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Natarajan RB, Pathania P, Singh H, Agrawal A, Subramani R. A Flow Cytometry-Based Assessment of the Genomic Size and Ploidy Level of Wild Musa Species in India. PLANTS (BASEL, SWITZERLAND) 2023; 12:3605. [PMID: 37896068 PMCID: PMC10609997 DOI: 10.3390/plants12203605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/12/2023] [Accepted: 10/15/2023] [Indexed: 10/29/2023]
Abstract
The genome size variation is an important attribute in evolutionary and species characterization. Musa L. is regarded as one of the taxonomically complicated genera within the order Zingiberales, with more than 75 species from wild seeded to seedless cultivars that may be diploid, triploid or tetraploid. The knowledge of total nuclear DNA content in terms of genome size and ploidy level in wild species of Musa is absolutely important in evolutionary and genomic studies. METHODS In this paper, chromosome spreading was performed via protoplast isolation and a fast air-dry dropping method and flow cytometry were used with Raphanus sativus L. (Brassicaceae) as a standard for ploidy and genome size estimation. RESULTS The results showed that genome size (2C) varied amongst Musa species, based on the ratio of G1 peak positions. The lowest genome size (2C) was found in M. balbisiana var. andamanica (1.051 ± 0.060 pg) and the highest genome size (2C) was recorded for Musa ABB.cv. Meitei-hei (1.812 ± 0.108 pg) for the section Eumusa. Among the species belonging to the section Rhodochlamys, M. rosae had the lowest 2C content of 1.194 ± 0.033 pg whereas the highest nuclear DNA content (2C) was observed in M. velutina (1.488 ± 0.203 pg). Cytogenetic analysis revealed that the chromosome number of 14 wild Musa species was 2n = 22, while 1 species-Ensete glaucum-showed a chromosome number of 2n = 18 (diploid), and for 3 species, the chromosome number was 2n = 33 (triploids). An association study based on the Pearson correlation coefficient showed 2C nuclear DNA content was significant and positively correlated with ploidy level (R = 0.9) and chromosome number (R = 0.84). CONCLUSIONS The present study provides reliable information on the genome size and ploidy level of wild Musa species from the Indian region through flow cytometric analysis, which could be further utilized in taxonomic and crop improvement programs. For the first time, the nuclear DNA content of eight wild diploid and three triploid Indian species were estimated and reported. Genome size could be an effective indicator in identification of species and evolutionary studies in Musa with varying ploidy levels and morphological similarities.
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Affiliation(s)
- Rithesh B Natarajan
- Division of Plant Genetic Resources, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012, India
| | - Pooja Pathania
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
| | - Hardeep Singh
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
| | - Anuradha Agrawal
- Division of Plant Genetic Resources, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012, India
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
- Indian Council of Agricultural Research, Pusa Campus, New Delhi 110012, India
| | - Rajkumar Subramani
- Division of Plant Genetic Resources, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012, India
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India
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Zhang LL, Feng RJ, Zhang YD. Evaluation of different methods of protein extraction and identification of differentially expressed proteins upon ethylene-induced early-ripening in banana peels. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2012; 92:2106-2115. [PMID: 22278681 DOI: 10.1002/jsfa.5591] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Revised: 08/19/2011] [Accepted: 11/28/2011] [Indexed: 05/31/2023]
Abstract
BACKGROUND Banana peels (Musa spp.) are a good example of a plant tissue where protein extraction is challenging due to the abundance of interfering metabolites. Sample preparation is a critical step in proteomic research and is critical for good results. RESULTS We sought to evaluate three methods of protein extraction: trichloroacetic acid (TCA)-acetone precipitation, phenol extraction, and TCA precipitation. We found that a modified phenol extraction protocol was the most optimal method. SDS-PAGE and two-dimensional gel electrophoresis (2-DE) demonstrated good protein separation and distinct spots of high quality protein. Approximately 300 and 550 protein spots were detected on 2-DE gels at pH values of 3-10 and 4-7, respectively. Several spots were excised from the 2-DE gels and identified by mass spectrometry. CONCLUSIONS The protein spots identified were found to be involved in glycolysis, the tricarboxylic acid cycle, and the biosynthesis of ethylene. Several of the identified proteins may play important roles in banana ripening.
