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Basit A, Lim KB. Systematic approach of polyploidy as an evolutionary genetic and genomic phenomenon in horticultural crops. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 348:112236. [PMID: 39186951 DOI: 10.1016/j.plantsci.2024.112236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 08/15/2024] [Accepted: 08/18/2024] [Indexed: 08/28/2024]
Abstract
Polyploidy is thought to be an evolutionary and systematic mechanism for gene flow and phenotypic advancement in flowering plants. It is a natural phenomenon that promotes diversity by creating new permutations enhancing the prime potentials as compared to progenitors. Two different pathways have been recognized in studying polyploidy in nature; mitotic or somatic chromosome doubling and cytogenetics variation. Secondly, the vital influence of being polyploid is its heritable property (unreduced reproductive cells) formed during first and second-division restitution (FDR & SDR). Different approaches either chemical (Colchicine, Oryzalin, Caffeine, Trifuralin, or phosphoric amides) or gaseous i.e. Nitrous oxide have been deliberated as strong polyploidy causing agents. A wide range of cytogenetic practices like chromosomes study, ploidy, genome analysis, and plant morphology and anatomy have been studied in different plant species. Flow cytometry for ploidy and chromosome analysis through fluorescence and genomic in situ hybridization (FISH & GISH) are the basic methods to evaluate heredity substances sampled from leaves and roots. Many horticultural crops have been developed successfully and released commercially for consumption. Moreover, some deep detailed studies are needed to check the strong relationship between unique morphological features and genetic makeup concerning genes and hormonal expression in a strong approach.
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Affiliation(s)
- Abdul Basit
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, South Korea.
| | - Ki-Byung Lim
- Department of Horticultural Science, Kyungpook National University, Daegu 41566, South Korea; Institute of Agricultural Science and Technology, Kyungpook National University, Daegu, South Korea.
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Dhakate P, Tyagi S, Singh A, Singh A. Functional characterization of a novel Brassica LEAFY homolog from Indian mustard: Expression pattern and gain-of-function studies. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 258:29-44. [PMID: 28330561 DOI: 10.1016/j.plantsci.2017.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 01/13/2017] [Accepted: 02/10/2017] [Indexed: 06/06/2023]
Abstract
LEAFY plays a central role in regulation of flowering time and floral meristem identity in plants. Unfortunately, LFY function remains uncharacterized in agronomicaly important Brassicas. Herein, we illustrate fine-mapping of expression domains of LFY in 15 cultivars of 6 Brassica species and describe gain-of-function phenotypes in Arabidopsis and Brassica. We depict early flowering and altered fatty-acid composition in transgenic seed. The cDNA encoding BjuLFY (417aa) shared only 85% identity with reported homolog of B.juncea implying distinctness. Quantitative RT-PCR based coarse expression mapping of BjuLFY in tissue samples representing 3 time points at specific days after sowing (DAS), pre-flowering (30 DAS), flowering (75 DAS) and post-flowering (110 DAS), depicted an intense pulse of BjuLFY expression restricted to primary floral buds (75 DAS) which subsided in secondary floral buds (110 DAS); expression in root samples was also recorded implying neo-functionalization. Fine-mapping of expression during flowering confirmed tightly regulated LFY expression during early stages of bud development in 15 cultivars of 6 Brassica species implying functional conservation. Ectopic expression of BjuLFY in A. thaliana and B. juncea caused floral meristem defects and precocious flowering. B. juncea transgenics (T1) over-expressing BjuLFY flowered 20days earlier produced normal flowers. GC-MS analysis of mature seed from Brassica transgenics showed an altered fatty-acid profile suggestive of seed maturation occurring at lower temperatures vis-à-vis control. Our findings implicate BjuLFY as a regulator of flowering in B. juncea and suggest its application in developing climate resilient crops.
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Affiliation(s)
- Priyanka Dhakate
- Department of Biotechnology, TERI University, 10 Institutional Area, Vasant Kunj, Delhi 110070, India
| | - Shikha Tyagi
- Department of Biotechnology, TERI University, 10 Institutional Area, Vasant Kunj, Delhi 110070, India
| | - Anupama Singh
- Department of Biotechnology, TERI University, 10 Institutional Area, Vasant Kunj, Delhi 110070, India
| | - Anandita Singh
- Department of Biotechnology, TERI University, 10 Institutional Area, Vasant Kunj, Delhi 110070, India.
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Babula-Skowrońska D, Ludwików A, Cieśla A, Olejnik A, Cegielska-Taras T, Bartkowiak-Broda I, Sadowski J. Involvement of genes encoding ABI1 protein phosphatases in the response of Brassica napus L. to drought stress. PLANT MOLECULAR BIOLOGY 2015; 88:445-57. [PMID: 26059040 PMCID: PMC4486095 DOI: 10.1007/s11103-015-0334-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Accepted: 05/22/2015] [Indexed: 05/21/2023]
Abstract
In this report we characterized the Arabidopsis ABI1 gene orthologue and Brassica napus gene paralogues encoding protein phosphatase 2C (PP2C, group A), which is known to be a negative regulator of the ABA signaling pathway. Six homologous B. napus sequences were identified and characterized as putative PP2C group A members. To gain insight into the conservation of ABI1 function in Brassicaceae, and understand better its regulatory effects in the drought stress response, we generated transgenic B. napus plants overexpressing A. thaliana ABI1. Transgenic plants subjected to drought showed a decrease in relative water content, photosynthetic pigments content and expression level of RAB18- and RD19A-drought-responsive marker genes relative to WT plants. We present the characterization of the drought response of B. napus with the participation of ABI1-like paralogues. The expression pattern of two evolutionarily distant paralogues, BnaA01.ABI1.a and BnaC07.ABI1.b in B. napus and their promoter activity in A. thaliana showed differences in the induction of the paralogues under dehydration stress. Comparative sequence analysis of both BnaABI1 promoters showed variation in positions of cis-acting elements that are especially important for ABA- and stress-inducible expression. Together, these data reveal that subfunctionalization following gene duplication may be important in the maintenance and functional divergence of the BnaABI1 paralogues. Our results provide a framework for a better understanding of (1) the role of ABI1 as a hub protein regulator of the drought response, and (2) the differential involvement of the duplicated BnaABI1 genes in the response of B. napus to dehydration-related stresses.
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Affiliation(s)
- Danuta Babula-Skowrońska
- />Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznan, Poland
| | - Agnieszka Ludwików
- />Department of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Agata Cieśla
- />Department of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Anna Olejnik
- />Plant Breeding and Acclimatization Institute – National Research Institute, Research Division in Poznań, Strzeszyńska 36, 60-479 Poznan, Poland
| | - Teresa Cegielska-Taras
- />Plant Breeding and Acclimatization Institute – National Research Institute, Research Division in Poznań, Strzeszyńska 36, 60-479 Poznan, Poland
| | - Iwona Bartkowiak-Broda
- />Plant Breeding and Acclimatization Institute – National Research Institute, Research Division in Poznań, Strzeszyńska 36, 60-479 Poznan, Poland
| | - Jan Sadowski
- />Department of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
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Cho YI, Ahn YK, Tripathi S, Kim JH, Lee HE, Kim DS. Comparative analysis of disease-linked single nucleotide polymorphic markers from Brassica rapa for their applicability to Brassica oleracea. PLoS One 2015; 10:e0120163. [PMID: 25790283 PMCID: PMC4366180 DOI: 10.1371/journal.pone.0120163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 01/12/2015] [Indexed: 11/18/2022] Open
Abstract
Numerous studies using single nucleotide polymorphisms (SNPs) have been conducted in humans, and other animals, and in major crops, including rice, soybean, and Chinese cabbage. However, the number of SNP studies in cabbage is limited. In this present study, we evaluated whether 7,645 SNPs previously identified as molecular markers linked to disease resistance in the Brassica rapa genome could be applied to B. oleracea. In a BLAST analysis using the SNP sequences of B. rapa and B. oleracea genomic sequence data registered in the NCBI database, 256 genes for which SNPs had been identified in B. rapa were found in B. oleracea. These genes were classified into three functional groups: molecular function (64 genes), biological process (96 genes), and cellular component (96 genes). A total of 693 SNP markers, including 145 SNP markers [BRH—developed from the B. rapa genome for high-resolution melt (HRM) analysis], 425 SNP markers (BRP—based on the B. rapa genome that could be applied to B. oleracea), and 123 new SNP markers (BRS—derived from BRP and designed for HRM analysis), were investigated for their ability to amplify sequences from cabbage genomic DNA. In total, 425 of the SNP markers (BRP-based on B. rapa genome), selected from 7,645 SNPs, were successfully applied to B. oleracea. Using PCR, 108 of 145 BRH (74.5%), 415 of 425 BRP (97.6%), and 118 of 123 BRS (95.9%) showed amplification, suggesting that it is possible to apply SNP markers developed based on the B. rapa genome to B. oleracea. These results provide valuable information that can be utilized in cabbage genetics and breeding programs using molecular markers derived from other Brassica species.
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Affiliation(s)
- Young-Il Cho
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, Republic of Korea
| | - Yul-Kyun Ahn
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, Republic of Korea
- * E-mail:
| | - Swati Tripathi
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, Republic of Korea
| | - Jeong-Ho Kim
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, Republic of Korea
| | - Hye-Eun Lee
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, Republic of Korea
| | - Do-Sun Kim
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, Republic of Korea
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Brulle F, Bernard F, Vandenbulcke F, Cuny D, Dumez S. Identification of suitable qPCR reference genes in leaves of Brassica oleracea under abiotic stresses. ECOTOXICOLOGY (LONDON, ENGLAND) 2014; 23:459-71. [PMID: 24566730 DOI: 10.1007/s10646-014-1209-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/08/2014] [Indexed: 05/20/2023]
Abstract
Real-time quantitative PCR is nowadays a standard method to study gene expression variations in various samples and experimental conditions. However, to interpret results accurately, data normalization with appropriate reference genes appears to be crucial. The present study describes the identification and the validation of suitable reference genes in Brassica oleracea leaves. Expression stability of eight candidates was tested following drought and cold abiotic stresses by using three different softwares (BestKeeper, NormFinder and geNorm). Four genes (BolC.TUB6, BolC.SAND1, BolC.UBQ2 and BolC.TBP1) emerged as the most stable across the tested conditions. Further gene expression analysis of a drought- and a cold-responsive gene (BolC.DREB2A and BolC.ELIP, respectively), confirmed the stability and the reliability of the identified reference genes when used for normalization in the leaves of B. oleracea. These four genes were finally tested upon a benzene exposure and all appeared to be useful reference genes along this toxicological condition. These results provide a good starting point for future studies involving gene expression measurement on leaves of B. oleracea exposed to environmental modifications.
