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Li X, Jiang Z, Zhang C, Cai K, Wang H, Pan W, Sun X, Gao Y, Xu K. Comparative genomics analysis provide insights into evolution and stress responses of Lhcb genes in Rosaceae fruit crops. BMC PLANT BIOLOGY 2023; 23:484. [PMID: 37817059 PMCID: PMC10566169 DOI: 10.1186/s12870-023-04438-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/04/2023] [Indexed: 10/12/2023]
Abstract
BACKGROUND Light-harvesting chlorophyll a/b b evelopment of higher plants and in response to abiotic stress. Previous works has demonstrated that that Lhcb genes were involved in the phytochrome regulation and responded to the different light and temperature conditions in Poaceae (such as maize). However, the evolution and functions of Lhcb genes remains poorly characterized in important Rosaceae species. RESULTS In this investigation, we conducted a genome-wide analysis and identified a total of 212 Lhcb genes across nine Rosaceae species. Specifically, we found 23 Lhcb genes in Fragaria vesca, 20 in Prunus armeniaca, 33 in Malus domestica 'Gala', 21 in Prunus persica, 33 in Rosa chinensis, 29 in Pyrus bretschneideri, 18 in Rubus occidentalis, 20 in Prunus mume, and 15 in Prunus salicina. Phylogenetic analysis revealed that the Lhcb gene family could be classified into seven major subfamilies, with members of each subfamily sharing similar conserved motifs. And, the functions of each subfamily was predicted based on the previous reports from other species. The Lhcb proteins were highly conserved within their respective subfamilies, suggesting similar functions. Interestingly, we observed similar peaks in Ks values (0.1-0.2) for Lhcb genes in apple and pear, indicating a recent whole genome duplication event (about 30 to 45 million years ago). Additionally, a few Lhcb genes underwent tandem duplication and were located across all chromosomes of nine species of Rosaceae. Furthermore, the analysis of the cis-acting elements in the 2000 bp promoter region upstream of the pear Lhcb gene revealed four main categories: light response correlation, stress response correlation, hormone response correlation, and plant growth. Quantitative expression analysis demonstrated that Lhcb genes exhibited tissue-specific expression patterns and responded differently to low-temperature stress in Rosaceae species. CONCLUSIONS These findings shed light on the evolution and phylogeny of Lhcb genes in Rosaceae and highlight the critical role of Lhcb in pear's response to low temperatures. The results obtained provide valuable insights for further investigations into the functions of Lhcb genes in Rosaceae, and these functional genes will be used for further fruit tree breeding and improvement to cope with the current climate changes.
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Affiliation(s)
- Xiaolong Li
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Zeyu Jiang
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Chaofan Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Kefan Cai
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Hui Wang
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Weiyi Pan
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Xuepeng Sun
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China
| | - Yongbin Gao
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China.
| | - Kai Xu
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, Zhejiang, China.
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Aono AH, Pimenta RJG, Dambroz CMDS, Costa FCL, Kuroshu RM, de Souza AP, Pereira WA. Genome-wide characterization of the common bean kinome: Catalog and insights into expression patterns and genetic organization. Gene 2023; 855:147127. [PMID: 36563714 DOI: 10.1016/j.gene.2022.147127] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/06/2022] [Accepted: 12/16/2022] [Indexed: 12/25/2022]
Abstract
The protein kinase (PK) superfamily is one of the largest superfamilies in plants and is the core regulator of cellular signaling. Even considering this substantial importance, the kinome of common bean (Phaseolus vulgaris) has not been profiled yet. Here, we identified and characterised the complete set of kinases of common bean, performing an in-depth investigation with phylogenetic analyses and measurements of gene distribution, structural organization, protein properties, and expression patterns over a large set of RNA-Sequencing data. Being composed of 1,203 PKs distributed across all P. vulgaris chromosomes, this set represents 3.25% of all predicted proteins for the species. These PKs could be classified into 20 groups and 119 subfamilies, with a more pronounced abundance of subfamilies belonging to the receptor-like kinase (RLK)-Pelle group. In addition to provide a vast and rich reservoir of data, our study supplied insights into the compositional similarities between PK subfamilies, their evolutionary divergences, highly variable functional profile, structural diversity, and expression patterns, modeled with coexpression networks for investigating putative interactions associated with stress response.
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Affiliation(s)
- Alexandre Hild Aono
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil.
| | | | | | | | - Reginaldo Massanobu Kuroshu
- Instituto de Ciência e Tecnologia, Universidade Federal de São Paulo (UNIFESP), São José dos Campos, Brazil.
| | - Anete Pereira de Souza
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil; Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), Campinas, Brazil.
