CandiSSR: An Efficient Pipeline used for Identifying Candidate Polymorphic SSRs Based on Multiple Assembled Sequences

Xia, Enhua; Yao, Qiu-Yang; Zhang, Hai-Bin; Jiang, Jianjun; Zhang, Liping; Gao, Li‐Zhi

doi:10.3389/fpls.2015.01171

Cited by 55 publications

(59 citation statements)

References 48 publications

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“…This tool was built to help users to massively detect polymorphic SSRs (PolySSR) in tea plant, an import and widely used genetic markers for tea plant population genetic study and molecular breeding. Our previously developed CandiSSR pipeline was deployed online to achieve this goal (Xia et al ., ). Users can upload the assembled transcript sequences, or genomic sequences, or even organelle sequences to search polySSRs.…”

Section: Facilities and Toolsmentioning

confidence: 97%

See 1 more Smart Citation

Tea Plant Information Archive: a comprehensive genomics and bioinformatics platform for tea plant

Xia

Tong

et al. 2019

Plant Biotechnology Journal

236

181

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Summary Tea is the world's widely consumed nonalcohol beverage with essential economic and health benefits. Confronted with the increasing large‐scale omics‐data set particularly the genome sequence released in tea plant, the construction of a comprehensive knowledgebase is urgently needed to facilitate the utilization of these data sets towards molecular breeding. We hereby present the first integrative and specially designed web‐accessible database, Tea Plant Information Archive (TPIA; http://tpia.teaplant.org). The current release of TPIA employs the comprehensively annotated tea plant genome as framework and incorporates with abundant well‐organized transcriptomes, gene expressions (across species, tissues and stresses), orthologs and characteristic metabolites determining tea quality. It also hosts massive transcription factors, polymorphic simple sequence repeats, single nucleotide polymorphisms, correlations, manually curated functional genes and globally collected germplasm information. A variety of versatile analytic tools (e.g. JBrowse, blast, enrichment analysis, etc.) are established helping users to perform further comparative, evolutionary and functional analysis. We show a case application of TPIA that provides novel and interesting insights into the phytochemical content variation of section Thea of genus Camellia under a well‐resolved phylogenetic framework. The constructed knowledgebase of tea plant will serve as a central gateway for global tea community to better understand the tea plant biology that largely benefits the whole tea industry.

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Section: Facilities and Toolsmentioning

confidence: 97%

“…The CandiSSR pipeline (Xia et al ., ) was used to identify PloySSRs between tea plant and other 19 representative Camellia species. In total, 1663 polymorphic EST‐SSRs were identified.…”

Section: Data Contentmentioning

confidence: 99%

Tea Plant Information Archive: a comprehensive genomics and bioinformatics platform for tea plant

Xia

Tong

et al. 2019

Plant Biotechnology Journal

236

181

View full text Add to dashboard Cite

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“…CandiSSR was used to identify potential polymorphic genic SSRs among the six unigenes datasets of T. mongolica [39]. The parameters used in the pipeline were: flanking sequence length 100 bp, blast e-value cutoff 1.0 × e −10 , blast identity cutoff 95%, and blast coverage cutoff 95% [39,40].…”

Section: Identification Of Potential Polymorphic Genic Ssrsmentioning

confidence: 99%

Identification of Genic SSRs Provide a Perspective for Studying Environmental Adaptation in the Endemic Shrub Tetraena mongolica

