Genome-wide identification, molecular evolution, and expression analysis provide new insights into the APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factor superfamily in Dimocarpus longan Lour

Abstract Backgroud: APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factors perform indispensable roles in various biological processes, and it has been identified in many plants. However, little is known about the AP2/ERF superfamily in longan (Dimocarpus longan Lour.). The release of the whole-genome sequence of longan provided us an opportunity to perform a genome-wide investigation of AP2/ERF superfamily. Results: In the present study, we performed a genome-wide survey of AP2/ERF superfamily longan (DlAP2/ERF), including the gene structure, motif composition, phylogenetic, cis-acting element, single nucleotide polymorphisms (SNPs), insertions and deletions (InDels), alternative splicing (AS) events and the expression patterns. In total, 125 DlAP2/ERF genes were identified and classified into four families, including AP2 (19 members), ERF (101 members), RAV (four members) and Soliost (one member) in the longan genome. The AP2 and soloist genes possessed one to ten introns, while 87 genes within the ERF and RAV family had no introns. A large number of hormone signaling and stress response cis-acting elements were also identified. Besides, a large number of SNPs existed in the DlAP2/ERF superfamily, they may be deverse in the early somatic embryogenesis and stem of longan. However, the numbers of InDels was far less than SNPs. In addition, the AP2 family members existed a large number of AS events in different developmental processes of longan. Expression patterns analysis revealed that the AP2 family may promote the early somatic embryogenesis of longan, and DlAP2/ERF genes were specifically expressed in various organs such as seed, root, flower and young-fruit. The DlAP2/ERF genes can response to exogenous phytohormones, such as 2,4-Dichlorophenoxyacetic acid (2,4-D), Abscisic acid (ABA), Methyl jasmonate (MeJA) and Salicylic acid (SA). Protein interactions prediction indicated that the Baby Boom (BBM) protein may interacted with LALF/AGL15 network and was up-regulated expression at the transcriptional level in the early somatic embryogenesis of longan. Conclusions: A comprehensive analysis of molecular evolution and expression patterns showed that AP2/ERF superfamily played an important role in longan, especially in the early somatic embryogenesis, seed, root, flower and young-fruit. This systematic analysis provided the foundation for further functional characterization of AP2/ERF superfamily with an aim of longan improvement.

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Genome-wide identification, molecular evolution, and expression analysis provide new insights into the APETALA2/ethylene responsive factor (AP2/ERF) superfamily in Dimocarpus longan Lour

10.21203/rs.2.11288/v3 ◽

2019 ◽

Author(s):

Shuting Zhang ◽

Chen Zhu ◽

Yumeng Lyu ◽

Yan Chen ◽

Zihao Zhang ◽

...

Keyword(s):

Molecular Evolution ◽

Stress Responses ◽

Expression Patterns ◽

Functional Characterization ◽

Transcriptional Level ◽

Developmental Processes ◽

Genome Wide ◽

A Genome ◽

Dimocarpus Longan ◽

Ethylene Responsive Factor

Abstract Background: The APETALA2/ethylene responsive factor (AP2/ERF) superfamily members are transcription factors that regulate diverse developmental processes and stress responses in plants. They have been identified in many plants. However, little is known about the AP2/ERF superfamily in longan (Dimocarpus longan Lour.), which is an important tropical/subtropical evergreen fruit tree that produces a variety of bioactive compounds with rich nutritional and medicinal value. We conducted a genome-wide analysis of the AP2/ERF superfamily and its roles in somatic embryogenesis (SE) and developmental processes in longan. Results: A genome-wide survey of the AP2/ERF superfamily was carried out to discover its evolution and function in longan. We identified 125 longan AP2/ERF genes and classified them into the ERF (101 members), AP2 (19 members), RAV (four members) families, and one Soloist. The AP2 and Soloist genes contained one to ten introns, whereas 87 genes in the ERF and RAV families had no introns. Hormone signaling molecules such as methyl jasmonate (MeJA), abscisic acid (ABA), gibberellin, auxin, and salicylic acid (SA), and stress response cis-acting element low-temperature (55) and defense (49) boxes also were identified. We detected diverse single nucleotide polymorphisms (SNPs) between the 'Hong He Zi' (HHZ) and 'SI JI MI' (SJM) cultivars. The number of insertions and deletions (InDels) was far fewer than SNPs. The AP2 family members exhibited more alternative splicing (AS) events in different developmental processes of longan than members of the other families. Expression pattern analysis revealed that some AP2/ERF members regulated early SE and developmental processes in longan seed, root, and flower, and responded to exogenous hormones such as MeJA, SA, and ABA, and 2,4-D, a synthetic auxin. Protein interaction predictions indicated that the Baby Boom (BBM) transcription factor, which was up-regulated at the transcriptional level in early SE, may interact with the LALF/AGL15 network. Conclusions: The comprehensive analysis of molecular evolution and expression patterns suggested that the AP2/ERF superfamily may plays an important role in longan, especially in early SE, and in seed, root, flower, and young fruit. This systematic analysis provides a foundation for further functional characterization of the AP2/ERF superfamily with the aim of longan improvement.

