101
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Guo L, Qiu J, Han Z, Ye Z, Chen C, Liu C, Xin X, Ye CY, Wang YY, Xie H, Wang Y, Bao J, Tang S, Xu J, Gui Y, Fu F, Wang W, Zhang X, Zhu Q, Guang X, Wang C, Cui H, Cai D, Ge S, Tuskan GA, Yang X, Qian Q, He SY, Wang J, Zhou XP, Fan L. A host plant genome (Zizania latifolia) after a century-long endophyte infection. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:600-609. [PMID: 26072920 DOI: 10.1111/tpj.12912] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 05/26/2015] [Accepted: 06/08/2015] [Indexed: 06/04/2023]
Abstract
Despite the importance of host-microbe interactions in natural ecosystems, agriculture and medicine, the impact of long-term (especially decades or longer) microbial colonization on the dynamics of host genomes is not well understood. The vegetable crop 'Jiaobai' with enlarged edible stems was domesticated from wild Zizania latifolia (Oryzeae) approximately 2000 years ago as a result of persistent infection by a fungal endophyte, Ustilago esculenta. Asexual propagation via infected rhizomes is the only means of Jiaobai production, and the Z. latifolia-endophyte complex has been maintained continuously for two centuries. Here, genomic analysis revealed that cultivated Z. latifolia has a significantly smaller repertoire of immune receptors compared with wild Z. latifolia. There are widespread gene losses/mutations and expression changes in the plant-pathogen interaction pathway in Jiaobai. These results show that continuous long-standing endophyte association can have a major effect on the evolution of the structural and transcriptomic components of the host genome.
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Affiliation(s)
- Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Jie Qiu
- Department of Agronomy & Zhejiang Key Laboratory of Crop Germplasm Resources, Zhejiang University, Hangzhou, 310058, China
| | | | - Zihong Ye
- College of Life Science, China Jiliang University, Hangzhou, 310018, China
| | - Chao Chen
- BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Xiufang Xin
- Howard Hughes Medical Institute, Department of Energy Plant Research Laboratory, and Department of Plant Biology, Michigan State University, East Lansing, MI, 48864, USA
| | - Chu-Yu Ye
- Department of Agronomy & Zhejiang Key Laboratory of Crop Germplasm Resources, Zhejiang University, Hangzhou, 310058, China
| | - Ying-Ying Wang
- Department of Agronomy & Zhejiang Key Laboratory of Crop Germplasm Resources, Zhejiang University, Hangzhou, 310058, China
| | | | - Yu Wang
- Department of Agronomy & Zhejiang Key Laboratory of Crop Germplasm Resources, Zhejiang University, Hangzhou, 310058, China
| | - Jiandong Bao
- Department of Agronomy & Zhejiang Key Laboratory of Crop Germplasm Resources, Zhejiang University, Hangzhou, 310058, China
| | - She Tang
- Department of Agronomy & Zhejiang Key Laboratory of Crop Germplasm Resources, Zhejiang University, Hangzhou, 310058, China
| | - Jie Xu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Yijie Gui
- Department of Agronomy & Zhejiang Key Laboratory of Crop Germplasm Resources, Zhejiang University, Hangzhou, 310058, China
| | - Fei Fu
- Department of Agronomy & Zhejiang Key Laboratory of Crop Germplasm Resources, Zhejiang University, Hangzhou, 310058, China
| | - Weidi Wang
- Department of Agronomy & Zhejiang Key Laboratory of Crop Germplasm Resources, Zhejiang University, Hangzhou, 310058, China
| | - Xingchen Zhang
- Department of Agronomy & Zhejiang Key Laboratory of Crop Germplasm Resources, Zhejiang University, Hangzhou, 310058, China
| | | | | | | | - Haifeng Cui
- College of Life Science, China Jiliang University, Hangzhou, 310018, China
| | - Daguang Cai
- Department of Molecular Phytopathology, Christian-Albrechts-University of Kiel, D-24118, Kiel, Germany
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Sheng Yang He
- Howard Hughes Medical Institute, Department of Energy Plant Research Laboratory, and Department of Plant Biology, Michigan State University, East Lansing, MI, 48864, USA
| | - Jun Wang
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xue-Ping Zhou
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, 310058, China
| | - Longjiang Fan
- Department of Agronomy & Zhejiang Key Laboratory of Crop Germplasm Resources, Zhejiang University, Hangzhou, 310058, China
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102
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Chumová Z, Krejčíková J, Mandáková T, Suda J, Trávníček P. Evolutionary and Taxonomic Implications of Variation in Nuclear Genome Size: Lesson from the Grass Genus Anthoxanthum (Poaceae). PLoS One 2015; 10:e0133748. [PMID: 26207824 PMCID: PMC4514812 DOI: 10.1371/journal.pone.0133748] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 06/16/2015] [Indexed: 11/19/2022] Open
Abstract
The genus Anthoxanthum (sweet vernal grass, Poaceae) represents a taxonomically intricate polyploid complex with large phenotypic variation and its evolutionary relationships still poorly resolved. In order to get insight into the geographic distribution of ploidy levels and assess the taxonomic value of genome size data, we determined C- and Cx-values in 628 plants representing all currently recognized European species collected from 197 populations in 29 European countries. The flow cytometric estimates were supplemented by conventional chromosome counts. In addition to diploids, we found two low (rare 3x and common 4x) and one high (~16x-18x) polyploid levels. Mean holoploid genome sizes ranged from 5.52 pg in diploid A. alpinum to 44.75 pg in highly polyploid A. amarum, while the size of monoploid genomes ranged from 2.75 pg in tetraploid A. alpinum to 9.19 pg in diploid A. gracile. In contrast to Central and Northern Europe, which harboured only limited cytological variation, a much more complex pattern of genome sizes was revealed in the Mediterranean, particularly in Corsica. Eight taxonomic groups that partly corresponded to traditionally recognized species were delimited based on genome size values and phenotypic variation. Whereas our data supported the merger of A. aristatum and A. ovatum, eastern Mediterranean populations traditionally referred to as diploid A. odoratum were shown to be cytologically distinct, and may represent a new taxon. Autopolyploid origin was suggested for 4x A. alpinum. In contrast, 4x A. odoratum seems to be an allopolyploid, based on the amounts of nuclear DNA. Intraspecific variation in genome size was observed in all recognized species, the most striking example being the A. aristatum/ovatum complex. Altogether, our study showed that genome size can be a useful taxonomic marker in Anthoxathum to not only guide taxonomic decisions but also help resolve evolutionary relationships in this challenging grass genus.
