Transcriptome sequencing and SNP detection in Phoebe chekiangensis

  title={Transcriptome sequencing and SNP detection in Phoebe chekiangensis},
  author={Bing He and Yin-Gang Li and Zhouxian Ni and Li-an Xu},
Background Phoebe chekiangensis is a rare tree species that is only distributed in south-eastern China. Although this species is famous for its excellent wood properties, it has not been extensively studied at the molecular level. Results Here, the transcriptome of P. chekiangensis was sequenced using next-generation sequencing technology, and 75,647 transcripts with 48,011 unigenes were assembled and annotated. In addition, 162,938 putative single nucleotide polymorphisms (SNPs) were predicted… 
Development of EST-based SSR and SNP markers in Gastrodia elata (herbal medicine) by sequencing, de novo assembly and annotation of the transcriptome
A huge number of genes that were responsible for the growth, development, and metabolism of bioactive components, but also a large number of molecular markers were detected for future studies on the conservation genetics and molecular breeding of G. elata.
Transcriptomic signature of drought response in pearl millet (Pennisetum glaucum (L.) and development of web-genomic resources
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Responses of Taxus chinensis and Phoebe chekiangensis seedlings to controlled-release fertilizer in various formulations and application rates
Findings will guide nursery practice in the production of high-quality seedlings for optimum survival and growth in the field and show that CRF formulation can affect nutritional attributes, while application rate modified seedling growth and nutritional attributes.
Establishment of a fluorescent PCR melting curve method for detecting asthma susceptibility using gene SNP typing
The fluorescence PCR melting curve method is economical, simple, and efficient, and is suitable for the screening of the susceptible gene SNPs in a large-scale population of patients with BA.


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The results provided significant data related to the conservation and management of P. zhennan and equipped land managers with better tools allowing them to more effectively protect this species and its limited genetic diversity.
Applications of single nucleotide polymorphisms in crop genetics.
  • A. Rafalski
  • Biology, Medicine
    Current opinion in plant biology
  • 2002
Haplotype-based analysis is more informative than analysis based on individual SNPs, and has more power in analyzing association with phenotypes in crop species such as corn and soybean.
Genotyping-by-Sequencing (GBS): A Novel, Efficient and Cost-Effective Genotyping Method for Cattle Using Next-Generation Sequencing
GBS technique is novel, flexible, sufficiently high-throughput, and capable of providing acceptable marker density for genomic selection or genome-wide association studies at roughly one third of the cost of currently available genotyping technologies.
SNP detection for massively parallel whole-genome resequencing.
A consensus-calling and SNP-detection method for sequencing-by-synthesis Illumina Genome Analyzer technology that has a very low false call rate at any sequencing depth and excellent genome coverage at a high sequencing depth.
Identification of indels in next-generation sequencing data
A set of algorithms and heuristics collectively called indelMINER is developed to identify indels from whole genome resequencing datasets using paired-end reads using a split-read approach to identify the precise breakpoints for indels of size less than a user specified threshold.
Genotyping microsatellites in next-generation sequencing data
A microsatellite genotyping algorithm is begun that addresses the issues of SNPs and compound repeats, providing high accuracy as well as more detailed analysis ofMicrosatellite loci, and is validated using high depth amplicon sequencing data of microsatellites near the AVPR1A gene.
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
It is shown that accurate gene-level abundance estimates are best obtained with large numbers of short single-end reads, and estimates of the relative frequencies of isoforms within single genes may be improved through the use of paired- end reads, depending on the number of possible splice forms for each gene.
Mining SNPs from DNA sequence data; computational approaches to SNP discovery and analysis.
The bioinformatics tools required to analyze DNA sequence data for SNP mining are discussed, a general approach for the consecutive steps in the mining process is described and commonly used SNP discovery pipelines are presented.
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis
This protocol provides a workflow for genome-independent transcriptome analysis leveraging the Trinity platform and presents Trinity-supported companion utilities for downstream applications, including RSEM for transcript abundance estimation, R/Bioconductor packages for identifying differentially expressed transcripts across samples and approaches to identify protein-coding genes.
ESTScan: A Program for Detecting, Evaluating, and Reconstructing Potential Coding Regions in EST Sequences
It is shown that ESTScan can detect and extract coding regions from low-quality sequences with high selectivity and sensitivity, and is able to accurately correct frameshift errors.