Investigating unexplained genetic variation and its expression in the arbuscular mycorrhizal fungus Rhizophagus irregularis: A comparison of whole genome and RAD sequencing data.

Details

Serval ID
serval:BIB_C5D5E35029AD
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Investigating unexplained genetic variation and its expression in the arbuscular mycorrhizal fungus Rhizophagus irregularis: A comparison of whole genome and RAD sequencing data.
Journal
PloS one
Author(s)
Masclaux F.G., Wyss T., Pagni M., Rosikiewicz P., Sanders I.R.
ISSN
1932-6203 (Electronic)
ISSN-L
1932-6203
Publication state
Published
Issued date
2019
Peer-reviewed
Oui
Volume
14
Number
12
Pages
e0226497
Language
english
Notes
Publication types: Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: epublish
Abstract
Arbuscular mycorrhizal fungi (AMF) are important symbionts of plants. Recently, studies of the AMF Rhizophagus irregularis recorded within-isolate genetic variation that does not completely match the proposed homokaryon or heterokaryon state (where heterokaryons comprise a population of two distinct nucleus genotypes). We re-analysed published data showing that bi-allelic sites (and their frequencies), detected in proposed homo- and heterokaryote R. irregularis isolates, were similar across independent studies using different techniques. This indicated that observed within-fungus genetic variation was not an artefact of sequencing and that such within- fungus genetic variation possibly exists. We then looked to see if bi-allelic transcripts from three R. irregularis isolates matched those observed in the genome as this would give a strong indication of whether bi-allelic sites recorded in the genome were reliable variants. In putative homokaryon isolates, very few bi-allelic transcripts matched those in the genome. In a putative heterokaryon, a large number of bi-allelic transcripts matched those in the genome. Bi-allelic transcripts also occurred in the same frequency in the putative heterokaryon as predicted from allele frequency in the genome. Our results indicate that while within-fungus genome variation in putative homokaryon and heterokaryon AMF was highly similar in 2 independent studies, there was little support that this variation is transcribed in homokaryons. In contrast, within-fungus variation thought to be segregated among two nucleus genotypes in a heterokaryon isolate was indeed transcribed in a way that is proportional to that seen in the genome.
Keywords
Fungal Proteins/genetics, Gene Expression Profiling/methods, Gene Expression Regulation, Fungal, Gene Frequency, Genetic Variation, Glomeromycota/genetics, High-Throughput Nucleotide Sequencing, Sequence Analysis, RNA, Whole Genome Sequencing/methods
Pubmed
Web of science
Open Access
Yes
Create date
06/12/2019 18:06
Last modification date
03/04/2020 6:19
Usage data