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Chen Y, Ma T, Zhang T, Ma L. Trends in the evolution of intronless genes in Poaceae. FRONTIERS IN PLANT SCIENCE 2023; 14:1065631. [PMID: 36875616 PMCID: PMC9978806 DOI: 10.3389/fpls.2023.1065631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
Intronless genes (IGs), which are a feature of prokaryotes, are a fascinating group of genes that are also present in eukaryotes. In the current study, a comparison of Poaceae genomes revealed that the origin of IGs may have involved ancient intronic splicing, reverse transcription, and retrotranspositions. Additionally, IGs exhibit the typical features of rapid evolution, including recent duplications, variable copy numbers, low divergence between paralogs, and high non-synonymous to synonymous substitution ratios. By tracing IG families along the phylogenetic tree, we determined that the evolutionary dynamics of IGs differed among Poaceae subfamilies. IG families developed rapidly before the divergence of Pooideae and Oryzoideae and expanded slowly after the divergence. In contrast, they emerged gradually and consistently in the Chloridoideae and Panicoideae clades during evolution. Furthermore, IGs are expressed at low levels. Under relaxed selection pressure, retrotranspositions, intron loss, and gene duplications and conversions may promote the evolution of IGs. The comprehensive characterization of IGs is critical for in-depth studies on intron functions and evolution as well as for assessing the importance of introns in eukaryotes.
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Affiliation(s)
- Yong Chen
- *Correspondence: Tingting Zhang, ; Lei Ma,
| | | | | | - Lei Ma
- *Correspondence: Tingting Zhang, ; Lei Ma,
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Ferreira-Neto JRC, de Araújo FC, de Oliveira Silva RL, de Melo NF, Pandolfi V, Frosi G, de Lima Morais DA, da Silva MD, Rivas R, Santos MG, de Tarso Aidar S, Morgante CV, Benko-Iseppon AM. Dehydration response in Stylosanthes scabra: Transcriptional, biochemical, and physiological modulations. PHYSIOLOGIA PLANTARUM 2022; 174:e13821. [PMID: 36345266 DOI: 10.1111/ppl.13821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/22/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
Stylosanthes scabra, popularly known as stylo, is native to the Brazilian Caatinga semiarid region and stands out as a drought-tolerant shrub forage crop. This work provides information about the plant response during the first 48 h of water deficit, followed by a rehydration treatment. Besides root transcriptomics data, 13 physiological or biochemical parameters were scrutinized. Additionally, RNA-Seq annotated transcripts not associated with the "Viridiplantae" clade were taxonomically categorized. It was found that S. scabra quickly perceives and recovers from the oscillations of the imposed water regime. Physiologically, mechanisms that minimize evapotranspiration or protect the photosynthetic apparatus stood out. Biochemically, it was found that the root tissue invests in synthesizing compounds that can act as osmolytes (proline and sugars), emphasizing the importance of osmoregulation to water deficit acclimation. Consistently, transcriptome and qPCR analyses showed that a set of enriched biological processes with upregulated (UR) transcripts were involved in protective functions against reactive oxygen species or encoding enzymes of important metabolic pathways, which might contribute to S. scabra response to water deficit. Additionally, several UR kinases and transcription factors were identified. Finally, in an innovative approach, some naturally occurring microbial groups (such as Schizosaccharomyces, Bradyrhizobium, etc.) were identified in the S. scabra roots. This study reveals insights into the physiological, biochemical, and molecular mechanisms underlying the S. scabra response to water deficit and provides candidate genes that may be useful in developing drought-tolerant crop varieties through biotechnological applications.