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Affiliation(s)
- Franck Brulle
- Laboratoire des Sciences Végétales et Fongiques, Faculté des Sciences Pharmaceutiques et Biologiques, Université Lille Nord de France, EA 4483, Lille 2, B.P. 83, 59006, Lille Cedex, France
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Suwabe K, Suzuki G, Nunome T, Hatakeyama K, Mukai Y, Fukuoka H, Matsumoto S. Microstructure of a Brassica rapa genome segment homoeologous to the resistance gene cluster on Arabidopsis chromosome 4. BREEDING SCIENCE 2012; 62:170-7. [PMID: 23136528 PMCID: PMC3405966 DOI: 10.1270/jsbbs.62.170] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 03/28/2012] [Indexed: 05/23/2023]
Abstract
Genome evolution is a continuous process and genomic rearrangement occurs both within and between species. With the sequencing of the Arabidopsis thaliana genome, comparative genetics and genomics offer new insights into plant biology. The genus Brassica offers excellent opportunities with which to compare genomic synteny so as to reveal genome evolution. During a previous genetic analysis of clubroot resistance in Brassica rapa, we identified a genetic region that is highly collinear with Arabidopsis chromosome 4. This region corresponds to a disease resistance gene cluster in the A. thaliana genome. Relying on synteny with Arabidopsis, we fine-mapped the region and found that the location and order of the markers showed good correspondence with those in Arabidopsis. Microsynteny on a physical map indicated an almost parallel correspondence, with a few rearrangements such as inversions and insertions. The results show that this genomic region of Brassica is conserved extensively with that of Arabidopsis and has potential as a disease resistance gene cluster, although the genera diverged 20 million years ago.
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Affiliation(s)
- Keita Suwabe
- Graduate School of Bioresources, Mie University, 1577 Kurima-machiya, Tsu, Mie 514-8507, Japan
- NARO Institute of Vegetable and Tea Science, 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Go Suzuki
- Division of Natural Science, Osaka Kyoiku University, 4-698-1 Asahigaoka, Kashiwara, Osaka 582-8582, Japan
| | - Tsukasa Nunome
- NARO Institute of Vegetable and Tea Science, 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Katsunori Hatakeyama
- NARO Institute of Vegetable and Tea Science, 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Yasuhiko Mukai
- Division of Natural Science, Osaka Kyoiku University, 4-698-1 Asahigaoka, Kashiwara, Osaka 582-8582, Japan
| | - Hiroyuki Fukuoka
- NARO Institute of Vegetable and Tea Science, 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Satoru Matsumoto
- NARO Institute of Vegetable and Tea Science, 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
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Xia S, Cheng L, Zu F, Dun X, Zhou Z, Yi B, Wen J, Ma C, Shen J, Tu J, Fu T. Mapping of BnMs4 and BnRf to a common microsyntenic region of Arabidopsis thaliana chromosome 3 using intron polymorphism markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:1193-200. [PMID: 22246313 DOI: 10.1007/s00122-011-1779-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Accepted: 12/22/2011] [Indexed: 05/09/2023]
Abstract
A recessive epistatic genic male sterile two-type line, 7365AB (Bnms3ms3ms4msRrfRf/BnMs3ms3ms4ms4RfRf), combined with the fertile interim-maintainer 7365C (Bnms3ms3ms4ms4rfrf) is an effective pollination control system in hybrid rapeseed production. We report an effective strategy used to fine map BnMs4 and BnRf. The two genes were both defined to a common microsyntenic region with Arabidopsis chromosome 3 using intron polymorphism (IP) markers developed according to Arabidopsis genome information and published genome organization of the A genome. The near-isogenic lines 7365AC (Bnms3ms3ms4ms4Rfrf/Bnms3ms3ms4ms4rfrf) of BnRf and 736512AB (Bnms3ms3Ms4ms4RfRf/Bnms3ms3ms4ms4RfRf) of BnMs4 were constructed to screen developed markers and create genetic linkage maps. Nine polymorphic IP markers (P1-P9) were identified. Of these, P2, P3, P4, and P6 were linked to both BnMs4 and BnRf with genetic distances <0.6 cM. Three simple sequence repeat markers, SR2, SR3, and SR5, were also identified by using public information. Subsequently, all markers linked to the two genes were used to compare the micro-collinearity of the regions flanking the two genes with Brassica rapa and Arabidopsis. The flanking regions showed rearrangements and inversion with fragments of different Arabidopsis chromosomes, but a high collinearity with B. rapa. This collinearity provided extremely valuable reference for map-based cloning in polyploid Brassica species. These IP markers could be exploited for comparative genomic studies within and between Brassica species, providing an economically feasible approach for molecular marker-assisted selection breeding, accelerating the process of gene cloning, and providing more direct evidence for the presence of multiple alleles between BnMs4 and BnRf.
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Affiliation(s)
- Shengqian Xia
- National Key Laboratory of Crop Genetic Improvement, National Sub-center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan 430070, China
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Kim JA, Kim JS, Hong JK, Lee YH, Choi BS, Seol YJ, Jeon CH. Comparative mapping, genomic structure, and expression analysis of eight pseudo-response regulator genes in Brassica rapa. Mol Genet Genomics 2012; 287:373-88. [PMID: 22466714 DOI: 10.1007/s00438-012-0682-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 02/15/2012] [Indexed: 12/30/2022]
Abstract
Circadian clocks regulate plant growth and development in response to environmental factors. In this function, clocks influence the adaptation of species to changes in location or climate. Circadian-clock genes have been subject of intense study in models such as Arabidopsis thaliana but the results may not necessarily reflect clock functions in species with polyploid genomes, such as Brassica species, that include multiple copies of clock-related genes. The triplicate genome of Brassica rapa retains high sequence-level co-linearity with Arabidopsis genomes. In B. rapa we had previously identified five orthologs of the five known Arabidopsis pseudo-response regulator (PRR) genes that are key regulators of the circadian clock in this species. Three of these B. rapa genes, BrPRR1, BrPPR5, and BrPPR7, are present in two copies each in the B. rapa genome, for a total of eight B. rapa PRR (BrPRR) orthologs. We have now determined sequences and expression characteristics of the eight BrPRR genes and mapped their positions in the B. rapa genome. Although both members of each paralogous pair exhibited the same expression pattern, some variation in their gene structures was apparent. The BrPRR genes are tightly linked to several flowering genes. The knowledge about genome location, copy number variation and structural diversity of these B. rapa clock genes will improve our understanding of clock-related functions in this important crop. This will facilitate the development of Brassica crops for optimal growth in new environments and under changing conditions.
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Affiliation(s)
- Jin A Kim
- Department of Agricultural Bio-resources, National Academy of Agricultural Science, Rural Development Administration, Suinro Gwonseon-gu, Suwon, Gyeonggi-do, Republic of Korea
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Kim H, Choi SR, Bae J, Hong CP, Lee SY, Hossain MJ, Van Nguyen D, Jin M, Park BS, Bang JW, Bancroft I, Lim YP. Sequenced BAC anchored reference genetic map that reconciles the ten individual chromosomes of Brassica rapa. BMC Genomics 2009; 10:432. [PMID: 19751531 PMCID: PMC2761421 DOI: 10.1186/1471-2164-10-432] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2008] [Accepted: 09/15/2009] [Indexed: 11/10/2022] Open
Abstract
Background In view of the immense value of Brassica rapa in the fields of agriculture and molecular biology, the multinational Brassica rapa Genome Sequencing Project (BrGSP) was launched in 2003 by five countries. The developing BrGSP has valuable resources for the community, including a reference genetic map and seed BAC sequences. Although the initial B. rapa linkage map served as a reference for the BrGSP, there was ambiguity in reconciling the linkage groups with the ten chromosomes of B. rapa. Consequently, the BrGSP assigned each of the linkage groups to the project members as chromosome substitutes for sequencing. Results We identified simple sequence repeat (SSR) motifs in the B. rapa genome with the sequences of seed BACs used for the BrGSP. By testing 749 amplicons containing SSR motifs, we identified polymorphisms that enabled the anchoring of 188 BACs onto the B. rapa reference linkage map consisting of 719 loci in the 10 linkage groups with an average distance of 1.6 cM between adjacent loci. The anchored BAC sequences enabled the identification of 30 blocks of conserved synteny, totaling 534.9 cM in length, between the genomes of B. rapa and Arabidopsis thaliana. Most of these were consistent with previously reported duplication and rearrangement events that differentiate these genomes. However, we were able to identify the collinear regions for seven additional previously uncharacterized sections of the A genome. Integration of the linkage map with the B. rapa cytogenetic map was accomplished by FISH with probes representing 20 BAC clones, along with probes for rDNA and centromeric repeat sequences. This integration enabled unambiguous alignment and orientation of the maps representing the 10 B. rapa chromosomes. Conclusion We developed a second generation reference linkage map for B. rapa, which was aligned unambiguously to the B. rapa cytogenetic map. Furthermore, using our data, we confirmed and extended the comparative genome analysis between B. rapa and A. thaliana. This work will serve as a basis for integrating the genetic, physical, and chromosome maps of the BrGSP, as well as for studies on polyploidization, speciation, and genome duplication in the genus Brassica.
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Affiliation(s)
- Hyeran Kim
- Plant Genomics Institute, Chungnam National University, Daejeon, 305-764 Korea.
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Piao Z, Ramchiary N, Lim YP. Genetics of Clubroot Resistance in Brassica Species. JOURNAL OF PLANT GROWTH REGULATION 2009; 28:252-264. [PMID: 0 DOI: 10.1007/s00344-009-9093-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
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Structural analysis of 83-kb genomic DNA from Thellungiella halophila: sequence features and microcolinearity between salt cress and Arabidopsis thaliana. Genomics 2009; 94:324-32. [PMID: 19646522 DOI: 10.1016/j.ygeno.2009.07.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2009] [Revised: 07/12/2009] [Accepted: 07/18/2009] [Indexed: 11/22/2022]
Abstract
Salt cress (Thellungiella halophila) has become a desirable plant model for molecular analysis of the mechanisms of salt tolerance. Analysis of its physiological action and expressed EST has resulted in better understanding. However, less is known about its genomic features. Here we determined a continuous sequence approximately 83 kb from a salt cress BAC clone, providing the first insight into the genomic feature for this species. The gene density is approximately one gene per 3.6 kb in this sequence. Many types of repetitive sequences are present in this salt cress sequence, including LTR retroelements, DNA transposons and a number of simple sequence repeats. Comparison of sequence similarity indicated that salt cress shares a close relationship with Arabidopsis. Extensive conservation and high-level microcolinearity were uncovered for both genomes. Our study also indicated that genomic DNA alternations (involving chromosome inversion, sequence loss and gene translocation) contributed to the genomic discrepancies between salt cress and Arabidopsis.
