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Manzoor MA, Manzoor MM, Li G, Abdullah M, Han W, Wenlong H, Shakoor A, Riaz MW, Rehman S, Cai Y. Genome-wide identification and characterization of bZIP transcription factors and their expression profile under abiotic stresses in Chinese pear (Pyrus bretschneideri). BMC PLANT BIOLOGY 2021; 21:413. [PMID: 34503442 PMCID: PMC8427902 DOI: 10.1186/s12870-021-03191-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 08/28/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND In plants, basic leucine zipper transcription factors (TFs) play important roles in multiple biological processes such as anthesis, fruit growth & development and stress responses. However, systematic investigation and characterization of bZIP-TFs remain unclear in Chinese white pear. Chinese white pear is a fruit crop that has important nutritional and medicinal values. RESULTS In this study, 62 bZIP genes were comprehensively identified from Chinese Pear, and 54 genes were distributed among 17 chromosomes. Frequent whole-genome duplication (WGD) and dispersed duplication (DSD) were the major driving forces underlying the bZIP gene family in Chinese white pear. bZIP-TFs are classified into 13 subfamilies according to the phylogenetic tree. Subsequently, purifying selection plays an important role in the evolution process of PbbZIPs. Synteny analysis of bZIP genes revealed that 196 orthologous gene pairs were identified between Pyrus bretschneideri, Fragaria vesca, Prunus mume, and Prunus persica. Moreover, cis-elements that respond to various stresses and hormones were found on the promoter regions of PbbZIP, which were induced by stimuli. Gene structure (intron/exon) and different compositions of motifs revealed that functional divergence among subfamilies. Expression pattern of PbbZIP genes differential expressed under hormonal treatment abscisic acid, salicylic acid, and methyl jasmonate in pear fruits by real-time qRT-PCR. CONCLUSIONS Collectively, a systematic analysis of gene structure, motif composition, subcellular localization, synteny analysis, and calculation of synonymous (Ks) and non-synonymous (Ka) was performed in Chinese white pear. Sixty-two bZIP-TFs in Chinese pear were identified, and their expression profiles were comprehensively analyzed under ABA, SA, and MeJa hormones, which respond to multiple abiotic stresses and fruit growth and development. PbbZIP gene occurred through Whole-genome duplication and dispersed duplication events. These results provide a basic framework for further elucidating the biological function characterizations under multiple developmental stages and abiotic stress responses.
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Affiliation(s)
| | | | - Guohui Li
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Muhammad Abdullah
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Wang Han
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Han Wenlong
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Awais Shakoor
- Department of Environment and Soil Sciences, University of Lleida, Avinguda Alcalde Rovira Roure 191, 25198, Lleida, Spain
| | | | - Shamsur Rehman
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
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De Coninck T, Gistelinck K, Janse van Rensburg HC, Van den Ende W, Van Damme EJM. Sweet Modifications Modulate Plant Development. Biomolecules 2021; 11:756. [PMID: 34070047 PMCID: PMC8158104 DOI: 10.3390/biom11050756] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 04/28/2021] [Accepted: 05/12/2021] [Indexed: 02/07/2023] Open
Abstract
Plant development represents a continuous process in which the plant undergoes morphological, (epi)genetic and metabolic changes. Starting from pollination, seed maturation and germination, the plant continues to grow and develops specialized organs to survive, thrive and generate offspring. The development of plants and the interplay with its environment are highly linked to glycosylation of proteins and lipids as well as metabolism and signaling of sugars. Although the involvement of these protein modifications and sugars is well-studied, there is still a long road ahead to profoundly comprehend their nature, significance, importance for plant development and the interplay with stress responses. This review, approached from the plants' perspective, aims to focus on some key findings highlighting the importance of glycosylation and sugar signaling for plant development.
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Affiliation(s)
- Tibo De Coninck
- Laboratory of Glycobiology & Biochemistry, Department of Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (T.D.C.); (K.G.)
| | - Koen Gistelinck
- Laboratory of Glycobiology & Biochemistry, Department of Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (T.D.C.); (K.G.)
| | - Henry C. Janse van Rensburg
- Laboratory of Molecular Plant Biology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium; (H.C.J.v.R.); (W.V.d.E.)
| | - Wim Van den Ende
- Laboratory of Molecular Plant Biology, Department of Biology, KU Leuven, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium; (H.C.J.v.R.); (W.V.d.E.)
| | - Els J. M. Van Damme
- Laboratory of Glycobiology & Biochemistry, Department of Biotechnology, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium; (T.D.C.); (K.G.)
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Wu S, Wang X, Reddy U, Sun H, Bao K, Gao L, Mao L, Patel T, Ortiz C, Abburi VL, Nimmakayala P, Branham S, Wechter P, Massey L, Ling K, Kousik C, Hammar SA, Tadmor Y, Portnoy V, Gur A, Katzir N, Guner N, Davis A, Hernandez AG, Wright CL, McGregor C, Jarret R, Zhang X, Xu Y, Wehner TC, Grumet R, Levi A, Fei Z. Genome of 'Charleston Gray', the principal American watermelon cultivar, and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:2246-2258. [PMID: 31022325 PMCID: PMC6835170 DOI: 10.1111/pbi.13136] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 04/16/2019] [Accepted: 04/18/2019] [Indexed: 05/14/2023]
Abstract
Years of selection for desirable fruit quality traits in dessert watermelon (Citrullus lanatus) has resulted in a narrow genetic base in modern cultivars. Development of novel genomic and genetic resources offers great potential to expand genetic diversity and improve important traits in watermelon. Here, we report a high-quality genome sequence of watermelon cultivar 'Charleston Gray', a principal American dessert watermelon, to complement the existing reference genome from '97103', an East Asian cultivar. Comparative analyses between genomes of 'Charleston Gray' and '97103' revealed genomic variants that may underlie phenotypic differences between the two cultivars. We then genotyped 1365 watermelon plant introduction (PI) lines maintained at the U.S. National Plant Germplasm System using genotyping-by-sequencing (GBS). These PI lines were collected throughout the world and belong to three Citrullus species, C. lanatus, C. mucosospermus and C. amarus. Approximately 25 000 high-quality single nucleotide polymorphisms (SNPs) were derived from the GBS data using the 'Charleston Gray' genome as the reference. Population genomic analyses using these SNPs discovered a close relationship between C. lanatus and C. mucosospermus and identified four major groups in these two species correlated to their geographic locations. Citrullus amarus was found to have a distinct genetic makeup compared to C. lanatus and C. mucosospermus. The SNPs also enabled identification of genomic regions associated with important fruit quality and disease resistance traits through genome-wide association studies. The high-quality 'Charleston Gray' genome and the genotyping data of this large collection of watermelon accessions provide valuable resources for facilitating watermelon research, breeding and improvement.