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Affiliation(s)
- Zuzana Chumová
- Department of Botany, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Jana Krejčíková
- Department of Botany, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Terezie Mandáková
- Central-European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jan Suda
- Department of Botany, Faculty of Science, Charles University in Prague, Prague, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czech Republic
| | - Pavel Trávníček
- Department of Botany, Faculty of Science, Charles University in Prague, Prague, Czech Republic
- Institute of Botany, The Czech Academy of Sciences, Průhonice, Czech Republic
- Biotechnological Centre, Faculty of Agriculture, University of South Bohemia, České Budějovice, Czech Republic
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103
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Copetti D, Zhang J, El Baidouri M, Gao D, Wang J, Barghini E, Cossu RM, Angelova A, Maldonado L CE, Roffler S, Ohyanagi H, Wicker T, Fan C, Zuccolo A, Chen M, Costa de Oliveira A, Han B, Henry R, Hsing YI, Kurata N, Wang W, Jackson SA, Panaud O, Wing RA. RiTE database: a resource database for genus-wide rice genomics and evolutionary biology. BMC Genomics 2015; 16:538. [PMID: 26194356 PMCID: PMC4508813 DOI: 10.1186/s12864-015-1762-3] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 07/09/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Comparative evolutionary analysis of whole genomes requires not only accurate annotation of gene space, but also proper annotation of the repetitive fraction which is often the largest component of most if not all genomes larger than 50 kb in size. RESULTS Here we present the Rice TE database (RiTE-db)--a genus-wide collection of transposable elements and repeated sequences across 11 diploid species of the genus Oryza and the closely-related out-group Leersia perrieri. The database consists of more than 170,000 entries divided into three main types: (i) a classified and curated set of publicly-available repeated sequences, (ii) a set of consensus assemblies of highly-repetitive sequences obtained from genome sequencing surveys of 12 species; and (iii) a set of full-length TEs, identified and extracted from 12 whole genome assemblies. CONCLUSIONS This is the first report of a repeat dataset that spans the majority of repeat variability within an entire genus, and one that includes complete elements as well as unassembled repeats. The database allows sequence browsing, downloading, and similarity searches. Because of the strategy adopted, the RiTE-db opens a new path to unprecedented direct comparative studies that span the entire nuclear repeat content of 15 million years of Oryza diversity.
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Affiliation(s)
- Dario Copetti
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, United States.
- International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna, Philippines.
| | - Jianwei Zhang
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, United States.
| | - Moaine El Baidouri
- Laboratoire Génome et Développement des Plantes and CNRS and Laboratoire Génome et Développements des Plantes, Université de Perpignan Via Domitia, UMR CNRS/UPVD 5096, 66860, Perpignan, France.
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, United States.
| | - Dongying Gao
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, United States.
| | - Jun Wang
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, United States.
| | - Elena Barghini
- Department of Agriculture, Food, and Environment, University of Pisa, 56124, Pisa, Italy.
| | - Rosa M Cossu
- Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127, Pisa, Italy.
| | - Angelina Angelova
- School of Life Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, Scotland.
| | - Carlos E Maldonado L
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, United States.
| | - Stefan Roffler
- Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland.
| | - Hajime Ohyanagi
- Plant Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.
| | - Thomas Wicker
- Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland.
| | - Chuanzhu Fan
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, United States.
| | - Andrea Zuccolo
- Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127, Pisa, Italy.
| | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology Chinese Academy of Sciences, Beijing, 100101, China.
| | | | - Bin Han
- National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Beijing, 100029, China.
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia.
| | - Yue-Ie Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei, 11529, Taiwan.
| | - Nori Kurata
- Plant Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, Yunnan, 650223, China.
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, United States.
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes and CNRS and Laboratoire Génome et Développements des Plantes, Université de Perpignan Via Domitia, UMR CNRS/UPVD 5096, 66860, Perpignan, France.
| | - Rod A Wing
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, United States.
- International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna, Philippines.
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104
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Zolotarov Y, Strömvik M. De Novo Regulatory Motif Discovery Identifies Significant Motifs in Promoters of Five Classes of Plant Dehydrin Genes. PLoS One 2015; 10:e0129016. [PMID: 26114291 PMCID: PMC4482647 DOI: 10.1371/journal.pone.0129016] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 05/04/2015] [Indexed: 12/03/2022] Open
Abstract
Plants accumulate dehydrins in response to osmotic stresses. Dehydrins are divided into five different classes, which are thought to be regulated in different manners. To better understand differences in transcriptional regulation of the five dehydrin classes, de novo motif discovery was performed on 350 dehydrin promoter sequences from a total of 51 plant genomes. Overrepresented motifs were identified in the promoters of five dehydrin classes. The Kn dehydrin promoters contain motifs linked with meristem specific expression, as well as motifs linked with cold/dehydration and abscisic acid response. KS dehydrin promoters contain a motif with a GATA core. SKn and YnSKn dehydrin promoters contain motifs that match elements connected with cold/dehydration, abscisic acid and light response. YnKn dehydrin promoters contain motifs that match abscisic acid and light response elements, but not cold/dehydration response elements. Conserved promoter motifs are present in the dehydrin classes and across different plant lineages, indicating that dehydrin gene regulation is likely also conserved.
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Affiliation(s)
- Yevgen Zolotarov
- Department of Plant Science, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Martina Strömvik
- Department of Plant Science, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC, H9X 3V9, Canada
- * E-mail:
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105
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Huang X, Zhao Q, Han B. Comparative Population Genomics Reveals Strong Divergence and Infrequent Introgression between Asian and African Rice. MOLECULAR PLANT 2015; 8:958-960. [PMID: 25615591 DOI: 10.1016/j.molp.2015.01.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 01/12/2015] [Accepted: 01/12/2015] [Indexed: 06/04/2023]
Affiliation(s)
- Xuehui Huang
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China.
| | - Qiang Zhao
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Bin Han
- National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
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106
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Yang H, Li C, Lam HM, Clements J, Yan G, Zhao S. Sequencing consolidates molecular markers with plant breeding practice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:779-95. [PMID: 25821196 DOI: 10.1007/s00122-015-2499-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 03/14/2015] [Indexed: 05/20/2023]
Abstract
Plenty of molecular markers have been developed by contemporary sequencing technologies, whereas few of them are successfully applied in breeding, thus we present a review on how sequencing can facilitate marker-assisted selection in plant breeding. The growing global population and shrinking arable land area require efficient plant breeding. Novel strategies assisted by certain markers have proven effective for genetic gains. Fortunately, cutting-edge sequencing technologies bring us a deluge of genomes and genetic variations, enlightening the potential of marker development. However, a large gap still exists between the potential of molecular markers and actual plant breeding practices. In this review, we discuss marker-assisted breeding from a historical perspective, describe the road from crop sequencing to breeding, and highlight how sequencing facilitates the application of markers in breeding practice.
