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Genome-wide identification and expression analysis of the ERF transcription factor family in pineapple (Ananas comosus (L.) Merr.)

Pineapple (Ananas comosus (L.) Merr.) is an important tropical fruit with high economic value. The quality and yield of pineapple will be affected by various environmental conditions. Under adverse conditions, plants can produce a complex reaction mechanism to enhance their resistance. It has been r...

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Autores principales: Huang, Youmei, Liu, Yanhui, Zhang, Man, Chai, Mengnan, He, Qing, Jakada, Bello Hassan, Chen, Fangqian, Chen, Huihuang, Jin, Xingyue, Cai, Hanyang, Qin, Yuan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7518161/
https://www.ncbi.nlm.nih.gov/pubmed/33024641
http://dx.doi.org/10.7717/peerj.10014
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author Huang, Youmei
Liu, Yanhui
Zhang, Man
Chai, Mengnan
He, Qing
Jakada, Bello Hassan
Chen, Fangqian
Chen, Huihuang
Jin, Xingyue
Cai, Hanyang
Qin, Yuan
author_facet Huang, Youmei
Liu, Yanhui
Zhang, Man
Chai, Mengnan
He, Qing
Jakada, Bello Hassan
Chen, Fangqian
Chen, Huihuang
Jin, Xingyue
Cai, Hanyang
Qin, Yuan
author_sort Huang, Youmei
collection PubMed
description Pineapple (Ananas comosus (L.) Merr.) is an important tropical fruit with high economic value. The quality and yield of pineapple will be affected by various environmental conditions. Under adverse conditions, plants can produce a complex reaction mechanism to enhance their resistance. It has been reported that the member of ethylene responsive transcription factors (ERFs) plays a crucial role in plant developmental process and stress response. However, the function of these proteins in pineapple remains limited. In this study, a total of 74 ERF genes (AcoERFs) were identified in pineapple genome, named from AcoERF1 to AcoERF74, and divided into 13 groups based on phylogenetic analysis. We also analyzed gene structure, conserved motif and chromosomal location of AcoERFs, and the AcoERFs within the same group possess similar gene structures and motif compositions. Three genes (AcoERF71, AcoERF73 and AcoERF74) were present on unanchored scaffolds, so they could not be conclusively mapped on chromosome. Synteny and cis-elements analysis of ERF genes provided deep insight into the evolution and function of pineapple ERF genes. Furthermore, we analyzed the expression profiling of AcoERF in different tissues and developmental stages, and 22 AcoERF genes were expressed in all examined tissues, in which five genes (AcoERF13, AcoERF16, AcoERF31, AcoERF42, and AcoERF65) had high expression levels. Additionally, nine AcoERF genes were selected for functional verification by qRT-PCR. These results provide useful information for further investigating the evolution and functions of ERF family in pineapple.
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spelling pubmed-75181612020-10-05 Genome-wide identification and expression analysis of the ERF transcription factor family in pineapple (Ananas comosus (L.) Merr.) Huang, Youmei Liu, Yanhui Zhang, Man Chai, Mengnan He, Qing Jakada, Bello Hassan Chen, Fangqian Chen, Huihuang Jin, Xingyue Cai, Hanyang Qin, Yuan PeerJ Agricultural Science Pineapple (Ananas comosus (L.) Merr.) is an important tropical fruit with high economic value. The quality and yield of pineapple will be affected by various environmental conditions. Under adverse conditions, plants can produce a complex reaction mechanism to enhance their resistance. It has been reported that the member of ethylene responsive transcription factors (ERFs) plays a crucial role in plant developmental process and stress response. However, the function of these proteins in pineapple remains limited. In this study, a total of 74 ERF genes (AcoERFs) were identified in pineapple genome, named from AcoERF1 to AcoERF74, and divided into 13 groups based on phylogenetic analysis. We also analyzed gene structure, conserved motif and chromosomal location of AcoERFs, and the AcoERFs within the same group possess similar gene structures and motif compositions. Three genes (AcoERF71, AcoERF73 and AcoERF74) were present on unanchored scaffolds, so they could not be conclusively mapped on chromosome. Synteny and cis-elements analysis of ERF genes provided deep insight into the evolution and function of pineapple ERF genes. Furthermore, we analyzed the expression profiling of AcoERF in different tissues and developmental stages, and 22 AcoERF genes were expressed in all examined tissues, in which five genes (AcoERF13, AcoERF16, AcoERF31, AcoERF42, and AcoERF65) had high expression levels. Additionally, nine AcoERF genes were selected for functional verification by qRT-PCR. These results provide useful information for further investigating the evolution and functions of ERF family in pineapple. PeerJ Inc. 2020-09-22 /pmc/articles/PMC7518161/ /pubmed/33024641 http://dx.doi.org/10.7717/peerj.10014 Text en ©2020 Huang et al. https://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Agricultural Science
Huang, Youmei
Liu, Yanhui
Zhang, Man
Chai, Mengnan
He, Qing
Jakada, Bello Hassan
Chen, Fangqian
Chen, Huihuang
Jin, Xingyue
Cai, Hanyang
Qin, Yuan
Genome-wide identification and expression analysis of the ERF transcription factor family in pineapple (Ananas comosus (L.) Merr.)
title Genome-wide identification and expression analysis of the ERF transcription factor family in pineapple (Ananas comosus (L.) Merr.)
title_full Genome-wide identification and expression analysis of the ERF transcription factor family in pineapple (Ananas comosus (L.) Merr.)
title_fullStr Genome-wide identification and expression analysis of the ERF transcription factor family in pineapple (Ananas comosus (L.) Merr.)
title_full_unstemmed Genome-wide identification and expression analysis of the ERF transcription factor family in pineapple (Ananas comosus (L.) Merr.)
title_short Genome-wide identification and expression analysis of the ERF transcription factor family in pineapple (Ananas comosus (L.) Merr.)
title_sort genome-wide identification and expression analysis of the erf transcription factor family in pineapple (ananas comosus (l.) merr.)
topic Agricultural Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7518161/
https://www.ncbi.nlm.nih.gov/pubmed/33024641
http://dx.doi.org/10.7717/peerj.10014
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