Large-Scale Structural Variation Detection in Subterranean Clover Subtypes Using Optical Mapping

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61389030%3A_____%2F18%3A00492763" target="_blank" >RIV/61389030:_____/18:00492763 - isvavai.cz</a>

Výsledek na webu

<a href="http://dx.doi.org/10.3389/fpls.2018.00971" target="_blank" >http://dx.doi.org/10.3389/fpls.2018.00971</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.3389/fpls.2018.00971" target="_blank" >10.3389/fpls.2018.00971</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Large-Scale Structural Variation Detection in Subterranean Clover Subtypes Using Optical Mapping

Popis výsledku v původním jazyce

We selected two genetically diverse subspecies of the Trifolium model species, subterranean clover cvs. Daliak and Yarloop. The structural variations (SVs) discovered by Bionano optical mapping (BOM) were validated using Illumina short reads. In the analysis, BOM identified 12 large-scale regions containing deletions and 19 regions containing insertions in Yarloop. The 12 large-scale regions contained 71 small deletions when validated by Illumina short reads. The results suggest that BOM could detect the total size of deletions and insertions, but it could not precisely report the location and actual quantity of SVs in the genome. Nucleotide-level validation is crucial to confirm and characterize SVs reported by optical mapping. The accuracy of SV detection by BOM is highly dependent on the quality of reference genomes and the density of selected nickases.

Název v anglickém jazyce

Large-Scale Structural Variation Detection in Subterranean Clover Subtypes Using Optical Mapping

Popis výsledku anglicky

We selected two genetically diverse subspecies of the Trifolium model species, subterranean clover cvs. Daliak and Yarloop. The structural variations (SVs) discovered by Bionano optical mapping (BOM) were validated using Illumina short reads. In the analysis, BOM identified 12 large-scale regions containing deletions and 19 regions containing insertions in Yarloop. The 12 large-scale regions contained 71 small deletions when validated by Illumina short reads. The results suggest that BOM could detect the total size of deletions and insertions, but it could not precisely report the location and actual quantity of SVs in the genome. Nucleotide-level validation is crucial to confirm and characterize SVs reported by optical mapping. The accuracy of SV detection by BOM is highly dependent on the quality of reference genomes and the density of selected nickases.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10611 - Plant sciences, botany

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2018

Kód důvěrnosti údajů

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

Název periodika

Frontiers in Plant Science

ISSN

1664-462X

e-ISSN

—

Svazek periodika

9

Číslo periodika v rámci svazku

JUL 17

Stát vydavatele periodika

CH - Švýcarská konfederace

Počet stran výsledku

5

Strana od-do

—

Kód UT WoS článku

000438902900001

EID výsledku v databázi Scopus

2-s2.0-85050749479