Relative performance of customized and universal probe sets in target enrichment: a case study in subtribe Malinae

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F67985939%3A_____%2F21%3A00545471" target="_blank" >RIV/67985939:_____/21:00545471 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/00216208:11310/21:10441377

Výsledek na webu

<a href="https://doi.org/10.1002/aps3.11442" target="_blank" >https://doi.org/10.1002/aps3.11442</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1002/aps3.11442" target="_blank" >10.1002/aps3.11442</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Relative performance of customized and universal probe sets in target enrichment: a case study in subtribe Malinae

Popis výsledku v původním jazyce

Custom probe design for target enrichment in phylogenetics is tedious and often hinders broader phylogenetic synthesis. The universal angiosperm probe set Angiosperms353 may be the solution. Here, we test the relative performance of Angiosperms353 on the Rosaceae subtribe Malinae in comparison with custom probes that we specifically designed for this clade. We then address the impact of bioinformatically altering the performance of Angiosperms353 by replacing the original probe sequences with orthologs extracted from the Malus domestica genome. Locus recovery was highest for our custom Malinae probe set, and replacing the original Angiosperms353 sequences with a Malus representative improved the locus recovery relative to Angiosperms353. The proportion of parsimony-informative sites was similar between all probe sets, while the gene tree discordance was lower in the case of the custom probes. A custom probe set benefits from data completeness and can be tailored toward the specificities of the project of choice, however, Angiosperms353 was equally as phylogenetically informative as the custom probes. We therefore recommend using both a custom probe set and Angiosperms353 to facilitate large-scale systematic studies, where financially possible.

Název v anglickém jazyce

Relative performance of customized and universal probe sets in target enrichment: a case study in subtribe Malinae

Popis výsledku anglicky

Custom probe design for target enrichment in phylogenetics is tedious and often hinders broader phylogenetic synthesis. The universal angiosperm probe set Angiosperms353 may be the solution. Here, we test the relative performance of Angiosperms353 on the Rosaceae subtribe Malinae in comparison with custom probes that we specifically designed for this clade. We then address the impact of bioinformatically altering the performance of Angiosperms353 by replacing the original probe sequences with orthologs extracted from the Malus domestica genome. Locus recovery was highest for our custom Malinae probe set, and replacing the original Angiosperms353 sequences with a Malus representative improved the locus recovery relative to Angiosperms353. The proportion of parsimony-informative sites was similar between all probe sets, while the gene tree discordance was lower in the case of the custom probes. A custom probe set benefits from data completeness and can be tailored toward the specificities of the project of choice, however, Angiosperms353 was equally as phylogenetically informative as the custom probes. We therefore recommend using both a custom probe set and Angiosperms353 to facilitate large-scale systematic studies, where financially possible.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10611 - Plant sciences, botany

Projekt

<a href="/cs/project/GJ16-15134Y" target="_blank" >GJ16-15134Y: Nový pohled na starou problematiku: role celogenomových procesů v adaptivní radiaci rostlin studovaná pomocí moderních sekvenačních technik</a><br>

Návaznosti

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Rok uplatnění

2021

Kód důvěrnosti údajů

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

Název periodika

Applications in Plant Sciences

ISSN

2168-0450

e-ISSN

2168-0450

Svazek periodika

9

Číslo periodika v rámci svazku

7

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

22

Strana od-do

e11442

Kód UT WoS článku

000676110800001

EID výsledku v databázi Scopus

2-s2.0-85108886737