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A Comprehensive Identification and Expression Analysis of VQ Motif-Containing Proteins in Sugarcane (Saccharum spontaneum L.) under Phytohormone Treatment and Cold Stress. Int J Mol Sci 2022; 23:ijms23116334. [PMID: 35683012 PMCID: PMC9181594 DOI: 10.3390/ijms23116334] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 05/30/2022] [Accepted: 06/03/2022] [Indexed: 11/18/2022] Open
Abstract
The VQ motif-containing proteins play a vital role in various processes such as growth, resistance to biotic and abiotic stresses and development. However, there is currently no report on the VQ genes in sugarcane (Saccharum spp.). Herein, 78 VQ genes in Saccharum spontaneum were identified and classified into nine subgroups (I-IX) by comparative genomic analyses. Each subgroup had a similar structural and conservative motif. These VQ genes expanded mainly through whole-genome segmental duplication. The cis-regulatory elements (CREs) of the VQ genes were widely involved in stress responses, phytohormone responses and physiological regulation. The RNA-seq data showed that SsVQ gene expression patterns in 10 different samples, including different developmental stages, revealed distinct temporal and spatial patterns. A total of 23 SsVQ genes were expressed in all tissues, whereas 13 SsVQ genes were not expressed in any tissues. Sequence Read Archive (SRA) data showed that the majority of SsVQs responded to cold and drought stress. In addition, quantitative real-time PCR analysis showed that the SsVQs were variously expressed under salicylic acid (SA), jasmonic acid (JA), abscisic acid (ABA) and cold treatment. This study conducted a full-scale analysis of the VQ gene family in sugarcane, which could be beneficial for the functional characterization of sugarcane VQ genes and provide candidate genes for molecular resistance breeding in cultivated sugarcane in the future.
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Liu C, Liu H, Zhou C, Timko MP. Genome-Wide Identification of the VQ Protein Gene Family of Tobacco ( Nicotiana tabacum L.) and Analysis of Its Expression in Response to Phytohormones and Abiotic and Biotic Stresses. Genes (Basel) 2020; 11:E284. [PMID: 32156048 PMCID: PMC7140788 DOI: 10.3390/genes11030284] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 03/04/2020] [Accepted: 03/04/2020] [Indexed: 12/30/2022] Open
Abstract
VQ motif-containing proteins (VQ proteins) are transcriptional regulators that work independently or in combination with other transcription factors (TFs) to control plant growth and development and responses to biotic and abiotic stresses. VQ proteins contain a conserved FxxhVQxhTG amino acid motif that is the main element of its interaction with WRKY TFs. We identified 59 members of the tobacco (Nicotiana tabacum L.) NtVQ gene family by in silico analysis and examined their differential expression in response to phytohormonal treatments and following exposure to biotic and abiotic stressors. NtVQ proteins clustered into eight groups based upon their amino acid sequence and presence of various conserved domains. Groups II, IV, V, VI, and VIII contained the largest proportion of NtVQ gene family members differentially expressed in response to one or more phytohormone, and NtVQ proteins with similar domain structures had similar patterns of response to different phytohormones. NtVQ genes differentially expressed in response to temperature alterations and mechanical wounding were also identified. Over half of the NtVQ genes were significantly induced in response to Ralstonia solanacearum infection. This first comprehensive characterization of the NtVQ genes in tobacco lays the foundation for further studies of the NtVQ-mediated regulatory network in plant growth, developmental, and stress-related processes.