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Affiliation(s)
- Huaan Yang
- Department of Agriculture and Food Western Australia, 3 Baron-Hay Court, South Perth, 6151, Australia,
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107
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Singh S, Chand S, Singh NK, Sharma TR. Genome-Wide Distribution, Organisation and Functional Characterization of Disease Resistance and Defence Response Genes across Rice Species. PLoS One 2015; 10:e0125964. [PMID: 25902056 PMCID: PMC4406684 DOI: 10.1371/journal.pone.0125964] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2011] [Accepted: 03/28/2015] [Indexed: 11/19/2022] Open
Abstract
The resistance (R) genes and defense response (DR) genes have become very important resources for the development of disease resistant cultivars. In the present investigation, genome-wide identification, expression, phylogenetic and synteny analysis was done for R and DR-genes across three species of rice viz: Oryza sativa ssp indica cv 93-11, Oryza sativa ssp japonica and wild rice species, Oryza brachyantha. We used the in silico approach to identify and map 786 R -genes and 167 DR-genes, 672 R-genes and 142 DR-genes, 251 R-genes and 86 DR-genes in the japonica, indica and O. brachyanth a genomes, respectively. Our analysis showed that 60.5% and 55.6% of the R-genes are tandemly repeated within clusters and distributed over all the rice chromosomes in indica and japonica genomes, respectively. The phylogenetic analysis along with motif distribution shows high degree of conservation of R- and DR-genes in clusters. In silico expression analysis of R-genes and DR-genes showed more than 85% were expressed genes showing corresponding EST matches in the databases. This study gave special emphasis on mechanisms of gene evolution and duplication for R and DR genes across species. Analysis of paralogs across rice species indicated 17% and 4.38% R-genes, 29% and 11.63% DR-genes duplication in indica and Oryza brachyantha, as compared to 20% and 26% duplication of R-genes and DR-genes in japonica respectively. We found that during the course of duplication only 9.5% of R- and DR-genes changed their function and rest of the genes have maintained their identity. Syntenic relationship across three genomes inferred that more orthology is shared between indica and japonica genomes as compared to brachyantha genome. Genome wide identification of R-genes and DR-genes in the rice genome will help in allele mining and functional validation of these genes, and to understand molecular mechanism of disease resistance and their evolution in rice and related species.
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Affiliation(s)
- Sangeeta Singh
- National Research Center on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
- School of Life Sciences, Devi Ahilya University, Khandwa Road, Indore, 452017, India
| | - Suresh Chand
- School of Life Sciences, Devi Ahilya University, Khandwa Road, Indore, 452017, India
| | - N. K. Singh
- National Research Center on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Tilak Raj Sharma
- National Research Center on Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
- * E-mail:
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108
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Piednoël M, Sousa A, Renner SS. Transposable elements in a clade of three tetraploids and a diploid relative, focusing on Gypsy amplification. Mob DNA 2015; 6:5. [PMID: 25834645 PMCID: PMC4381496 DOI: 10.1186/s13100-015-0034-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 02/10/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Polyploidization can activate specific transposable elements, leading to their accumulation. At the same time, the preferential loss of repetitive elements in polyploids may be central to diploidization. The paucity of studies of transposable element (TE) dynamics in closely related diploid and polyploid species, however, prevents generalizations about these patterns. Here, we use low-coverage Illumina sequencing data for a clade of three tetraploid Orobanche species and a diploid relative to quantify the abundance and relative frequencies of different types of TEs. We confirmed tetraploidy in the sequenced individuals using standard cytogenetic methods and inferred the time of origin of the tetraploid clade with a rate-calibrated molecular clock. FINDINGS The sequenced individuals of Orobanche austrohispanica, Orobanche densiflora, and Orobanche gracilis have 2n = 76 chromosomes, are tetraploid, and shared a most recent common ancestor some 6.7 Ma ago. Comparison of TE classifications from the Illumina data with classification from 454 data for one of the species revealed strong effects of sequencing technology on the detection of certain types of repetitive DNA. The three tetraploids show repeat enrichment especially of Gypsy TE families compared to eight previously analyzed Orobanchaceae. However, the diploid Orobanche rapum-genistae genome also has a very high proportion (30%) of Gypsy elements. CONCLUSIONS We had earlier suggested that tetraploidization might have contributed to an amplification of Gypsy elements, particularly of the Tekay clade, and that O. gracilis underwent genome downsizing following polyploidization. The new data reveal that Gypsy amplification in Orobanchaceae does not consistently relate to tetraploidy and that more species sampling is required to generalize about Tekay accumulation patterns.
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Affiliation(s)
- Mathieu Piednoël
- Systematic Botany and Mycology, University of Munich (LMU), Botanisches Institut, Menzinger Str. 67, Munich, 80638 Germany ; Department of Plant Developmental Biology, Max-Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne, 50829 Germany
| | - Aretuza Sousa
- Systematic Botany and Mycology, University of Munich (LMU), Botanisches Institut, Menzinger Str. 67, Munich, 80638 Germany
| | - Susanne S Renner
- Systematic Botany and Mycology, University of Munich (LMU), Botanisches Institut, Menzinger Str. 67, Munich, 80638 Germany
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109
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de los Reyes BG, Mohanty B, Yun SJ, Park MR, Lee DY. Upstream regulatory architecture of rice genes: summarizing the baseline towards genus-wide comparative analysis of regulatory networks and allele mining. RICE (NEW YORK, N.Y.) 2015; 8:14. [PMID: 25844119 PMCID: PMC4385054 DOI: 10.1186/s12284-015-0041-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Accepted: 01/12/2015] [Indexed: 05/23/2023]
Abstract
Dissecting the upstream regulatory architecture of rice genes and their cognate regulator proteins is at the core of network biology and its applications to comparative functional genomics. With the rapidly advancing comparative genomics resources in the genus Oryza, a reference genome annotation that defines the various cis-elements and trans-acting factors that interface each gene locus with various intrinsic and extrinsic signals for growth, development, reproduction and adaptation must be established to facilitate the understanding of phenotypic variation in the context of regulatory networks. Such information is also important to establish the foundation for mining non-coding sequence variation that defines novel alleles and epialleles across the enormous phenotypic diversity represented in rice germplasm. This review presents a synthesis of the state of knowledge and consensus trends regarding the various cis-acting and trans-acting components that define spatio-temporal regulation of rice genes based on representative examples from both foundational studies in other model and non-model plants, and more recent studies in rice. The goal is to summarize the baseline for systematic upstream sequence annotation of the rapidly advancing genome sequence resources in Oryza in preparation for genus-wide functional genomics. Perspectives on the potential applications of such information for gene discovery, network engineering and genomics-enabled rice breeding are also discussed.