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Affiliation(s)
- Li-Li Zhang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou 571101, P.R. China
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Zhao C, Zhang T, Zhang X, Hu S, Xiang J. Sequencing and analysis of four BAC clones containing innate immune genes from the Zhikong scallop (Chlamys farreri). Gene 2012; 502:9-15. [PMID: 22542508 DOI: 10.1016/j.gene.2012.04.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 02/29/2012] [Accepted: 04/05/2012] [Indexed: 11/17/2022]
Abstract
The sequencing of BAC clones (~100 kb) can reveal some characteristics of a genome that are challenging to obtain based on short sequences. Additionally, although the immune genes of the Zhikong scallop (Chlamys farreri) have been studied widely, few analyses have been conducted at the DNA level. In this study, four C. farreri BAC clones containing innate immune genes, including hsp70, l gbp (lipopolysaccharide and beta-1,3-glucan binding protein), serine protease and a gene with an immunoglobulin-like domain, were sequenced and analyzed both to explore the genomic characteristics of C. farreri based on long DNA sequences and to promote the study of C. farreri immune genes at the DNA level. The total length of the four BACs was 389.98 kb. A total of 34 genes were predicted in these sequences, and several features of protein-coding regions in the C. farreri genome were inferred based on this information. Two LGBP genes were located close together in a 22-kb region in one BAC clone, indicating the physical linkage of some immune genes in C. farreri. A cluster of membrane transport genes was also observed; these genes might play important roles in eliminating toxins in C. farreri, which lives as a filter feeder. Further analysis showed 15.43% of the BAC sequence was repetitive. Tandem repeats were the most abundant repeat type, followed by transposable elements. A total of 31 SSRs were predicted in the four BACs. An IS10 family transposon was identified, and a suspected regulatory non-coding RNA gene for this transposon (RNA-OUT) was observed to overlap with it complementarily. This work will promote future studies on the genomics, immune system and non-coding regions of C. farreri.
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Affiliation(s)
- Cui Zhao
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
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Henry IM, Carpentier SC, Pampurova S, Van Hoylandt A, Panis B, Swennen R, Remy S. Structure and regulation of the Asr gene family in banana. PLANTA 2011; 234:785-98. [PMID: 21630042 PMCID: PMC3180632 DOI: 10.1007/s00425-011-1421-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Accepted: 04/17/2011] [Indexed: 05/17/2023]
Abstract
Abscisic acid, stress, ripening proteins (ASR) are a family of plant-specific small hydrophilic proteins. Studies in various plant species have highlighted their role in increased resistance to abiotic stress, including drought, but their specific function remains unknown. As a first step toward their potential use in crop improvement, we investigated the structure and regulation of the Asr gene family in Musa species (bananas and plantains). We determined that the Musa Asr gene family contained at least four members, all of which exhibited the typical two exons, one intron structure of Asr genes and the "ABA/WDS" (abscisic acid/water deficit stress) domain characteristic of Asr genes. Phylogenetic analyses determined that the Musa Asr genes were closely related to each other, probably as the product of recent duplication events. For two of the four members, two versions corresponding to the two sub-genomes of Musa, acuminata and balbisiana were identified. Gene expression and protein analyses were performed and Asr expression could be detected in meristem cultures, root, pseudostem, leaf and cormus. In meristem cultures, mAsr1 and mAsr3 were induced by osmotic stress and wounding, while mAsr3 and mAsr4 were induced by exposure to ABA. mASR3 exhibited the most variation both in terms of amino acid sequence and expression pattern, making it the most promising candidate for further functional study and use in crop improvement.