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Affiliation(s)
- Cuihua Liu
- Citrus Research Institute, Southwest University, Chongqing 400712, China;
- Department of Biology, University of Virginia, Charlottesville, VA 22903, USA;
| | - Hai Liu
- Department of Biology, University of Virginia, Charlottesville, VA 22903, USA;
| | - Changyong Zhou
- Citrus Research Institute, Southwest University, Chongqing 400712, China;
| | - Michael P. Timko
- Department of Biology, University of Virginia, Charlottesville, VA 22903, USA;
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Chen P, Jing X, Liao B, Zhu Y, Xu J, Liu R, Zhao Y, Li X. BioNano Genome Map Resource for Oryza sativa ssp. japonica and indica and Its Application in Rice Genome Sequence Correction and Gap Filling. MOLECULAR PLANT 2017; 10:895-898. [PMID: 28212831 DOI: 10.1016/j.molp.2017.02.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 01/25/2017] [Accepted: 02/06/2017] [Indexed: 05/09/2023]
Affiliation(s)
- Ping Chen
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xinyun Jing
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Baosheng Liao
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yan Zhu
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jiang Xu
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Renyi Liu
- Shanghai Centre for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Yinhong Zhao
- China National Center for Biotechnology Development, Building 4, No.16, Xisihuanzhonglu, Beijing 100036, China
| | - Xuan Li
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Deng Y, Pan Y, Luo M. Detection and correction of assembly errors of rice Nipponbare reference sequence. PLANT BIOLOGY (STUTTGART, GERMANY) 2014; 16:643-650. [PMID: 24224543 DOI: 10.1111/plb.12090] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 07/06/2013] [Indexed: 06/02/2023]
Abstract
A complete and high-quality genome reference sequence of an organism provides a solid foundation for a wide research community and determines the outcomes of relevant genomic, genetic, molecular and evolutionary research. Rice is an important food crop and a model plant for grasses, and therefore was the first chosen crop plant for whole genome sequencing. The genome of the japonica representative rice variety, Nipponbare, was sequenced using a gold standard, map-based clone-by-clone strategy. However, although the Nipponbare reference sequence (RefSeq) has the best quality for existing crop genome sequences, it still contains many assembly errors and gaps. To improve the Nipponbare RefSeq, first a robust method is required to detect the hidden assembly errors. Through alignments between BAC-end sequences (BESs) embedded in the Nipponbare bacterial artificial chromosome (BAC) physical map and the Nipponbare RefSeq, we detected locations on the Nipponbare RefSeq that were inversely matched with BESs and could therefore be candidates for spurious inversions of assembly. We performed further analysis of five potential locations and confirmed assembly errors at those locations; four of them, two on chr4 and two on chr11 of the Nipponbare RefSeq (IRGSP build 5), were found to be caused by reverse repetitive sequences flanking the locations. Our approach is effective in detecting spurious inversions in the Nipponbare RefSeq and can be applied for improving the sequence qualities of other genomes as well.
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Affiliation(s)
- Y Deng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
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Pan Y, Deng Y, Lin H, Kudrna DA, Wing RA, Li L, Zhang Q, Luo M. Comparative BAC-based physical mapping of Oryza sativa ssp. indica var. 93-11 and evaluation of the two rice reference sequence assemblies. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 77:795-805. [PMID: 24330235 DOI: 10.1111/tpj.12412] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Revised: 12/03/2013] [Accepted: 12/09/2013] [Indexed: 05/10/2023]
Abstract
Reference sequences are sequences that are used for public consultation, and therefore must be of high quality. Using the whole-genome shotgun/next-generation sequencing approach, many genome sequences of complex higher plants have been generated in recent years, and are generally considered reference sequences. However, none of these sequences has been experimentally evaluated at the whole-genome sequence assembly level. Rice has a relatively simple plant genome, and the genome sequences for its two sub-species obtained using different sequencing approaches were published approximately 10 years ago. This provides a unique system for a case study to evaluate the qualities and utilities of published plant genome sequences. We constructed a robust BAC physical map embedding a large number of BAC end sequences forrice variety 93-11. Through BAC end sequence alignments and tri-assembly comparisons of the 93-11 physical map and the two reference sequences, we found that the Nipponbare reference sequence generated using the clone-by-clone approach has a high quality but still contains small artifact inversions and missing sequences. In contrast, the 93-11 reference sequence generated using the whole-genome shotgun approach contains many large and varied assembly errors, such as inversions, duplications and translocations, as well as missing sequences. The 93-11 physical map provides an invaluable resource for evaluation and improvements toward completion of both Nipponbare and 93-11 reference sequences.