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Soltis DE, Albert VA, Leebens-Mack J, Bell CD, Paterson AH, Zheng C, Sankoff D, Depamphilis CW, Wall PK, Soltis PS. Polyploidy and angiosperm diversification. AMERICAN JOURNAL OF BOTANY 2009; 96:336-48. [PMID: 21628192 DOI: 10.3732/ajb.0800079] [Citation(s) in RCA: 663] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Polyploidy has long been recognized as a major force in angiosperm evolution. Recent genomic investigations not only indicate that polyploidy is ubiquitous among angiosperms, but also suggest several ancient genome-doubling events. These include ancient whole genome duplication (WGD) events in basal angiosperm lineages, as well as a proposed paleohexaploid event that may have occurred close to the eudicot divergence. However, there is currently no evidence for WGD in Amborella, the putative sister species to other extant angiosperms. The question is no longer "What proportion of angiosperms are polyploid?", but "How many episodes of polyploidy characterize any given lineage?" New algorithms provide promise that ancestral genomes can be reconstructed for deep divergences (e.g., it may be possible to reconstruct the ancestral eudicot or even the ancestral angiosperm genome). Comparisons of diversification rates suggest that genome doubling may have led to a dramatic increase in species richness in several angiosperm lineages, including Poaceae, Solanaceae, Fabaceae, and Brassicaceae. However, additional genomic studies are needed to pinpoint the exact phylogenetic placement of the ancient polyploidy events within these lineages and to determine when novel genes resulting from polyploidy have enabled adaptive radiations.
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Affiliation(s)
- Douglas E Soltis
- Department of Botany, University of Florida, Gainesville, Florida 32611 USA
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Delourme R, Piel N, Horvais R, Pouilly N, Domin C, Vallée P, Falentin C, Manzanares-Dauleux MJ, Renard M. Molecular and phenotypic characterization of near isogenic lines at QTL for quantitative resistance to Leptosphaeria maculans in oilseed rape (Brassica napus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:1055-67. [PMID: 18696043 DOI: 10.1007/s00122-008-0844-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2008] [Revised: 06/20/2008] [Accepted: 06/28/2008] [Indexed: 05/09/2023]
Abstract
The most common and effective way to control phoma stem canker (blackleg) caused by Leptosphaeria maculans in oilseed rape (Brassica napus) is by breeding resistant cultivars. Specific resistance genes have been identified in B. napus and related species but in some B. napus cultivars resistance is polygenic [mediated by quantitative trait loci (QTL)], postulated to be race non-specific and durable. The genetic basis of quantitative resistance in the French winter oilseed rape 'Darmor', which was derived from 'Jet Neuf', was previously examined in two genetic backgrounds. Stable QTL involved in blackleg resistance across year and genetic backgrounds were identified. In this study, near isogenic lines (NILs) were produced in the susceptible background 'Yudal' for four of these QTL using marker-assisted selection. Various strategies were used to develop new molecular markers, which were mapped in these QTL regions. These were used to characterize the length and homozygosity of the 'Darmor-bzh' introgressed segment in the NILs. Individuals from each NIL were evaluated in blackleg disease field trials and assessed for their level of stem canker in comparison to the recurrent line 'Yudal'. The effect of QTL LmA2 was clearly validated and to a lesser extent, QTL LmA9 also showed an effect on the disease level. This work provides valuable material that can be used to study the mode of action of genetic factors involved in L. maculans quantitative resistance.
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Affiliation(s)
- R Delourme
- UMR 118 Amélioration des Plantes et Biotechnologies Végétales, INRA, BP 35327, 35653 Le Rheu Cedex, France.
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Rahman M, Sun Z, McVetty PBE, Li G. High throughput genome-specific and gene-specific molecular markers for erucic acid genes in Brassica napus (L.) for marker-assisted selection in plant breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:895-904. [PMID: 18633592 DOI: 10.1007/s00122-008-0829-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2008] [Accepted: 06/11/2008] [Indexed: 05/21/2023]
Abstract
A single base change in the Bn-FAE1.1 gene in the A genome and a two-base deletion in the Bn-FAE1.2 gene in the C genome produce the nearly zero content of erucic acid observed in canola. A BAC clone anchoring Bn-FAE1.1 from a B. rapa BAC library and a BAC clone anchoring Bn-FAE1.2 from a B. oleracea BAC library were used in this research. After sequencing the gene flanking regions, it was found that the dissimilarity of the flanking sequences of these two FAE1 homologs facilitated the design of genome-specific primers that could amplify the corresponding genome in allotetraploid B. napus. The two-base deletion in the C genome gene was detected as a sequence-characterized amplified region (SCAR) marker. To increase the throughput, one genome-specific primer was labeled with four fluorescence dyes and combined with 20 different primers to produce PCR products with different fragment sizes. Eventually, a super pool of 80 samples was detected simultaneously. This dramatically reduces the cost of marker detection. The single base change in the Bn-FAE1.1 gene was detected as single nucleotide polymorphic (SNP) marker with an ABI SNaPshot kit. A multiplexing primer set was designed by adding a polyT to the 5' primer end to increase SNP detection throughput through sample pooling. Furthermore, the Bn-FAE1.1 and Bn-FAE1.2 were integrated into the N8 and N13 linkage groups of our previously reported high-density sequence-related amplified polymorphism (SRAP) map, respectively. There were 124 SRAP markers in a N8 bin in which the Bn-FAE1.1 gene-specific SCAR marker was located and 46 SRAP markers in a N13 bin into which the Bn-FAE1.2 SNP marker was integrated. These three kinds of high throughput molecular markers have been successfully implemented in our canola/rapeseed breeding programs.
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Affiliation(s)
- Mukhlesur Rahman
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, Canada, R3T 2N2
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15
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Lu K, Chai YR, Zhang K, Wang R, Chen L, Lei B, Lu J, Xu XF, Li JN. Cloning and characterization of phosphorus starvation inducible Brassica napus PURPLE ACID PHOSPHATASE 12 gene family, and imprinting of a recently evolved MITE-minisatellite twin structure. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:963-75. [PMID: 18716755 DOI: 10.1007/s00122-008-0836-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2008] [Accepted: 06/24/2008] [Indexed: 05/03/2023]
Abstract
Purple acid phosphatase (PAP) is important for phosphorus assimilation and in planta redistribution. In this study, seven Brassica napus PAP12 (BnPAP12) genes orthologous to Arabidopsis thaliana PAP12 (AtPAP12) are isolated and characterized. NCBI BLASTs, multi-alignments, conserved domain prediction, and featured motif/residue characterization indicate that all BnPAP12 members encode dimeric high molecular weight plant PAPs. BnPAP12-1, BnPAP12-2, BnPAP12-3 and BnPAP12-7 (Group I) have six introns and encode 469-aa polypeptides structurally comparable to AtPAP12. BnPAP12-4 and BnPAP12-6 (Group II) have seven introns and encode 526-aa PAP12s. Encoding a 475-aa polypeptide, BnPAP12-5 (Group III) is evolved from a chimera of 5' part of Group I and 3' part of Group II. Sequence characterization and Southern detection suggest that there are about five BnPAP12 alleles. Homoeologous non-allelic fragment exchanges exist among BnPAP12 genes. BnPAP12-4 and BnPAP12-6 are imprinted with a Tourist-like miniature inverted-repeat transposable element (MITE) which is tightly associated with a novel minisatellite composed of four 36-bp tandem repeats. Existing solely in B. rapa/oleracea lineage, this recently evolved MITE-minisatellite twin structure does not impair transcription and coding capacity of the imprinted genes, and could be used to identify close relatives of B. rapa/oleracea lineage within Brassica. It is also useful for studying MITE activities especially possible involvement in minisatellite formation and gene structure evolution. BnPAP12-6 is silent in transcription. All other BnPAP12 genes basically imitate AtPAP12 in tissue specificity and Pi-starvation induced expression pattern, but divergence and complementation are distinct among them. Alternative polyadenylation and intron retention also exist in BnPAP12 mRNAs.
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Affiliation(s)
- Kun Lu
- Chongqing Rapeseed Engineering Research Center, Southwest University, Tiansheng Road 216#, Beibei, Chongqing 400716, PR China
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16
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Abstract
Comparative genomics is a powerful tool for gaining insight into genomic function and evolution. However, in plants, sequence data that would enable detailed comparisons of both coding and noncoding regions have been limited in availability. Here we report the generation and analysis of sequences for an unduplicated conserved syntenic segment (CSS) in the genomes of five members of the agriculturally important plant family Solanaceae. This CSS includes a 105-kb region of tomato chromosome 2 and orthologous regions of the potato, eggplant, pepper, and petunia genomes. With a total neutral divergence of 0.73-0.78 substitutions/site, these sequences are similar enough that most noncoding regions can be aligned, yet divergent enough to be informative about evolutionary dynamics and selective pressures. The CSS contains 17 distinct genes with generally conserved order and orientation, but with numerous small-scale differences between species. Our analysis indicates that the last common ancestor of these species lived approximately 27-36 million years ago, that more than one-third of short genomic segments (5-15 bp) are under selection, and that more than two-thirds of selected bases fall in noncoding regions. In addition, we identify genes under positive selection and analyze hundreds of conserved noncoding elements. This analysis provides a window into 30 million years of plant evolution in the absence of polyploidization.