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Affiliation(s)
- José Ribamar Costa Ferreira-Neto
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Flávia Czekalski de Araújo
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Roberta Lane de Oliveira Silva
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | | | - Valesca Pandolfi
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Gabriella Frosi
- Départament de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | | | - Manassés Daniel da Silva
- Laboratório de Genética Molecular, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Rebeca Rivas
- Laboratório de Genética Molecular, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Mauro Guida Santos
- Laboratório de Fisiologia Vegetal, Departamento de Botânica, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Saulo de Tarso Aidar
- Empresa Brasileira de Pesquisa Agropecuária (SEMIÁRIDO), Petrolina, Pernambuco, Brazil
| | | | - Ana Maria Benko-Iseppon
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
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Zhu K, Fan P, Liu H, Tan P, Ma W, Mo Z, Zhao J, Chu G, Peng F. Insight into the CBL and CIPK gene families in pecan (Carya illinoinensis): identification, evolution and expression patterns in drought response. BMC PLANT BIOLOGY 2022; 22:221. [PMID: 35484502 PMCID: PMC9047272 DOI: 10.1186/s12870-022-03601-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 04/18/2022] [Indexed: 05/05/2023]
Abstract
BACKGROUND Calcium (Ca2+) serves as a ubiquitous second messenger and plays a pivotal role in signal transduction. Calcineurin B-like proteins (CBLs) are plant-specific Ca2+ sensors that interact with CBL-interacting protein kinases (CIPKs) to transmit Ca2+ signals. CBL-CIPK complexes have been reported to play pivotal roles in plant development and response to drought stress; however, limited information is available about the CBL and CIPK genes in pecan, an important nut crop. RESULTS In the present study, a total of 9 CBL and 30 CIPK genes were identified from the pecan genome and divided into four and five clades based on phylogeny, respectively. Gene structure and distribution of conserved sequence motif analysis suggested that family members in the same clade commonly exhibited similar exon-intron structures and motif compositions. The segmental duplication events contributed largely to the expansion of pecan CBL and CIPK gene families, and Ka/Ks values revealed that all of them experienced strong negative selection. Phylogenetic analysis of CIPK proteins from 14 plant species revealed that CIPKs in the intron-poor clade originated in seed plants. Tissue-specific expression profiles of CiCBLs and CiCIPKs were analysed, presenting functional diversity. Expression profiles derived from RNA-Seq revealed distinct expression patterns of CiCBLs and CiCIPKs under drought treatment in pecan. Moreover, coexpression network analysis helped to elucidate the relationships between these genes and identify potential candidates for the regulation of drought response, which were verified by qRT-PCR analysis. CONCLUSIONS The characterization and analysis of CBL and CIPK genes in pecan genome could provide a basis for further functional analysis of CiCBLs and CiCIPKs in the drought stress response of pecan.
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Affiliation(s)
- Kaikai Zhu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Pinghua Fan
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Hui Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Pengpeng Tan
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Wenjuan Ma
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Zhenghai Mo
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014 Jiangsu China
| | - Juan Zhao
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Guolin Chu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Fangren Peng
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
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Ferreira-Neto JRC, Borges ANDC, da Silva MD, Morais DADL, Bezerra-Neto JP, Bourque G, Kido EA, Benko-Iseppon AM. The Cowpea Kinome: Genomic and Transcriptomic Analysis Under Biotic and Abiotic Stresses. FRONTIERS IN PLANT SCIENCE 2021; 12:667013. [PMID: 34194450 PMCID: PMC8238008 DOI: 10.3389/fpls.2021.667013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/26/2021] [Indexed: 06/13/2023]
Abstract
The present work represents a pioneering effort, being the first to analyze genomic and transcriptomic data from Vigna unguiculata (cowpea) kinases. We evaluated the cowpea kinome considering its genome-wide distribution and structural characteristics (at the gene and protein levels), sequence evolution, conservation among Viridiplantae species, and gene expression in three cowpea genotypes under different stress situations, including biotic (injury followed by virus inoculation-CABMV or CPSMV) and abiotic (root dehydration). The structural features of cowpea kinases (VuPKs) indicated that 1,293 bona fide VuPKs covered 20 groups and 118 different families. The RLK-Pelle was the largest group, with 908 members. Insights on the mechanisms of VuPK genomic expansion and conservation among Viridiplantae species indicated dispersed and tandem duplications as major forces for VuPKs' distribution pattern and high orthology indexes and synteny with other legume species, respectively. K a /K s ratios showed that almost all (91%) of the tandem duplication events were under purifying selection. Candidate cis-regulatory elements were associated with different transcription factors (TFs) in the promoter regions of the RLK-Pelle group. C2H2 TFs were closely associated with the promoter regions of almost all scrutinized families for the mentioned group. At the transcriptional level, it was suggested that VuPK up-regulation was stress, genotype, or tissue dependent (or a combination of them). The most prominent families in responding (up-regulation) to all the analyzed stresses were RLK-Pelle_DLSV and CAMK_CAMKL-CHK1. Concerning root dehydration, it was suggested that the up-regulated VuPKs are associated with ABA hormone signaling, auxin hormone transport, and potassium ion metabolism. Additionally, up-regulated VuPKs under root dehydration potentially assist in a critical physiological strategy of the studied cowpea genotype in this assay, with activation of defense mechanisms against biotic stress while responding to root dehydration. This study provides the foundation for further studies on the evolution and molecular function of VuPKs.
