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Ramos MJN, Coito JL, Fino J, Cunha J, Silva H, de Almeida PG, Costa MMR, Amâncio S, Paulo OS, Rocheta M. Deep analysis of wild Vitis flower transcriptome reveals unexplored genome regions associated with sex specification. PLANT MOLECULAR BIOLOGY 2017; 93:151-170. [PMID: 27778293 DOI: 10.1007/s11103-016-0553-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 10/15/2016] [Indexed: 06/06/2023]
Abstract
RNA-seq of Vitis during early stages of bud development, in male, female and hermaphrodite flowers, identified new loci outside of annotated gene models, suggesting their involvement in sex establishment. The molecular mechanisms responsible for flower sex specification remain unclear for most plant species. In the case of V. vinifera ssp. vinifera, it is not fully understood what determines hermaphroditism in the domesticated subspecies and male or female flowers in wild dioecious relatives (Vitis vinifera ssp. sylvestris). Here, we describe a de novo assembly of the transcriptome of three flower developmental stages from the three Vitis vinifera flower types. The validation of de novo assembly showed a correlation of 0.825. The main goals of this work were the identification of V. v. sylvestris exclusive transcripts and the characterization of differential gene expression during flower development. RNA from several flower developmental stages was used previously to generate Illumina sequence reads. Through a sequential de novo assembly strategy one comprehensive transcriptome comprising 95,516 non-redundant transcripts was assembled. From this dataset 81,064 transcripts were annotated to V. v. vinifera reference transcriptome and 11,084 were annotated against V. v. vinifera reference genome. Moreover, we found 3368 transcripts that could not be mapped to Vitis reference genome. From all the non-redundant transcripts that were assembled, bioinformatics analysis identified 133 specific of V. v. sylvestris and 516 transcripts differentially expressed among the three flower types. The detection of transcription from areas of the genome not currently annotated suggests active transcription of previously unannotated genomic loci during early stages of bud development.
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Affiliation(s)
- Miguel Jesus Nunes Ramos
- Universidade de Lisboa, Instituto Superior de Agronomia, LEAF, Linking Landscape, Environment, Agriculture and Food, Tapada da Ajuda, 1359-017, Lisboa, Portugal
| | - João Lucas Coito
- Universidade de Lisboa, Instituto Superior de Agronomia, LEAF, Linking Landscape, Environment, Agriculture and Food, Tapada da Ajuda, 1359-017, Lisboa, Portugal
| | - Joana Fino
- Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Jorge Cunha
- Instituto Nacional de Investigação Agrária e Veterinária, Quinta d'Almoinha, Dois Portos, Portugal
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Helena Silva
- BioSystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Centre, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Patrícia Gomes de Almeida
- Development and Evolutionary Morphogenesis, Centre for Ecology, Evolution and Environmental Change, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Maria Manuela Ribeiro Costa
- BioSystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Centre, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Sara Amâncio
- Universidade de Lisboa, Instituto Superior de Agronomia, LEAF, Linking Landscape, Environment, Agriculture and Food, Tapada da Ajuda, 1359-017, Lisboa, Portugal
| | - Octávio S Paulo
- Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Margarida Rocheta
- Universidade de Lisboa, Instituto Superior de Agronomia, LEAF, Linking Landscape, Environment, Agriculture and Food, Tapada da Ajuda, 1359-017, Lisboa, Portugal.
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Abbasi Holasou H, Abdollahi Mandoulakani B, Jafari M, Bernousi I. Use of IRAP and REMAP markers to interpret the population structure of Linum usitatissimum from Iran. Biologia (Bratisl) 2016. [DOI: 10.1515/biolog-2016-0042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Ismail NA, Rafii MY, Mahmud TMM, Hanafi MM, Miah G. Molecular markers: a potential resource for ginger genetic diversity studies. Mol Biol Rep 2016; 43:1347-1358. [PMID: 27585572 DOI: 10.1007/s11033-016-4070-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 08/22/2016] [Indexed: 10/21/2022]
Abstract
Ginger is an economically important and valuable plant around the world. Ginger is used as a food, spice, condiment, medicine and ornament. There is available information on biochemical aspects of ginger, but few studies have been reported on its molecular aspects. The main objective of this review is to accumulate the available molecular marker information and its application in diverse ginger studies. This review article was prepared by combing material from published articles and our own research. Molecular markers allow the identification and characterization of plant genotypes through direct access to hereditary material. In crop species, molecular markers are applied in different aspects and are useful in breeding programs. In ginger, molecular markers are commonly used to identify genetic variation and classify the relatedness among varieties, accessions, and species. Consequently, it provides important input in determining resourceful management strategies for ginger improvement programs. Alternatively, a molecular marker could function as a harmonizing tool for documenting species. This review highlights the application of molecular markers (isozyme, RAPD, AFLP, SSR, ISSR and others such as RFLP, SCAR, NBS and SNP) in genetic diversity studies of ginger species. Some insights on the advantages of the markers are discussed. The detection of genetic variation among promising cultivars of ginger has significance for ginger improvement programs. This update of recent literature will help researchers and students select the appropriate molecular markers for ginger-related research.