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Affiliation(s)
- Isabelle M. Henry
- Division of Crop Biotechnics, Laboratory of Tropical Crop Improvement, K.U.Leuven, Kasteelpark Arenberg 13, Bus 2455, 3001 Leuven, Belgium
- Present Address: Department of Plant Biology and Genome Center, University of California Davis, 451 E. Health Sciences Drive, Davis, CA 95616 USA
| | - Sebastien C. Carpentier
- Division of Crop Biotechnics, Laboratory of Tropical Crop Improvement, K.U.Leuven, Kasteelpark Arenberg 13, Bus 2455, 3001 Leuven, Belgium
| | - Suzana Pampurova
- Division of Crop Biotechnics, Laboratory of Tropical Crop Improvement, K.U.Leuven, Kasteelpark Arenberg 13, Bus 2455, 3001 Leuven, Belgium
- VIB Department of Molecular Microbiology, Institute of Botany and Microbiology, K.U.Leuven Laboratory of Molecular Cell Biology, Kasteelpark Arenberg 31, Bus 2438, 3001 Leuven, Belgium
| | - Anais Van Hoylandt
- Division of Crop Biotechnics, Laboratory of Tropical Crop Improvement, K.U.Leuven, Kasteelpark Arenberg 13, Bus 2455, 3001 Leuven, Belgium
| | - Bart Panis
- Division of Crop Biotechnics, Laboratory of Tropical Crop Improvement, K.U.Leuven, Kasteelpark Arenberg 13, Bus 2455, 3001 Leuven, Belgium
| | - Rony Swennen
- Division of Crop Biotechnics, Laboratory of Tropical Crop Improvement, K.U.Leuven, Kasteelpark Arenberg 13, Bus 2455, 3001 Leuven, Belgium
- Bioversity International, Kasteelpark Arenberg 13, Bus 2455, 3001 Leuven, Belgium
| | - Serge Remy
- Division of Crop Biotechnics, Laboratory of Tropical Crop Improvement, K.U.Leuven, Kasteelpark Arenberg 13, Bus 2455, 3001 Leuven, Belgium
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Hřibová E, Neumann P, Matsumoto T, Roux N, Macas J, Doležel J. Repetitive part of the banana (Musa acuminata) genome investigated by low-depth 454 sequencing. BMC PLANT BIOLOGY 2010; 10:204. [PMID: 20846365 PMCID: PMC2956553 DOI: 10.1186/1471-2229-10-204] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Accepted: 09/16/2010] [Indexed: 05/18/2023]
Abstract
BACKGROUND Bananas and plantains (Musa spp.) are grown in more than a hundred tropical and subtropical countries and provide staple food for hundreds of millions of people. They are seed-sterile crops propagated clonally and this makes them vulnerable to a rapid spread of devastating diseases and at the same time hampers breeding improved cultivars. Although the socio-economic importance of bananas and plantains cannot be overestimated, they remain outside the focus of major research programs. This slows down the study of nuclear genome and the development of molecular tools to facilitate banana improvement. RESULTS In this work, we report on the first thorough characterization of the repeat component of the banana (M. acuminata cv. 'Calcutta 4') genome. Analysis of almost 100 Mb of sequence data (0.15× genome coverage) permitted partial sequence reconstruction and characterization of repetitive DNA, making up about 30% of the genome. The results showed that the banana repeats are predominantly made of various types of Ty1/copia and Ty3/gypsy retroelements representing 16 and 7% of the genome respectively. On the other hand, DNA transposons were found to be rare. In addition to new families of transposable elements, two new satellite repeats were discovered and found useful as cytogenetic markers. To help in banana sequence annotation, a specific Musa repeat database was created, and its utility was demonstrated by analyzing the repeat composition of 62 genomic BAC clones. CONCLUSION A low-depth 454 sequencing of banana nuclear genome provided the largest amount of DNA sequence data available until now for Musa and permitted reconstruction of most of the major types of DNA repeats. The information obtained in this study improves the knowledge of the long-range organization of banana chromosomes, and provides sequence resources needed for repeat masking and annotation during the Musa genome sequencing project. It also provides sequence data for isolation of DNA markers to be used in genetic diversity studies and in marker-assisted selection.