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Affiliation(s)
| | | | - Manassés Daniel da Silva
- Laboratory of Molecular Genetics, Genetics Department, Federal University of Pernambuco, Recife, Brazil
| | | | - João Pacífico Bezerra-Neto
- Laboratory of Plant Genetics and Biotechnology, Genetics Department, Federal University of Pernambuco, Recife, Brazil
| | - Guillaume Bourque
- Génome Québec Innovation Centre, McGill University, Montréal, QC, Canada
| | - Ederson Akio Kido
- Laboratory of Molecular Genetics, Genetics Department, Federal University of Pernambuco, Recife, Brazil
| | - Ana Maria Benko-Iseppon
- Laboratory of Plant Genetics and Biotechnology, Genetics Department, Federal University of Pernambuco, Recife, Brazil
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Liu H, Lyu HM, Zhu K, de Peer YV, Cheng ZM(M. The emergence and evolution of intron-poor and intronless genes in intron-rich plant gene families. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1072-1082. [PMID: 33217085 PMCID: PMC7116809 DOI: 10.1111/tpj.15088] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 10/30/2020] [Accepted: 11/09/2020] [Indexed: 05/02/2023]
Abstract
Eukaryotic genes can be classified into intronless (no introns), intron-poor (three or fewer introns per gene) or intron-rich. Early eukaryotic genes were mostly intron-rich, and their alternative splicing into multiple transcripts, giving rise to different proteins, might have played pivotal roles in adaptation and evolution. Interestingly, extant plant genomes contain many gene families with one or sometimes few sub-families with genes that are intron-poor or intronless, and it remains unknown when and how these intron-poor or intronless genes have originated and evolved, and what their possible functions are. In this study, we identified 33 such gene families that contained intronless and intron-poor sub-families. Intronless genes seemed to have first emerged in early land plant evolution, while intron-poor sub-families seemed first to have appeared in green algae. In contrast to intron-rich genes, intronless genes in intron-poor sub-families occurred later, and were subject to stronger functional constraints. Based on RNA-seq analyses in Arabidopsis and rice, intronless or intron-poor genes in AP2, EF-hand_7, bZIP, FAD_binding_4, STE_STE11, CAMK_CAMKL-CHK1 and C2 gene families were more likely to play a role in response to drought and salt stress, compared with intron-rich genes in the same gene families, whereas intronless genes in the B_lectin and S_locus_glycop gene family were more likely to participate in epigenetic processes and plant development. Understanding the origin and evolutionary trajectory, as well as the potential functions, of intronless and intron-poor sub-families provides further insight into plant genome evolution and the functional divergence of genes.
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Affiliation(s)
- Hui Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Hai-Meng Lyu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Kaikai Zhu
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Yves Van de Peer
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, South Africa
| | - Zong-Ming (Max) Cheng
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Department of Plant Sciences, University of Tennessee, Knoxville 37996, USA
- Corresponding author (, )
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Aono AH, Pimenta RJG, Garcia ALB, Correr FH, Hosaka GK, Carrasco MM, Cardoso-Silva CB, Mancini MC, Sforça DA, dos Santos LB, Nagai JS, Pinto LR, Landell MGDA, Carneiro MS, Balsalobre TW, Quiles MG, Pereira WA, Margarido GRA, de Souza AP. The Wild Sugarcane and Sorghum Kinomes: Insights Into Expansion, Diversification, and Expression Patterns. FRONTIERS IN PLANT SCIENCE 2021; 12:668623. [PMID: 34305969 PMCID: PMC8294386 DOI: 10.3389/fpls.2021.668623] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 03/17/2021] [Indexed: 05/11/2023]
Abstract
The protein kinase (PK) superfamily is one of the largest superfamilies in plants and the core regulator of cellular signaling. Despite this substantial importance, the kinomes of sugarcane and sorghum have not been profiled. Here, we identified and profiled the complete kinomes of the polyploid Saccharum spontaneum (Ssp) and Sorghum bicolor (Sbi), a close diploid relative. The Sbi kinome was composed of 1,210 PKs; for Ssp, we identified 2,919 PKs when disregarding duplications and allelic copies, and these were related to 1,345 representative gene models. The Ssp and Sbi PKs were grouped into 20 groups and 120 subfamilies and exhibited high compositional similarities and evolutionary divergences. By utilizing the collinearity between the species, this study offers insights into Sbi and Ssp speciation, PK differentiation and selection. We assessed the PK subfamily expression profiles via RNA-Seq and identified significant similarities between Sbi and Ssp. Moreover, coexpression networks allowed inference of a core structure of kinase interactions with specific key elements. This study provides the first categorization of the allelic specificity of a kinome and offers a wide reservoir of molecular and genetic information, thereby enhancing the understanding of Sbi and Ssp PK evolutionary history.