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Panjabi P, Jagannath A, Bisht NC, Padmaja KL, Sharma S, Gupta V, Pradhan AK, Pental D. Comparative mapping of Brassica juncea and Arabidopsis thaliana using Intron Polymorphism (IP) markers: homoeologous relationships, diversification and evolution of the A, B and C Brassica genomes. BMC Genomics 2008; 9:113. [PMID: 18315867 PMCID: PMC2277410 DOI: 10.1186/1471-2164-9-113] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Accepted: 03/03/2008] [Indexed: 11/25/2022] Open
Abstract
Background Extensive mapping efforts are currently underway for the establishment of comparative genomics between the model plant, Arabidopsis thaliana and various Brassica species. Most of these studies have deployed RFLP markers, the use of which is a laborious and time-consuming process. We therefore tested the efficacy of PCR-based Intron Polymorphism (IP) markers to analyze genome-wide synteny between the oilseed crop, Brassica juncea (AABB genome) and A. thaliana and analyzed the arrangement of 24 (previously described) genomic block segments in the A, B and C Brassica genomes to study the evolutionary events contributing to karyotype variations in the three diploid Brassica genomes. Results IP markers were highly efficient and generated easily discernable polymorphisms on agarose gels. Comparative analysis of the segmental organization of the A and B genomes of B. juncea (present study) with the A and B genomes of B. napus and B. nigra respectively (described earlier), revealed a high degree of colinearity suggesting minimal macro-level changes after polyploidization. The ancestral block arrangements that remained unaltered during evolution and the karyotype rearrangements that originated in the Oleracea lineage after its divergence from Rapa lineage were identified. Genomic rearrangements leading to the gain or loss of one chromosome each between the A-B and A-C lineages were deciphered. Complete homoeology in terms of block organization was found between three linkage groups (LG) each for the A-B and A-C genomes. Based on the homoeology shared between the A, B and C genomes, a new nomenclature for the B genome LGs was assigned to establish uniformity in the international Brassica LG nomenclature code. Conclusion IP markers were highly effective in generating comparative relationships between Arabidopsis and various Brassica species. Comparative genomics between the three Brassica lineages established the major rearrangements, translocations and fusions pivotal to karyotype diversification between the A, B and C genomes of Brassica species. The inter-relationships established between the Brassica lineages vis-à-vis Arabidopsis would facilitate the identification and isolation of candidate genes contributing to traits of agronomic value in crop Brassicas and the development of unified tools for Brassica genomics.
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Affiliation(s)
- Priya Panjabi
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India.
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18
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Hong CP, Kwon SJ, Kim JS, Yang TJ, Park BS, Lim YP. Progress in understanding and sequencing the genome of Brassica rapa. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2008; 2008:582837. [PMID: 18288250 PMCID: PMC2233773 DOI: 10.1155/2008/582837] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2007] [Accepted: 11/21/2007] [Indexed: 05/24/2023]
Abstract
Brassica rapa, which is closely related to Arabidopsis thaliana, is an important crop and a model plant for studying genome evolution via polyploidization. We report the current understanding of the genome structure of B. rapa and efforts for the whole-genome sequencing of the species. The tribe Brassicaceae, which comprises ca. 240 species, descended from a common hexaploid ancestor with a basic genome similar to that of Arabidopsis. Chromosome rearrangements, including fusions and/or fissions, resulted in the present-day "diploid" Brassica species with variation in chromosome number and phenotype. Triplicated genomic segments of B. rapa are collinear to those of A. thaliana with InDels. The genome triplication has led to an approximately 1.7-fold increase in the B. rapa gene number compared to that of A. thaliana. Repetitive DNA of B. rapa has also been extensively amplified and has diverged from that of A. thaliana. For its whole-genome sequencing, the Brassica rapa Genome Sequencing Project (BrGSP) consortium has developed suitable genomic resources and constructed genetic and physical maps. Ten chromosomes of B. rapa are being allocated to BrGSP consortium participants, and each chromosome will be sequenced by a BAC-by-BAC approach. Genome sequencing of B. rapa will offer a new perspective for plant biology and evolution in the context of polyploidization.
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Affiliation(s)
- Chang Pyo Hong
- Department of Horticulture,
College of Agriculture and Life Science,
Chungnam National University,
Daejeon 305764,
South Korea
| | - Soo-Jin Kwon
- Brassica Genomics Team,
National Institute of Agricultural Biotechnology (NIAB),
Rural Development Administration (RDA),
Suwon 441707,
South Korea
| | - Jung Sun Kim
- Brassica Genomics Team,
National Institute of Agricultural Biotechnology (NIAB),
Rural Development Administration (RDA),
Suwon 441707,
South Korea
| | - Tae-Jin Yang
- Department of Plant Science,
College of Agriculture and Life Sciences,
Seoul National University,
Seoul 151921,
South Korea
| | - Beom-Seok Park
- Brassica Genomics Team,
National Institute of Agricultural Biotechnology (NIAB),
Rural Development Administration (RDA),
Suwon 441707,
South Korea
| | - Yong Pyo Lim
- Department of Horticulture,
College of Agriculture and Life Science,
Chungnam National University,
Daejeon 305764,
South Korea
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19
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Razi H, Howell EC, Newbury HJ, Kearsey MJ. Does sequence polymorphism of FLC paralogues underlie flowering time QTL in Brassica oleracea? TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 116:179-92. [PMID: 17938878 DOI: 10.1007/s00122-007-0657-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2007] [Accepted: 09/21/2007] [Indexed: 05/09/2023]
Abstract
Previous locations of flowering time (FT) QTL in several Brassica species, coupled with Arabidopsis synteny, suggest that orthologues of the genes FLC, FY or CONSTANS might be the candidates. We focused on FLC, and cloned paralogous copies in Brassica oleracea, obtained their genomic DNA sequences, and confirmed their locations relative to those of known FT-QTL by genetical mapping. They varied in total length mainly due to the variable size of the first and last introns. A high level of identity was observed among Brassica FLC genes at the amino acid level but non-synonymous differences were present. Comparative analysis of the promoter and intragenic regions of BoFLC paralogues with Arabidopsis FLC revealed extensive differences in overall structure and organisation but showed high conservation within those segments known to be essential in regulating FLC expression. Four B. oleracea FLC copies (BoFLC1, BoFLC3, BoFLC4 and BoFLC5) were located to their respective linkage groups based on allelic sequence variation in lines from a doubled haploid population. All except BoFLC4 were within the confidence intervals of known FT-QTL. Sequence data indicated that relevant non-synonymous polymorphisms were present between parents A12DHd and GDDH33 for BoFLC genes. However, BoFLC alleles segregated independently of FT in backcrosses while the study provided evidence that BoFLC4 and BoFLC5 contain premature stop codons and so could not contribute to flowering time variation. Therefore, there is strong evidence against any of the 4 BoFLC being FT-QTL candidates in this population.
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Affiliation(s)
- H Razi
- School of Biosciences, The University of Birmingham, Birmingham B15 2TT, UK.
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20
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Weier D, Mittasch J, Strack D, Milkowski C. The genes BnSCT1 and BnSCT2 from Brassica napus encoding the final enzyme of sinapine biosynthesis: molecular characterization and suppression. PLANTA 2008; 227:375-85. [PMID: 17882453 DOI: 10.1007/s00425-007-0624-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Accepted: 08/30/2007] [Indexed: 05/16/2023]
Abstract
This study describes the molecular characterization of the genes BnSCT1 and BnSCT2 from oilseed rape (Brassica napus) encoding the enzyme 1-O-sinapoyl-beta-glucose:choline sinapoyltransferase (SCT; EC 2.3.1.91). SCT catalyzes the 1-O-beta-acetal ester-dependent biosynthesis of sinapoylcholine (sinapine), the most abundant phenolic compound in seeds of B. napus. GUS fusion experiments indicated that seed specificity of BnSCT1 expression is caused by an inducible promoter confining transcription to embryo tissues and the aleurone layer. A dsRNAi construct designed to silence seed-specifically the BnSCT1 gene was effective in reducing the sinapine content of Arabidopsis seeds thus defining SCT genes as targets for molecular breeding of low sinapine cultivars of B. napus. Sequence analyses revealed that in the allotetraploid genome of B. napus the gene BnSCT1 represents the C genome homologue from the B. oleracea progenitor whereas BnSCT2 was derived from the Brassica A genome of B. rapa. The BnSCT1 and BnSCT2 loci showed colinearity with the homologous Arabidopsis SNG2 gene locus although the genomic microstructure revealed the deletion of a cluster of three genes and several coding regions in the B. napus genome.
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Affiliation(s)
- Diana Weier
- Department of Secondary Metabolism, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
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21
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Timms L, Jimenez R, Chase M, Lavelle D, McHale L, Kozik A, Lai Z, Heesacker A, Knapp S, Rieseberg L, Michelmore R, Kesseli R. Analyses of synteny between Arabidopsis thaliana and species in the Asteraceae reveal a complex network of small syntenic segments and major chromosomal rearrangements. Genetics 2006; 173:2227-35. [PMID: 16783026 PMCID: PMC1569713 DOI: 10.1534/genetics.105.049205] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2005] [Accepted: 06/07/2006] [Indexed: 11/18/2022] Open
Abstract
Comparative genomic studies among highly divergent species have been problematic because reduced gene similarities make orthologous gene pairs difficult to identify and because colinearity is expected to be low with greater time since divergence from the last common ancestor. Nevertheless, synteny between divergent taxa in several lineages has been detected over short chromosomal segments. We have examined the level of synteny between the model species Arabidopsis thaliana and species in the Compositae, one of the largest and most diverse plant families. While macrosyntenic patterns covering large segments of the chromosomes are not evident, significant levels of local synteny are detected at a fine scale covering segments of 1-Mb regions of A. thaliana and regions of <5 cM in lettuce and sunflower. These syntenic patches are often not colinear, however, and form a network of regions that have likely evolved by duplications followed by differential gene loss.
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Affiliation(s)
- Lee Timms
- Biology Department, University of Massachusetts, Boston 02125, USA
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22
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Suwabe K, Tsukazaki H, Iketani H, Hatakeyama K, Kondo M, Fujimura M, Nunome T, Fukuoka H, Hirai M, Matsumoto S. Simple sequence repeat-based comparative genomics between Brassica rapa and Arabidopsis thaliana: the genetic origin of clubroot resistance. Genetics 2006; 173:309-19. [PMID: 16723420 PMCID: PMC1461432 DOI: 10.1534/genetics.104.038968] [Citation(s) in RCA: 167] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
An SSR-based linkage map was constructed in Brassica rapa. It includes 113 SSR, 87 RFLP, and 62 RAPD markers. It consists of 10 linkage groups with a total distance of 1005.5 cM and an average distance of 3.7 cM. SSRs are distributed throughout the linkage groups at an average of 8.7 cM. Synteny between B. rapa and a model plant, Arabidopsis thaliana, was analyzed. A number of small genomic segments of A. thaliana were scattered throughout an entire B. rapa linkage map. This points out the complex genomic rearrangements during the course of evolution in Cruciferae. A 282.5-cM region in the B. rapa map was in synteny with A. thaliana. Of the three QTL (Crr1, Crr2, and Crr4) for clubroot resistance identified, synteny analysis revealed that two major QTL regions, Crr1 and Crr2, overlapped in a small region of Arabidopsis chromosome 4. This region belongs to one of the disease-resistance gene clusters (MRCs) in the A. thaliana genome. These results suggest that the resistance genes for clubroot originated from a member of the MRCs in a common ancestral genome and subsequently were distributed to the different regions they now inhabit in the process of evolution.