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Affiliation(s)
- Shan Wu
- Boyce Thompson InstituteCornell UniversityIthacaNYUSA
| | - Xin Wang
- Boyce Thompson InstituteCornell UniversityIthacaNYUSA
| | - Umesh Reddy
- Department of BiologyWest Virginia State UniversityInstituteWVUSA
| | - Honghe Sun
- Boyce Thompson InstituteCornell UniversityIthacaNYUSA
- National Engineering Research Center for VegetablesBeijing Academy of Agriculture and Forestry SciencesKey Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)BeijingChina
| | - Kan Bao
- Boyce Thompson InstituteCornell UniversityIthacaNYUSA
| | - Lei Gao
- Boyce Thompson InstituteCornell UniversityIthacaNYUSA
| | - Linyong Mao
- Boyce Thompson InstituteCornell UniversityIthacaNYUSA
- Department of Biochemistry and Molecular BiologyHoward University College of MedicineWashingtonDCUSA
| | - Takshay Patel
- Horticultural Science DepartmentNorth Carolina State UniversityRaleighNCUSA
| | - Carlos Ortiz
- Department of BiologyWest Virginia State UniversityInstituteWVUSA
| | | | | | - Sandra Branham
- U.S. Department of Agriculture‐Agricultural Research ServiceU.S. Vegetable LaboratoryCharlestonSCUSA
| | - Pat Wechter
- U.S. Department of Agriculture‐Agricultural Research ServiceU.S. Vegetable LaboratoryCharlestonSCUSA
| | - Laura Massey
- U.S. Department of Agriculture‐Agricultural Research ServiceU.S. Vegetable LaboratoryCharlestonSCUSA
| | - Kai‐Shu Ling
- U.S. Department of Agriculture‐Agricultural Research ServiceU.S. Vegetable LaboratoryCharlestonSCUSA
| | - Chandrasekar Kousik
- U.S. Department of Agriculture‐Agricultural Research ServiceU.S. Vegetable LaboratoryCharlestonSCUSA
| | - Sue A. Hammar
- Department of HorticultureMichigan State UniversityEast LansingMIUSA
| | - Yaakov Tadmor
- Department of Vegetable ResearchAgricultural Research OrganizationNewe Ya'ar Research CenterRamat YishayIsrael
| | - Vitaly Portnoy
- Department of Vegetable ResearchAgricultural Research OrganizationNewe Ya'ar Research CenterRamat YishayIsrael
| | - Amit Gur
- Department of Vegetable ResearchAgricultural Research OrganizationNewe Ya'ar Research CenterRamat YishayIsrael
| | - Nurit Katzir
- Department of Vegetable ResearchAgricultural Research OrganizationNewe Ya'ar Research CenterRamat YishayIsrael
| | | | - Angela Davis
- Sakata Seed AmericaWoodland Research StationWoodlandCAUSA
| | - Alvaro G. Hernandez
- Roy J. Carver Biotechnology CenterUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
| | - Chris L. Wright
- Roy J. Carver Biotechnology CenterUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
| | | | - Robert Jarret
- U.S. Department of Agriculture‐Agricultural Research ServicePlant Genetic Resources Conservation UnitGriffinGAUSA
| | | | - Yong Xu
- National Engineering Research Center for VegetablesBeijing Academy of Agriculture and Forestry SciencesKey Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)BeijingChina
| | - Todd C. Wehner
- Horticultural Science DepartmentNorth Carolina State UniversityRaleighNCUSA
| | - Rebecca Grumet
- Department of HorticultureMichigan State UniversityEast LansingMIUSA
| | - Amnon Levi
- U.S. Department of Agriculture‐Agricultural Research ServiceU.S. Vegetable LaboratoryCharlestonSCUSA
| | - Zhangjun Fei
- Boyce Thompson InstituteCornell UniversityIthacaNYUSA
- U.S. Department of Agriculture‐Agricultural Research ServiceRobert W. Holley Center for Agriculture and HealthIthacaNYUSA
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Saminathan T, García M, Ghimire B, Lopez C, Bodunrin A, Nimmakayala P, Abburi VL, Levi A, Balagurusamy N, Reddy UK. Metagenomic and Metatranscriptomic Analyses of Diverse Watermelon Cultivars Reveal the Role of Fruit Associated Microbiome in Carbohydrate Metabolism and Ripening of Mature Fruits. FRONTIERS IN PLANT SCIENCE 2018; 9:4. [PMID: 29403516 PMCID: PMC5780703 DOI: 10.3389/fpls.2018.00004] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 01/03/2018] [Indexed: 05/06/2023]
Abstract
The plant microbiome is a key determinant of plant health and productivity, and changes in the plant microbiome can alter the tolerance to biotic and abiotic stresses and the quality of end produce. Little is known about the microbial diversity and its effect on carbohydrate metabolism in ripe fruits. In this study, we aimed to understand the diversity and function of microorganisms in relation to carbohydrate metabolism of ripe watermelon fruits. We used 16S metagenomics and RNAseq metatranscriptomics for analysis of red (PI459074, Congo, and SDRose) and yellow fruit-flesh cultivars (PI227202, PI435990, and JBush) of geographically and metabolically diverse watermelon cultivars. Metagenomics data showed that Proteobacteria were abundant in SDRose and PI227202, whereas Cyanobacteria were most abundant in Congo and PI4559074. In the case of metatranscriptome data, Proteobacteria was the most abundant in all cultivars. High expression of genes linked to infectious diseases and the expression of peptidoglycan hydrolases associated to pathogenicity of eukaryotic hosts was observed in SDRose, which could have resulted in low microbial diversity in this cultivar. The presence of GH28, associated with polygalacturonase activity in JBush and SDRose could be related to cell wall modifications including de-esterification and depolymerization, and consequent loss of galacturonic acid and neutral sugars. Moreover, based on the KEGG annotation of the expressed genes, nine α-galactosidase genes involved in key processes of galactosyl oligosaccharide metabolism, such as raffinose family were identified and galactose metabolism pathway was reconstructed. Results of this study underline the links between the host and fruit-associated microbiome in carbohydrate metabolism of the ripe fruits. The cultivar difference in watermelon reflects the quantum and diversity of the microbiome, which would benefit watermelon and other plant breeders aiming at the holobiont concept to incorporate associated microbiomes in breeding programs.