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Affiliation(s)
- Eva Hřibová
- Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany, Sokolovská 6, Olomouc, CZ-77200, Czech Republic
| | - Pavel Neumann
- Biology Centre ASCR, Institute of Plant Molecular Biology, Branišovská 31, České Budĕjovice, CZ-37005, Czech Republic
| | - Takashi Matsumoto
- National Institute of Agrobiological Sciences, Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Nicolas Roux
- Commodities for Livelihoods Programme, Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Jiří Macas
- Biology Centre ASCR, Institute of Plant Molecular Biology, Branišovská 31, České Budĕjovice, CZ-37005, Czech Republic
| | - Jaroslav Doležel
- Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany, Sokolovská 6, Olomouc, CZ-77200, Czech Republic
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Vertommen A, Panis B, Swennen R, Carpentier SC. Evaluation of chloroform/methanol extraction to facilitate the study of membrane proteins of non-model plants. PLANTA 2010; 231:1113-25. [PMID: 20177697 PMCID: PMC2840667 DOI: 10.1007/s00425-010-1121-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2010] [Accepted: 01/27/2010] [Indexed: 05/10/2023]
Abstract
Membrane proteins are of great interest to plant physiologists because of their important function in many physiological processes. However, their study is hampered by their low abundance and poor solubility in aqueous buffers. Proteomics studies of non-model plants are generally restricted to gel-based methods. Unfortunately, all gel-based techniques for membrane proteomics lack resolving power. Therefore, a very stringent enrichment method is needed before protein separation. In this study, protein extraction in a mixture of chloroform and methanol in combination with gel electrophoresis is evaluated as a method to study membrane proteins in non-model plants. Benefits as well as disadvantages of the method are discussed. To demonstrate the pitfalls of working with non-model plants and to give a proof of principle, the method was first applied to whole leaves of the model plant Arabidopsis. Subsequently, a comparison with proteins extracted from leaves of the non-model plant, banana, was made. To estimate the tissue and organelle specificity of the method, it was also applied on banana meristems. Abundant membrane or lipid-associated proteins could be identified in both tissues, with the leaf extract yielding a higher number of membrane proteins.
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Affiliation(s)
- Annelies Vertommen
- Division of Crop Biotechnics, Department of Biosystems, K U Leuven, Leuven, Belgium.
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Davey MW, Graham NS, Vanholme B, Swennen R, May ST, Keulemans J. Heterologous oligonucleotide microarrays for transcriptomics in a non-model species; a proof-of-concept study of drought stress in Musa. BMC Genomics 2009; 10:436. [PMID: 19758430 PMCID: PMC2761422 DOI: 10.1186/1471-2164-10-436] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Accepted: 09/16/2009] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND 'Systems-wide' approaches such as microarray RNA-profiling are ideally suited to the study of the complex overlapping responses of plants to biotic and abiotic stresses. However, commercial microarrays are only available for a limited number of plant species and development costs are so substantial as to be prohibitive for most research groups. Here we evaluate the use of cross-hybridisation to Affymetrix oligonucleotide GeneChip(R) microarrays to profile the response of the banana (Musa spp.) leaf transcriptome to drought stress using a genomic DNA (gDNA)-based probe-selection strategy to improve the efficiency of detection of differentially expressed Musa transcripts. RESULTS Following cross-hybridisation of Musa gDNA to the Rice GeneChip(R) Genome Array, ~33,700 gene-specific probe-sets had a sufficiently high degree of homology to be retained for transcriptomic analyses. In a proof-of-concept approach, pooled RNA representing a single biological replicate of control and drought stressed leaves of the Musa cultivar 'Cachaco' were hybridised to the Affymetrix Rice Genome Array. A total of 2,910 Musa gene homologues with a >2-fold difference in expression levels were subsequently identified. These drought-responsive transcripts included many functional classes associated with plant biotic and abiotic stress responses, as well as a range of regulatory genes known to be involved in coordinating abiotic stress responses. This latter group included members of the ERF, DREB, MYB, bZIP and bHLH transcription factor families. Fifty-two of these drought-sensitive Musa transcripts were homologous to genes underlying QTLs for drought and cold tolerance in rice, including in 2 instances QTLs associated with a single underlying gene. The list of drought-responsive transcripts also included genes identified in publicly-available comparative transcriptomics experiments. CONCLUSION Our results demonstrate that despite the general paucity of nucleotide sequence data in Musa and only distant phylogenetic relations to rice, gDNA probe-based cross-hybridisation to the Rice GeneChip(R) is a highly promising strategy to study complex biological responses and illustrates the potential of such strategies for gene discovery in non-model species.