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Affiliation(s)
| | - Bijayalaxmi Mohanty
- />Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117576 Singapore
| | - Song Joong Yun
- />Department of Crop Science and Institute of Agricultural Science and Technology, Chonbuk National University, Chonju, 561-756 Korea
| | - Myoung-Ryoul Park
- />School of Biology and Ecology, University of Maine, Orono, ME 04469 USA
| | - Dong-Yup Lee
- />Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, 117576 Singapore
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110
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De novo assembly and characterization of Oryza officinalis leaf transcriptome by using RNA-seq. BIOMED RESEARCH INTERNATIONAL 2015; 2015:982065. [PMID: 25713814 PMCID: PMC4332758 DOI: 10.1155/2015/982065] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Accepted: 01/04/2015] [Indexed: 01/13/2023]
Abstract
Although endeavors have been made to identify useful wild rice genes that can be used to improve cultivated rice, the virtual reservoir of genetic variation hidden within the wild relatives of cultivated rice is largely untapped. Here, using next-generation sequencing technology, we investigated the leaf transcriptome of a wild rice O. officinalis with CC genome. Approximately 23 million reads were produced in the species leaf transcriptome analysis and de novo assembly methods constructed 68,132 unigenes. Functional annotations for the unigenes were conducted using sequence similarity comparisons against the following databases: the nonredundant nucleotide database, the nonredundant protein database, the SWISS-PROT database, the Clusters of Orthologous Groups of proteins database, the Kyoto Encyclopedia of Genes and Genomes database, the Gene Ontology Consortium database, and the InterPro domains database. In addition, a total of 476 unigenes related to disease resistance were identified in O. officinalis, and these unigenes can serve as important genetic resources for cultivated rice breeding and quality improvement. The present study broadens our understanding of the genetic background of non-AA genomic wild rice species and it also provides a bridge to extend studies to other Oryza species with CC genomes.
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111
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Unamba CIN, Nag A, Sharma RK. Next Generation Sequencing Technologies: The Doorway to the Unexplored Genomics of Non-Model Plants. FRONTIERS IN PLANT SCIENCE 2015; 6:1074. [PMID: 26734016 PMCID: PMC4679907 DOI: 10.3389/fpls.2015.01074] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 11/16/2015] [Indexed: 05/04/2023]
Abstract
Non-model plants i.e., the species which have one or all of the characters such as long life cycle, difficulty to grow in the laboratory or poor fecundity, have been schemed out of sequencing projects earlier, due to high running cost of Sanger sequencing. Consequently, the information about their genomics and key biological processes are inadequate. However, the advent of fast and cost effective next generation sequencing (NGS) platforms in the recent past has enabled the unearthing of certain characteristic gene structures unique to these species. It has also aided in gaining insight about mechanisms underlying processes of gene expression and secondary metabolism as well as facilitated development of genomic resources for diversity characterization, evolutionary analysis and marker assisted breeding even without prior availability of genomic sequence information. In this review we explore how different Next Gen Sequencing platforms, as well as recent advances in NGS based high throughput genotyping technologies are rewarding efforts on de-novo whole genome/transcriptome sequencing, development of genome wide sequence based markers resources for improvement of non-model crops that are less costly than phenotyping.
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Affiliation(s)
- Chibuikem I. N. Unamba
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource TechnologyPalampur, India
- Department of Plant Science and Biotechnology, Imo State UniversityOwerri, Nigeria
| | - Akshay Nag
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource TechnologyPalampur, India
| | - Ram K. Sharma
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource TechnologyPalampur, India
- *Correspondence: Ram K. Sharma ;
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Fleischmann A, Michael TP, Rivadavia F, Sousa A, Wang W, Temsch EM, Greilhuber J, Müller KF, Heubl G. Evolution of genome size and chromosome number in the carnivorous plant genus Genlisea (Lentibulariaceae), with a new estimate of the minimum genome size in angiosperms. ANNALS OF BOTANY 2014; 114:1651-63. [PMID: 25274549 PMCID: PMC4649684 DOI: 10.1093/aob/mcu189] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 08/07/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND AND AIMS Some species of Genlisea possess ultrasmall nuclear genomes, the smallest known among angiosperms, and some have been found to have chromosomes of diminutive size, which may explain why chromosome numbers and karyotypes are not known for the majority of species of the genus. However, other members of the genus do not possess ultrasmall genomes, nor do most taxa studied in related genera of the family or order. This study therefore examined the evolution of genome sizes and chromosome numbers in Genlisea in a phylogenetic context. The correlations of genome size with chromosome number and size, with the phylogeny of the group and with growth forms and habitats were also examined. METHODS Nuclear genome sizes were measured from cultivated plant material for a comprehensive sampling of taxa, including nearly half of all species of Genlisea and representing all major lineages. Flow cytometric measurements were conducted in parallel in two laboratories in order to compare the consistency of different methods and controls. Chromosome counts were performed for the majority of taxa, comparing different staining techniques for the ultrasmall chromosomes. KEY RESULTS Genome sizes of 15 taxa of Genlisea are presented and interpreted in a phylogenetic context. A high degree of congruence was found between genome size distribution and the major phylogenetic lineages. Ultrasmall genomes with 1C values of <100 Mbp were almost exclusively found in a derived lineage of South American species. The ancestral haploid chromosome number was inferred to be n = 8. Chromosome numbers in Genlisea ranged from 2n = 2x = 16 to 2n = 4x = 32. Ascendant dysploid series (2n = 36, 38) are documented for three derived taxa. The different ploidy levels corresponded to the two subgenera, but were not directly correlated to differences in genome size; the three different karyotype ranges mirrored the different sections of the genus. The smallest known plant genomes were not found in G. margaretae, as previously reported, but in G. tuberosa (1C ≈ 61 Mbp) and some strains of G. aurea (1C ≈ 64 Mbp). CONCLUSIONS Genlisea is an ideal candidate model organism for the understanding of genome reduction as the genus includes species with both relatively large (∼1700 Mbp) and ultrasmall (∼61 Mbp) genomes. This comparative, phylogeny-based analysis of genome sizes and karyotypes in Genlisea provides essential data for selection of suitable species for comparative whole-genome analyses, as well as for further studies on both the molecular and cytogenetic basis of genome reduction in plants.
