Open Access
Plants, volume 11, issue 1, pages 5
Searching for a Needle in a Haystack: Cas9-Targeted Nanopore Sequencing and DNA Methylation Profiling of Full-Length Glutenin Genes in a Big Cereal Genome
Kirov Ilya
1, 2
,
Dudnikov Maxim
1, 2
,
Merkulov Pavel
1
,
Vlasova Anastasia
1
,
Soloviev Alexander
1, 3
2
Publication type: Journal Article
Publication date: 2021-12-21
Plant Science
Ecology, Evolution, Behavior and Systematics
Ecology
Abstract
Sequencing and epigenetic profiling of target genes in plants are important tasks with various applications ranging from marker design for plant breeding to the study of gene expression regulation. This is particularly interesting for plants with big genome size for which whole-genome sequencing can be time-consuming and costly. In this study, we asked whether recently proposed Cas9-targeted nanopore sequencing (nCATS) is efficient for target gene sequencing for plant species with big genome size. We applied nCATS to sequence the full-length glutenin genes (Glu-1Ax, Glu-1Bx and Glu-1By) and their promoters in hexaploid triticale (X Triticosecale, AABBRR, genome size is 24 Gb). We showed that while the target gene enrichment per se was quite high for the three glutenin genes (up to 645×), the sequencing depth that was achieved from two MinION flowcells was relatively low (5–17×). However, this sequencing depth was sufficient for various tasks including detection of InDels and single-nucleotide variations (SNPs), read phasing and methylation profiling. Using nCATS, we uncovered SNP and InDel variation of full-length glutenin genes providing useful information for marker design and deciphering of variation of individual Glu-1By alleles. Moreover, we demonstrated that glutenin genes possess a ‘gene-body’ methylation epigenetic profile with hypermethylated CDS part and hypomethylated promoter region. The obtained information raised an interesting question on the role of gene-body methylation in glutenin gene expression regulation. Taken together, our work disclosures the potential of the nCATS approach for sequencing of target genes in plants with big genome size.
Citations by journals
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1
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Frontiers in Plant Science
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Frontiers in Plant Science
1 publication, 12.5%
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New Biotechnology
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New Biotechnology
1 publication, 12.5%
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International Journal of Molecular Sciences
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International Journal of Molecular Sciences
1 publication, 12.5%
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Journal of Integrative Plant Biology
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Journal of Integrative Plant Biology
1 publication, 12.5%
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Phytopathology
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Phytopathology
1 publication, 12.5%
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Agronomy
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Agronomy
1 publication, 12.5%
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1
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Citations by publishers
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1
2
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Multidisciplinary Digital Publishing Institute (MDPI)
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Multidisciplinary Digital Publishing Institute (MDPI)
2 publications, 25%
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Frontiers Media S.A.
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Frontiers Media S.A.
1 publication, 12.5%
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Elsevier
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Elsevier
1 publication, 12.5%
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Wiley
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Wiley
1 publication, 12.5%
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American Phytopathological Society
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American Phytopathological Society
1 publication, 12.5%
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1
2
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- We do not take into account publications that without a DOI.
- Statistics recalculated only for publications connected to researchers, organizations and labs registered on the platform.
- Statistics recalculated weekly.
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Kirov I. et al. Searching for a Needle in a Haystack: Cas9-Targeted Nanopore Sequencing and DNA Methylation Profiling of Full-Length Glutenin Genes in a Big Cereal Genome // Plants. 2021. Vol. 11. No. 1. p. 5.
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Kirov I., Polkhovskaya E., Dudnikov M., Merkulov P., Vlasova A., Karlov G. I., Soloviev A. Searching for a Needle in a Haystack: Cas9-Targeted Nanopore Sequencing and DNA Methylation Profiling of Full-Length Glutenin Genes in a Big Cereal Genome // Plants. 2021. Vol. 11. No. 1. p. 5.
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TY - JOUR
DO - 10.3390/plants11010005
UR - https://doi.org/10.3390%2Fplants11010005
TI - Searching for a Needle in a Haystack: Cas9-Targeted Nanopore Sequencing and DNA Methylation Profiling of Full-Length Glutenin Genes in a Big Cereal Genome
T2 - Plants
AU - Polkhovskaya, Ekaterina
AU - Dudnikov, Maxim
AU - Vlasova, Anastasia
AU - Kirov, Ilya
AU - Merkulov, Pavel
AU - Karlov, Gennady I.
AU - Soloviev, Alexander
PY - 2021
DA - 2021/12/21 00:00:00
PB - Multidisciplinary Digital Publishing Institute (MDPI)
SP - 5
IS - 1
VL - 11
SN - 2223-7747
ER -
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@article{2021_Kirov,
author = {Ekaterina Polkhovskaya and Maxim Dudnikov and Anastasia Vlasova and Ilya Kirov and Pavel Merkulov and Gennady I. Karlov and Alexander Soloviev},
title = {Searching for a Needle in a Haystack: Cas9-Targeted Nanopore Sequencing and DNA Methylation Profiling of Full-Length Glutenin Genes in a Big Cereal Genome},
journal = {Plants},
year = {2021},
volume = {11},
publisher = {Multidisciplinary Digital Publishing Institute (MDPI)},
month = {dec},
url = {https://doi.org/10.3390%2Fplants11010005},
number = {1},
pages = {5},
doi = {10.3390/plants11010005}
}
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Kirov, Ilya, et al. “Searching for a Needle in a Haystack: Cas9-Targeted Nanopore Sequencing and DNA Methylation Profiling of Full-Length Glutenin Genes in a Big Cereal Genome.” Plants, vol. 11, no. 1, Dec. 2021, p. 5. https://doi.org/10.3390%2Fplants11010005.
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