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Affiliation(s)
- Alexandre Hild Aono
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Ricardo José Gonzaga Pimenta
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Ana Letycia Basso Garcia
- Department of Genetics, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Fernando Henrique Correr
- Department of Genetics, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Guilherme Kenichi Hosaka
- Department of Genetics, Luiz de Queiroz College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil
| | - Marishani Marin Carrasco
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | | | - Melina Cristina Mancini
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Danilo Augusto Sforça
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - Lucas Borges dos Santos
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
| | - James Shiniti Nagai
- Faculty of Medicine, Institute for Computational Genomics, RWTH Aachen University, Aachen, Germany
| | - Luciana Rossini Pinto
- Advanced Center of Sugarcane Agrobusiness Technological Research, Agronomic Institute of Campinas (IAC), Ribeirão Preto, Brazil
| | | | - Monalisa Sampaio Carneiro
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
| | - Thiago Willian Balsalobre
- Departamento de Biotecnologia e Produção Vegetal e Animal, Centro de Ciências Agrárias, Universidade Federal de São Carlos (UFSCar), São Carlos, Brazil
| | - Marcos Gonçalves Quiles
- Instituto de Ciência e Tecnologia (ICT), Universidade Federal de São Paulo (Unifesp), São José dos Campos, Brazil
| | | | | | - Anete Pereira de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), Campinas, Brazil
- Department of Plant Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
- *Correspondence: Anete Pereira de Souza,
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Confirmation and Fine Mapping of the Resistance Locus Ren9 from the Grapevine Cultivar 'Regent'. PLANTS 2020; 10:plants10010024. [PMID: 33374373 PMCID: PMC7823669 DOI: 10.3390/plants10010024] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 12/21/2020] [Accepted: 12/22/2020] [Indexed: 12/15/2022]
Abstract
Grapevine (Vitis vinifera ssp. vinifera) is a major fruit crop with high economic importance. Due to its susceptibility towards fungal and oomycete pathogens such as Erysiphe necator and Plasmopara viticola, the causal agents of powdery and downy mildew (PM and DM, respectively), grapevine growers annually face a major challenge in coping with shortfalls of yield caused by these diseases. Here we report the confirmation of a genetic resource for grapevine resistance breeding against PM. During the delimitation process of Ren3 on chromosome 15 from the cultivar ‘Regent’, a second resistance-encoding region on chromosome 15 termed Ren9 was characterized. It mediates a trailing necrosis associated with the appressoria of E. necator and restricts pathogen growth. In this study, we confirm this QTL in a related mapping population of ‘Regent’ × ‘Cabernet Sauvignon’. The data show that this locus is located at the upper arm of chromosome 15 between markers GF15-58 (0.15 Mb) and GF15-53 (4 Mb). The efficiency of the resistance against one of the prominent European PM isolates (EU-B) is demonstrated. Based on fine-mapping and literature knowledge we propose two possible regions of interest and supply molecular markers to follow both regions in marker-assisted selection.
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Venios X, Korkas E, Nisiotou A, Banilas G. Grapevine Responses to Heat Stress and Global Warming. PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9121754. [PMID: 33322341 PMCID: PMC7763569 DOI: 10.3390/plants9121754] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/05/2020] [Accepted: 12/09/2020] [Indexed: 05/08/2023]
Abstract
The potential effects of the forthcoming climate change include the rising of the average annual temperature and the accumulation of extreme weather events, like frequent and severe heatwaves, a phenomenon known as global warming. Temperature is an important environmental factor affecting almost all aspects of growth and development in plants. The grapevine (Vitis spp.) is quite sensitive to extreme temperatures. Over the current century, temperatures are projected to continue rising with negative impacts on viticulture. These consequences range from short-term effects on wine quality to long-term issues such as the suitability of certain varieties and the sustainability of viticulture in traditional wine regions. Many viticultural zones, particularly in Mediterranean climate regions, may not be suitable for growing winegrapes in the near future unless we develop heat-stress-adapted genotypes or identify and exploit stress-tolerant germplasm. Grapevines, like other plants, have developed strategies to maintain homeostasis and cope with high-temperature stress. These mechanisms include physiological adaptations and activation of signaling pathways and gene regulatory networks governing heat stress response and acquisition of thermotolerance. Here, we review the major impacts of global warming on grape phenology and viticulture and focus on the physiological and molecular responses of the grapevine to heat stress.