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Genome-wide identification, molecular evolution, and expression analysis provide new insights into the APETALA2/ethylene responsive factor (AP2/ERF) superfamily in Dimocarpus longan Lour.

10.21203/rs.2.11288/v2 ◽

2019 ◽

Author(s):

Shuting Zhang ◽

Chen Zhu ◽

Yumeng Lyu ◽

Yan Chen ◽

Zihao Zhang ◽

...

Keyword(s):

Molecular Evolution ◽

Stress Responses ◽

Expression Patterns ◽

Functional Characterization ◽

Transcriptional Level ◽

Developmental Processes ◽

Genome Wide ◽

A Genome ◽

Dimocarpus Longan ◽

Ethylene Responsive Factor

Abstract Background: The APETALA2/ethylene responsive factor (AP2/ERF) superfamily members are transcription factors that regulate diverse developmental processes and stress responses in plants. They have been identified in many plants. However, little is known about the AP2/ERF superfamily in longan (Dimocarpus longan Lour.), which is an important tropical/subtropical evergreen fruit tree that produces a variety of bioactive compounds with rich nutritional and medicinal value. We conducted a genome-wide analysis of the AP2/ERF superfamily and its roles in somatic embryogenesis (SE) and developmental processes in longan. Results: A genome-wide survey of the AP2/ERF superfamily was carried out to discover its evolution and function in longan. We identified 125 longan AP2/ERF genes and classified them into the ERF (101 members), AP2 (19 members), RAV (four members), and Soloist (one member) families. The AP2 and soloist genes contained one to ten introns, whereas 87 genes in the ERF and RAV families had no introns. Hormone signaling molecules such as methyl jasmonate (MeJA), abscisic acid (ABA), gibberellin, auxin, and salicylic acid (SA), and stress response cis-acting element low-temperature (55) and defense (49) boxes also were identified. We detected diverse single nucleotide polymorphisms (SNPs) between the 'Hong He Zi' (HHZ) and 'SI JI MI' (SJM) cultivars. The number of insertions and deletions (InDels) was far fewer than SNPs. The AP2 family members exhibited more alternative splicing (AS) events in different developmental processes of longan than members of the other families. Expression pattern analysis revealed that some AP2/ERF members regulated early SE and developmental processes in longan seed, root, and flower, and responded to exogenous hormones such as MeJA, SA, and ABA, and 2,4-D, a synthetic auxin. Protein interaction predictions indicated that the Baby Boom (BBM) transcription factor, which was up-regulated at the transcriptional level in early SE, may interact with the LALF/AGL15 network. Conclusions: The comprehensive analysis of molecular evolution and expression patterns suggested that the AP2/ERF superfamily may play an important role in longan, especially in early SE, and in seed, root, flower, and young fruit. This systematic analysis provides a foundation for further functional characterization of the AP2/ERF superfamily with the aim of longan improvement.

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Identification and Analysis of the AP2 Subfamily Transcription Factors in the Pecan (Carya illinoinensis)

International Journal of Molecular Sciences ◽

10.3390/ijms222413568 ◽

2021 ◽

Vol 22 (24) ◽

pp. 13568

Author(s):

Zhengfu Yang ◽

Hongmiao Jin ◽

Junhao Chen ◽

Caiyun Li ◽

Jiani Wang ◽

...

