A bioinformatic platform to integrate target capture and whole genome sequences of various read depths for phylogenomics

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60076658%3A12310%2F21%3A43904322" target="_blank" >RIV/60076658:12310/21:43904322 - isvavai.cz</a>

Alternative codes found

RIV/60077344:_____/21:00547831

Result on the web

<a href="https://onlinelibrary.wiley.com/doi/10.1111/mec.16240" target="_blank" >https://onlinelibrary.wiley.com/doi/10.1111/mec.16240</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1111/mec.16240" target="_blank" >10.1111/mec.16240</a>

Result language

angličtina

Original language name

A bioinformatic platform to integrate target capture and whole genome sequences of various read depths for phylogenomics

Original language description

The increasing availability of short-read whole genome sequencing (WGS) provides unprecedented opportunities to study ecological and evolutionary processes. Although loci of interest can be extracted from WGS data and combined with target sequence data, this requires suitable bioinformatic workflows. Here, we test different assembly and locus extraction strategies and implement them into secapr, a pipeline that processes short-read data into multilocus alignments for phylogenetics and molecular ecology analyses. We integrate the processing of data from low-coverage WGS (&lt;30x) and target sequence capture into a flexible framework, while optimizing de novo contig assembly and loci extraction. Specifically, we test different assembly strategies by contrasting their ability to recover loci from targeted butterfly protein-coding genes, using four data sets: a WGS data set across different average coverages (10x, 5x and 2x) and a data set for which these loci were enriched prior to sequencing via target sequence capture. Using the resulting de novo contigs, we account for potential errors within contigs and infer phylogenetic trees to evaluate the ability of each assembly strategy to recover species relationships. We demonstrate that choosing multiple sizes of kmer simultaneously for assembly results in the highest yield of extracted loci from de novo assembled contigs, while data sets derived from sequencing read depths as low as 5x recovers the expected species relationships in phylogenetic trees. By making the tested assembly approaches available in the secapr pipeline, we hope to inspire future studies to incorporate complementary data and make an informed choice on the optimal assembly strategy.

Czech name

—

Czech description

—

Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10618 - Ecology

Project

<a href="/en/project/GJ20-18566Y" target="_blank" >GJ20-18566Y: The role of species interactions in the diversification of Neotropical butterflies at the macroevolutionary and microevolutionary scales</a><br>

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2021

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Molecular Ecology

ISSN

0962-1083

e-ISSN

—

Volume of the periodical

30

Issue of the periodical within the volume

23

Country of publishing house

US - UNITED STATES

Number of pages

15

Pages from-to

6021-6035

UT code for WoS article

000712974600001

EID of the result in the Scopus database

2-s2.0-85118255763