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Affiliation(s)
- Xenophon Venios
- Department of Wine, Vine and Beverage Sciences, University of West Attica, Ag. Spyridonos 28, 12243 Athens, Greece; (X.V.); (E.K.)
| | - Elias Korkas
- Department of Wine, Vine and Beverage Sciences, University of West Attica, Ag. Spyridonos 28, 12243 Athens, Greece; (X.V.); (E.K.)
| | - Aspasia Nisiotou
- Institute of Technology of Agricultural Products, Hellenic Agricultural Organization “Demeter”, Sofokli Venizelou 1, 14123 Lykovryssi, Greece;
| | - Georgios Banilas
- Department of Wine, Vine and Beverage Sciences, University of West Attica, Ag. Spyridonos 28, 12243 Athens, Greece; (X.V.); (E.K.)
- Correspondence:
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Liu H, Qu W, Zhu K, Cheng ZMM. The wild strawberry kinome: identification, classification and transcript profiling of protein kinases during development and in response to gray mold infection. BMC Genomics 2020; 21:635. [PMID: 32928117 PMCID: PMC7490889 DOI: 10.1186/s12864-020-07053-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 09/04/2020] [Indexed: 12/22/2022] Open
Abstract
Background Protein kinases (PKs) play an important role in signaling cascades and are one of the largest and most conserved protein super families in plants. Despite their importance, the woodland strawberry (Fragaria vesca) kinome and expression patterns of PK genes remain to be characterized. Results Here, we report on the identification and classification of 954 Fragaria vesca PK genes, which were classified into nine groups and 124 gene families. These genes were distributed unevenly among the seven chromosomes, and the number of introns per gene varied from 0 to 47. Almost half of the putative PKs were predicted to localize to the nucleus and 24.6% were predicted to localize to the cell membrane. The expansion of the woodland strawberry PK gene family occurred via different duplication mechanisms and tandem duplicates occurred relatively late as compared to other duplication types. Moreover, we found that tandem and transposed duplicated PK gene pairs had undergone stronger diversifying selection and evolved relatively faster than WGD genes. The GO enrichment and transcriptome analysis implicates the involvement of strawberry PK genes in multiple biological processes and molecular functions in differential tissues, especially in pollens. Finally, 109 PKs, mostly the receptor-like kinases (RLKs), were found transcriptionally responsive to Botrytis cinerea infection. Conclusions The findings of this research expand the understanding of the evolutionary dynamics of PK genes in plant species and provide a potential link between cell signaling pathways and pathogen attack.
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Affiliation(s)
- Hui Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wei Qu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kaikai Zhu
- College of Forestry, Nanjing Forestry University, Nanjing, 210037, China
| | - Zong-Ming Max Cheng
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China. .,Department of Plant Sciences, University of Tennessee, Knoxville, 37996, USA.
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Zhang W, Chen Z, Kang Y, Fan Y, Liu Y, Yang X, Shi M, Yao K, Qin S. Genome-wide analysis of lectin receptor-like kinases family from potato ( Solanum tuberosum L.). PeerJ 2020; 8:e9310. [PMID: 32566405 PMCID: PMC7293193 DOI: 10.7717/peerj.9310] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 05/17/2020] [Indexed: 12/29/2022] Open
Abstract
Lectin receptor-like kinases (LecRLKs) are involved in responses to diverse environmental stresses and pathogenic microbes. A comprehensive acknowledgment of the family members in potato (Solanum tuberosum) genome is largely limited until now. In total, 113 potato LecRLKs (StLecRLKs) were first identified, including 85 G-type, 26 L-type and 2 C-type members. Based on phylogenetic analysis, StLecRLKs were sub-grouped into seven clades, including C-type, L-type, G-I, G-II, G-III G-IV and G-V. Chromosomal distribution and gene duplication analysis revealed the expansion of StLecRLKs occurred majorly through tandem duplication although the whole-genome duplication (WGD)/segmental duplication events were found. Cis-elements in the StLecRLKs promoter region responded mainly to signals of defense and stress, phytohormone, biotic or abiotic stress. Moreover, expressional investigations indicated that the family members of the clades L-type, G-I, G-IV and G-V were responsive to both bacterial and fungal infection. Based on qRT-PCR analysis, the expressions of PGSC0003DMP400055136 and PGSC0003DMP400067047 were strongly induced in all treatments by both Fusarium sulphureum (Fs) and Phytophthora infestans (Pi) inoculation. The present study provides valuable information for LecRLKs gene family in potato genome, and establishes a foundation for further research into the functional analysis.