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Affiliation(s)
- Mark W Davey
- Laboratory for Fruit Breeding and Biotechnology, Department of Biosystems, Katholieke Universiteit Leuven, Box 2747, Willem De Croylaan 42, B-3001, Heverlee, Leuven, Belgium
| | - Neil S Graham
- Nottingham Arabidopsis Stock Centre, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Bartel Vanholme
- Department of Plant Systems Biology, VIB, and Department of Molecular Genetics, Universiteit Gent, Technologiepark 927, B-9052 Gent, Belgium
| | - Rony Swennen
- Department of Biosystems, Katholieke Universiteit Leuven, Kasteelpark Arenberg 13 Box 2455, B - 3001 Leuven, Belgium
| | - Sean T May
- Nottingham Arabidopsis Stock Centre, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK
| | - Johan Keulemans
- Laboratory for Fruit Breeding and Biotechnology, Department of Biosystems, Katholieke Universiteit Leuven, Box 2747, Willem De Croylaan 42, B-3001, Heverlee, Leuven, Belgium
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Hribová E, Dolezelová M, Town CD, Macas J, Dolezel J. Isolation and characterization of the highly repeated fraction of the banana genome. Cytogenet Genome Res 2008; 119:268-74. [PMID: 18253041 DOI: 10.1159/000112073] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2007] [Indexed: 01/04/2023] Open
Abstract
Although the nuclear genome of banana (Musa spp.) is relatively small (1C approximately 610 Mbp for M. acuminata), the results obtained from other sequenced genomes suggest that more than half of the banana genome may be composed of repetitive and non-coding DNA sequences. Knowledge of repetitive DNA can facilitate mapping of important traits, phylogenetic studies, BAC-based physical mapping, and genome sequencing/annotation. However, only a few repetitive DNA sequences have been characterized in banana. In this work, we used DNA reassociation kinetics to isolate the highly repeated fraction of the banana genome (M. acuminata 'Calcutta 4'). Two libraries, one prepared from Cot </=0.05 DNA (2,688 clones) and one from Cot </=0.1 sequences (4,608 clones), were constructed, and 614 DNA clones were chosen randomly for sequencing and further characterization. Dot-plot analysis revealed that 14% of the sequenced clones contained various semi-tandem and palindromic repeated sequences. 'BLAST' homology searches showed that, in addition to tandem repeats, the Cot libraries were composed mainly of different types of retrotransposons, the most frequent being the Ty3/gypsy type monkey retrotransposon. Selected sequences displaying tandem organization properties were mapped by PRimed IN Situ DNA labeling (PRINS) to the secondary constriction on metaphase chromosomes of M. acuminata 'Calcutta 4'. Southern hybridization with selected BAC clones carrying 45S rDNA confirmed the presence of the tandem repeats in the 45S rDNA unit. This work significantly expands the knowledge of the repetitive fraction of the Musa genome and organization of its chromosomes.