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Affiliation(s)
- Thangasamy Saminathan
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, United States
| | - Marleny García
- Laboratorio de Biorremediación, Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, Torreón, Mexico
| | - Bandana Ghimire
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, United States
| | - Carlos Lopez
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, United States
- Laboratorio de Biorremediación, Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, Torreón, Mexico
| | - Abiodun Bodunrin
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, United States
| | - Padma Nimmakayala
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, United States
| | - Venkata L. Abburi
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, United States
| | - Amnon Levi
- U.S. Vegetable Laboratory, Agricultural Research Service, United States Department of Agriculture, Charleston, SC, United States
| | - Nagamani Balagurusamy
- Laboratorio de Biorremediación, Facultad de Ciencias Biológicas, Universidad Autónoma de Coahuila, Torreón, Mexico
| | - Umesh K. Reddy
- Gus R. Douglass Institute and Department of Biology, West Virginia State University, Institute, WV, United States
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5
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Albornos L, Martín I, Labrador E, Dopico B. Three members of Medicago truncatula ST family are ubiquitous during development and modulated by nutritional status (MtST1) and dehydration (MtST2 and MtST3). BMC PLANT BIOLOGY 2017; 17:117. [PMID: 28693485 PMCID: PMC5504553 DOI: 10.1186/s12870-017-1061-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 06/22/2017] [Indexed: 05/30/2023]
Abstract
BACKGROUND ShooT specific/Specific Tissue (ST) belong to a protein family of unknown function characterized by the DUF2775 domain and produced in specific taxonomic plant families, mainly Fabaceae and Asteraceae, with the Medicago truncatula ST family being the largest. The putative roles proposed for this family are cell elongation, biotic interactions, abiotic stress and N reserve. The aim of this work was to go deeper into the role of three M. truncatula ST proteins, namely ST1, ST2 and ST3. Our starting hypothesis was that each member of the family could perform a specific role, and hence, each ST gene would be subjected to a different type of regulation. RESULTS The search for cis-acting regulatory elements (CREs) in silico in pST1, pST2 and pST3 promoters showed prevalence of tissue/organ specific motifs, especially root- and seed-specific ones. Light, hormone, biotic and abiotic related motifs were also present. None of these pSTs showed the same combination of CREs, or presented the same activity pattern. In general, pST activity was associated with the vascular cylinder, mainly in roots. Promoter activation was highly specific and dissimilar during reproductive development. The ST1, ST2 and ST3 transcripts accumulated in most of the organs and developmental stages analysed - decreasing with age - and expression was higher in the roots than in the aerial parts and more abundant in light-grown plants. The effect of the different treatments on transcript accumulation indicated that ST1 behaved differently from ST2 and ST3, mainly in response to several hormones and dehydration treatments (NaCl or mannitol), upon which ST1 transcript levels decreased and ST2 and ST3 levels increased. Finally, the ST1 protein was located in the cell wall whereas ST2 and ST3 were present both in the cytoplasm and in the cell wall. CONCLUSIONS The ST proteins studied are ubiquitous proteins that could perform distinct/complementary roles in plant biology as they are encoded by differentially regulated genes. Based on these differences we have established two functional groups among the three STs. ST1 would participate in processes affected by nutritional status, while ST2 and ST3 seem to act when plants are challenged with abiotic stresses related to water stress and in physiologically controlled desiccation processes such as the seed maturation.
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Affiliation(s)
- Lucía Albornos
- Departamento de Botánica y Fisiología Vegetal. Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), University of Salamanca. C/ Licenciado Méndez Nieto s/n, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Ignacio Martín
- Departamento de Botánica y Fisiología Vegetal. Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), University of Salamanca. C/ Licenciado Méndez Nieto s/n, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Emilia Labrador
- Departamento de Botánica y Fisiología Vegetal. Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), University of Salamanca. C/ Licenciado Méndez Nieto s/n, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Berta Dopico
- Departamento de Botánica y Fisiología Vegetal. Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), University of Salamanca. C/ Licenciado Méndez Nieto s/n, Campus Miguel de Unamuno, 37007 Salamanca, Spain
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6
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Zhu Q, Gao P, Liu S, Zhu Z, Amanullah S, Davis AR, Luan F. Comparative transcriptome analysis of two contrasting watermelon genotypes during fruit development and ripening. BMC Genomics 2017; 18:3. [PMID: 28049426 PMCID: PMC5209866 DOI: 10.1186/s12864-016-3442-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 12/19/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] is an economically important crop with an attractive ripe fruit that has colorful flesh. Fruit ripening is a complex, genetically programmed process. RESULTS In this study, a comparative transcriptome analysis was performed to identify the regulators and pathways that are involved in the fruit ripening of pale-yellow-flesh cultivated watermelon (COS) and red-flesh cultivated watermelon (LSW177). We first identified 797 novel genes to extend the available reference gene set. Second, 3958 genes in COS and 3503 genes in LSW177 showed at least two-fold variation in expression, and a large number of these differentially expressed genes (DEGs) during fruit ripening were related to carotenoid biosynthesis, plant hormone pathways, and sugar and cell wall metabolism. Third, we noted a correlation between ripening-associated transcripts and metabolites and the key function of these metabolic pathways during fruit ripening. CONCLUSION The results revealed several ripening-associated actions and provide novel insights into the molecular mechanisms underlying the regulation of watermelon fruit ripening.
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Affiliation(s)
- Qianglong Zhu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Harbin, Heilongjiang, 150030, China
- Horticulture College, Northeast Agricultural University, 59 Mucai Street, Harbin, Heilongjiang, 150030, China
| | - Peng Gao
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Harbin, Heilongjiang, 150030, China
- Horticulture College, Northeast Agricultural University, 59 Mucai Street, Harbin, Heilongjiang, 150030, China
| | - Shi Liu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Harbin, Heilongjiang, 150030, China
- Horticulture College, Northeast Agricultural University, 59 Mucai Street, Harbin, Heilongjiang, 150030, China
| | - Zicheng Zhu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Harbin, Heilongjiang, 150030, China
- Horticulture College, Northeast Agricultural University, 59 Mucai Street, Harbin, Heilongjiang, 150030, China
| | - Sikandar Amanullah
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Harbin, Heilongjiang, 150030, China
- Horticulture College, Northeast Agricultural University, 59 Mucai Street, Harbin, Heilongjiang, 150030, China
| | - Angela R Davis
- South Central Agricultural Research Laboratory, Agricultural Research Service, U.S. Department of Agriculture, Currently with HM. Clause 9241 Mace Blvd, Davis, CA, 95618, USA
| | - Feishi Luan
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture, Harbin, Heilongjiang, 150030, China.