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Affiliation(s)
- Yonglong Pan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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Lin H, Xia P, A Wing R, Zhang Q, Luo M. Dynamic intra-japonica subspecies variation and resource application. MOLECULAR PLANT 2012; 5:218-30. [PMID: 21984334 DOI: 10.1093/mp/ssr085] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We constructed a physical map of O. sativa ssp. japonica cv. ZH11 and compared it and its random sample sequences with the Nipponbare RefSeq derived from the same subspecies. This comparison showed that the two japonica genomes were highly syntenic but revealed substantial differences in terms of structural variations, rates of substitutions and indels, and transposable element content. For example, contractions/expansions as large as 450 kb and repeat sequences that were present in high copy numbers only in ZH11 were detected. In tri-alignment regions using the indica variety 93-11 sequence as an outgroup, we found that: (1) the substitution rates of the two japonica-indica inter-subspecies comparison combinations were close but almost a magnitude higher than the substitution rate between the japonica rice varieties ZH11 and Nipponbare; (2) of the substitutions found between ZH11 and Nipponbare, 47.2% occurred in ZH11 and 52.6% in Nipponbare; (3) of the indels found between ZH11 and Nipponbare, the indels that occurred in ZH11 were 15.8 times of those in Nipponbare. Of the indels that occurred in ZH11, 75.67% were insertions and 24.33% deletions. Of the indels that occurred in Nipponbare, 48.23% were insertions and 51.77% were deletions. The ZH11 comparative map covered four Nipponbare physical gaps, detected assembly errors in the Nipponbare sequence, and was integrated with the FSTs of a large ZH11 T-DNA insertion mutant library. ZH11 BAC clones can be browsed, searched, and obtained at our website, http://GResource.hzau.edu.cn.
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Affiliation(s)
- Haiyan Lin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Moroldo M, Paillard S, Marconi R, Fabrice L, Canaguier A, Cruaud C, De Berardinis V, Guichard C, Brunaud V, Le Clainche I, Scalabrin S, Testolin R, Di Gaspero G, Morgante M, Adam-Blondon AF. A physical map of the heterozygous grapevine 'Cabernet Sauvignon' allows mapping candidate genes for disease resistance. BMC PLANT BIOLOGY 2008; 8:66. [PMID: 18554400 PMCID: PMC2442077 DOI: 10.1186/1471-2229-8-66] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2008] [Accepted: 06/13/2008] [Indexed: 05/18/2023]
Abstract
BACKGROUND Whole-genome physical maps facilitate genome sequencing, sequence assembly, mapping of candidate genes, and the design of targeted genetic markers. An automated protocol was used to construct a Vitis vinifera 'Cabernet Sauvignon' physical map. The quality of the result was addressed with regard to the effect of high heterozygosity on the accuracy of contig assembly. Its usefulness for the genome-wide mapping of genes for disease resistance, which is an important trait for grapevine, was then assessed. RESULTS The physical map included 29,727 BAC clones assembled into 1,770 contigs, spanning 715,684 kbp, and corresponding to 1.5-fold the genome size. Map inflation was due to high heterozygosity, which caused either the separation of allelic BACs in two different contigs, or local mis-assembly in contigs containing BACs from the two haplotypes. Genetic markers anchored 395 contigs or 255,476 kbp to chromosomes. The fully automated assembly and anchorage procedures were validated by BAC-by-BAC blast of the end sequences against the grape genome sequence, unveiling 7.3% of chimerical contigs. The distribution across the physical map of candidate genes for non-host and host resistance, and for defence signalling pathways was then studied. NBS-LRR and RLK genes for host resistance were found in 424 contigs, 133 of them (32%) were assigned to chromosomes, on which they are mostly organised in clusters. Non-host and defence signalling genes were found in 99 contigs dispersed without a discernable pattern across the genome. CONCLUSION Despite some limitations that interfere with the correct assembly of heterozygous clones into contigs, the 'Cabernet Sauvignon' physical map is a useful and reliable intermediary step between a genetic map and the genome sequence. This tool was successfully exploited for a quick mapping of complex families of genes, and it strengthened previous clues of co-localisation of major NBS-LRR clusters and disease resistance loci in grapevine.