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Affiliation(s)
- Andreas Fleischmann
- Department of Biology, Systematic Botany and Mycology and Geo-Bio Center LMU, Ludwig-Maximilians-Universität München, Menzinger Strasse 67, D 80638 Munich, Germany
| | - Todd P Michael
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | | | - Aretuza Sousa
- Department of Biology, Systematic Botany and Mycology and Geo-Bio Center LMU, Ludwig-Maximilians-Universität München, Menzinger Strasse 67, D 80638 Munich, Germany
| | - Wenqin Wang
- Waksman Institute of Microbiology, Rutgers University, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA
| | - Eva M Temsch
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, A 1030 Vienna, Austria
| | - Johann Greilhuber
- Department of Botany and Biodiversity Research, Faculty of Life Sciences, University of Vienna, Rennweg 14, A 1030 Vienna, Austria
| | - Kai F Müller
- Institute for Evolution and Biodiversity, University of Muenster, Hüfferstrasse 1, D 48149 Münster, Germany
| | - Günther Heubl
- Department of Biology, Systematic Botany and Mycology and Geo-Bio Center LMU, Ludwig-Maximilians-Universität München, Menzinger Strasse 67, D 80638 Munich, Germany
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113
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Rapid diversification of five Oryza AA genomes associated with rice adaptation. Proc Natl Acad Sci U S A 2014; 111:E4954-62. [PMID: 25368197 DOI: 10.1073/pnas.1418307111] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Comparative genomic analyses among closely related species can greatly enhance our understanding of plant gene and genome evolution. We report de novo-assembled AA-genome sequences for Oryza nivara, Oryza glaberrima, Oryza barthii, Oryza glumaepatula, and Oryza meridionalis. Our analyses reveal massive levels of genomic structural variation, including segmental duplication and rapid gene family turnover, with particularly high instability in defense-related genes. We show, on a genomic scale, how lineage-specific expansion or contraction of gene families has led to their morphological and reproductive diversification, thus enlightening the evolutionary process of speciation and adaptation. Despite strong purifying selective pressures on most Oryza genes, we documented a large number of positively selected genes, especially those genes involved in flower development, reproduction, and resistance-related processes. These diversifying genes are expected to have played key roles in adaptations to their ecological niches in Asia, South America, Africa and Australia. Extensive variation in noncoding RNA gene numbers, function enrichment, and rates of sequence divergence might also help account for the different genetic adaptations of these rice species. Collectively, these resources provide new opportunities for evolutionary genomics, numerous insights into recent speciation, a valuable database of functional variation for crop improvement, and tools for efficient conservation of wild rice germplasm.
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114
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Lee SI, Kim NS. Transposable elements and genome size variations in plants. Genomics Inform 2014; 12:87-97. [PMID: 25317107 PMCID: PMC4196380 DOI: 10.5808/gi.2014.12.3.87] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Revised: 08/18/2014] [Accepted: 08/22/2014] [Indexed: 02/01/2023] Open
Abstract
Although the number of protein-coding genes is not highly variable between plant taxa, the DNA content in their genomes is highly variable, by as much as 2,056-fold from a 1C amount of 0.0648 pg to 132.5 pg. The mean 1C-value in plants is 2.4 pg, and genome size expansion/contraction is lineage-specific in plant taxonomy. Transposable element fractions in plant genomes are also variable, as low as ~3% in small genomes and as high as ~85% in large genomes, indicating that genome size is a linear function of transposable element content. Of the 2 classes of transposable elements, the dynamics of class 1 long terminal repeat (LTR) retrotransposons is a major contributor to the 1C value differences among plants. The activity of LTR retrotransposons is under the control of epigenetic suppressing mechanisms. Also, genome-purging mechanisms have been adopted to counter-balance the genome size amplification. With a wealth of information on whole-genome sequences in plant genomes, it was revealed that several genome-purging mechanisms have been employed, depending on plant taxa. Two genera, Lilium and Fritillaria, are known to have large genomes in angiosperms. There were twice times of concerted genome size evolutions in the family Liliaceae during the divergence of the current genera in Liliaceae. In addition to the LTR retrotransposons, non-LTR retrotransposons and satellite DNAs contributed to the huge genomes in the two genera by possible failure of genome counter-balancing mechanisms.
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Affiliation(s)
- Sung-Il Lee
- Department of Molecular Bioscience, Kangwon National University, Chuncheon 200-701, Korea
| | - Nam-Soo Kim
- Department of Molecular Bioscience, Kangwon National University, Chuncheon 200-701, Korea
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115
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Baker K, Bayer M, Cook N, Dreißig S, Dhillon T, Russell J, Hedley PE, Morris J, Ramsay L, Colas I, Waugh R, Steffenson B, Milne I, Stephen G, Marshall D, Flavell AJ. The low-recombining pericentromeric region of barley restricts gene diversity and evolution but not gene expression. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:981-92. [PMID: 24947331 PMCID: PMC4309411 DOI: 10.1111/tpj.12600] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 06/10/2014] [Accepted: 06/12/2014] [Indexed: 05/02/2023]
Abstract
The low-recombining pericentromeric region of the barley genome contains roughly a quarter of the genes of the species, embedded in low-recombining DNA that is rich in repeats and repressive chromatin signatures. We have investigated the effects of pericentromeric region residency upon the expression, diversity and evolution of these genes. We observe no significant difference in average transcript level or developmental RNA specificity between the barley pericentromeric region and the rest of the genome. In contrast, all of the evolutionary parameters studied here show evidence of compromised gene evolution in this region. First, genes within the pericentromeric region of wild barley show reduced diversity and significantly weakened purifying selection compared with the rest of the genome. Second, gene duplicates (ohnolog pairs) derived from the cereal whole-genome duplication event ca. 60MYa have been completely eliminated from the barley pericentromeric region. Third, local gene duplication in the pericentromeric region is reduced by 29% relative to the rest of the genome. Thus, the pericentromeric region of barley is a permissive environment for gene expression but has restricted gene evolution in a sizeable fraction of barley's genes.