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Affiliation(s)
- Nor Asiah Ismail
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Malaysia Agricultural Research and Development Institute, Serdang, Selangor, Malaysia
| | - M Y Rafii
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
- Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
| | - T M M Mahmud
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - M M Hanafi
- Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Department of Land Management, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Gous Miah
- Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
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Wang X, Zhang MM, Wang YJ, Gao YT, Li R, Wang GF, Li WQ, Liu WT, Chen KM. The plasma membrane NADPH oxidase OsRbohA plays a crucial role in developmental regulation and drought-stress response in rice. PHYSIOLOGIA PLANTARUM 2016; 156:421-43. [PMID: 26400148 DOI: 10.1111/ppl.12389] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 07/19/2015] [Accepted: 07/30/2015] [Indexed: 05/20/2023]
Abstract
Plasma membrane NADPH oxidases are major producers of reactive oxygen species (ROS) in plant cells under normal growth and stress conditions. In the present study the total activity of rice NADPH oxidases and the transcription of OsRbohA, which encodes an Oryza sativa plasma membrane NADPH oxidase, were stimulated by drought. OsRbohA was expressed in all tissues examined throughout development. Its mRNA was upregulated by a number of factors, including heat, drought, salt, oxidative stress and methyl jasmonate treatment. Compared with wild-type (WT), the OsRbohA-knockout mutant osrbohA exhibited upregulated expression of other respiratory burst oxidase homolog genes and multiple abnormal agronomic traits, including reduced biomass, low germination rate and decreased pollen viability and seed fertility. However, OsRbohA-overexpressing transgenic plants showed no differences in these traits compared with WT. Although osrbohA leaves and roots produced more ROS than WT, the mutant had lesser intracellular ROS. In contrast, OsRbohA-overexpressing transgenic plants exhibited higher ROS production at the intracellular level and in tissues. Ablation of OsRbohA impaired the tolerance of plants to various water stresses, whereas its overexpression enhanced the tolerance. In addition, a number of genes related to energy supply, substrate transport, stress response and transcriptional regulation were differentially expressed in osrbohA plants even under normal growth conditions, suggesting that OsRbohA has fundamental and broad functions in rice. These results indicate that OsRbohA-mediated processes are governed by complex signaling pathways that function during the developmental regulation and drought-stress response in rice.
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Affiliation(s)
- Xiang Wang
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Mao-Mao Zhang
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Ya-Jing Wang
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Yin-Tao Gao
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Ri Li
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Gang-Feng Wang
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Wen-Qiang Li
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Wen-Ting Liu
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Kun-Ming Chen
- State Key Laboratory of Crop Stress Biology in Arid Area/College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
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Hertweck KL. Assembly and comparative analysis of transposable elements from low coverage genomic sequence data in Asparagales. Genome 2013; 56:487-94. [PMID: 24168669 DOI: 10.1139/gen-2013-0042] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The research field of comparative genomics is moving from a focus on genes to a more holistic view including the repetitive complement. This study aimed to characterize relative proportions of the repetitive fraction of large, complex genomes in a nonmodel system. The monocotyledonous plant order Asparagales (onion, asparagus, agave) comprises some of the largest angiosperm genomes and represents variation in both genome size and structure (karyotype). Anonymous, low coverage, single-end Illumina data from 11 exemplar Asparagales taxa were assembled using a de novo method. Resulting contigs were annotated using a reference library of available monocot repetitive sequences. Mapping reads to contigs provided rough estimates of relative proportions of each type of transposon in the nuclear genome. The results were parsed into general repeat types and synthesized with genome size estimates and a phylogenetic context to describe the pattern of transposable element evolution among these lineages. The major finding is that although some lineages in Asparagales exhibit conservation in repeat proportions, there is generally wide variation in types and frequency of repeats. This approach is an appropriate first step in characterizing repeats in evolutionary lineages with a paucity of genomic resources.
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Affiliation(s)
- Kate L Hertweck
- National Evolutionary Synthesis Center, 2024 West Main Street, Suite A200, Durham, NC 27705, USA
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Effectiveness of AFLPs and Retrotransposon-Based Markers for the Identification of Portuguese Grapevine Cultivars and Clones. Mol Biotechnol 2011; 52:26-39. [DOI: 10.1007/s12033-011-9470-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Evrensel C, Yilmaz S, Temel A, Gozukirmizi N. Variations in BARE-1 insertion patterns in barley callus cultures. GENETICS AND MOLECULAR RESEARCH 2011; 10:980-7. [PMID: 21710447 DOI: 10.4238/vol10-2gmr965] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The stability of aging barley calli was investigated with the barley retroelement 1 (BARE-1) retrotransposon specific inter-retrotransposon amplified polymorphism (IRAP) technique. Mature embryos of barley (Hordeum vulgare cv. Zafer-160) were cultured on callus induction MS medium supplemented with 3 mg/L 2,4-D and maintained on the same medium for 60 days. Ten IRAP primers were used in 25 different combinations. The similarity index between 30-day-old and 45-day-old calli was 84%; however, the similarity index between mature embryos and 45-day-old calli was 75%. These culture conditions caused BARE-1 retrotransposon alterations to appear as different band profiles. This is the first report of the use of the IRAP technique in barley in an investigation of callus development.
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Affiliation(s)
- C Evrensel
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Vezneciler, Istanbul, Turkey
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