Comparisons of de novo transcriptome assemblers in diploid and polyploid species using peanut (Arachis spp.) RNA-Seq data (Q30882415)

16 October 2017

Comparisons of de novo transcriptome assemblers in diploid and polyploid species using peanut (Arachis spp.) RNA-Seq data (English)

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16 October 2017

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Arachis

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Ratan Chopra

1

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author name string

Gloria Burow

2

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16 October 2017

Andrew Farmer

3

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16 October 2017

Joann Mudge

4

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16 October 2017

Charles E Simpson

5

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16 October 2017

Mark D Burow

6

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16 October 2017

language of work or name

English

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publication date

31 December 2014

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16 October 2017

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16 October 2017

9

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16 October 2017

e115055

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16 October 2017

12

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Creative Commons CC0 License

16 October 2017

start time

31 December 2014

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April 2022 Public Data File from Crossref

copyright status

copyrighted, dedicated to the public domain by copyright holder

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cites work

Next-generation transcriptome sequencing, SNP discovery and validation in four market classes of peanut, Arachis hypogaea L.

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SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads.

21 June 2018

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A high-density genetic map of Arachis duranensis, a diploid ancestor of cultivated peanut.

21 June 2018

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Optimizing de novo common wheat transcriptome assembly using short-read RNA-Seq data

21 June 2018

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Global transcriptome analysis of two wild relatives of peanut under drought and fungi infection

21 June 2018

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Transcriptome sequencing of field pea and faba bean for discovery and validation of SSR genetic markers

21 June 2018

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De novo assembly and characterisation of the transcriptome during seed development, and generation of genic-SSR markers in peanut (Arachis hypogaea L.).

21 June 2018

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Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

21 June 2018

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Transcriptomic analysis of Chinese bayberry (Myrica rubra) fruit development and ripening using RNA-Seq.

21 June 2018

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RNA-seq in grain unveils fate of neo- and paleopolyploidization events in bread wheat (Triticum aestivum L.).

21 June 2018

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Cell walls of developing wheat starchy endosperm: comparison of composition and RNA-Seq transcriptome

21 June 2018

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De novo sequence assembly and characterization of the floral transcriptome in cross- and self-fertilizing plants

21 June 2018

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Genomic relationships between the cultivated peanut (Arachis hypogaea, Leguminosae) and its close relatives revealed by double GISH.

21 June 2018

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Full-length transcriptome assembly from RNA-Seq data without a reference genome

21 June 2018

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De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq.

21 June 2018

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De novo assembly and analysis of RNA-seq data.

21 June 2018

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Optimization of de novo transcriptome assembly from next-generation sequencing data

21 June 2018

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Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

21 June 2018

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Fast and accurate long-read alignment with Burrows-Wheeler transform

21 June 2018

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De novo transcriptome assembly with ABySS.

21 June 2018

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The Sequence Alignment/Map format and SAMtools

21 June 2018

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Fast and accurate short read alignment with Burrows-Wheeler transform

21 June 2018

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21 June 2018

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Database resources of the National Center for Biotechnology Information

21 June 2018

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Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4281230

Versatile and open software for comparing large genomes

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4281230

Transmission genetics of chromatin from a synthetic amphidiploid to cultivated peanut (Arachis hypogaea L.). broadening the gene pool of a monophyletic polyploid species

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4281230

Genome evolution in polyploids

21 June 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4281230

21 June 2018

https://pubmed.ncbi.nlm.nih.gov/25551607

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

CAP3: A DNA sequence assembly program

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4281230

Combined use of sequence similarity and codon bias for coding region identification

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4281230

Basic local alignment search tool

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4281230

Genome size variation in Arachis hypogaea and A. monticola re-evaluated.

21 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0115055

Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing.

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0115055

10.1371/JOURNAL.PONE.0115055

21 January 2018

Identifiers

DOI

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16 October 2017

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16 October 2017

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