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Affiliation(s)
- Marco Moroldo
- UMR de Génomique Végétale, INRA-CNRS-UEVE, 2, Rue Gaston Crémieux, CP5708, 91057 Evry Cedex, France
| | - Sophie Paillard
- UMR de Génomique Végétale, INRA-CNRS-UEVE, 2, Rue Gaston Crémieux, CP5708, 91057 Evry Cedex, France
- UMR118, INRA-Agrocampus, University of Rennes, Amélioration des Plantes et Biotechnologies Végétales, F-35650 Le Rheu, France
| | - Raffaella Marconi
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, via delle Scienze 208, 33100 Udine, Italy
| | - Legeai Fabrice
- Unité de Recherche Génomique-Info, URGI, Tour Evry 2, 523, Place des Terrasses de l'Agora, 91034 Evry Cedex, France
| | - Aurelie Canaguier
- UMR de Génomique Végétale, INRA-CNRS-UEVE, 2, Rue Gaston Crémieux, CP5708, 91057 Evry Cedex, France
| | - Corinne Cruaud
- Gnoscope, 2, rue Gaston Crémieux, CP5706, 91057 Evry Cedex, France
| | | | - Cecile Guichard
- UMR de Génomique Végétale, INRA-CNRS-UEVE, 2, Rue Gaston Crémieux, CP5708, 91057 Evry Cedex, France
| | - Veronique Brunaud
- UMR de Génomique Végétale, INRA-CNRS-UEVE, 2, Rue Gaston Crémieux, CP5708, 91057 Evry Cedex, France
| | - Isabelle Le Clainche
- UMR de Génomique Végétale, INRA-CNRS-UEVE, 2, Rue Gaston Crémieux, CP5708, 91057 Evry Cedex, France
| | - Simone Scalabrin
- Dipartimento di Scienze Matematiche, University of Udine, via delle Scienze 208, 33100 Udine, Italy
- Istituto di Genomica Applicata, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100 Udine, Italy
| | - Raffaele Testolin
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, via delle Scienze 208, 33100 Udine, Italy
- Istituto di Genomica Applicata, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100 Udine, Italy
| | - Gabriele Di Gaspero
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, via delle Scienze 208, 33100 Udine, Italy
- Istituto di Genomica Applicata, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100 Udine, Italy
| | - Michele Morgante
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, via delle Scienze 208, 33100 Udine, Italy
- Istituto di Genomica Applicata, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100 Udine, Italy
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Schlueter JA, Lin JY, Schlueter SD, Vasylenko-Sanders IF, Deshpande S, Yi J, O'Bleness M, Roe BA, Nelson RT, Scheffler BE, Jackson SA, Shoemaker RC. Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing. BMC Genomics 2007; 8:330. [PMID: 17880721 PMCID: PMC2077340 DOI: 10.1186/1471-2164-8-330] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2007] [Accepted: 09/19/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Soybean, Glycine max (L.) Merr., is a well documented paleopolyploid. What remains relatively under characterized is the level of sequence identity in retained homeologous regions of the genome. Recently, the Department of Energy Joint Genome Institute and United States Department of Agriculture jointly announced the sequencing of the soybean genome. One of the initial concerns is to what extent sequence identity in homeologous regions would have on whole genome shotgun sequence assembly. RESULTS Seventeen BACs representing approximately 2.03 Mb were sequenced as representative potential homeologous regions from the soybean genome. Genetic mapping of each BAC shows that 11 of the 20 chromosomes are represented. Sequence comparisons between homeologous BACs shows that the soybean genome is a mosaic of retained paleopolyploid regions. Some regions appear to be highly conserved while other regions have diverged significantly. Large-scale "batch" reassembly of all 17 BACs combined showed that even the most homeologous BACs with upwards of 95% sequence identity resolve into their respective homeologous sequences. Potential assembly errors were generated by tandemly duplicated pentatricopeptide repeat containing genes and long simple sequence repeats. Analysis of a whole-genome shotgun assembly of 80,000 randomly chosen JGI-DOE sequence traces reveals some new soybean-specific repeat sequences. CONCLUSION This analysis investigated both the structure of the paleopolyploid soybean genome and the potential effects retained homeology will have on assembling the whole genome shotgun sequence. Based upon these results, homeologous regions similar to those characterized here will not cause major assembly issues.
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Affiliation(s)
| | - Jer-Young Lin
- Purdue Genetics Program, Purdue University, West Lafayette, IN 47907, USA
| | | | | | - Shweta Deshpande
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Jing Yi
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Majesta O'Bleness
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Bruce A Roe
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Rex T Nelson
- USDA-ARS, Corn Insect and Crop Genetics Research Unit, and Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | | | - Scott A Jackson
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA
| | - Randy C Shoemaker
- USDA-ARS, Corn Insect and Crop Genetics Research Unit, and Department of Agronomy, Iowa State University, Ames, IA 50011, USA
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Schlueter JA, Lin JY, Schlueter SD, Vasylenko-Sanders IF, Deshpande S, Yi J, O'Bleness M, Roe BA, Nelson RT, Scheffler BE, Jackson SA, Shoemaker RC. Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing. BMC Genomics 2007. [PMID: 17880721 DOI: 10.1186/1471‐2164‐8‐330] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Soybean, Glycine max (L.) Merr., is a well documented paleopolyploid. What remains relatively under characterized is the level of sequence identity in retained homeologous regions of the genome. Recently, the Department of Energy Joint Genome Institute and United States Department of Agriculture jointly announced the sequencing of the soybean genome. One of the initial concerns is to what extent sequence identity in homeologous regions would have on whole genome shotgun sequence assembly. RESULTS Seventeen BACs representing approximately 2.03 Mb were sequenced as representative potential homeologous regions from the soybean genome. Genetic mapping of each BAC shows that 11 of the 20 chromosomes are represented. Sequence comparisons between homeologous BACs shows that the soybean genome is a mosaic of retained paleopolyploid regions. Some regions appear to be highly conserved while other regions have diverged significantly. Large-scale "batch" reassembly of all 17 BACs combined showed that even the most homeologous BACs with upwards of 95% sequence identity resolve into their respective homeologous sequences. Potential assembly errors were generated by tandemly duplicated pentatricopeptide repeat containing genes and long simple sequence repeats. Analysis of a whole-genome shotgun assembly of 80,000 randomly chosen JGI-DOE sequence traces reveals some new soybean-specific repeat sequences. CONCLUSION This analysis investigated both the structure of the paleopolyploid soybean genome and the potential effects retained homeology will have on assembling the whole genome shotgun sequence. Based upon these results, homeologous regions similar to those characterized here will not cause major assembly issues.
