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Agronomy, volume 13, issue 2, pages 292

Long-Read cDNA Sequencing Revealed Novel Expressed Genes and Dynamic Transcriptome Landscape of Triticale (x Triticosecale Wittmack) Seed at Different Developing Stages

Polkhovskaya Ekaterina ¹

Bolotina Anna ^{1, 2}

Merkulov Pavel ^{1, 2}

Dudnikov Maxim ^{1, 2}

Soloviev Alexander ^{1, 3}

Kirov Ilya ^{1, 2}

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All-Russia Research Institute of Agricultural Biotechnology, Moscow 127550, Russia |

Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia |

N.V. Tsitsin Main Botanical Garden of the Russian Academy of Sciences, Botanicheskaya Str. 4, 127276 Moscow, Russia |

Publication type: Journal Article

Publication date: 2023-01-18

Multidisciplinary Digital Publishing Institute (MDPI)

Journal: Agronomy

Quartile SCImago

Quartile WOS

Impact factor: 3.7

ISSN: 20734395

DOI: 10.3390/agronomy13020292

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Agronomy and Crop Science

Abstract

Developing seed is a unique stage of plant development with highly dynamic changes in transcriptome. Here, we aimed to detect the novel previously unannotated, genes of the triticale (x Triticosecale Wittmack, AABBRR genome constitution) genome that are expressed during different stages and at different parts of the developing seed. For this, we carried out the Oxford Nanopore sequencing of cDNA obtained for middle (15 days post-anthesis, dpa) and late (20 dpa) stages of seed development. The obtained data together with our previous direct RNA sequencing of early stage (10 dpa) of seed development revealed 39,914 expressed genes including 7128 (17.6%) genes that were not previously annotated in A, B, and R genomes. The bioinformatic analysis showed that the identified genes belonged to long non-coding RNAs (lncRNAs), protein-coding RNAs, and TE-derived RNAs. The gene set analysis revealed the transcriptome dynamics during seed development with distinct patterns of over-represented gene functions in early and middle/late stages. We performed analysis of the lncRNA genes polymorphism and showed that the genes of some of the tested lncRNAs are indeed polymorphic in the triticale collection. Altogether, our results provide information on thousands of novel loci expressed during seed development that can be used as new targets for GWAS analysis, the marker-assisted breeding of triticale, and functional elucidation.

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Polkhovskaya E. et al. Long-Read cDNA Sequencing Revealed Novel Expressed Genes and Dynamic Transcriptome Landscape of Triticale (x Triticosecale Wittmack) Seed at Different Developing Stages // Agronomy. 2023. Vol. 13. No. 2. p. 292.

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Polkhovskaya E., Bolotina A., Merkulov P., Dudnikov M., Soloviev A., Kirov I. Long-Read cDNA Sequencing Revealed Novel Expressed Genes and Dynamic Transcriptome Landscape of Triticale (x Triticosecale Wittmack) Seed at Different Developing Stages // Agronomy. 2023. Vol. 13. No. 2. p. 292.

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RIS Copy

TY - JOUR

DO - 10.3390/agronomy13020292

UR - https://doi.org/10.3390%2Fagronomy13020292

TI - Long-Read cDNA Sequencing Revealed Novel Expressed Genes and Dynamic Transcriptome Landscape of Triticale (x Triticosecale Wittmack) Seed at Different Developing Stages

T2 - Agronomy

AU - Polkhovskaya, Ekaterina

AU - Bolotina, Anna

AU - Merkulov, Pavel

AU - Dudnikov, Maxim

AU - Soloviev, Alexander

AU - Kirov, Ilya

PY - 2023

DA - 2023/01/18 00:00:00

PB - Multidisciplinary Digital Publishing Institute (MDPI)

SP - 292

IS - 2

VL - 13

SN - 2073-4395

ER -

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@article{2023_Polkhovskaya,

author = {Ekaterina Polkhovskaya and Anna Bolotina and Pavel Merkulov and Maxim Dudnikov and Alexander Soloviev and Ilya Kirov},

title = {Long-Read cDNA Sequencing Revealed Novel Expressed Genes and Dynamic Transcriptome Landscape of Triticale (x Triticosecale Wittmack) Seed at Different Developing Stages},

journal = {Agronomy},

year = {2023},

volume = {13},

publisher = {Multidisciplinary Digital Publishing Institute (MDPI)},

month = {jan},

url = {https://doi.org/10.3390%2Fagronomy13020292},

number = {2},

pages = {292},

doi = {10.3390/agronomy13020292}

}

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Polkhovskaya, Ekaterina, et al. “Long-Read cDNA Sequencing Revealed Novel Expressed Genes and Dynamic Transcriptome Landscape of Triticale (x Triticosecale Wittmack) Seed at Different Developing Stages.” Agronomy, vol. 13, no. 2, Jan. 2023, p. 292. https://doi.org/10.3390%2Fagronomy13020292.

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Publisher

Multidisciplinary Digital Publishing Institute (MDPI)

Journal

Agronomy

Quartile SCImago

Quartile WOS

Impact factor

3.7

ISSN

20734395 (Electronic)

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