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Affiliation(s)
- Weina Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Zhongjian Chen
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yichen Kang
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Yanling Fan
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Yuhui Liu
- Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
| | - Xinyu Yang
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Mingfu Shi
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Kai Yao
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Shuhao Qin
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
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Wu Y, Henderson SW, Wege S, Zheng F, Walker AR, Walker RR, Gilliham M. The grapevine NaE sodium exclusion locus encodes sodium transporters with diverse transport properties and localisation. JOURNAL OF PLANT PHYSIOLOGY 2020; 246-247:153113. [PMID: 32044673 DOI: 10.1016/j.jplph.2020.153113] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/22/2019] [Accepted: 12/29/2019] [Indexed: 06/10/2023]
Abstract
Grapevine (Vitis vinifera L.) is a valuable crop for human consumption and wine production, and is prone to suffering from salinity stress in arid regions or when exposed to low quality irrigation water. A previous study identified a quantitative trait locus (QTL) NaE, containing six High-affinity Potassium Transporter 1 genes, that was associated with shoot Na+ exclusion in grapevine. While HKT1;1 was predicted to be the most likely gene within this QTL to encode for this important salinity tolerance sub-trait, four other HKTs within the QTL remained uncharacterised; VviHKT1;2 encodes a truncated transcript unlikely to form a functional transporter. In this study, two allelic variants for each of VviHKT1;6, VviHKT1;7 and VviHKT1;8 from the heterozygous grapevine variety Cabernet Sauvignon were functionally characterised. Using the Xenopus laevis oocyte heterologous expression system, as well as transient expression in tobacco leaves, we found that the VviHKT1;6 and VviHKT1;7 alleles encoded plasma membrane localised proteins that facilitated significant non-rectifying Na+ transport. Conversely, proteins encoded by the VviHKT1;8 alleles were inwardly-rectifying, weak Na+ transporters that localised to intracellular organelles. Mining of previous RNA-seq gene expression data suggested that VviHKT1;6-8 are weakly expressed in grapevine roots, flower buds, and seeds under normal conditions and different nutrient regimes. We propose that VviHKT1;6 and VviHKT1;7 are likely to have a less significant role in grapevine leaf Na+ exclusion than VviHKT1;1, and that VviHKT1;8 is involved in endomembrane Na+ transport.
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Affiliation(s)
- Yue Wu
- ARC Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine & Waite Research Institute, University of Adelaide, Glen Osmond, 5064, Australia
| | - Sam W Henderson
- ARC Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine & Waite Research Institute, University of Adelaide, Glen Osmond, 5064, Australia
| | - Stefanie Wege
- ARC Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine & Waite Research Institute, University of Adelaide, Glen Osmond, 5064, Australia
| | - Fei Zheng
- ARC Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine & Waite Research Institute, University of Adelaide, Glen Osmond, 5064, Australia
| | - Amanda R Walker
- CSIRO Agriculture and Food, Locked Bag 2, Glen Osmond, 5064, Australia
| | - Rob R Walker
- CSIRO Agriculture and Food, Locked Bag 2, Glen Osmond, 5064, Australia
| | - Matthew Gilliham
- ARC Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine & Waite Research Institute, University of Adelaide, Glen Osmond, 5064, Australia; ARC Industrial Transformation Training Centre for Innovative Wine Production, School of Agriculture, Food and Wine & Waite Research Institute, University of Adelaide, Glen Osmond, 5064, Australia.
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Wang G, Tian C, Wang Y, Wan F, Hu L, Xiong A, Tian J. Selection of reliable reference genes for quantitative RT-PCR in garlic under salt stress. PeerJ 2019; 7:e7319. [PMID: 31341748 PMCID: PMC6640627 DOI: 10.7717/peerj.7319] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 06/18/2019] [Indexed: 12/21/2022] Open
Abstract
Quantitative real-time reverse-transcriptase PCR (qRT-PCR) has been frequently used for detecting gene expression. To obtain reliable results, selection of suitable reference genes is a fundamental and necessary step. Garlic (Allium sativum), a member from Alliaceae family, has been used both as a food flavoring and as a traditional medicine. In the present study, garlic plants were exposed to salt stress (200 mM NaCl) for 0, 1, 4 and 12 h, and garlic roots, bulbs, and leaves were harvested for subsequent analysis. The expression stability of eight candidate reference genes, eukaryotic translation initiation factor 4α (eIF-4α), actin (ACTIN), tubulin β-7 (TUB7), TAP42-interacting protein of 41 kDa (TIP41), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), SAND family protein (SAND), elongation factor 1 alpha (EF-1α), and protein phosphatase 2A (PP2A) were evaluated by geNorm, NormFinder, and BestKeeper. All genes tested displayed variable expression profiles under salt stress. In the leaf and root group, ACTIN was the best reference gene for normalizing gene expression. In garlic clove, ACTIN and SAND were the least variable, and were suitable for gene expression studies under salt stress; these two genes also performed well in all samples tested. Based on our results, we recommend that it is essential to use specific reference genes in different situations to obtain accurate results. Using a combination of multiple stable reference genes, such as ACTIN and SAND, to normalize gene expression is encouraged. The results from the study will be beneficial for accurate determination of gene expression in garlic and other plants.