Keyword(s):

Transcriptional Activation ◽

Expression Patterns ◽

Carya Illinoinensis ◽

Expression Levels ◽

Cis Acting ◽

Similar Expression ◽

Genome Wide ◽

A Genome ◽

Genome Wide Search ◽

Ethylene Responsive Factor

The AP2 transcriptional factors (TFs) belong to the APETALA2/ ethylene-responsive factor (AP2/ERF) superfamily and regulate various biological processes of plant growth and development, as well as response to biotic and abiotic stresses. However, genome-wide research on the AP2 subfamily TFs in the pecan (Carya illinoinensis) is rarely reported. In this paper, we identify 30 AP2 subfamily genes from pecans through a genome-wide search, and they were unevenly distributed on the pecan chromosomes. Then, a phylogenetic tree, gene structure and conserved motifs were further analyzed. The 30 AP2 genes were divided into euAP2, euANT and basalANT three clades. Moreover, the cis-acting elements analysis showed many light responsive elements, plant hormone-responsive elements and abiotic stress responsive elements are found in CiAP2 promoters. Furthermore, a qPCR analysis showed that genes clustered together usually shared similar expression patterns in euAP2 and basalANT clades, while the expression pattern in the euANT clade varied greatly. In developing pecan fruits, CiAP2-5, CiANT1 and CiANT2 shared similar expression patterns, and their expression levels decreased with fruit development. CiANT5 displayed the highest expression levels in developing fruits. The subcellular localization and transcriptional activation activity assay demonstrated that CiANT5 is located in the nucleus and functions as a transcription factor with transcriptional activation activity. These results help to comprehensively understand the pecan AP2 subfamily TFs and lay the foundation for further functional research on pecan AP2 family genes.

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Genome-wide identification and expression analyses of Sm genes reveal their involvement in early somatic embryogenesis in Dimocarpus longan Lour

PLoS ONE ◽

10.1371/journal.pone.0230795 ◽

2020 ◽

Vol 15 (4) ◽

pp. e0230795

Author(s):

Xue Li ◽

Yan Chen ◽

Shuting Zhang ◽

Liyao Su ◽

Xiaoping Xu ◽

...

Keyword(s):

Somatic Embryogenesis ◽

Genome Wide ◽

Dimocarpus Longan ◽

Early Somatic Embryogenesis

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Genome-wide identification and comprehensive analyses of NAC transcription factor gene family and expression patterns during somatic embryogenesis in Dimocarpus longan Lour

Plant Physiology and Biochemistry ◽

10.1016/j.plaphy.2020.10.009 ◽

2020 ◽

Vol 157 ◽

pp. 169-184

Author(s):

Nigarish Munir ◽

Chen Yukun ◽

Chen Xiaohui ◽

Muhammad Azher Nawaz ◽

Junaid Iftikhar ◽

...

Keyword(s):

Transcription Factor ◽

Somatic Embryogenesis ◽

Gene Family ◽

Expression Patterns ◽

Nac Transcription Factor ◽

Transcription Factor Gene ◽

Factor Gene ◽

Genome Wide ◽

Dimocarpus Longan ◽

Transcription Factor Gene Family

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Genome-wide identification, molecular evolution, and expression analysis provide new insights into the APETALA2/ethylene responsive factor (AP2/ERF) superfamily in Dimocarpus longan Lour

BMC Genomics ◽

10.1186/s12864-020-6469-4 ◽

2020 ◽

Vol 21 (1) ◽

Cited By ~ 4

Author(s):

Shuting Zhang ◽

Chen Zhu ◽

Yumeng Lyu ◽

Yan Chen ◽

Zihao Zhang ◽

...

Keyword(s):

Molecular Evolution ◽

Expression Analysis ◽

Genome Wide ◽

Dimocarpus Longan ◽

Ethylene Responsive Factor

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Genome-wide identification and characterization of long non-coding RNAs involved in the early somatic embryogenesis in Dimocarpus longan Lour

BMC Genomics ◽

10.1186/s12864-018-5158-z ◽

2018 ◽

Vol 19 (1) ◽

Cited By ~ 3

Author(s):

Yan Chen ◽

Xue Li ◽

Liyao Su ◽

Xu Chen ◽

Shuting Zhang ◽

...