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Affiliation(s)
- Keita Suwabe
- Department of Quality Science, National Institute of Vegetable and Tea Science, Ano, Mie, Japan
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23
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Ziolkowski PA, Kaczmarek M, Babula D, Sadowski J. Genome evolution in Arabidopsis/Brassica: conservation and divergence of ancient rearranged segments and their breakpoints. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2006; 47:63-74. [PMID: 16824180 DOI: 10.1111/j.1365-313x.2006.02762.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Since the tetraploidization of the Arabidopsis thaliana ancestor 30-35 million years ago (Mya), a wave of chromosomal rearrangements have modified its genome architecture. The dynamics of this process is unknown, as it has so far been impossible to date individual rearrangement events. In this paper, we present evidence demonstrating that the majority of rearrangements occurred before the Arabidopsis-Brassica split 20-24 Mya, and that the segmental architecture of the A. thaliana genome is predominantly conserved in Brassica. This finding is based on the conservation of four rearrangement breakpoints analysed by fluorescence in situ hybridization (FISH) and RFLP mapping of three A. thaliana chromosomal regions. For this purpose, 95 Arabidopsis bacterial artificial chromosomes (BACs) spanning a total of 8.25 Mb and 81 genetic loci for 36 marker genes were studied in the Brassica oleracea genome. All the regions under study were triplicated in the B. oleracea genome, confirming the hypothesis of Brassica ancestral genome triplication. However, whilst one of the breakpoints was conserved at one locus, it was not at the two others. Further comparison of their organization may indicate that the evolution of the hexaploid Brassica progenitor proceeded by several events, separated in time. Genetic mapping and reprobing with rDNA allowed assignment of the regions to particular Brassica chromosomes. Based on this study of regional organization and evolution, a new insight into polyploidization/diploidization cycles is proposed.
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Affiliation(s)
- Piotr A Ziolkowski
- Department of Biotechnology, Adam Mickiewicz University, Miedzychodzka 5, 60-371 Poznań, Poland
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24
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Town CD, Cheung F, Maiti R, Crabtree J, Haas BJ, Wortman JR, Hine EE, Althoff R, Arbogast TS, Tallon LJ, Vigouroux M, Trick M, Bancroft I. Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy. THE PLANT CELL 2006; 18:1348-59. [PMID: 16632643 PMCID: PMC1475499 DOI: 10.1105/tpc.106.041665] [Citation(s) in RCA: 280] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2006] [Revised: 03/21/2006] [Accepted: 03/28/2006] [Indexed: 05/08/2023]
Abstract
We sequenced 2.2 Mb representing triplicated genome segments of Brassica oleracea, which are each paralogous with one another and homologous with a segmentally duplicated region of the Arabidopsis thaliana genome. Sequence annotation identified 177 conserved collinear genes in the B. oleracea genome segments. Analysis of synonymous base substitution rates indicated that the triplicated Brassica genome segments diverged from a common ancestor soon after divergence of the Arabidopsis and Brassica lineages. This conclusion was corroborated by phylogenetic analysis of protein families. Using A. thaliana as an outgroup, 35% of the genes inferred to be present when genome triplication occurred in the Brassica lineage have been lost, most likely via a deletion mechanism, in an interspersed pattern. Genes encoding proteins involved in signal transduction or transcription were not found to be significantly more extensively retained than those encoding proteins classified with other functions, but putative proteins predicted in the A. thaliana genome were underrepresented in B. oleracea. We identified one example of gene loss from the Arabidopsis lineage. We found evidence for the frequent insertion of gene fragments of nuclear genomic origin and identified four apparently intact genes in noncollinear positions in the B. oleracea and A. thaliana genomes.
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25
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Gao M, Li G, Potter D, McCombie WR, Quiros CF. Comparative analysis of methylthioalkylmalate synthase (MAM) gene family and flanking DNA sequences in Brassica oleracea and Arabidopsis thaliana. PLANT CELL REPORTS 2006; 25:592-8. [PMID: 16432629 DOI: 10.1007/s00299-005-0078-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2005] [Revised: 09/27/2005] [Accepted: 10/02/2005] [Indexed: 05/06/2023]
Abstract
Gene BoGSL-PRO is associated with presence of 3-carbon side-chain glucosinolates (GSL). This gene is a member of the methylthioalkylmalate synthase (MAM) gene family. A BAC clone of Brassica oleracea, B21F5, containing this gene, was sequenced, annotated and compared to its corresponding region in Arabidopsis thaliana. Twelve protein-coding genes and 10 transposable elements were found in this clone. The corresponding region in A. thaliana chromosome I has 14 genes and no transposable elements. Analysis of MAM gene family in both species, which also include genes controlling 4-carbon side-chain GSL, separated the genes in two groups based on exon numbers and function. Phylogenetic analysis of the amino acid sequences encoded by these genes suggest that these two groups were produced by a duplication that must have occurred before the divergence of the Rosid and Asterid lineages of angiosperms. Comparison with putative orthologs from several prokaryotes further suggest that the members of the gene family with 10 exons, which encode proteins involved in 4-carbon side-chain GSL biosynthesis, were derived via truncation of the 3' end from ancestral genes more similar in length to those with 12 exons, which encode proteins involved in 3-carbon side-chain GSL biosynthesis. Lower gene density in B. oleracea compared to A. thaliana is due in part to presence of transposable elements (TE) mostly in inter-genic regions.
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Affiliation(s)
- Muqiang Gao
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
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26
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Yang TJ, Kim JS, Kwon SJ, Lim KB, Choi BS, Kim JA, Jin M, Park JY, Lim MH, Kim HI, Lim YP, Kang JJ, Hong JH, Kim CB, Bhak J, Bancroft I, Park BS. Sequence-level analysis of the diploidization process in the triplicated FLOWERING LOCUS C region of Brassica rapa. THE PLANT CELL 2006; 18:1339-47. [PMID: 16632644 PMCID: PMC1475497 DOI: 10.1105/tpc.105.040535] [Citation(s) in RCA: 160] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Strong evidence exists for polyploidy having occurred during the evolution of the tribe Brassiceae. We show evidence for the dynamic and ongoing diploidization process by comparative analysis of the sequences of four paralogous Brassica rapa BAC clones and the homologous 124-kb segment of Arabidopsis thaliana chromosome 5. We estimated the times since divergence of the paralogous and homologous lineages. The three paralogous subgenomes of B. rapa triplicated 13 to 17 million years ago (MYA), very soon after the Arabidopsis and Brassica divergence occurred at 17 to 18 MYA. In addition, a pair of BACs represents a more recent segmental duplication, which occurred approximately 0.8 MYA, and provides an exception to the general expectation of three paralogous segments within the B. rapa genome. The Brassica genome segments show extensive interspersed gene loss relative to the inferred structure of the ancestral genome, whereas the Arabidopsis genome segment appears little changed. Representatives of all 32 genes in the Arabidopsis genome segment are represented in Brassica, but the hexaploid complement of 96 has been reduced to 54 in the three subgenomes, with compression of the genomic region lengths they occupy to between 52 and 110 kb. The gene content of the recently duplicated B. rapa genome segments is identical, but intergenic sequences differ.
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Affiliation(s)
- Tae-Jin Yang
- Brassica Genomics Team, National Institute of Agricultural Biotechnology, Rural Development Administration, Suwon 441-707, Korea
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27
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Schranz ME, Mitchell-Olds T. Independent ancient polyploidy events in the sister families Brassicaceae and Cleomaceae. THE PLANT CELL 2006; 18:1152-65. [PMID: 16617098 PMCID: PMC1456871 DOI: 10.1105/tpc.106.041111] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Recent studies have elucidated the ancient polyploid history of the Arabidopsis thaliana (Brassicaceae) genome. The studies concur that there was at least one polyploidy event occurring some 14.5 to 86 million years ago (Mya), possibly near the divergence of the Brassicaceae from its sister family, Cleomaceae. Using a comparative genomics approach, we asked whether this polyploidy event was unique to members of the Brassicaceae, shared with the Cleomaceae, or an independent polyploidy event in each lineage. We isolated and sequenced three genomic regions from diploid Cleome spinosa (Cleomaceae) that are each homoeologous to a duplicated region shared between At3 and At5, centered on the paralogs of SEPALLATA (SEP) and CONSTANS (CO). Phylogenetic reconstructions and analysis of synonymous substitution rates support the hypothesis that a genomic triplication in Cleome occurred independently of and more recently than the duplication event in the Brassicaceae. There is a strong correlation in the copy number (single versus duplicate) of individual genes, suggesting functionally consistent influences operating on gene copy number in these two independently evolving lineages. However, the amount of gene loss in Cleome is greater than in Arabidopsis. The genome of C. spinosa is only 1.9 times the size of A. thaliana, enabling comparative genome analysis of separate but related polyploidy events.
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Affiliation(s)
- M Eric Schranz
- Department of Genetics and Evolution, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany.
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Schranz ME, Mitchell-Olds T. Independent ancient polyploidy events in the sister families Brassicaceae and Cleomaceae. THE PLANT CELL 2006; 18:1152-1165. [PMID: 16617098 DOI: 10.1105/tpc.106.041111.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Recent studies have elucidated the ancient polyploid history of the Arabidopsis thaliana (Brassicaceae) genome. The studies concur that there was at least one polyploidy event occurring some 14.5 to 86 million years ago (Mya), possibly near the divergence of the Brassicaceae from its sister family, Cleomaceae. Using a comparative genomics approach, we asked whether this polyploidy event was unique to members of the Brassicaceae, shared with the Cleomaceae, or an independent polyploidy event in each lineage. We isolated and sequenced three genomic regions from diploid Cleome spinosa (Cleomaceae) that are each homoeologous to a duplicated region shared between At3 and At5, centered on the paralogs of SEPALLATA (SEP) and CONSTANS (CO). Phylogenetic reconstructions and analysis of synonymous substitution rates support the hypothesis that a genomic triplication in Cleome occurred independently of and more recently than the duplication event in the Brassicaceae. There is a strong correlation in the copy number (single versus duplicate) of individual genes, suggesting functionally consistent influences operating on gene copy number in these two independently evolving lineages. However, the amount of gene loss in Cleome is greater than in Arabidopsis. The genome of C. spinosa is only 1.9 times the size of A. thaliana, enabling comparative genome analysis of separate but related polyploidy events.
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Affiliation(s)
- M Eric Schranz
- Department of Genetics and Evolution, Max Planck Institute for Chemical Ecology, D-07745 Jena, Germany.
