Genome-wide identification of RING finger genes in flax (Linum usitatissimum) and analyses of their evolution

Background Flax (Linum usitatissimum) is an important crop for its seed oil and stem fiber. Really Interesting New Gene (RING) finger genes play essential roles in growth, development, and biotic and abiotic stress responses in plants. However, little is known about these genes in flax. Methods Here...

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Autores principales: Xianwen Meng, Jing Liu, Mingde Zhao
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Lenguaje:EN
Publicado: PeerJ Inc. 2021
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Acceso en línea:https://doaj.org/article/0b9f57b912784e1fbb4ed201694a0732
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spelling oai:doaj.org-article:0b9f57b912784e1fbb4ed201694a07322021-11-17T15:05:17ZGenome-wide identification of RING finger genes in flax (Linum usitatissimum) and analyses of their evolution10.7717/peerj.124912167-8359https://doaj.org/article/0b9f57b912784e1fbb4ed201694a07322021-11-01T00:00:00Zhttps://peerj.com/articles/12491.pdfhttps://peerj.com/articles/12491/https://doaj.org/toc/2167-8359Background Flax (Linum usitatissimum) is an important crop for its seed oil and stem fiber. Really Interesting New Gene (RING) finger genes play essential roles in growth, development, and biotic and abiotic stress responses in plants. However, little is known about these genes in flax. Methods Here, we performed a systematic genome-wide analysis to identify RING finger genes in flax. Results We identified 587 RING domains in 574 proteins and classified them into RING-H2 (292), RING-HCa (181), RING-HCb (23), RING-v (53), RING-C2 (31), RING-D (2), RING-S/T (3), and RING-G (2). These proteins were further divided into 45 groups according to domain organization. These genes were located in 15 chromosomes and clustered into three clades according to their phylogenetic relationships. A total of 312 segmental duplicated gene pairs were inferred from 411 RING finger genes, indicating a major contribution of segmental duplications to the RING finger gene family expansion. The non-synonymous/synonymous substitution ratio of the segmentally duplicated gene pairs was less than 1, suggesting that the gene family was under negative selection since duplication. Further, most RING genes in flax were differentially expressed during seed development or in the shoot apex. This study provides useful information for further functional analysis of RING finger genes in flax and to develop gene-derived molecular markers in flax breeding.Xianwen MengJing LiuMingde ZhaoPeerJ Inc.articleFlaxRING finger geneEvolutionExpression patternsMedicineRENPeerJ, Vol 9, p e12491 (2021)
institution DOAJ
collection DOAJ
language EN
topic Flax
RING finger gene
Evolution
Expression patterns
Medicine
R
spellingShingle Flax
RING finger gene
Evolution
Expression patterns
Medicine
R
Xianwen Meng
Jing Liu
Mingde Zhao
Genome-wide identification of RING finger genes in flax (Linum usitatissimum) and analyses of their evolution
description Background Flax (Linum usitatissimum) is an important crop for its seed oil and stem fiber. Really Interesting New Gene (RING) finger genes play essential roles in growth, development, and biotic and abiotic stress responses in plants. However, little is known about these genes in flax. Methods Here, we performed a systematic genome-wide analysis to identify RING finger genes in flax. Results We identified 587 RING domains in 574 proteins and classified them into RING-H2 (292), RING-HCa (181), RING-HCb (23), RING-v (53), RING-C2 (31), RING-D (2), RING-S/T (3), and RING-G (2). These proteins were further divided into 45 groups according to domain organization. These genes were located in 15 chromosomes and clustered into three clades according to their phylogenetic relationships. A total of 312 segmental duplicated gene pairs were inferred from 411 RING finger genes, indicating a major contribution of segmental duplications to the RING finger gene family expansion. The non-synonymous/synonymous substitution ratio of the segmentally duplicated gene pairs was less than 1, suggesting that the gene family was under negative selection since duplication. Further, most RING genes in flax were differentially expressed during seed development or in the shoot apex. This study provides useful information for further functional analysis of RING finger genes in flax and to develop gene-derived molecular markers in flax breeding.
format article
author Xianwen Meng
Jing Liu
Mingde Zhao
author_facet Xianwen Meng
Jing Liu
Mingde Zhao
author_sort Xianwen Meng
title Genome-wide identification of RING finger genes in flax (Linum usitatissimum) and analyses of their evolution
title_short Genome-wide identification of RING finger genes in flax (Linum usitatissimum) and analyses of their evolution
title_full Genome-wide identification of RING finger genes in flax (Linum usitatissimum) and analyses of their evolution
title_fullStr Genome-wide identification of RING finger genes in flax (Linum usitatissimum) and analyses of their evolution
title_full_unstemmed Genome-wide identification of RING finger genes in flax (Linum usitatissimum) and analyses of their evolution
title_sort genome-wide identification of ring finger genes in flax (linum usitatissimum) and analyses of their evolution
publisher PeerJ Inc.
publishDate 2021
url https://doaj.org/article/0b9f57b912784e1fbb4ed201694a0732
work_keys_str_mv AT xianwenmeng genomewideidentificationofringfingergenesinflaxlinumusitatissimumandanalysesoftheirevolution
AT jingliu genomewideidentificationofringfingergenesinflaxlinumusitatissimumandanalysesoftheirevolution
AT mingdezhao genomewideidentificationofringfingergenesinflaxlinumusitatissimumandanalysesoftheirevolution
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