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Affiliation(s)
- Katie Baker
- University of Dundee at JHI, InvergowrieDundee, DD2 5DA, UK
| | - Micha Bayer
- James Hutton Institute, InvergowrieDundee, DD2 5DA, UK
| | - Nicola Cook
- University of Dundee at JHI, InvergowrieDundee, DD2 5DA, UK
| | - Steven Dreißig
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg06120, Halle, Germany
| | - Taniya Dhillon
- University of Dundee at JHI, InvergowrieDundee, DD2 5DA, UK
| | | | - Pete E Hedley
- James Hutton Institute, InvergowrieDundee, DD2 5DA, UK
| | - Jenny Morris
- James Hutton Institute, InvergowrieDundee, DD2 5DA, UK
| | - Luke Ramsay
- James Hutton Institute, InvergowrieDundee, DD2 5DA, UK
| | | | - Robbie Waugh
- University of Dundee at JHI, InvergowrieDundee, DD2 5DA, UK
- James Hutton Institute, InvergowrieDundee, DD2 5DA, UK
| | - Brian Steffenson
- Department of Plant Pathology, University of MinnesotaSt. Paul, MN, 55108, USA
| | - Iain Milne
- James Hutton Institute, InvergowrieDundee, DD2 5DA, UK
| | | | | | - Andrew J Flavell
- University of Dundee at JHI, InvergowrieDundee, DD2 5DA, UK
- *For correspondence (e-mail )
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116
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Tae H, Karunasena E, Bavarva JH, McIver LJ, Garner HR. Large scale comparison of non-human sequences in human sequencing data. Genomics 2014; 104:453-8. [PMID: 25173571 DOI: 10.1016/j.ygeno.2014.08.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Revised: 08/17/2014] [Accepted: 08/19/2014] [Indexed: 11/19/2022]
Abstract
Several studies have demonstrated that unmapped reads in next generation sequencing data could be used to identify infectious agents or structural variants, but there has been no intensive effort to analyze and classify all non-human sequences found in individual large data sets. To identify commonality in non-human sequences by infectious agents and putative contamination events, we analyzed non-human sequences in 150 genomic sequencing data files from the 1000 Genomes Project and observed that 0.13% of reads on average showed similarities to non-human genomes. We compared results among different sample groups divided based on ethnicities, sequencing centers and enrichment methods (whole genome sequencing vs. exome sequencing) and found that sequencing centers had specific signatures of contaminating genomes as 'time stamps'. We also observed many unmapped reads that falsely indicated contamination because of the high similarity of human sequences to sequences in non-human genome assemblies such as mouse and Nicotiana.
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Affiliation(s)
- Hongseok Tae
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA
| | - Enusha Karunasena
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA
| | - Jasmin H Bavarva
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA
| | - Lauren J McIver
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA
| | - Harold R Garner
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA.
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117
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Wang M, Yu Y, Haberer G, Marri PR, Fan C, Goicoechea JL, Zuccolo A, Song X, Kudrna D, Ammiraju JSS, Cossu RM, Maldonado C, Chen J, Lee S, Sisneros N, de Baynast K, Golser W, Wissotski M, Kim W, Sanchez P, Ndjiondjop MN, Sanni K, Long M, Carney J, Panaud O, Wicker T, Machado CA, Chen M, Mayer KFX, Rounsley S, Wing RA. The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nat Genet 2014; 46:982-8. [PMID: 25064006 PMCID: PMC7036042 DOI: 10.1038/ng.3044] [Citation(s) in RCA: 282] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Accepted: 06/30/2014] [Indexed: 12/19/2022]
Abstract
Mingsheng Chen, Klaus Mayer, Steve Rounsley, Rod Wing and colleagues report the genome sequence of African rice (Oryza glaberrima), a different species than Asian rice. The authors resequenced 20 O. glaberrima accessions and 94 Oryza barthii accessions (the putative progenitor species of O. glaberrima), and their analyses support the hypothesis that O. glaberrima was domesticated in a single region along the upper Niger river. The cultivation of rice in Africa dates back more than 3,000 years. Interestingly, African rice is not of the same origin as Asian rice (Oryza sativa L.) but rather is an entirely different species (i.e., Oryza glaberrima Steud.). Here we present a high-quality assembly and annotation of the O. glaberrima genome and detailed analyses of its evolutionary history of domestication and selection. Population genomics analyses of 20 O. glaberrima and 94 Oryza barthii accessions support the hypothesis that O. glaberrima was domesticated in a single region along the Niger river as opposed to noncentric domestication events across Africa. We detected evidence for artificial selection at a genome-wide scale, as well as with a set of O. glaberrima genes orthologous to O. sativa genes that are known to be associated with domestication, thus indicating convergent yet independent selection of a common set of genes during two geographically and culturally distinct domestication processes.
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Affiliation(s)
- Muhua Wang
- 1] Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA. [2]
| | - Yeisoo Yu
- 1] Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA. [2]
| | - Georg Haberer
- 1] Plant Genome and Systems Biology, Helmholtz Center Munich, Neuherberg, Germany. [2]
| | | | - Chuanzhu Fan
- 1] Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA. [2] Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Jose Luis Goicoechea
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Andrea Zuccolo
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Xiang Song
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Dave Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Jetty S S Ammiraju
- 1] Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA. [2] DuPont Pioneer, Johnston, Iowa, USA
| | - Rosa Maria Cossu
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Carlos Maldonado
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Jinfeng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Seunghee Lee
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Nick Sisneros
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Kristi de Baynast
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Wolfgang Golser
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Marina Wissotski
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Woojin Kim
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Paul Sanchez
- 1] Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA. [2] US Arid Land Agricultural Research Center, Maricopa, Arizona, USA
| | | | | | - Manyuan Long
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA
| | - Judith Carney
- Department of Geography, Institute of the Environment and Sustainability, University of California, Los Angeles, California, USA
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes, UMR CNRS/Institut de Recherche pour le Développement/l'Université de Perpignan Via Domitia, Université de Perpignan, Perpignan, France
| | - Thomas Wicker
- Institute of Plant Biology, University of Zurich, Zurich, Switzerland
| | - Carlos A Machado
- Department of Biology, University of Maryland, College Park, Maryland, USA
| | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Center Munich, Neuherberg, Germany
| | | | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
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118
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Agren JÅ, Wang W, Koenig D, Neuffer B, Weigel D, Wright SI. Mating system shifts and transposable element evolution in the plant genus Capsella. BMC Genomics 2014; 15:602. [PMID: 25030755 PMCID: PMC4112209 DOI: 10.1186/1471-2164-15-602] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 07/10/2014] [Indexed: 11/11/2022] Open
Abstract
Background Despite having predominately deleterious fitness effects, transposable elements (TEs) are major constituents of eukaryote genomes in general and of plant genomes in particular. Although the proportion of the genome made up of TEs varies at least four-fold across plants, the relative importance of the evolutionary forces shaping variation in TE abundance and distributions across taxa remains unclear. Under several theoretical models, mating system plays an important role in governing the evolutionary dynamics of TEs. Here, we use the recently sequenced Capsella rubella reference genome and short-read whole genome sequencing of multiple individuals to quantify abundance, genome distributions, and population frequencies of TEs in three recently diverged species of differing mating system, two self-compatible species (C. rubella and C. orientalis) and their self-incompatible outcrossing relative, C. grandiflora. Results We detect different dynamics of TE evolution in our two self-compatible species; C. rubella shows a small increase in transposon copy number, while C. orientalis shows a substantial decrease relative to C. grandiflora. The direction of this change in copy number is genome wide and consistent across transposon classes. For insertions near genes, however, we detect the highest abundances in C. grandiflora. Finally, we also find differences in the population frequency distributions across the three species. Conclusion Overall, our results suggest that the evolution of selfing may have different effects on TE evolution on a short and on a long timescale. Moreover, cross-species comparisons of transposon abundance are sensitive to reference genome bias, and efforts to control for this bias are key when making comparisons across species. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-602) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- J Ågren Agren
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.