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29
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Suwabe K, Tsukazaki H, Iketani H, Hatakeyama K, Kondo M, Fujimura M, Nunome T, Fukuoka H, Hirai M, Matsumoto S. Simple sequence repeat-based comparative genomics between Brassica rapa and Arabidopsis thaliana: the genetic origin of clubroot resistance. Genetics 2006. [PMID: 16723420 DOI: 10.1534/genetics.104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023] Open
Abstract
An SSR-based linkage map was constructed in Brassica rapa. It includes 113 SSR, 87 RFLP, and 62 RAPD markers. It consists of 10 linkage groups with a total distance of 1005.5 cM and an average distance of 3.7 cM. SSRs are distributed throughout the linkage groups at an average of 8.7 cM. Synteny between B. rapa and a model plant, Arabidopsis thaliana, was analyzed. A number of small genomic segments of A. thaliana were scattered throughout an entire B. rapa linkage map. This points out the complex genomic rearrangements during the course of evolution in Cruciferae. A 282.5-cM region in the B. rapa map was in synteny with A. thaliana. Of the three QTL (Crr1, Crr2, and Crr4) for clubroot resistance identified, synteny analysis revealed that two major QTL regions, Crr1 and Crr2, overlapped in a small region of Arabidopsis chromosome 4. This region belongs to one of the disease-resistance gene clusters (MRCs) in the A. thaliana genome. These results suggest that the resistance genes for clubroot originated from a member of the MRCs in a common ancestral genome and subsequently were distributed to the different regions they now inhabit in the process of evolution.
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Affiliation(s)
- Keita Suwabe
- Department of Quality Science, National Institute of Vegetable and Tea Science, Ano, Mie, Japan
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30
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Babula D, Misztal LH, Jakubowicz M, Kaczmarek M, Nowak W, Sadowski J. Genes involved in biosynthesis and signalisation of ethylene in Brassica oleracea and Arabidopsis thaliana: identification and genome comparative mapping of specific gene homologues. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 112:410-20. [PMID: 16311726 DOI: 10.1007/s00122-005-0136-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2005] [Accepted: 10/24/2005] [Indexed: 05/05/2023]
Abstract
The study reported was aimed at the identification and determination of the chromosomal organisation of genes involved in the ethylene biosynthesis and signalling pathways in Brassica oleracea, on the basis of the Arabidopsis thaliana DNA probes and in silico genome analysis. Because of its polyploidal origin, the B. oleracea genome is characterised by extensive gene redundancy. Therefore, an important aspect of gene expression in B. oleracea response to environmental stimuli is to identify the specific gene copy involved. This aspect should also be taken into consideration while studying the genetic basis of biosynthesis and signal transduction in relation to basic phytohormones. Our present work concerns the identification of homologue genes involved in ethylene biosynthesis such as SAM, ACS and ACO, as well as those involved in the ethylene signalling pathway, mainly ETR1, CTR1, MKK4, MKK5, EIN2, EIN3, EREBP, ERF5 and ERF7 on the basis of the restriction fragment length polymorphism (RFLP) and PCR mapping. In the case of ACC synthases, (ACSs) the in silico analysis of gene variants in the genome of A. thaliana was followed by the identification of homologues to ACS2, ACS6 and ACS7 in the B. oleracea database. In total, 22 loci with sequence homology to the genes under analysis were included in the existing B. oleracea RFLP chromosomal map. Based on the stress responsiveness of most of the A. thaliana genes analysed in this study, we performed initial functional analysis of some gene homologues mapped. With the use of the RT-PCR approach the conservation of differential transcriptional induction of ACS homologues in the B. oleracea and A. thaliana was demonstrated during ozone stress.
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Affiliation(s)
- D Babula
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479 Poznań, Poland
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31
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Howell EC, Armstrong SJ, Barker GC, Jones GH, King GJ, Ryder CD, Kearsey MJ. Physical organization of the major duplication onBrassica oleraceachromosome O6 revealed through fluorescence in situ hybridization withArabidopsisandBrassicaBAC probes. Genome 2005; 48:1093-103. [PMID: 16391678 DOI: 10.1139/g05-069] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The close relationship between Brassica oleracea and Arabidopsis thaliana has been used to explore the genetic and physical collinearity of the two species, focusing on an inverted segmental chromosome duplication within linkage group O6 of B. oleracea. Genetic evidence suggests that these segments share a common origin with a region of Arabidopsis chromosome 1. Brassica oleracea and Arabidopsis bacterial artificial chromosome probes have been used for fluorescence in situ hybridization analysis of B. oleracea pachytene chromosomes to further characterize the inverted duplication. This has been highly effective in increasing the local resolution of the cytogenetic map. We have shown that the physical order of corresponding genetic markers is highly conserved between the duplicated regions in B. oleracea and the physical lengths of the regions at pachytene are similar, while the genetic distances are considerably different. The physical marker order is also well conserved between Arabidopsis and B. oleracea, with only one short inversion identified. Furthermore, the relative physical distances between the markers in one segment of B. oleracea and Arabidopsis have stayed approximately the same. The efficacy of using fluorescence in situ hybridization, together with other forms of physical and genetic mapping, for elucidating such issues relating to synteny is discussed.Key words: collinearity, cytogenetic map, pachytene chromosomes, Brassica, Arabidopsis.
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Affiliation(s)
- E C Howell
- School of Biosciences, University of Birmingham, UK.
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32
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Park JY, Koo DH, Hong CP, Lee SJ, Jeon JW, Lee SH, Yun PY, Park BS, Kim HR, Bang JW, Plaha P, Bancroft I, Lim YP. Physical mapping and microsynteny of Brassica rapa ssp. pekinensis genome corresponding to a 222 kbp gene-rich region of Arabidopsis chromosome 4 and partially duplicated on chromosome 5. Mol Genet Genomics 2005; 274:579-88. [PMID: 16283385 DOI: 10.1007/s00438-005-0041-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2005] [Accepted: 08/05/2005] [Indexed: 11/28/2022]
Abstract
We constructed a bacterial artificial chromosome (BAC) library, designated as KBrH, from high molecular weight genomic DNA of Brassica rapa ssp. pekinensis (Chinese cabbage). This library, which was constructed using HindIII-cleaved genomic DNA, consists of 56,592 clones with average insert size of 115 kbp. Using a partially duplicated DNA sequence of Arabidopsis, represented by 19 and 9 predicted genes on chromosome 4 and 5, respectively, and BAC clones from the KBrH library, we studied conservation and microsynteny corresponding to the Arabidopsis regions in B. rapa ssp. pekinensis. The BAC contigs assembled according to the Arabidopsis homoeologues revealed triplication and rearrangements in the Chinese cabbage. In general, collinearity of genes in the paralogous segments was maintained, but gene contents were highly variable with interstitial losses. We also used representative BAC clones, from the assembled contigs, as probes and hybridized them on mitotic (metaphase) and/or meiotic (leptotene/pachytene/metaphase I) chromosomes of Chinese cabbage using bicolor fluorescence in situ hybridization. The hybridization pattern physically identified the paralogous segments of the Arabidopsis homoeologues on B. rapa ssp. pekinensis chromosomes. The homoeologous segments corresponding to chromosome 4 of Arabidopsis were located on chromosomes 2, 8 and 7, whereas those of chromosome 5 were present on chromosomes 6, 1 and 4 of B. rapa ssp. pekinensis.
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Affiliation(s)
- J Y Park
- Department of Horticulture, Chungnam National University, Kung-Dong 220, Yusong-Gu, Daejeon 305-764, South Korea
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33
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Maluszynska J, Hasterok R. Identification of individual chromosomes and parental genomes in Brassica juncea using GISH and FISH. Cytogenet Genome Res 2005; 109:310-4. [PMID: 15753591 DOI: 10.1159/000082414] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2003] [Accepted: 02/25/2004] [Indexed: 11/19/2022] Open
Abstract
The three diploid (B. nigra, B. oleracea, B. campestris) and three allotetraploid (B. carinata, B. juncea, B. napus) species of Brassica, known as the "U-triangle" are one of the best model systems for the study of polyploidy. Numerous molecular investigations have provided a wealth of new insights into the polyploid origin and changes during the evolution of Brassica, but there are still many controversial aspects of their relationship and evolution. Interpretation of genome changes during evolution requires individual chromosome identification within the genome and clear distinction of genomes within the allotetraploid. The aim of this study was to identify individual chromosomes of B. juncea (genome AABB; 2n = 4x = 36) and to determine their genomic origin. Fluorescence in situ hybridization with 5S and 45S rDNA probes enabled discrimination of a substantial number of chromosomes, providing chromosomal landmarks for 20 out of 36 chromosomes of B. juncea. Additionally, along with double target genomic in situ hybridization, it allowed assignment of all chromosomes to either the A or B genomes.
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Affiliation(s)
- J Maluszynska
- Department of Plant Anatomy and Cytology, University of Silesia, Katowice, Poland.
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34
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Gao M, Li G, McCombie WR, Quiros CF. Comparative analysis of a transposon-rich Brassica oleracea BAC clone with its corresponding sequence in A. thaliana. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 111:949-55. [PMID: 16044267 DOI: 10.1007/s00122-005-0029-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2004] [Accepted: 11/15/2004] [Indexed: 05/03/2023]
Abstract
We compared the sequence of a 96.7 Kb-long BAC clone (B 19 N 3) from Brassica oleracea (broccoli) with its corresponding regions in Arabidopsis thaliana. B 19 N 3 contains eight genes and 15 transposable elements (TEs). The first two genes in this clone, Bo 1 and Bo 2, have its corresponding region at the end of chromosome V of Arabidopsis (24 Mb). The third gene, Bo 3, corresponds to an ortholog at the opposite end (2.6 Mb) of the same chromosome. The other five genes, Bo 4 to Bo 8 also have a corresponding region on the same chromosome but at 7.7 Mb . These five genes are colinear with those found in the corresponding region of Arabidopsis, which contains, however, 15 genes. Therefore, a cluster of 10 genes is missing in B. oleracea clone (B 19 N 3). All five genes in common have the same order and orientation in the genomes of both species. Their 36 exons constituting the eight homologous genes have high conservation in size and sequence identity in both species. Among these, there is a major gene involved in aliphatic glucosinolate biosynthesis, Bo GSL-ELONG (Bo 4). Similar to A. thaliana, this gene, has a tandem duplicate, Bo 5. A contig for this region was constructed by primer walking and BAC-end-sequencing, revealing general gene colinearity between both species. During the 20 million years separating A. thaliana from B. oleracea from a common ancestor both genomes have diverged by chromosomal rearrangements and differential TE activity. These events, in addition to changes in chromosome number are responsible for the evolution of the genomes of both species. In spite of these changes, both species conserve general colinearity for their corresponding genes.