Keyword(s):

Somatic Embryogenesis ◽

Genome Wide ◽

Dimocarpus Longan ◽

Non Coding Rnas ◽

Early Somatic Embryogenesis ◽

Identification And Characterization

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Characterization of MATE Gene Family And Its Role In Drought, Heat, And Salt Tolerance In Wheat (Triticum Aestivum L.)

10.21203/rs.3.rs-880815/v1 ◽

2021 ◽

Author(s):

Joseph Noble Amoah ◽

Yong Weon Seo

Keyword(s):

Salt Stress ◽

Expression Patterns ◽

Triticum Aestivum L ◽

Stress Conditions ◽

Crop Species ◽

Expression Levels ◽

Cis Acting ◽

Genome Wide ◽

A Genome

Abstract To explore the response of multidrug and toxic compound extrusion (MATE) proteins to drought, heat, and salt stress in wheat, a genome-wide identification and expression study was performed. 20 MATE genes located on 4 of the 12 chromosomes were identified and categorized into four (I-1V) subfamilies, based on phylogenetic analysis. Wheat MATE family expansion was primarily driven by whole-genome duplication (WGD) and tandem events. In the same subfamily, gene exon-intron structures and motif composition are more similar. TaMATE genes had cis-acting elements that were implicated in stress and defense response. Tae-miR5175e was identified as the highly expressed miRNA that targets TaMATEs by miRNA prediction. When compared to controls, the relative expression patterns of seven TaMATE genes were substantially elevated during drought stress. TaMATE2, 10, 13, and 14 expression levels considerably elevated after 15 days (d) of heat stress, whereas TaMATE2, 14, 18, and 20 expression levels were highly upregulated following 15 d of salt stress treatment, indicating the crucial role of TaMATEs under these abiotic stress conditions. Furthermore, drought, heat, and salt stress decreased wheat water content, but increased malondialdehyde (MDA), electrolyte leakage (EL), and proline content, whereas the expression of the 7 putative MATE genes was correlated with physio-biochemical indicators of these stress conditions. The findings contribute to a better understanding of the complexities of MATEs and present a theoretical base for future MATE gene discovery and application in wheat and other crop species.

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Calcium-Dependent Protein Kinase Genes in Glycyrrhiza Uralensis Appear to be Involved in Promoting the Biosynthesis of Glycyrrhizic Acid and Flavonoids under Salt Stress

Molecules ◽

10.3390/molecules24091837 ◽

2019 ◽

Vol 24 (9) ◽

pp. 1837 ◽

Cited By ~ 3

Author(s):

Xuechen Tong ◽

Aiping Cao ◽

Fei Wang ◽

Xifeng Chen ◽

Shuangquan Xie ◽

...

Keyword(s):

Salt Stress ◽

Glycyrrhizic Acid ◽

Expression Patterns ◽

Glycyrrhiza Uralensis ◽

Calcium Signal ◽

Cis Acting ◽

Calcium Dependent ◽

Genome Wide ◽

A Genome ◽

Dependent Protein

As calcium signal sensors, calcium-dependent protein kinases (CPKs) play vital roles in stimulating the production of secondary metabolites to participate in plant development and response to environmental stress. However, investigations of the Glycyrrhiza uralensis CPK family genes and their multiple functions are rarely reported. In this study, a total of 23 GuCPK genes in G. uralensis were identified, and their phylogenetic relationships, evolutionary characteristics, gene structure, motif distribution, and promoter cis-acting elements were analyzed. Ten GuCPKs showed root-specific preferential expressions, and GuCPKs indicated different expression patterns under treatments of CaCl2 and NaCl. In addition, under 2.5 mM of CaCl2 and 30 mM of NaCl treatments, the diverse, induced expression of GuCPKs and significant accumulations of glycyrrhizic acid and flavonoids suggested the possible important function of GuCPKs in regulating the production of glycyrrhizic acid and flavonoids. Our results provide a genome-wide characterization of CPK family genes in G. uralensis, and serve as a foundation for understanding the potential function and regulatory mechanism of GuCPKs in promoting the biosynthesis of glycyrrhizic acid and flavonoids under salt stress.

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