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Affiliation(s)
- Guanglong Wang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, Jiangsu, China
| | - Chang Tian
- Key Laboratory of Landscape Agriculture, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Yunpeng Wang
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, Jiangsu, China
| | - Faxiang Wan
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, Jiangsu, China
| | - Laibao Hu
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, Jiangsu, China
| | - Aisheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jie Tian
- Academy of Agriculture and Forestry Sciences of Qinghai University (Qinghai Academy of Agriculture and Forestry Sciences), Qinghai Key Laboratory of Vegetable Genetics and Physiology, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Qinghai, China
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Genome-Wide Identification, Characterization, and Expression Analysis of the Grapevine Superoxide Dismutase (SOD) Family. Int J Genomics 2019; 2019:7350414. [PMID: 30923713 PMCID: PMC6409070 DOI: 10.1155/2019/7350414] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 12/01/2018] [Accepted: 12/20/2018] [Indexed: 01/23/2023] Open
Abstract
Superoxide dismutase (SOD) is an essential enzyme of the plant antioxidant system that responds to oxidative damage caused by adverse conditions. However, little is known about the SOD gene family in Vitis vinifera (Vv). In the present study, ten SOD genes, including 6 copper/zinc SODs, 2 iron SODs, and 2 manganese SODs, were identified in the grapevine genome where they were unevenly distributed on 12 chromosomes. Ten VvSOD genes were divided into three main groups based on phylogenetic analysis, subcellular localization, and the distribution of conserved protein motifs. Additionally, many cis-elements related to different stresses were found in the promoters of the 10 VvSOD genes. Syntenic analysis revealed that VvMSD1 and VvMSD2 were derived from segmental duplication, and VvCSD4 and VvCSD5 belong to a pair of tandemly duplicated genes. Gene expression analysis based on microarray data showed that the 10 VvSOD genes were expressed in all the tested tissues. Interestingly, the segmentally duplicated gene pair (VvMSD1 and VvMSD2) exhibited differential expression patterns in various organs. In contrast, the tandemly duplicated gene pair (VvCSD4 and VvCSD5) displayed similar expression patterns in the tested organs. Our results provide a basis for further functional research on the SOD gene family in grapevine.
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Zhu K, Liu H, Chen X, Cheng Q, Cheng ZM(M. The kinome of pineapple: catalog and insights into functions in crassulacean acid metabolism plants. BMC PLANT BIOLOGY 2018; 18:199. [PMID: 30227850 PMCID: PMC6145126 DOI: 10.1186/s12870-018-1389-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 08/14/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Crassulacean acid metabolism (CAM) plants use water 20-80% more efficiently by shifting stomata opening and primary CO2 uptake and fixation to the nighttime. Protein kinases (PKs) play pivotal roles in this biological process. However, few PKs have been functionally analyzed precisely due to their abundance and potential functional redundancy (caused by numerous gene duplications). RESULTS In this study, we systematically identified a total of 758 predicted PK genes in the genome of a CAM plant, pineapple (Ananas comosus). The pineapple kinome was classified into 20 groups and 116 families based on the kinase domain sequences. The RLK was the largest group, containing 480 members, and over half of them were predicted to locate at the plasma membrane. Both segmental and tandem duplications make important contributions to the expansion of pineapple kinome based on the synteny analysis. Ka/Ks ratios showed all of the duplication events were under purifying selection. The global expression analysis revealed that pineapple PKs exhibit different tissue-specific and diurnal expression patterns. Forty PK genes in a cluster performed higher expression levels in green leaf tip than in white leaf base, and fourteen of them had strong differential expression patterns between the photosynthetic green leaf tip and the non-photosynthetic white leaf base tissues. CONCLUSIONS Our findings provide insights into the evolution and biological function of pineapple PKs and a foundation for further functional analysis of PKs in CAM plants. The gene duplication, expression, and coexpression analysis helped us to rapidly identify the key candidates in pineapple kinome, which may play roles in the carbon fixation process in pineapple and help engineering CAM pathway into C3 crops for improved drought tolerance.
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Affiliation(s)
- Kaikai Zhu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
| | - Hui Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Xinlu Chen
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
| | - Qunkang Cheng
- Department of Botany and Plant Pathology, Central Oregon Agricultural Research Center, Oregon State University, Madras, OR 97741 USA
| | - Zong-Ming (Max) Cheng
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996 USA
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