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Affiliation(s)
- Muqiang Gao
- Department of Vegetable Crops, University of California, Davis, CA 95616, USA
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35
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Windsor AJ, Reichelt M, Figuth A, Svatos A, Kroymann J, Kliebenstein DJ, Gershenzon J, Mitchell-Olds T. Geographic and evolutionary diversification of glucosinolates among near relatives of Arabidopsis thaliana (Brassicaceae). PHYTOCHEMISTRY 2005; 66:1321-33. [PMID: 15913672 DOI: 10.1016/j.phytochem.2005.04.016] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2004] [Revised: 01/21/2005] [Accepted: 04/07/2005] [Indexed: 05/02/2023]
Abstract
Glucosinolates are biologically active secondary metabolites that display both intra- and interspecific variation in the order Brassicales. Glucosinolate profiles have not been interpreted within a phylogenic framework and little is known regarding the processes that influence the evolution of glucosinolate diversity at a macroevolutionary scale. We have analyzed leaf glucosinolate profiles from members of the Brassicaceae that have diverged from Arabidopsis thaliana within the last 15 million years and interpreted our findings relative to the phylogeny of this group. We identified several interspecific polymorphisms in glucosinolate composition. A majority of these polymorphisms are lineage-specific secondary losses of glucosinolate characters, but a gain-of-character polymorphism was also detected. The genetic basis of most observed polymorphisms appears to be regulatory. In the case of A. lyrata, geographic distribution is also shown to contribute to glucosinolate metabolic diversity. Further, we observed evidence of gene-flow between sympatric species, parallel evolution, and the existence of genetic constraints on the evolution of glucosinolates within the Brassicaceae.
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Affiliation(s)
- Aaron J Windsor
- Max-Planck-Institute for Chemical Ecology, Genetics and Evolution, Hans-Knoell-Strasse 8, D-07745 Jena, Germany
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36
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Katari MS, Balija V, Wilson RK, Martienssen RA, McCombie WR. Comparing low coverage random shotgun sequence data from Brassica oleracea and Oryza sativa genome sequence for their ability to add to the annotation of Arabidopsis thaliana. Genome Res 2005; 15:496-504. [PMID: 15805491 PMCID: PMC1074364 DOI: 10.1101/gr.3239105] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Since the completion of the Arabidopsis thaliana genome sequence, there is an ongoing effort to annotate the genome as accurately as possible. Comparing genome sequences of related species complements the current annotation strategies by identifying genes and improving gene structure. A total of 595,321 Brassica oleracea shotgun reads were sequenced by TIGR (The Institute for Genome Research) and the collaboration of Washington University and Cold Spring Harbor. Vicogenta (a genome viewer based on GMOD and GBrowse) was created to view the current annotation and sequence alignments for Arabidopsis. Brassica reads were compared with the Arabidopsis genome and proteome databases using BLAST. Hypothetical genes and conserved unannotated regions on the short arm of chromosome 4 from Arabidopsis were experimentally verified using RT-PCR. We were able to improve the Arabidopsis annotation by identifying 25 genes that were missed, and confirming expression of 43 hypothetical genes in Arabidopsis. We were also able to detect conservation in genes whose transcription is normally suppressed due to methylation. We also examined how useful the O. sativa genome and ESTs from other species are, compared with Brassica, in improving the Arabidopsis annotation.
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Affiliation(s)
- Manpreet S Katari
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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37
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Ayele M, Haas BJ, Kumar N, Wu H, Xiao Y, Van Aken S, Utterback TR, Wortman JR, White OR, Town CD. Whole genome shotgun sequencing of Brassica oleracea and its application to gene discovery and annotation in Arabidopsis. Genome Res 2005; 15:487-95. [PMID: 15805490 PMCID: PMC1074363 DOI: 10.1101/gr.3176505] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Through comparative studies of the model organism Arabidopsis thaliana and its close relative Brassica oleracea, we have identified conserved regions that represent potentially functional sequences overlooked by previous Arabidopsis genome annotation methods. A total of 454,274 whole genome shotgun sequences covering 283 Mb (0.44 x) of the estimated 650 Mb Brassica genome were searched against the Arabidopsis genome, and conserved Arabidopsis genome sequences (CAGSs) were identified. Of these 229,735 conserved regions, 167,357 fell within or intersected existing gene models, while 60,378 were located in previously unannotated regions. After removal of sequences matching known proteins, CAGSs that were close to one another were chained together as potentially comprising portions of the same functional unit. This resulted in 27,347 chains of which 15,686 were sufficiently distant from existing gene annotations to be considered a novel conserved unit. Of 192 conserved regions examined, 58 were found to be expressed in our cDNA populations. Rapid amplification of cDNA ends (RACE) was used to obtain potentially full-length transcripts from these 58 regions. The resulting sequences led to the creation of 21 gene models at 17 new Arabidopsis loci and the addition of splice variants or updates to another 19 gene structures. In addition, CAGSs overlapping already annotated genes in Arabidopsis can provide guidance for manual improvement of existing gene models. Published genome-wide expression data based on whole genome tiling arrays and massively parallel signature sequencing were overlaid on the Brassica-Arabidopsis conserved sequences, and 1399 regions of intersection were identified. Collectively our results and these data sets suggest that several thousand new Arabidopsis genes remain to be identified and annotated.
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Affiliation(s)
- Mulu Ayele
- The Institute for Genomic Research, Rockville, Maryland 20850, USA
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38
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Gao M, Li G, Yang B, McCombie WR, Quiros CF. Comparative analysis of a Brassica BAC clone containing several major aliphatic glucosinolate genes with its corresponding Arabidopsis sequence. Genome 2005; 47:666-79. [PMID: 15284871 DOI: 10.1139/g04-021] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We compared the sequence of a 101-kb-long bacterial artificial chromosome (BAC) clone (B21H13) from Brassica oleracea with its homologous region in Arabidopsis thaliana. This clone contains a gene family involved in the synthesis of aliphatic glucosinolates. The A. thaliana homologs for this gene family are located on chromosome IV and correspond to three 2-oxoglutarate-dependent dioxygenase (AOP) genes. We found that B21H13 harbors 23 genes, whereas the equivalent region in Arabidopsis contains 37 genes. All 23 common genes have the same order and orientation in both Brassica and Arabidopsis. The 16 missing genes in the broccoli BAC clone were arranged in two major blocks of 5 and 7 contiguous genes, two singletons, and a twosome. The 118 exons comprising these 23 genes have high conservation between the two species. The arrangement of the AOP gene family in A. thaliana is as follows: AOP3 (GS-OHP) - AOP2 (GS-ALK) - pseudogene - AOP1. In contrast, in B. oleracea (broccoli and collard), two of the genes are duplicated and the third, AOP3, is missing. The remaining genes are arranged as follows: Bo-AOP2.1 (BoGSL-ALKa) - pseudogene - AOP2.2 (BoGSL-ALKb) - AOP1.1 - AOP1.2. When the survey was expanded to other Brassica accessions, we found variation in copy number and sequence for the Brassica AOP2 homologs. This study confirms that extensive rearrangements have taken place during the evolution of the Brassicacea at both gene and chromosomal levels.
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Affiliation(s)
- Muqiang Gao
- Departmernt of Vegetable Crops, University of California-Davis, Davis, CA 95616, USA
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39
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Kuittinen H, de Haan AA, Vogl C, Oikarinen S, Leppälä J, Koch M, Mitchell-Olds T, Langley CH, Savolainen O. Comparing the linkage maps of the close relatives Arabidopsis lyrata and A. thaliana. Genetics 2004; 168:1575-84. [PMID: 15579708 PMCID: PMC1448766 DOI: 10.1534/genetics.103.022343] [Citation(s) in RCA: 147] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2003] [Accepted: 06/01/2004] [Indexed: 11/18/2022] Open
Abstract
We have constructed a genetic map of Arabidopsis lyrata, a self-incompatible relative of the plant model species A. thaliana. A. lyrata is a diploid (n = 8) species that diverged from A. thaliana (n = 5) approximately 5 MYA. Mapping was conducted in a full-sib progeny of two unrelated F(1) hybrids between two European populations of A. lyrata ssp. petraea. We used the least-squares method of the Joinmap program for map construction. The gross chromosomal differences between the two species were most parsimoniously explained with three fusions, two reciprocal translocations, and one inversion. The total map length was 515 cM, and the distances were 12% larger than those between corresponding markers in the linkage map of A. thaliana. The 72 markers, consisting of microsatellites and gene-based markers, were spaced on average every 8 cM. Transmission ratio distortion was extensive, and most distortions were specific to each reciprocal cross, suggesting cytoplasmic interactions. We estimate locations and most probable genotype frequencies of transmission ratio distorting loci (TRDL) with a Bayesian method and discuss the possible reasons for the observed distortions.
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Affiliation(s)
- Helmi Kuittinen
- Department of Biology, University of Oulu, 90401 Oulu, Finland.
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40
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LUKENS LEWISN, QUIJADA PABLOA, UDALL JOSHUA, PIRES JCHRIS, SCHRANZ MERIC, OSBORN THOMASC. Genome redundancy and plasticity within ancient and recent Brassica crop species. Biol J Linn Soc Lond 2004. [DOI: 10.1111/j.1095-8312.2004.00352.x] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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41
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Basu C, Halfhill MD, Mueller TC, Stewart CN. Weed genomics: new tools to understand weed biology. TRENDS IN PLANT SCIENCE 2004; 9:391-8. [PMID: 15358270 DOI: 10.1016/j.tplants.2004.06.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
In spite of the large yield losses that weeds inflict on crops, we know little about the genomics of economically important weed species. Comparative genomics between plant model species and weeds, map-based approaches, genomic sequencing and functional genomics can play vital roles in understanding and dissecting weedy traits of agronomically important weed species that damage crops. Weed genomics research should increase our understanding of the evolution of herbicide resistance and of the basic genetics underlying traits that make weeds a successful group of plants. Here, we propose specific weed candidates as genomic models, including economically important plants that have evolved herbicide resistance on several occasions and weeds with good comparative genomic qualities that can be anchored to the genomics of Arabidopsis and Oryza sativa.
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Affiliation(s)
- Chhandak Basu
- Department of Plant Sciences, 2431 Joe Johnson Drive, University of Tennessee, Knoxville, TN 37996, USA
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42
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Varshney A, Mohapatra T, Sharma RP. Development and validation of CAPS and AFLP markers for white rust resistance gene in Brassica juncea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 109:153-159. [PMID: 14997300 DOI: 10.1007/s00122-004-1607-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2003] [Accepted: 01/19/2004] [Indexed: 05/24/2023]
Abstract
White rust, caused by Albugo candida, is a very serious disease in crucifers. In Indian mustard (Brassica juncea), it can cause a yield loss to the extent of 89.9%. The locus Ac2(t) controlling resistance to white rust in BEC-144, an exotic accession of mustard, was mapped using RAPD markers. In the present study, we developed: (1) a more tightly linked marker for the white rust resistance gene, using AFLP in conjunction with bulk segregant analysis, and (2) a PCR-based cleaved amplified polymorphic sequence (CAPS) marker for the closely linked RAPD marker, OPB06(1000). The data obtained on 94 RILs revealed that the CAPS marker for OPB06(1000) and the AFLP marker E-ACC/M-CAA(350) flank the Ac2(t) gene at 3.8 cM and 6.7 cM, respectively. Validation of the CAPS marker in two different F(2) populations of crosses Varuna x BEC-144 and Varuna x BEC-286 was also undertaken, which established its utility in marker-assisted selection (MAS) for white rust resistance. The use of both flanking markers in MAS would allow only 0.25% misclassification and thus provide greater efficiency to selection.