- Horticulture College, Northeast Agricultural University, 59 Mucai Street, Harbin, Heilongjiang, 150030, China.
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Dash PK, Rai R. Translating the "Banana Genome" to Delineate Stress Resistance, Dwarfing, Parthenocarpy and Mechanisms of Fruit Ripening. FRONTIERS IN PLANT SCIENCE 2016; 7:1543. [PMID: 27833619 PMCID: PMC5080353 DOI: 10.3389/fpls.2016.01543] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 09/30/2016] [Indexed: 05/07/2023]
Abstract
Evolutionary frozen, genetically sterile and globally iconic fruit "Banana" remained untouched by the green revolution and, as of today, researchers face intrinsic impediments for its varietal improvement. Recently, this wonder crop entered the genomics era with decoding of structural genome of double haploid Pahang (AA genome constitution) genotype of Musa acuminata. Its complex genome decoded by hybrid sequencing strategies revealed panoply of genes and transcription factors involved in the process of sucrose conversion that imparts sweetness to its fruit. Historically, banana has faced the wrath of pandemic bacterial, fungal, and viral diseases and multitude of abiotic stresses that has ruined the livelihood of small/marginal farmers' and destroyed commercial plantations. Decoding structural genome of this climacteric fruit has given impetus to a deeper understanding of the repertoire of genes involved in disease resistance, understanding the mechanism of dwarfing to develop an ideal plant type, unraveling the process of parthenocarpy, and fruit ripening for better fruit quality. Further, injunction of comparative genomics will usher in integration of information from its decoded genome and other monocots into field applications in banana related but not limited to yield enhancement, food security, livelihood assurance, and energy sustainability. In this mini review, we discuss pre- and post-genomic discoveries and highlight accomplishments in structural genomics, genetic engineering and forward genetic accomplishments with an aim to target genes and transcription factors for translational research in banana.
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Affiliation(s)
- Prasanta K. Dash
- ICAR-National Research Centre on Plant BiotechnologyNew Delhi, India
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Hu W, Wang L, Tie W, Yan Y, Ding Z, Liu J, Li M, Peng M, Xu B, Jin Z. Genome-wide analyses of the bZIP family reveal their involvement in the development, ripening and abiotic stress response in banana. Sci Rep 2016; 6:30203. [PMID: 27445085 PMCID: PMC4957152 DOI: 10.1038/srep30203] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 06/29/2016] [Indexed: 12/26/2022] Open
Abstract
The leucine zipper (bZIP) transcription factors play important roles in multiple biological processes. However, less information is available regarding the bZIP family in the important fruit crop banana. In this study, 121 bZIP transcription factor genes were identified in the banana genome. Phylogenetic analysis showed that MabZIPs were classified into 11 subfamilies. The majority of MabZIP genes in the same subfamily shared similar gene structures and conserved motifs. The comprehensive transcriptome analysis of two banana genotypes revealed the differential expression patterns of MabZIP genes in different organs, in various stages of fruit development and ripening, and in responses to abiotic stresses, including drought, cold, and salt. Interaction networks and co-expression assays showed that group A MabZIP-mediated networks participated in various stress signaling, which was strongly activated in Musa ABB Pisang Awak. This study provided new insights into the complicated transcriptional control of MabZIP genes and provided robust tissue-specific, development-dependent, and abiotic stress-responsive candidate MabZIP genes for potential applications in the genetic improvement of banana cultivars.
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Affiliation(s)
- Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, China
| | - Lianzhe Wang
- School of Life Science and Engineering, Henan University of Urban Construction, Pingdingshan, Henan, 467044, China
| | - Weiwei Tie
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, China
| | - Yan Yan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, China
| | - Zehong Ding
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, China
| | - Juhua Liu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, China
| | - Meiying Li
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, China
| | - Ming Peng
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, China
| | - Biyu Xu
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, China
| | - Zhiqiang Jin
- Key Laboratory of Genetic Improvement of Bananas, Hainan province, Haikou Experimental Station, China Academy of Tropical Agricultural Sciences, Haikou, Hainan, 570102, China
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9
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Kobayashi M, Ohyanagi H, Yano K. Databases for Solanaceae and Cucurbitaceae Research. BIOTECHNOLOGY IN AGRICULTURE AND FORESTRY 2016. [DOI: 10.1007/978-3-662-48535-4_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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10
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Kong Q, Yuan J, Gao L, Zhao L, Cheng F, Huang Y, Bie Z. Evaluation of Appropriate Reference Genes for Gene Expression Normalization during Watermelon Fruit Development. PLoS One 2015; 10:e0130865. [PMID: 26110539 PMCID: PMC4481515 DOI: 10.1371/journal.pone.0130865] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 05/26/2015] [Indexed: 01/02/2023] Open
Abstract
Gene expression analysis in watermelon (Citrullus lanatus) fruit has drawn considerable attention with the availability of genome sequences to understand the regulatory mechanism of fruit development and to improve its quality. Real-time quantitative reverse-transcription PCR (qRT-PCR) is a routine technique for gene expression analysis. However, appropriate reference genes for transcript normalization in watermelon fruits have not been well characterized. The aim of this study was to evaluate the appropriateness of 12 genes for their potential use as reference genes in watermelon fruits. Expression variations of these genes were measured in 48 samples obtained from 12 successive developmental stages of parthenocarpic and fertilized fruits of two watermelon genotypes by using qRT-PCR analysis. Considering the effects of genotype, fruit setting method, and developmental stage, geNorm determined clathrin adaptor complex subunit (ClCAC), β-actin (ClACT), and alpha tubulin 5 (ClTUA5) as the multiple reference genes in watermelon fruit. Furthermore, ClCAC alone or together with SAND family protein (ClSAND) was ranked as the single or two best reference genes by NormFinder. By using the top-ranked reference genes to normalize the transcript abundance of phytoene synthase (ClPSY1), a good correlation between lycopene accumulation and ClPSY1 expression pattern was observed in ripening watermelon fruit. These validated reference genes will facilitate the accurate measurement of gene expression in the studies on watermelon fruit biology.
