Evidence map›Paper›PMID 28989824›Full record

ArticleApplications in plant sciences2017

Development of single-copy nuclear intron markers for species-level phylogenetics: Case study with Paullinieae (Sapindaceae).

Joyce G Chery, Chodon Sass, Chelsea D Specht

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Article in Applications in plant sciences, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

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2 · The registry

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3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

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5 · Who and what money

Authors and funding

3 authors.

Joyce G CheryDepartment of Integrative Biology, University of California, Berkeley, 3040 Valley Life Sciences Building #3140, Berkeley, California 94720 USA.
Chodon SassUniversity and Jepson Herbaria, University of California, Berkeley, 1001 Valley Life Sciences Building #2465, Berkeley, California 94720 USA.
Chelsea D SpechtSchool of Integrative Plant Sciences, Section of Plant Biology, Cornell University, 412 Mann Library Building, Ithaca, New York 14853 USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

premise of the studyWe developed a bioinformatic pipeline that leverages a publicly available genome and published transcriptomes to design primers in conserved coding sequences flanking targeted introns of single-copy nuclear loci. Paullinieae (Sapindaceae) is used to demonstrate the pipeline. METHODS AND

resultsTranscriptome reads phylogenetically closer to the lineage of interest are aligned to the closest genome. Single-nucleotide polymorphisms are called, generating a "pseudoreference" closer to the lineage of interest. Several filters are applied to meet the criteria of single-copy nuclear loci with introns of a desired size. Primers are designed in conserved coding sequences flanking introns. Using this pipeline, we developed nine single-copy nuclear intron markers for Paullinieae.

conclusionsThis pipeline is highly flexible and can be used for any group with available genomic and transcriptomic resources. This pipeline led to the development of nine variable markers for phylogenetic study without generating sequence data de novo.

Indexed as

intronsnuclear marker developmentPaullinieaeSapindaceae

Identifiers

PMID28989824
PMCPMC5628028

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.