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Affiliation(s)
- A Varshney
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, 110012 New Delhi, India
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43
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Rombauts S, Florquin K, Lescot M, Marchal K, Rouzé P, van de Peer Y. Computational approaches to identify promoters and cis-regulatory elements in plant genomes. PLANT PHYSIOLOGY 2003; 132:1162-76. [PMID: 12857799 PMCID: PMC167057 DOI: 10.1104/pp.102.017715] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2002] [Revised: 01/10/2003] [Accepted: 03/17/2003] [Indexed: 05/19/2023]
Abstract
The identification of promoters and their regulatory elements is one of the major challenges in bioinformatics and integrates comparative, structural, and functional genomics. Many different approaches have been developed to detect conserved motifs in a set of genes that are either coregulated or orthologous. However, although recent approaches seem promising, in general, unambiguous identification of regulatory elements is not straightforward. The delineation of promoters is even harder, due to its complex nature, and in silico promoter prediction is still in its infancy. Here, we review the different approaches that have been developed for identifying promoters and their regulatory elements. We discuss the detection of cis-acting regulatory elements using word-counting or probabilistic methods (so-called "search by signal" methods) and the delineation of promoters by considering both sequence content and structural features ("search by content" methods). As an example of search by content, we explored in greater detail the association of promoters with CpG islands. However, due to differences in sequence content, the parameters used to detect CpG islands in humans and other vertebrates cannot be used for plants. Therefore, a preliminary attempt was made to define parameters that could possibly define CpG and CpNpG islands in Arabidopsis, by exploring the compositional landscape around the transcriptional start site. To this end, a data set of more than 5,000 gene sequences was built, including the promoter region, the 5'-untranslated region, and the first introns and coding exons. Preliminary analysis shows that promoter location based on the detection of potential CpG/CpNpG islands in the Arabidopsis genome is not straightforward. Nevertheless, because the landscape of CpG/CpNpG islands differs considerably between promoters and introns on the one side and exons (whether coding or not) on the other, more sophisticated approaches can probably be developed for the successful detection of "putative" CpG and CpNpG islands in plants.
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Affiliation(s)
- Stephane Rombauts
- Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, B-9000 Gent, Belgium
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Guo H, Moose SP. Conserved noncoding sequences among cultivated cereal genomes identify candidate regulatory sequence elements and patterns of promoter evolution. THE PLANT CELL 2003; 15:1143-58. [PMID: 12724540 PMCID: PMC153722 DOI: 10.1105/tpc.010181] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2002] [Accepted: 03/07/2003] [Indexed: 05/20/2023]
Abstract
Surveys for conserved noncoding sequences (CNS) among genes from monocot cereal species were conducted to assess the general properties of CNS in grass genomes and their correlation with known promoter regulatory elements. Initial comparisons of 11 orthologous maize-rice gene pairs found that previously defined regulatory motifs could be identified within short CNS but could not be distinguished reliably from random sequence matches. Among the different phylogenetic footprinting algorithms tested, the VISTA tool yielded the most informative alignments of noncoding sequence. VISTA was used to survey for CNS among all publicly available genomic sequences from maize, rice, wheat, barley, and sorghum, representing >300 gene comparisons. Comparisons of orthologous maize-rice and maize-sorghum gene pairs identified 20 bp as a minimal length criterion for a significant CNS among grass genes, with few such CNS found to be conserved across rice, maize, sorghum, and barley. The frequency and length of cereal CNS as well as nucleotide substitution rates within CNS were consistent with the known phylogenetic distances among the species compared. The implications of these findings for the evolution of cereal gene promoter sequences and the utility of using the nearly completed rice genome sequence to predict candidate regulatory elements in other cereal genes by phylogenetic footprinting are discussed.
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Affiliation(s)
- Hena Guo
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 61801, USA
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Lukens L, Zou F, Lydiate D, Parkin I, Osborn T. Comparison of a Brassica oleracea genetic map with the genome of Arabidopsis thaliana. Genetics 2003; 164:359-72. [PMID: 12750346 PMCID: PMC1462567 DOI: 10.1093/genetics/164.1.359] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Brassica oleracea is closely related to the model plant, Arabidopsis thaliana. Despite this relationship, it has been difficult to both identify the most closely related segments between the genomes and determine the degree of genome replication within B. oleracea relative to A. thaliana. These difficulties have arisen in part because both species have replicated genomes, and the criteria used to identify orthologous regions between the genomes are often ambiguous. In this report, we compare the positions of sequenced Brassica loci with a known position on a B. oleracea genetic map to the positions of their putative orthologs within the A. thaliana genome. We use explicit criteria to distinguish orthologous from paralogous loci. In addition, we develop a conservative algorithm to identify collinear loci between the genomes and a permutation test to evaluate the significance of these regions. The algorithm identified 34 significant A. thaliana regions that are collinear with >28% of the B. oleracea genetic map. These regions have a mean of 3.3 markers spanning 2.1 Mbp of the A. thaliana genome and 2.5 cM of the B. oleracea genetic map. Our findings are consistent with the hypothesis that the B. oleracea genome has been highly rearranged since divergence from A. thaliana, likely as a result of polyploidization.
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Affiliation(s)
- Lewis Lukens
- Department of Agronomy, University of Wisconsin, Madison, Wisconsin 53711, USA.
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Ziolkowski PA, Blanc G, Sadowski J. Structural divergence of chromosomal segments that arose from successive duplication events in the Arabidopsis genome. Nucleic Acids Res 2003; 31:1339-50. [PMID: 12582254 PMCID: PMC150220 DOI: 10.1093/nar/gkg201] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2002] [Revised: 11/04/2002] [Accepted: 12/12/2002] [Indexed: 11/14/2022] Open
Abstract
Using the extensive segmental duplications of the Arabidopsis thaliana genome, a comparative study of homoeologous segments occurring in chromosomes 1, 2, 4 and 5 was performed. The gene-by-gene BLASTP approach was applied to identify duplicated genes in homoeologues. The levels of synonymous substitutions between duplicated coding sequences suggest that these regions were formed by at least two rounds of duplications. Moreover, remnants of even more ancient duplication events were recognised by a whole-genome study. We describe a subchromosomal organisation of genes, including the tandemly repeated genes, and the distribution of transposable elements (TEs). In certain cases, evidence of the possible mechanisms of structural rearrangements within the segments could be found. We provide a probable scenario of the rearrangements that took place during the evolution of the homoeologous regions. Furthermore, on the basis of the comparative analysis of the chromosomal segments in the Columbia and Landsberg erecta accessions, an additional structural variation in the A.thaliana genome is described. Analysis of the segments, spanning 7 Mb or 5.6% of the genome, permitted us to propose a model of evolution at the subchromosomal level.
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Affiliation(s)
- Piotr A Ziolkowski
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479 Poznan, Poland
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Li G, Quiros CF. Genetic analysis, expression and molecular characterization of BoGSL-ELONG, a major gene involved in the aliphatic glucosinolate pathway of Brassica species. Genetics 2002; 162:1937-43. [PMID: 12524361 PMCID: PMC1462373 DOI: 10.1093/genetics/162.4.1937] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We cloned a major aliphatic glucosinolate (GSL) gene, BoGSL-ELONG in Brassica oleracea, using the Arabidopsis sequence database. We based our work on an Arabidopsis candidate gene forming part of a gene family coding for isopropyl malate synthetase-like enzymes (IPMS). This gene is presumably responsible for synthesis of GSL possessing side chains consisting of four carbons (4C). The similarity of the Brassica homolog IPMS-Bo from broccoli to its Arabidopsis counterpart IPMS-At was on the order of 78%, both sharing the same number of exons. A nonfunctional allele of the BoGSL-ELONG gene from white cauliflower, based on the absence of 4C GSL in this crop, displayed a 30-bp deletion, which allowed us to develop a codominant marker for 4C-GSL. Gene expression analysis based on RT-PCR revealed a splicing site mutation in the white cauliflower allele. This resulted in a longer transcript containing intron 3, which failed to excise. Perfect cosegregation was observed for broccoli and cauliflower alleles at the IPMS-Bo gene and 4C-GSL content, strongly indicating that this gene indeed corresponds to BoGSL-ELONG. Cloning of two other major genes, BoGSL-ALK and BoGSL-PRO, is underway. The availability of these genes and BoGSL-ELONG is essential for the manipulation of the aliphatic GSL profile of B. oleracea.
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Affiliation(s)
- Genyi Li
- Department of Vegetable Crops, University of California, Davis, California 95615, USA
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Hall AE, Fiebig A, Preuss D. Beyond the Arabidopsis genome: opportunities for comparative genomics. PLANT PHYSIOLOGY 2002; 129:1439-47. [PMID: 12177458 PMCID: PMC1540248 DOI: 10.1104/pp.004051] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Affiliation(s)
- Anne E Hall
- Howard Hughes Medical Institute, The University of Chicago, 1103 East 57th Street, Chicago, Illinois 60637, USA
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Colinas J, Birnbaum K, Benfey PN. Using cauliflower to find conserved non-coding regions in Arabidopsis. PLANT PHYSIOLOGY 2002; 129:451-4. [PMID: 12068091 PMCID: PMC1540231 DOI: 10.1104/pp.002501] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Affiliation(s)
- Juliette Colinas
- Department of Biology, 1009 Main Building, New York University, 100 Washington Square East, New York, NY 10003, USA
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Abstract
Evolutionary genomics combines functional and evolutionary analyses of genome conservation and differentiation. Gene duplication and polyploidy have fundamentally shaped the genomes of Arabidopsis and all angiosperms. Recent comparative studies have focussed on gene regulation, the function of untranscribed genomic regions, and the effects of natural selection on protein function. A large fraction of interspecific protein divergence is probably adaptive, and may be useful for experimental studies of genes and proteins.
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Affiliation(s)
- Thomas Mitchell-Olds
- Department of Genetics and Evolution, Max-Planck Institute of Chemical Ecology, 07745, Jena, Germany.
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