance of imported malaria cases in the United States and to aid in the adoption of this system at participating state public health laboratories, as well as by global partners.

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Development of 65 Novel Polymorphic cDNA-SSR Markers in Common Vetch (Vicia sativa subsp. sativa) Using Next Generation Sequencing

Molecules ◽

10.3390/molecules18078376 ◽

2013 ◽

Vol 18 (7) ◽

pp. 8376-8392 ◽

Cited By ~ 27

Author(s):

Jong-Wook Chung ◽

Tae-Sung Kim ◽

Sundan Suresh ◽

Sok-Young Lee ◽

Gyu-Taek Cho

Keyword(s):

Next Generation Sequencing ◽

Ssr Markers ◽

Vicia Sativa ◽

Next Generation ◽

Common Vetch ◽

Generation Sequencing

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Development of SSR markers by next-generation sequencing of Korean landraces of chamoe (Cucumis melo var. makuwa)

Molecular Biology Reports ◽

10.1007/s11033-013-2803-0 ◽

2013 ◽

Vol 40 (12) ◽

pp. 6855-6862 ◽

Cited By ~ 7

Author(s):

Inkyu Park ◽

Jungeun Kim ◽

Jeongyeo Lee ◽

Sewon Kim ◽

Okhee Cho ◽

...

Keyword(s):

Next Generation Sequencing ◽

Ssr Markers ◽

Cucumis Melo ◽

Next Generation ◽

Generation Sequencing

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Identification and Characterization of a Novel Parvovirus-Like Virus in Seronegative Hepatitis Patients by Next Generation Sequencing

Blood ◽

10.1182/blood.v120.21.273.273 ◽

2012 ◽

Vol 120 (21) ◽

pp. 273-273

Author(s):

Baoyan Xu ◽

Ning Zhi ◽

Gangqing Hu ◽

Zhihong Wan ◽

Sachiko Kajigaya ◽

...

Keyword(s):

Next Generation Sequencing ◽

Capsid Protein ◽

Conflicts Of Interest ◽

Virus Titer ◽

The United States ◽

Western China ◽

Healthy Controls ◽

Next Generation ◽

Specific Antibodies ◽

Generation Sequencing

Abstract Abstract 273 Seronegative hepatitis—non-hepatitis A, non-B, non-C, non-E—is poorly characterized but strongly associated with serious complications, especially aplastic anemia and fulminant hepatitis of childhood. Seronegative hepatitis is rare in the United States but more prevalent in Asia, constituting about 10–20% of acute cases. We applied next-generation sequencing to blood samples of patients from western China with seronegative hepatitis for virus discovery. A total of 92 plasma specimens were collected at Chongqing, China, between 1999 and 2007. Twenty-seven patients were diagnosed as having acute hepatitis by clinical and laboratory characteristics. Sixty-five patients had biopsy-proven chronic aggressive hepatitis, ten of which had cirrhosis. Serologic assays for hepatitis viruses A, B, C, E, HIV, Epstein-Barr virus and cytomegalovirus were all negative. Additional tests for antinuclear antibody, rheumatoid factor, anti-mitochondrial antibody also were normal. Ten plasma pools derived from 93 specimens of the patients were screened by Solexa deep sequencing. We discovered a 3780-bp contig present in all ten-pools that yielded tBLASTx E scores of 0.003 to 1.5 against parvoviruses. The sequence of the in silico assembled 3780-bp contig was confirmed by overlapping PCRs, indicating the contig that contained the nearly complete new virus genome indeed existed in the patient samples rather than being artificially generated by misassembly. The new virus is provisionally designated NIH-CQV. Further analysis revealed that the contig was composed of two major open reading frames (ORF). Protein Blast showed that ORF1 encoded a protein that contained a conserved P-loop NTPase domain, homologous to the replication-associated protein of bat circovirus (E score=4e-04). ORF2 was homologous to capsid protein of porcine parvovirus (E scores=7e-06). Phylogenetic analysis indicated that the NIH-CQV represents a new subfamily of parvovirus, located at the interface of Parvoviridae and Circoviridae (Figure 1). Prevalence of the NIH-CQV in hepatitis patients was investigated by qPCR. Sixty three out of 92 (69%) patient samples were positive, while all 45 healthy controls were negative. The average virus titer in the patients was 1.28 E4 copies/ul, and the highest one was 3.2 E4 copies/ul. Specific antibodies against NIH-CQV were sought by immunoblot using a recombinant capsid protein. No cross reactivity was detected between the capsid protein of NIH-CQV and other major human parvoviruses. Eighty five percent (78/92) of patients were positive for IgG, and 32% (29/92) of them were positive for IgM. In contrast, 78% (35/45) of healthy controls were positive for IgG and 16% (7/45) were positive for IgM. Viral particles were purified from IgM-positive patient plasma by ultracentrifugation through a 40% sucrose cushion and examined by electron microscopy: spherical, naked, parvovirus-like particles approximately 26–29 nm in diameter were visualized. There was no correlation between clinical diagnosis and the presence or absence of the viral DNA or specific antibodies. Although more work is needed to determine the etiologic role of NIH-CQV in human disease, our data indicate that a novel parvovirus-like virus is highly prevalent in a cohort of patients with seronegative hepatitis. Figure 1, whole-proteome tree of the new parvovirus and members of the families Parvoviridae and Circoviridae. Figure 1,. whole-proteome tree of the new parvovirus and members of the families Parvoviridae and Circoviridae. Disclosures: No relevant conflicts of interest to declare.

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