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Zhang Z, Deng Y, Tan J, Hu S, Yu J, Xue Q. A genome-wide microsatellite polymorphism database for the indica and japonica rice. DNA Res 2007; 14:37-45. [PMID: 17452422 PMCID: PMC2779893 DOI: 10.1093/dnares/dsm005] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Microsatellite (MS) polymorphism is an important source of genetic diversity, providing support for map-based cloning and molecular breeding. We have developed a new database that contains 52 845 polymorphic MS loci between indica and japonica, composed of ample Class II MS markers, and integrated 18 828 MS loci from IRGSP and genetic markers from RGP. Based on genetic marker positions on the rice genome (http://rise.genomics.org.cn/rice2/index.jsp ), we determined the approximate genetic distances of these MS loci and validated 100 randomly selected markers experimentally with 90% success rate. In addition, we recorded polymorphic MS positions in indica cv. 9311 that is the most important paternal parent of the two-line hybrid rice in China. Our database will undoubtedly facilitate the application of MS markers in genetic researches and marker-assisted breeding. The data set is freely available from www.wigs.zju.edu.cn/achievment/polySSR.
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Affiliation(s)
- Zhonghua Zhang
- James D. Watson Institute of Genome Science, Zhejiang University, Hangzhou 310008, China
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yajun Deng
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China
| | - Jun Tan
- Institute of Bioinformation, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Songnian Hu
- James D. Watson Institute of Genome Science, Zhejiang University, Hangzhou 310008, China
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China
| | - Jun Yu
- James D. Watson Institute of Genome Science, Zhejiang University, Hangzhou 310008, China
- Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 101300, China
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing 101300, China
| | - Qingzhong Xue
- James D. Watson Institute of Genome Science, Zhejiang University, Hangzhou 310008, China
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310029, China
- To whom correspondence should be addressed. Tel. +86-571-86971611. Fax. +86-571-86971117, E-mail:
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Yang S, Jiang K, Araki H, Ding J, Yang YH, Tian D. A molecular isolation mechanism associated with high intra-specific diversity in rice. Gene 2007; 394:87-95. [PMID: 17379459 DOI: 10.1016/j.gene.2007.02.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2006] [Revised: 02/10/2007] [Accepted: 02/12/2007] [Indexed: 11/21/2022]
Abstract
High levels of inter-specific diversity are expected due to genetic isolation, the reproductive or geographical barriers, which lead to the accumulation of nucleotide variation. However, high levels of genetic variation are repeatedly observed even within species, notably at loci of the human major histocompatability complex and of plant resistance genes. Are molecular isolations responsible for the high intra-specific variation? To address this issue, we performed a genome-wide survey of the relationship between the possible factors that could cause genetic isolation, and the level of polymorphism, based on two rice genome comparisons. Here, we show that the levels of polymorphism in rice genes are positively correlated with the proportions of non-alignable flanking sequences, and that the correlation is observed even in single-copy genes. The physical locations of the genes were also investigated, and a strong association between the asymmetric architecture of genomes and the levels of polymorphism was revealed. These results suggest that the flank heterogeneity and the asymmetric architecture between genomes serve as isolation mechanisms at the molecular level that result in accumulation of higher genetic variation. This mechanism is of fundamental importance to understand natural genetic variation within species.
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Affiliation(s)
- Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, Nanjing 210093, China
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