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Affiliation(s)
- Qiusheng Kong
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Jingxian Yuan
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Lingyun Gao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Liqiang Zhao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Fei Cheng
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Yuan Huang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
| | - Zhilong Bie
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, China
- * E-mail:
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Ren R, Ray R, Li P, Xu J, Zhang M, Liu G, Yao X, Kilian A, Yang X. Construction of a high-density DArTseq SNP-based genetic map and identification of genomic regions with segregation distortion in a genetic population derived from a cross between feral and cultivated-type watermelon. Mol Genet Genomics 2015; 290:1457-70. [PMID: 25702268 DOI: 10.1007/s00438-015-0997-7] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 01/17/2015] [Indexed: 11/25/2022]
Abstract
Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] is an economically important vegetable crop grown extensively worldwide. To facilitate the identification of agronomically important traits and provide new information for genetic and genomic research on this species, a high-density genetic linkage map of watermelon was constructed using an F2 population derived from a cross between elite watermelon cultivar K3 and wild watermelon germplasm PI 189225. Based on a sliding window approach, a total of 1,161 bin markers representing 3,465 SNP markers were mapped onto 11 linkage groups corresponding to the chromosome pair number of watermelon. The total length of the genetic map is 1,099.2 cM, with an average distance between bins of 1.0 cM. The number of markers in each chromosome varies from 62 in chromosome 07 to 160 in chromosome 05. The length of individual chromosomes ranged between 61.8 cM for chromosome 07 and 140.2 cM for chromosome 05. A total of 616 SNP bin markers showed significant (P < 0.05) segregation distortion across all 11 chromosomes, and 513 (83.3 %) of these distorted loci showed distortion in favor of the elite watermelon cultivar K3 allele and 103 were skewed toward PI 189225. The number of SNPs and InDels per Mb varied considerably across the segregation distorted regions (SDRs) on each chromosome, and a mixture of dense and sparse SNPs and InDel SDRs coexisted on some chromosomes suggesting that SDRs were randomly distributed throughout the genome. Recombination rates varied greatly among each chromosome, from 2.0 to 4.2 centimorgans per megabase (cM/Mb). An inconsistency was found between the genetic and physical positions on the map for a segment on chromosome 11. The high-density genetic map described in the present study will facilitate fine mapping of quantitative trait loci, the identification of candidate genes, map-based cloning, as well as marker-assisted selection (MAS) in watermelon breeding programs.
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Affiliation(s)
- Runsheng Ren
- Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing, 210014, China
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12
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Albornos L, Cabrera J, Hernández-Nistal J, Martín I, Labrador E, Dopico B. Organ accumulation and subcellular location of Cicer arietinum ST1 protein. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 224:44-53. [PMID: 24908505 DOI: 10.1016/j.plantsci.2014.03.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 03/06/2014] [Accepted: 03/29/2014] [Indexed: 06/03/2023]
Abstract
The ST (ShooT Specific) proteins are a new family of proteins characterized by a signal peptide, tandem repeats of 25/26 amino acids, and a domain of unknown function (DUF2775), whose presence is limited to a few families of dicotyledonous plants, mainly Fabaceae and Asteraceae. Their function remains unknown, although involvement in plant growth, fruit morphogenesis or in biotic and abiotic interactions have been suggested. This work is focused on ST1, a Cicer arietinum ST protein. We established the protein accumulation in different tissues and organs of chickpea seedlings and plants and its subcellular localization, which could indicate the possible function of ST1. The raising of specific antibodies against ST1 protein revealed that its accumulation in epicotyls and radicles was related to their elongation rate. Its pattern of tissue location in cotyledons during seed formation and early seed germination, as well as its localization in the perivascular fibres of epicotyls and radicles, indicated a possible involvement in seed germination and seedling growth. ST1 protein appears both inside the cell and in the cell wall. This double subcellular localization was found in every organ in which the ST1 protein was detected: seeds, cotyledons and seedling epicotyls and radicles.
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Affiliation(s)
- Lucía Albornos
- Dpto de Fisiología Vegetal. Facultad de Biología, Centro Hispano-Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Pza Doctores de la Reina s/n., Salamanca 37007, Spain.
| | - Javier Cabrera
- Dpto de Fisiología Vegetal. Facultad de Biología, Centro Hispano-Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Pza Doctores de la Reina s/n., Salamanca 37007, Spain.
| | - Josefina Hernández-Nistal
- Dpto de Fisiología Vegetal, Universidad de Santiago de Compostela, Campus de Lugo, Lugo 27002, Spain.
| | - Ignacio Martín
- Dpto de Fisiología Vegetal. Facultad de Biología, Centro Hispano-Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Pza Doctores de la Reina s/n., Salamanca 37007, Spain.
| | - Emilia Labrador
- Dpto de Fisiología Vegetal. Facultad de Biología, Centro Hispano-Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Pza Doctores de la Reina s/n., Salamanca 37007, Spain.
| | - Berta Dopico
- Dpto de Fisiología Vegetal. Facultad de Biología, Centro Hispano-Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Pza Doctores de la Reina s/n., Salamanca 37007, Spain.
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13
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Fan M, Huang Y, Zhong Y, Kong Q, Xie J, Niu M, Xu Y, Bie Z. Comparative transcriptome profiling of potassium starvation responsiveness in two contrasting watermelon genotypes. PLANTA 2014; 239:397-410. [PMID: 24185372 DOI: 10.1007/s00425-013-1976-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 10/11/2013] [Indexed: 05/09/2023]
Abstract
Potassium (K) is one of the essential nutrients for crops, and K⁺ deficiency highly restricts crop yield and quality. Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] is an economically important crop that often suffers from K⁺ deficiency. To elucidate the underlying tolerance mechanism of watermelon to K⁺ deficiency and to improve K efficiency of watermelon and other crops in the future, two watermelon genotypes, namely, YS and 8424, that exhibit contrasting K efficiencies were studied to compare their response mechanisms to K⁺ deficiency. YS was more tolerant of K⁺ deficiency and displayed less inhibited root growth than 8424. Roots of YS and 8424 seedlings with or without K⁺ supply were harvested at 6 and 120 h after treatment (HAT), and their transcriptomes were analyzed by Illumina RNA sequencing. Different regulation mechanisms of the root K⁺-uptake genes for short- and long-term stress were observed. Genes involved in jasmonic acid and reactive oxygen species production; Ca²⁺ and receptor-like kinase signaling; lignin biosynthesis; and other stress-related genes were repressed in YS, whereas a large number of such stress-related genes were induced in 8424 at 120 HAT. These results suggested that repressed defense and stress response can save energy for better root growth in YS, which can facilitate K⁺ uptake and increase K efficiency and tolerance to K⁺ deficiency. This study presents the first global root transcriptome in watermelon and provides new insights into the molecular mechanisms underlying tolerance to K⁺ deficiency of K-efficient watermelon genotypes.
