Open Access
Frontiers in Plant Science, volume 12
High-Resolution Transcriptome Atlas and Improved Genome Assembly of Common Buckwheat, Fagopyrum esculentum
Penin Aleksey A.
1
,
Kasianov Artem S.
1
,
Kirov Ilya V
2
,
Gerasimov Evgeny S
3
,
Fesenko Aleksey N.
4
,
Logacheva Maria D.
1, 5
4
Federal Scientific Center of Legumes and Groat Crops, Russia
|
Publication type: Journal Article
Publication date: 2021-03-16
Journal:
Frontiers in Plant Science
Quartile SCImago
Q1
Quartile WOS
Q1
Impact factor: 5.6
ISSN: 1664462X
Plant Science
Abstract
Common buckwheat (Fagopyrum esculentum) is an important non-cereal grain crop and a prospective component of functional food. Despite this, the genomic resources for this species and for the whole family Polygonaceae, to which it belongs, are scarce. Here, we report the assembly of the buckwheat genome using long-read technology and a high-resolution expression atlas including 46 organs and developmental stages. We found that the buckwheat genome has an extremely high content of transposable elements, including several classes of recently (0.5–1 Mya) multiplied TEs (“transposon burst”) and gradually accumulated TEs. The difference in TE content is a major factor contributing to the three-fold increase in the genome size ofF. esculentumcompared with its sister speciesF. tataricum. Moreover, we detected the differences in TE content between the wild ancestral subspeciesF. esculentumssp.ancestraleand buckwheat cultivars, suggesting that TE activity accompanied buckwheat domestication. Expression profiling allowed us to test a hypothesis about the genetic control of petaloidy of tepals in buckwheat. We showed that it is not mediated by B-class gene activity, in contrast to the prediction from the ABC model. Based on a survey of expression profiles and phylogenetic analysis, we identified the MYB family transcription factor gene tr_18111 as a potential candidate for the determination of conical cells in buckwheat petaloid tepals. The information on expression patterns has been integrated into the publicly available database TraVA:http://travadb.org/browse/Species=Fesc/. The improved genome assembly and transcriptomic resources will enable research on buckwheat, including practical applications.
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Citations by publishers
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1
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5
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5 publications, 31.25%
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Multidisciplinary Digital Publishing Institute (MDPI)
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3 publications, 18.75%
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1 publication, 6.25%
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Public Library of Science (PLoS)
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- We do not take into account publications that without a DOI.
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- Statistics recalculated weekly.
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Penin A. A. et al. High-Resolution Transcriptome Atlas and Improved Genome Assembly of Common Buckwheat, Fagopyrum esculentum // Frontiers in Plant Science. 2021. Vol. 12.
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Penin A. A., Kasianov A. S., Klepikova A. V., Kirov I. V., Gerasimov E. S., Fesenko A. N., Logacheva M. D. High-Resolution Transcriptome Atlas and Improved Genome Assembly of Common Buckwheat, Fagopyrum esculentum // Frontiers in Plant Science. 2021. Vol. 12.
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TY - JOUR
DO - 10.3389/fpls.2021.612382
UR - https://doi.org/10.3389%2Ffpls.2021.612382
TI - High-Resolution Transcriptome Atlas and Improved Genome Assembly of Common Buckwheat, Fagopyrum esculentum
T2 - Frontiers in Plant Science
AU - Penin, Aleksey A.
AU - Kasianov, Artem S.
AU - Klepikova, Anna V.
AU - Kirov, Ilya V
AU - Gerasimov, Evgeny S
AU - Fesenko, Aleksey N.
AU - Logacheva, Maria D.
PY - 2021
DA - 2021/03/16 00:00:00
PB - Frontiers Media S.A.
VL - 12
SN - 1664-462X
ER -
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@article{2021_Penin,
author = {Aleksey A. Penin and Artem S. Kasianov and Anna V. Klepikova and Ilya V Kirov and Evgeny S Gerasimov and Aleksey N. Fesenko and Maria D. Logacheva},
title = {High-Resolution Transcriptome Atlas and Improved Genome Assembly of Common Buckwheat, Fagopyrum esculentum},
journal = {Frontiers in Plant Science},
year = {2021},
volume = {12},
publisher = {Frontiers Media S.A.},
month = {mar},
url = {https://doi.org/10.3389%2Ffpls.2021.612382},
doi = {10.3389/fpls.2021.612382}
}