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119
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Zuo J, Li J. Molecular dissection of complex agronomic traits of rice: a team effort by Chinese scientists in recent years. Natl Sci Rev 2014. [DOI: 10.1093/nsr/nwt004] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Rice is a staple food for more than half of the worldwide population and is also a model species for biological studies on monocotyledons. Through a team effort, Chinese scientists have made rapid and important progresses in rice biology in recent years. Here, we briefly review these advances, emphasizing on the regulatory mechanisms of the complex agronomic traits that affect rice yield and grain quality. Progresses in rice genome biology and genome evolution have also been summarized.
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Affiliation(s)
- Jianru Zuo
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jiayang Li
- State Key Laboratory of Plant Genomics and National Plant Gene Research Center, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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120
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Jacquemin J, Ammiraju JSS, Haberer G, Billheimer DD, Yu Y, Liu LC, Rivera LF, Mayer K, Chen M, Wing RA. Fifteen million years of evolution in the Oryza genus shows extensive gene family expansion. MOLECULAR PLANT 2014; 7:642-56. [PMID: 24214894 DOI: 10.1093/mp/sst149] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
In analyzing gene families in the whole-genome sequences available for O. sativa (AA), O. glaberrima (AA), and O. brachyantha (FF), we observed large size expansions in the AA genomes compared to FF genomes for the super-families F-box and NB-ARC, and five additional families: the Aspartic proteases, BTB/POZ proteins (BTB), Glutaredoxins, Trypsin α-amylase inhibitor proteins, and Zf-Dof proteins. Their evolutionary dynamic was investigated to understand how and why such important size variations are observed between these closely related species. We show that expansions resulted from both amplification, largely by tandem duplications, and contraction by gene losses. For the F-box and NB-ARC gene families, the genes conserved in all species were under strong purifying selection while expanded orthologous genes were under more relaxed purifying selection. In F-box, NB-ARC, and BTB, the expanded groups were enriched in genes with little evidence of expression, in comparison with conserved groups. We also detected 87 loci under positive selection in the expanded groups. These results show that most of the duplicated copies in the expanded groups evolve neutrally after duplication because of functional redundancy but a fraction of these genes were preserved following neofunctionalization. Hence, the lineage-specific expansions observed between Oryza species were partly driven by directional selection.
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Affiliation(s)
- Julie Jacquemin
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
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121
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Michael TP. Plant genome size variation: bloating and purging DNA. Brief Funct Genomics 2014; 13:308-17. [DOI: 10.1093/bfgp/elu005] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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122
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Sui Y, Li B, Shi J, Chen M. Genomic, regulatory and epigenetic mechanisms underlying duplicated gene evolution in the natural allotetraploid Oryza minuta. BMC Genomics 2014; 15:11. [PMID: 24393121 PMCID: PMC3890553 DOI: 10.1186/1471-2164-15-11] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Accepted: 12/30/2013] [Indexed: 11/27/2022] Open
Abstract
Background Polyploid species contribute to Oryza diversity. However, the mechanisms underlying gene and genome evolution in Oryza polyploids remain largely unknown. The allotetraploid Oryza minuta, which is estimated to have formed less than one million years ago, along with its putative diploid progenitors (O. punctata and O. officinalis), are quite suitable for the study of polyploid genome evolution using a comparative genomics approach. Results Here, we performed a comparative study of a large genomic region surrounding the Shattering4 locus in O. minuta, as well as in O. punctata and O. officinalis. Duplicated genomes in O. minuta have maintained the diploid genome organization, except for several structural variations mediated by transposon movement. Tandem duplicated gene clusters are prevalent in the Sh4 region, and segmental duplication followed by random deletion is illustrated to explain the gene gain-and-loss process. Both copies of most duplicated genes still persist in O. minuta. Molecular evolution analysis suggested that these duplicated genes are equally evolved and mostly manipulated by purifying selection. However, cDNA-SSCP analysis revealed that the expression patterns were dramatically altered between duplicated genes: nine of 29 duplicated genes exhibited expression divergence in O. minuta. We further detected one gene silencing event that was attributed to gene structural variation, but most gene silencing could not be related to sequence changes. We identified one case in which DNA methylation differences within promoter regions that were associated with the insertion of one hAT element were probably responsible for gene silencing, suggesting a potential epigenetic gene silencing pathway triggered by TE movement. Conclusions Our study revealed both genetic and epigenetic mechanisms involved in duplicated gene silencing in the allotetraploid O. minuta.
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Affiliation(s)
| | | | | | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
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123
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Huang X, Han B. Natural variations and genome-wide association studies in crop plants. ANNUAL REVIEW OF PLANT BIOLOGY 2014; 65:531-51. [PMID: 24274033 DOI: 10.1146/annurev-arplant-050213-035715] [Citation(s) in RCA: 360] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Natural variants of crops are generated from wild progenitor plants under both natural and human selection. Diverse crops that are able to adapt to various environmental conditions are valuable resources for crop improvements to meet the food demands of the increasing human population. With the completion of reference genome sequences, the advent of high-throughput sequencing technology now enables rapid and accurate resequencing of a large number of crop genomes to detect the genetic basis of phenotypic variations in crops. Comprehensive maps of genome variations facilitate genome-wide association studies of complex traits and functional investigations of evolutionary changes in crops. These advances will greatly accelerate studies on crop designs via genomics-assisted breeding. Here, we first discuss crop genome studies and describe the development of sequencing-based genotyping and genome-wide association studies in crops. We then review sequencing-based crop domestication studies and offer a perspective on genomics-driven crop designs.