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Affiliation(s)
- Molin Fan
- Key Laboratory of Horticultural Plant Biology, Ministry of Education/College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
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14
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Albornos L, Martín I, Iglesias R, Jiménez T, Labrador E, Dopico B. ST proteins, a new family of plant tandem repeat proteins with a DUF2775 domain mainly found in Fabaceae and Asteraceae. BMC PLANT BIOLOGY 2012; 12:207. [PMID: 23134664 PMCID: PMC3499167 DOI: 10.1186/1471-2229-12-207] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Accepted: 10/12/2012] [Indexed: 06/01/2023]
Abstract
BACKGROUND Many proteins with tandem repeats in their sequence have been described and classified according to the length of the repeats: I) Repeats of short oligopeptides (from 2 to 20 amino acids), including structural cell wall proteins and arabinogalactan proteins. II) Repeats that range in length from 20 to 40 residues, including proteins with a well-established three-dimensional structure often involved in mediating protein-protein interactions. (III) Longer repeats in the order of 100 amino acids that constitute structurally and functionally independent units. Here we analyse ShooT specific (ST) proteins, a family of proteins with tandem repeats of unknown function that were first found in Leguminosae, and their possible similarities to other proteins with tandem repeats. RESULTS ST protein sequences were only found in dicotyledonous plants, limited to several plant families, mainly the Fabaceae and the Asteraceae. ST mRNAs accumulate mainly in the roots and under biotic interactions. Most ST proteins have one or several Domain(s) of Unknown Function 2775 (DUF2775). All deduced ST proteins have a signal peptide, indicating that these proteins enter the secretory pathway, and the mature proteins have tandem repeat oligopeptides that share a hexapeptide (E/D)FEPRP followed by 4 partially conserved amino acids, which could determine a putative N-glycosylation signal, and a fully conserved tyrosine. In a phylogenetic tree, the sequences clade according to taxonomic group. A possible involvement in symbiosis and abiotic stress as well as in plant cell elongation is suggested, although different STs could play different roles in plant development. CONCLUSIONS We describe a new family of proteins called ST whose presence is limited to the plant kingdom, specifically to a few families of dicotyledonous plants. They present 20 to 40 amino acid tandem repeat sequences with different characteristics (signal peptide, DUF2775 domain, conservative repeat regions) from the described group of 20 to 40 amino acid tandem repeat proteins and also from known cell wall proteins with repeat sequences. Several putative roles in plant physiology can be inferred from the characteristics found.
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Affiliation(s)
- Lucía Albornos
- Dpto. de Fisiología Vegetal, Centro Hispano Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Plaza Doctores de la Reina s/n. Campus Miguel Unamuno, Salamanca, 37007, Spain
| | - Ignacio Martín
- Dpto. de Fisiología Vegetal, Centro Hispano Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Plaza Doctores de la Reina s/n. Campus Miguel Unamuno, Salamanca, 37007, Spain
| | - Rebeca Iglesias
- Dpto. de Fisiología Vegetal, Centro Hispano Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Plaza Doctores de la Reina s/n. Campus Miguel Unamuno, Salamanca, 37007, Spain
| | - Teresa Jiménez
- Dpto. de Fisiología Vegetal, Centro Hispano Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Plaza Doctores de la Reina s/n. Campus Miguel Unamuno, Salamanca, 37007, Spain
| | - Emilia Labrador
- Dpto. de Fisiología Vegetal, Centro Hispano Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Plaza Doctores de la Reina s/n. Campus Miguel Unamuno, Salamanca, 37007, Spain
| | - Berta Dopico
- Dpto. de Fisiología Vegetal, Centro Hispano Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Plaza Doctores de la Reina s/n. Campus Miguel Unamuno, Salamanca, 37007, Spain
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15
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Nilo P. R, Campos-Vargas R, Orellana A. Assessment of Prunus persica fruit softening using a proteomics approach. J Proteomics 2012; 75:1618-38. [DOI: 10.1016/j.jprot.2011.11.037] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Revised: 11/25/2011] [Accepted: 11/29/2011] [Indexed: 12/23/2022]
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16
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Guo S, Liu J, Zheng Y, Huang M, Zhang H, Gong G, He H, Ren Y, Zhong S, Fei Z, Xu Y. Characterization of transcriptome dynamics during watermelon fruit development: sequencing, assembly, annotation and gene expression profiles. BMC Genomics 2011; 12:454. [PMID: 21936920 PMCID: PMC3197533 DOI: 10.1186/1471-2164-12-454] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 09/21/2011] [Indexed: 11/23/2022] Open
Abstract
Background Cultivated watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai var. lanatus] is an important agriculture crop world-wide. The fruit of watermelon undergoes distinct stages of development with dramatic changes in its size, color, sweetness, texture and aroma. In order to better understand the genetic and molecular basis of these changes and significantly expand the watermelon transcript catalog, we have selected four critical stages of watermelon fruit development and used Roche/454 next-generation sequencing technology to generate a large expressed sequence tag (EST) dataset and a comprehensive transcriptome profile for watermelon fruit flesh tissues. Results We performed half Roche/454 GS-FLX run for each of the four watermelon fruit developmental stages (immature white, white-pink flesh, red flesh and over-ripe) and obtained 577,023 high quality ESTs with an average length of 302.8 bp. De novo assembly of these ESTs together with 11,786 watermelon ESTs collected from GenBank produced 75,068 unigenes with a total length of approximately 31.8 Mb. Overall 54.9% of the unigenes showed significant similarities to known sequences in GenBank non-redundant (nr) protein database and around two-thirds of them matched proteins of cucumber, the most closely-related species with a sequenced genome. The unigenes were further assigned with gene ontology (GO) terms and mapped to biochemical pathways. More than 5,000 SSRs were identified from the EST collection. Furthermore we carried out digital gene expression analysis of these ESTs and identified 3,023 genes that were differentially expressed during watermelon fruit development and ripening, which provided novel insights into watermelon fruit biology and a comprehensive resource of candidate genes for future functional analysis. We then generated profiles of several interesting metabolites that are important to fruit quality including pigmentation and sweetness. Integrative analysis of metabolite and digital gene expression profiles helped elucidating molecular mechanisms governing these important quality-related traits during watermelon fruit development. Conclusion We have generated a large collection of watermelon ESTs, which represents a significant expansion of the current transcript catalog of watermelon and a valuable resource for future studies on the genomics of watermelon and other closely-related species. Digital expression analysis of this EST collection allowed us to identify a large set of genes that were differentially expressed during watermelon fruit development and ripening, which provide a rich source of candidates for future functional analysis and represent a valuable increase in our knowledge base of watermelon fruit biology.