Dang

Huang

Jia

et al. 2020

Genes

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Tetraena mongolica is a xerophytic shrub endemic to desert regions in Inner Mongolia. This species has evolved distinct survival strategies that allow it to adapt to hyper-drought and heterogeneous habitats. Simple sequence repeats (SSRs) may provide a molecular basis in plants for fast adaptation to environmental change. Thus, identifying SSRs and their possible effects on gene behavior has the potential to provide valuable information for studies of adaptation. In this study, we sequenced six individual transcriptomes of T. mongolica from heterogeneous habitats, focused on SSRs located in genes, and identified 811 polymorphic SSRs. Of the identified SSRs, 172, 470, and 76 were located in 5 UTRs, CDSs, and 3 UTRs in 591 transcripts; and AG/CT, AAC/GTT, and AT/AT were the most abundant repeats in each gene region. Functional annotation showed that many of the identified polymorphic SSRs were in genes that were enriched in several GO terms and KEGG pathways, suggesting the functional significance of these genes in the environmental adaptation process. The identification of polymorphic genic SSRs in our study lays a foundation for future studies investigating the contribution of SSRs to regulation of genes in natural populations of T. mongolica and their importance for adaptive evolution of this species.Genes 2020, 11, 322 2 of 13 is a good candidate for studies of plant origin, evolution, and adversity adaptation in such desert regions. Around these topics, a series of fundamental research investigations have been implemented, the results of which are of importance for comprehensively understanding the properties of T. mongolica. This pioneering work includes the studies of systematic, geographic, and taxonomic aspects [7-9]; morphology and anatomy [10][11][12]; physiological ecology [13][14][15][16]; chemometrics and biochemistry [17,18]; population genetics [5]; conservation biology [19][20][21]; abiotic stress response [3]; and medicinal phytochemistry [22,23]. In recent decades, the plant has suffered from serious habitat destruction in size and has even disappeared, leading to the general decline of the species and making the survival of T. mongolica much harder than before [24]. Correspondingly, one consideration for the ongoing survival of the species that has been paid much attention recently is an apparent decrease in genetic diversity due to loss of demographics, inbreeding depression, stochastic events, and other factors [5,24]. However, contrary to the assumption of diversity loss, it has been observed that the species has an intermediate or high level of genetic diversity as detected from analyses of inter-simple sequence repeats and nuclear microsatellites, respectively [5,24]. Therefore, further exploration of these hereditary characteristics and a potential link to adaptation strategies of the species is needed.Genic simple sequence repeats (SSRs) (also called genic microsatellites or expressed sequence tag (EST)-SSRs), a relatively newly established concept, are simple sequence repeats located in ...

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“…PolyMorphPredict (Das et al, ) and PSR (Cantarella & D'Agostino, ) lack the masking of mutations in primer design. PolySSR (Tang et al, ) and CandiSSR (Xia et al, ) depend on assembled sequences. iMSAT (Andersen & Mills, ) is dependent on (insertion and deletion) Indel calling and lacks the masking of mutations in primer design.…”

Section: Introductionmentioning

confidence: 99%

“…PolySSR (Tang et al, 2008) and CandiSSR (Xia et al, 2015) depend on assembled sequences. iMSAT (Andersen & Mills, 2014) is dependent on (insertion and deletion) Indel calling and lacks the masking of mutations in primer design.…”

Section: Introductionmentioning

confidence: 99%

MultiplexSSR: A pipeline for developing multiplex SSR‐PCR assays from resequencing data

Guo

Yang

et al. 2020

Ecology and Evolution

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Next‐generation sequencing has greatly promoted the investigation of single nucleotide polymorphisms, while studies of simple sequence repeats are sharply decreasing. However, simple sequence repeats still present some advantages in conservation genetics. In this study, an end‐to‐end pipeline referred to as MultiplexSSR was established to develop multiplex PCR assays in batches with highly polymorphic simple sequence repeats for capillary platforms from resequencing data. The distribution of single sequence repeats in the genome, the error profiles of genotypes and allelotypes, and the increase in the allele length range depending on the number of individuals were investigated. A total of 98% of single sequence repeats presented lengths of less than 100 bp. The error rate of the genotyping and allelotyping of dimeric patterns was ten times higher than those for other patterns. The error rate of allelotyping was less than that of genotyping. The allele length range reached approximate saturation with 10 individuals. This pipeline uses allele numbers to select highly polymorphic loci, masks loci with variation, and applies in silico PCR to improve primer specificity. The application of the developed multiplex SSR‐PCR assays validated the pipeline's robustness, showing higher polymorphism and stability for the developed simple sequence repeats and a lower cost for genotyping and providing low‐depth resequencing data from less than a dozen individuals for the development of markers. This pipeline fills the gap between next‐generation sequencing and multiplex SSR‐PCR.

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CandiSSR: An Efficient Pipeline used for Identifying Candidate Polymorphic SSRs Based on Multiple Assembled Sequences

Cited by 55 publications

References 48 publications

Tea Plant Information Archive: a comprehensive genomics and bioinformatics platform for tea plant

Tea Plant Information Archive: a comprehensive genomics and bioinformatics platform for tea plant

Identification of Genic SSRs Provide a Perspective for Studying Environmental Adaptation in the Endemic Shrub Tetraena mongolica

MultiplexSSR: A pipeline for developing multiplex SSR‐PCR assays from resequencing data

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