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Affiliation(s)
- Xuehui Huang
- National Center for Gene Research, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China; ,
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Bennetzen JL, Wang H. The contributions of transposable elements to the structure, function, and evolution of plant genomes. ANNUAL REVIEW OF PLANT BIOLOGY 2014; 65:505-30. [PMID: 24579996 DOI: 10.1146/annurev-arplant-050213-035811] [Citation(s) in RCA: 310] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Transposable elements (TEs) are the key players in generating genomic novelty by a combination of the chromosome rearrangements they cause and the genes that come under their regulatory sway. Genome size, gene content, gene order, centromere function, and numerous other aspects of nuclear biology are driven by TE activity. Although the origins and attitudes of TEs have the hallmarks of selfish DNA, there are numerous cases where TE components have been co-opted by the host to create new genes or modify gene regulation. In particular, epigenetic regulation has been transformed from a process to silence invading TEs and viruses into a key strategy for regulating plant genes. Most, perhaps all, of this epigenetic regulation is derived from TE insertions near genes or TE-encoded factors that act in trans. Enormous pools of genome data and new technologies for reverse genetics will lead to a powerful new era of TE analysis in plants.
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Affiliation(s)
- Jeffrey L Bennetzen
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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125
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Wambugu PW, Furtado A, Waters DLE, Nyamongo DO, Henry RJ. Conservation and utilization of African Oryza genetic resources. RICE (NEW YORK, N.Y.) 2013; 6:29. [PMID: 24280189 PMCID: PMC4883696 DOI: 10.1186/1939-8433-6-29] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 10/23/2013] [Indexed: 05/20/2023]
Abstract
Africa contains a huge diversity of both cultivated and wild rice species. The region has eight species representing six of the ten known genome types. Genetic resources of these species are conserved in various global germplasm repositories but they remain under collected and hence underrepresented in germplasm collections. Moreover, they are under characterized and therefore grossly underutilized. The lack of in situ conservation programs further exposes them to possible genetic erosion or extinction. In order to obtain maximum benefits from these resources, it is imperative that they are collected, efficiently conserved and optimally utilized. High throughput molecular approaches such as genome sequencing could be employed to more precisely study their genetic diversity and value and thereby enhance their use in rice improvement. Oryza sativa was the first crop plant to have its reference genome sequence released marking a major milestone that opened numerous opportunities for functional characterization of the entire rice genome. Studies have however demonstrated that one reference genome sequence is not enough to fully explore the genetic variation in the Oryza genus, hence the need to have reference sequences for other species in the genus. An overview of the state of conservation and utilization of African Oryza is hereby presented. Progress in the release of reference genome sequences for these species is also highlighted.
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Affiliation(s)
- Peterson W Wambugu
- />Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, St Lucia, Qld Australia
- />Kenya Agricultural Research Institute, Nairobi, Kenya
| | - Agnelo Furtado
- />Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, St Lucia, Qld Australia
| | - Daniel LE Waters
- />Southern Cross Plant Science, Southern Cross University, Lismore, NSW Australia
| | | | - Robert J Henry
- />Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, St Lucia, Qld Australia
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126
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Zhu T, Xu PZ, Liu JP, Peng S, Mo XC, Gao LZ. Phylogenetic relationships and genome divergence among the AA- genome species of the genus Oryza as revealed by 53 nuclear genes and 16 intergenic regions. Mol Phylogenet Evol 2013; 70:348-61. [PMID: 24148990 DOI: 10.1016/j.ympev.2013.10.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2012] [Revised: 08/17/2013] [Accepted: 10/09/2013] [Indexed: 12/17/2022]
Abstract
Rapid radiations have long been regarded as the most challenging issue for elucidating poorly resolved phylogenies in evolutionary biology. The eight diploid AA- genome species in the genus Oryza represent a typical example of a closely spaced series of recent speciation events in plants. However, questions regarding when and how they diversified have long been an issue of extensive interest but remain a mystery. Here, a data set comprising >60 kb of 53 singleton fragments and 16 intergenic regions is used to perform phylogenomic analyses of all eight AA- genome species plus four diploid Oryza species with BB-, CC-, EE- and GG- genomes. We fully reconstruct phylogenetic relationships of AA- genome species with confidence. Oryza meridionalis, native to Australia, is found to be the earliest divergent lineage around 2.93 mya, whereas O. punctata, a BB- genome species, serves as the best outgroup to distinguish their phylogenetic relationships. They separated from O. punctata approximately 9.11 mya during the Miocene epoch, and subsequently radiated to generate the entire AA- genome lineage diversity. The success in resolving the phylogeny of AA- genome species highlights the potential of phylogenomics to determine their divergence and evolutionary histories.
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Affiliation(s)
- Ting Zhu
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, The Chinese Academy of Sciences, Kunming 650204, China; University of the Chinese Academy of Sciences, Beijing 100039, China.
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Garg R, Verma M, Agrawal S, Shankar R, Majee M, Jain M. Deep transcriptome sequencing of wild halophyte rice, Porteresia coarctata, provides novel insights into the salinity and submergence tolerance factors. DNA Res 2013; 21:69-84. [PMID: 24104396 PMCID: PMC3925395 DOI: 10.1093/dnares/dst042] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Porteresia coarctata is a wild relative of rice with capability of high salinity and submergence tolerance. The transcriptome analyses of Porteresia can lead to the identification of candidate genes involved in salinity and submergence tolerance. We sequenced the transcriptome of Porteresia under different conditions using Illumina platform and generated about 375 million high-quality reads. After optimized assembly, a total of 152 367 unique transcript sequences with average length of 794 bp were obtained. Many of these sequences might represent fragmented transcripts. Functional annotation revealed the presence of genes involved in diverse cellular processes and 2749 transcription factor (TF)-encoding genes in Porteresia. The differential gene expression analyses identified a total of 15 158 genes involved in salinity and/or submergence response(s). The stress-responsive members of different TF families, including MYB, bHLH, AP2-EREBP, WRKY, bZIP and NAC, were identified. We also revealed key metabolic pathways, including amino acid biosynthesis, hormone biosynthesis, secondary metabolite biosynthesis, carbohydrate metabolism and cell wall structures, involved in stress tolerance in Porteresia. The transcriptome analyses of Porteresia are expected to highlight genes/pathways involved in salinity and submergence tolerance of this halophyte species. The data can serve as a resource for unravelling the underlying mechanism and devising strategies to engineer salinity and submergence tolerance in rice.
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Affiliation(s)
- Rohini Garg
- Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
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