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Affiliation(s)
- Shaogui Guo
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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17
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Costa F, Alba R, Schouten H, Soglio V, Gianfranceschi L, Serra S, Musacchi S, Sansavini S, Costa G, Fei Z, Giovannoni J. Use of homologous and heterologous gene expression profiling tools to characterize transcription dynamics during apple fruit maturation and ripening. BMC PLANT BIOLOGY 2010; 10:229. [PMID: 20973957 PMCID: PMC3095317 DOI: 10.1186/1471-2229-10-229] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Accepted: 10/25/2010] [Indexed: 05/18/2023]
Abstract
BACKGROUND Fruit development, maturation and ripening consists of a complex series of biochemical and physiological changes that in climacteric fruits, including apple and tomato, are coordinated by the gaseous hormone ethylene. These changes lead to final fruit quality and understanding of the functional machinery underlying these processes is of both biological and practical importance. To date many reports have been made on the analysis of gene expression in apple. In this study we focused our investigation on the role of ethylene during apple maturation, specifically comparing transcriptomics of normal ripening with changes resulting from application of the hormone receptor competitor 1-methylcyclopropene. RESULTS To gain insight into the molecular process regulating ripening in apple, and to compare to tomato (model species for ripening studies), we utilized both homologous and heterologous (tomato) microarray to profile transcriptome dynamics of genes involved in fruit development and ripening, emphasizing those which are ethylene regulated.The use of both types of microarrays facilitated transcriptome comparison between apple and tomato (for the later using data previously published and available at the TED: tomato expression database) and highlighted genes conserved during ripening of both species, which in turn represent a foundation for further comparative genomic studies. The cross-species analysis had the secondary aim of examining the efficiency of heterologous (specifically tomato) microarray hybridization for candidate gene identification as related to the ripening process. The resulting transcriptomics data revealed coordinated gene expression during fruit ripening of a subset of ripening-related and ethylene responsive genes, further facilitating the analysis of ethylene response during fruit maturation and ripening. CONCLUSION Our combined strategy based on microarray hybridization enabled transcriptome characterization during normal climacteric apple ripening, as well as definition of ethylene-dependent transcriptome changes. Comparison with tomato fruit maturation and ethylene responsive transcriptome activity facilitated identification of putative conserved orthologous ripening-related genes, which serve as an initial set of candidates for assessing conservation of gene activity across genomes of fruit bearing plant species.
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Affiliation(s)
- Fabrizio Costa
- Department of Fruit Tree and Woody Plant Science, University of Bologna, Viale Fanin 46, 40121 Bologna, Italy
- IASMA Research and Innovation Centre, Foundation Edmund Mach, Via E. Mach 1, 38010 San Michele all'Adige, Trento, Italy
| | - Rob Alba
- Boyce Thompson Institute for Plant Research, Cornell University Campus, Ithaca, New York, 14853, USA
| | - Henk Schouten
- Plant Breeding, Wageningen-UR, Droevendaalsesteeg 1,6700 AA Wageningen, The Netherlands
| | - Valeria Soglio
- Dept. of Biomolecular Sciences and Biotechnology, University of Milano, via Celoria 26, 20133 Milano, Italy
| | - Luca Gianfranceschi
- Dept. of Biomolecular Sciences and Biotechnology, University of Milano, via Celoria 26, 20133 Milano, Italy
| | - Sara Serra
- Department of Fruit Tree and Woody Plant Science, University of Bologna, Viale Fanin 46, 40121 Bologna, Italy
| | - Stefano Musacchi
- Department of Fruit Tree and Woody Plant Science, University of Bologna, Viale Fanin 46, 40121 Bologna, Italy
| | - Silviero Sansavini
- Department of Fruit Tree and Woody Plant Science, University of Bologna, Viale Fanin 46, 40121 Bologna, Italy
| | - Guglielmo Costa
- Department of Fruit Tree and Woody Plant Science, University of Bologna, Viale Fanin 46, 40121 Bologna, Italy
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, Cornell University Campus, Ithaca, New York, 14853, USA
- U.S. Department of Agriculture, Agricultural Research Service, Robert W. Holley Center, Ithaca, New York, 14853, USA
| | - James Giovannoni
- Boyce Thompson Institute for Plant Research, Cornell University Campus, Ithaca, New York, 14853, USA
- U.S. Department of Agriculture, Agricultural Research Service, Robert W. Holley Center, Ithaca, New York, 14853, USA
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18
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Nilo R, Saffie C, Lilley K, Baeza-Yates R, Cambiazo V, Campos-Vargas R, González M, Meisel LA, Retamales J, Silva H, Orellana A. Proteomic analysis of peach fruit mesocarp softening and chilling injury using difference gel electrophoresis (DIGE). BMC Genomics 2010; 11:43. [PMID: 20082721 PMCID: PMC2822761 DOI: 10.1186/1471-2164-11-43] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2009] [Accepted: 01/18/2010] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Peach fruit undergoes a rapid softening process that involves a number of metabolic changes. Storing fruit at low temperatures has been widely used to extend its postharvest life. However, this leads to undesired changes, such as mealiness and browning, which affect the quality of the fruit. In this study, a 2-D DIGE approach was designed to screen for differentially accumulated proteins in peach fruit during normal softening as well as under conditions that led to fruit chilling injury. RESULTS The analysis allowed us to identify 43 spots -representing about 18% of the total number analyzed- that show statistically significant changes. Thirty-nine of the proteins could be identified by mass spectrometry. Some of the proteins that changed during postharvest had been related to peach fruit ripening and cold stress in the past. However, we identified other proteins that had not been linked to these processes. A graphical display of the relationship between the differentially accumulated proteins was obtained using pairwise average-linkage cluster analysis and principal component analysis. Proteins such as endopolygalacturonase, catalase, NADP-dependent isocitrate dehydrogenase, pectin methylesterase and dehydrins were found to be very important for distinguishing between healthy and chill injured fruit. A categorization of the differentially accumulated proteins was performed using Gene Ontology annotation. The results showed that the 'response to stress', 'cellular homeostasis', 'metabolism of carbohydrates' and 'amino acid metabolism' biological processes were affected the most during the postharvest. CONCLUSIONS Using a comparative proteomic approach with 2-D DIGE allowed us to identify proteins that showed stage-specific changes in their accumulation pattern. Several proteins that are related to response to stress, cellular homeostasis, cellular component organization and carbohydrate metabolism were detected as being differentially accumulated. Finally, a significant proportion of the proteins identified had not been associated with softening, cold storage or chilling injury-altered fruit before; thus, comparative proteomics has proven to be a valuable tool for understanding fruit softening and postharvest.