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Affiliation(s)
- E Hribová
- Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany, Olomouc, Czech Republic
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Lescot M, Piffanelli P, Ciampi AY, Ruiz M, Blanc G, Leebens-Mack J, da Silva FR, Santos CMR, D'Hont A, Garsmeur O, Vilarinhos AD, Kanamori H, Matsumoto T, Ronning CM, Cheung F, Haas BJ, Althoff R, Arbogast T, Hine E, Pappas GJ, Sasaki T, Souza MT, Miller RNG, Glaszmann JC, Town CD. Insights into the Musa genome: syntenic relationships to rice and between Musa species. BMC Genomics 2008; 9:58. [PMID: 18234080 PMCID: PMC2270835 DOI: 10.1186/1471-2164-9-58] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2007] [Accepted: 01/30/2008] [Indexed: 01/10/2023] Open
Abstract
Background Musa species (Zingiberaceae, Zingiberales) including bananas and plantains are collectively the fourth most important crop in developing countries. Knowledge concerning Musa genome structure and the origin of distinct cultivars has greatly increased over the last few years. Until now, however, no large-scale analyses of Musa genomic sequence have been conducted. This study compares genomic sequence in two Musa species with orthologous regions in the rice genome. Results We produced 1.4 Mb of Musa sequence from 13 BAC clones, annotated and analyzed them along with 4 previously sequenced BACs. The 443 predicted genes revealed that Zingiberales genes share GC content and distribution characteristics with eudicot and Poaceae genomes. Comparison with rice revealed microsynteny regions that have persisted since the divergence of the Commelinid orders Poales and Zingiberales at least 117 Mya. The previously hypothesized large-scale duplication event in the common ancestor of major cereal lineages within the Poaceae was verified. The divergence time distributions for Musa-Zingiber (Zingiberaceae, Zingiberales) orthologs and paralogs provide strong evidence for a large-scale duplication event in the Musa lineage after its divergence from the Zingiberaceae approximately 61 Mya. Comparisons of genomic regions from M. acuminata and M. balbisiana revealed highly conserved genome structure, and indicated that these genomes diverged circa 4.6 Mya. Conclusion These results point to the utility of comparative analyses between distantly-related monocot species such as rice and Musa for improving our understanding of monocot genome evolution. Sequencing the genome of M. acuminata would provide a strong foundation for comparative genomics in the monocots. In addition a genome sequence would aid genomic and genetic analyses of cultivated Musa polyploid genotypes in research aimed at localizing and cloning genes controlling important agronomic traits for breeding purposes.
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Affiliation(s)
- Magali Lescot
- French Agricultural Research Center for International Development, UMR 1096, Avenue Agropolis, TA40/03, FR-34398, Montpellier, Cedex 5, France.
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Cheung F, Town CD. A BAC end view of the Musa acuminata genome. BMC PLANT BIOLOGY 2007; 7:29. [PMID: 17562019 PMCID: PMC1904220 DOI: 10.1186/1471-2229-7-29] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2006] [Accepted: 06/11/2007] [Indexed: 05/04/2023]
Abstract
BACKGROUND Musa species contain the fourth most important crop in developing countries. Here, we report the analysis of 6,252 BAC end-sequences, in order to view the sequence composition of the Musa acuminata genome in a cost effective and efficient manner. RESULTS BAC end sequencing generated 6,252 reads representing 4,420,944 bp, including 2,979 clone pairs with an average read length after cleaning and filtering of 707 bp. All sequences have been submitted to GenBank, with the accession numbers DX451975-DX458350. The BAC end-sequences, were searched against several databases and significant homology was found to mitochondria and chloroplast (2.6%), transposons and repetitive sequences (36%) and proteins (11%). Functional interpretation of the protein matches was carried out by Gene Ontology assignments from matches to Arabidopsis and was shown to cover a broad range of categories. From protein matching regions of Musa BAC end-sequences, it was determined that the GC content of coding regions was 47%. Where protein matches encompassed a start codon, GC content as a function of position (5' to 3') across 129 bp sliding windows generates a "rice-like" gradient. A total of 352 potential SSR markers were discovered. The most abundant simple sequence repeats in four size categories were AT-rich. After filtering mitochondria and chloroplast matches, thousands of BAC end-sequences had a significant BLASTN match to the Oryza sativa and Arabidopsis genome sequence. Of these, a small number of BAC end-sequence pairs were shown to map to neighboring regions of the Oryza sativa genome representing regions of potential microsynteny. CONCLUSION Database searches with the BAC end-sequences and ab initio analysis identified those reads likely to contain transposons, repeat sequences, proteins and simple sequence repeats. Approximately 600 BAC end-sequences contained protein sequences that were not found in the existing available Musa expressed sequence tags, repeat or transposon databases. In addition, gene statistics, GC content and profile could also be estimated based on the region matching the top protein hit. A small number of BAC end pair sequences can be mapped to neighboring regions of the Oryza sativa representing regions of potential microsynteny. These results suggest that a large-scale BAC end sequencing strategy has the potential to anchor a small proportion of the genome of Musa acuminata to the genomes of Oryza sativa and possibly Arabidopsis.