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Affiliation(s)
- Ricardo Nilo
- Centro de Biotecnología Vegetal, Universidad Andrés Bello, Santiago, Chile
- Millennium Nucleus in Plant Cell Biotechnology (MN-PCB), Santiago, Chile
| | - Carlos Saffie
- Centro de Biotecnología Vegetal, Universidad Andrés Bello, Santiago, Chile
- Millennium Nucleus in Plant Cell Biotechnology (MN-PCB), Santiago, Chile
| | - Kathryn Lilley
- Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK
| | | | - Verónica Cambiazo
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, Santiago, Chile
- Millennium Nucleus Center for Genomics of the Cell (CGC), Santiago, Chile
| | - Reinaldo Campos-Vargas
- Centro de Biotecnología Vegetal, Universidad Andrés Bello, Santiago, Chile
- Millennium Nucleus in Plant Cell Biotechnology (MN-PCB), Santiago, Chile
- Institute of Agricultural Research (INIA-La Platina), Santiago, Chile
| | - Mauricio González
- Laboratorio de Bioinformática y Expresión Génica, INTA-Universidad de Chile, Santiago, Chile
| | - Lee A Meisel
- Centro de Biotecnología Vegetal, Universidad Andrés Bello, Santiago, Chile
- Millennium Nucleus in Plant Cell Biotechnology (MN-PCB), Santiago, Chile
| | - Julio Retamales
- Facultad de Ciencias Agronómicas, Universidad de Chile, Santiago, Chile
| | - Herman Silva
- Millennium Nucleus in Plant Cell Biotechnology (MN-PCB), Santiago, Chile
- Plant Functional Genomics & Bioinformatics Lab, Universidad Andrés Bello, Santiago, Chile
| | - Ariel Orellana
- Centro de Biotecnología Vegetal, Universidad Andrés Bello, Santiago, Chile
- Millennium Nucleus in Plant Cell Biotechnology (MN-PCB), Santiago, Chile
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19
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Wechter WP, Levi A, Harris KR, Davis AR, Fei Z, Katzir N, Giovannoni JJ, Salman-Minkov A, Hernandez A, Thimmapuram J, Tadmor Y, Portnoy V, Trebitsh T. Gene expression in developing watermelon fruit. BMC Genomics 2008; 9:275. [PMID: 18534026 PMCID: PMC2440768 DOI: 10.1186/1471-2164-9-275] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Accepted: 06/05/2008] [Indexed: 11/23/2022] Open
Abstract
Background Cultivated watermelon form large fruits that are highly variable in size, shape, color, and content, yet have extremely narrow genetic diversity. Whereas a plethora of genes involved in cell wall metabolism, ethylene biosynthesis, fruit softening, and secondary metabolism during fruit development and ripening have been identified in other plant species, little is known of the genes involved in these processes in watermelon. A microarray and quantitative Real-Time PCR-based study was conducted in watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai var. lanatus] in order to elucidate the flow of events associated with fruit development and ripening in this species. RNA from three different maturation stages of watermelon fruits, as well as leaf, were collected from field grown plants during three consecutive years, and analyzed for gene expression using high-density photolithography microarrays and quantitative PCR. Results High-density photolithography arrays, composed of probes of 832 EST-unigenes from a subtracted, fruit development, cDNA library of watermelon were utilized to examine gene expression at three distinct time-points in watermelon fruit development. Analysis was performed with field-grown fruits over three consecutive growing seasons. Microarray analysis identified three hundred and thirty-five unique ESTs that are differentially regulated by at least two-fold in watermelon fruits during the early, ripening, or mature stage when compared to leaf. Of the 335 ESTs identified, 211 share significant homology with known gene products and 96 had no significant matches with any database accession. Of the modulated watermelon ESTs related to annotated genes, a significant number were found to be associated with or involved in the vascular system, carotenoid biosynthesis, transcriptional regulation, pathogen and stress response, and ethylene biosynthesis. Ethylene bioassays, performed with a closely related watermelon genotype with a similar phenotype, i.e. seeded, bright red flesh, dark green rind, etc., determined that ethylene levels were highest during the green fruit stage followed by a decrease during the white and pink fruit stages. Additionally, quantitative Real-Time PCR was used to validate modulation of 127 ESTs that were differentially expressed in developing and ripening fruits based on array analysis. Conclusion This study identified numerous ESTs with putative involvement in the watermelon fruit developmental and ripening process, in particular the involvement of the vascular system and ethylene. The production of ethylene during fruit development in watermelon gives further support to the role of ethylene in fruit development in non-climacteric fruits.
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Affiliation(s)
- W Patrick Wechter
- USDA, ARS, US Vegetable Lab, 2700 Savannah Highway, Charleston, SC, USA.
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Nakagawa T, Nakatsuka A, Yano K, Yasugahira S, Nakamura R, Sun N, Itai A, Suzuki T, Itamura H. Expressed sequence tags from persimmon at different developmental stages. PLANT CELL REPORTS 2008; 27:931-938. [PMID: 18301901 DOI: 10.1007/s00299-008-0518-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2007] [Revised: 01/28/2008] [Accepted: 02/10/2008] [Indexed: 05/26/2023]
Abstract
Persimmon (Diospyros kaki Thunb.) is an important fruit in Asian countries, where it is eaten as a fresh fruit and is also used for many other purposes. To understand the molecular mechanism of fruit development and ripening in persimmon, we generated a total of 9,952 expressed sequence tags (ESTs) from randomly selected clones of two different cDNA libraries. One cDNA library was derived from fruit of "Saijo" persimmon at an early stage of development, and the other from ripening fruit. These ESTs were clustered into 6,700 non-redundant sequences. Of the 6,700 non-redundant sequences evaluated, the deduced amino acid sequences of 4,356 (65%) showed significant homology to known proteins, and 2,344 (35%) showed no significant similarity to any known proteins in Arabidopsis databases. We report comparison of genes identified in the two cDNA libraries and describe some putative genes involved in proanthocyanidin and carotenoid synthesis. This study provides the first global overview of a set of genes that are expressed during fruit development and ripening in persimmon.
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Affiliation(s)
- T Nakagawa
- Department of Molecular and Functional Genomics, Center for Integrated Research in Science, Shimane University, Matsue 690-8504, Japan
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