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Affiliation(s)
- Foo Cheung
- J Craig Venter Institute, 9712 Medical Center Drive, Rockville, MD 20850 USA
| | - Christopher D Town
- J Craig Venter Institute, 9712 Medical Center Drive, Rockville, MD 20850 USA
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Carpentier SC, Witters E, Laukens K, Deckers P, Swennen R, Panis B. Preparation of protein extracts from recalcitrant plant tissues: an evaluation of different methods for two-dimensional gel electrophoresis analysis. Proteomics 2005; 5:2497-507. [PMID: 15912556 DOI: 10.1002/pmic.200401222] [Citation(s) in RCA: 369] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
This study focuses on the specific problems of protein extraction from recalcitrant plant tissues and evaluates several methods to bypass them. Sample preparation is a critical step in a two-dimensional gel electrophoresis proteome approach and is absolutely essential for good results. We evaluated four methods: the classical trichloroacetic acid (TCA)/acetone precipitation, TCA/acetone precipitation and fractionation, an alternative based on fractionation and without precipitation, and phenol extraction methanol/ammonium acetate precipitation. We optimized the phenol extraction protocol for small amounts of tissue, which is essential when the study material is limited. The protocol was optimized for banana (Musa spp.) and was subsequently applied to two other plant species: apple (Malus domestica L.) and potato (Solanum tuberosum L.). Banana (Musa spp.) is a good representative of a "difficult" plant species since it contains many interfering metabolites. Only classical TCA/acetone precipitation and phenol extraction methods proved useful as standard methods. Both methods are associated with a minor but reproducible loss of proteins. Every extraction method and the subsequent analytical procedure have their physicochemical limitations; both methods should be investigated before selecting an appropriate protocol. The study, which is presented in this paper, is useful for guiding the experimental setup of many other nonmodel species, containing various interfering elements.
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Coemans B, Matsumura H, Terauchi R, Remy S, Swennen R, Sági L. SuperSAGE combined with PCR walking allows global gene expression profiling of banana (Musa acuminata), a non-model organism. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 111:1118-26. [PMID: 16133315 DOI: 10.1007/s00122-005-0039-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2005] [Accepted: 07/04/2005] [Indexed: 05/04/2023]
Abstract
Super-serial analysis of gene expression (SuperSAGE) was used to characterize, for the first time, the global gene expression pattern in banana (Musa acuminata). A total of 10,196 tags were generated from leaf tissue, representing 5,292 expressed genes. Forty-nine tags of the top 100 most abundantly expressed transcripts were annotated by homology to cDNA or EST sequences. Typically for leaf tissue, analysis of the transcript profiles showed that the majority of the abundant transcripts are involved in energy production, mainly photosynthesis. However, the most abundant tag was derived from a type 3 metallothionein transcript, which accounted for nearly 3% of total transcripts analysed. Furthermore, the 26-bp long SuperSAGE tags were applied in 3'-rapid amplification of cDNA ends (3'RACE) for the identification of unknown tags. In combination with thermal asymmetric interlaced PCR (TAIL-PCR), this allowed the recovery of a full gene sequence of a novel NADPH:protochlorophyllide oxidoreductase, the key enzyme in chlorophyll biosynthesis. SuperSAGE in conjunction with 3'RACE and TAIL-PCR will be a powerful tool for transcriptomics of non-model, but otherwise important organisms.
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Affiliation(s)
- Bert Coemans
- Laboratory of Tropical Crop Improvement, Katholieke Universiteit Leuven, Kasteelpark Arenberg 13, 3001 Leuven, Belgium.
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Abstract
Plant domestication ranks as one of the most important developments in human history, giving human populations the potential to harness unprecedented quantities of the earth's resources. But domestication has also played a more subtle historical role as the foundation of the modern study of evolution and adaptation. Until recently, however, researchers interested in domestication were limited to studying phenotypic changes or the genetics of simple Mendelian traits, when often the characters of most interest--fruit size, yield, height, flowering time, etc.--are quantitative in nature. The goals of this paper are to review some of the recent work on the quantitative genetics of plant domestication, identify some of the common trends found in this literature, and offer some novel interpretations of the data that is currently available.
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