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Christine TD, Clothilde C, Mathieu B, Laurence A, Valentin K, Cédric M, Wing Rod A, Yves V, Francois S. FrangiPANe, a tool for creating a panreference using left behind reads. NAR Genom Bioinform 2023; 5:lqad013. [PMID: 36814455 PMCID: PMC9940456 DOI: 10.1093/nargab/lqad013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 12/21/2022] [Accepted: 02/02/2023] [Indexed: 02/22/2023] Open
Abstract
We present here FrangiPANe, a pipeline developed to build panreference using short reads through a map-then-assemble strategy. Applying it to 248 African rice genomes using an improved CG14 reference genome, we identified an average of 8 Mb of new sequences and 5290 new contigs per individual. In total, 1.4 G of new sequences, consisting of 1 306 676 contigs, were assembled. We validated 97.7% of the contigs of the TOG5681 cultivar individual assembly from short reads on a newly long reads genome assembly of the same TOG5681 cultivar. FrangiPANe also allowed the anchoring of 31.5% of the new contigs within the CG14 reference genome, with a 92.5% accuracy at 2 kb span. We annotated in addition 3252 new genes absent from the reference. FrangiPANe was developed as a modular and interactive application to simplify the construction of a panreference using the map-then-assemble approach. It is available as a Docker image containing (i) a Jupyter notebook centralizing codes, documentation and interactive visualization of results, (ii) python scripts and (iii) all the software and libraries requested for each step of the analysis. We foreseen our approach will help leverage large-scale illumina dataset for pangenome studies in GWAS or detection of selection.
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Affiliation(s)
| | | | - Blaison Mathieu
- DIADE, Univ Montpellier, CIRAD, IRD, 911 Avenue Agropolis 34934, 34830 Montpellier Cedex 5, France
| | - Albar Laurence
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Klein Valentin
- DIADE, Univ Montpellier, CIRAD, IRD, 911 Avenue Agropolis 34934, 34830 Montpellier Cedex 5, France
| | - Mariac Cédric
- DIADE, Univ Montpellier, CIRAD, IRD, 911 Avenue Agropolis 34934, 34830 Montpellier Cedex 5, France
| | - A. Wing Rod
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
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2
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Li J, Shen J, Wang R, Chen Y, Zhang T, Wang H, Guo C, Qi J. The nearly complete assembly of the Cercis chinensis genome and Fabaceae phylogenomic studies provide insights into new gene evolution. PLANT COMMUNICATIONS 2023; 4:100422. [PMID: 35957520 PMCID: PMC9860166 DOI: 10.1016/j.xplc.2022.100422] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 08/02/2022] [Accepted: 08/05/2022] [Indexed: 05/27/2023]
Abstract
Fabaceae is a large family of angiosperms with high biodiversity that contains a variety of economically important crops and model plants for the study of biological nitrogen fixation. Polyploidization events have been extensively studied in some Fabaceae plants, but the occurrence of new genes is still concealed, owing to a lack of genomic information on certain species of the basal clade of Fabaceae. Cercis chinensis (Cercidoideae) is one such species; it diverged earliest from Fabaceae and is essential for phylogenomic studies and new gene predictions in Fabaceae. To facilitate genomic studies on Fabaceae, we performed genome sequencing of C. chinensis and obtained a 352.84 Mb genome, which was further assembled into seven pseudochromosomes with 30 612 predicted protein-coding genes. Compared with other legume genomes, that of C. chinensis exhibits no lineage-specific polyploidization event. Further phylogenomic analyses of 22 legumes and 11 other angiosperms revealed that many gene families are lineage specific before and after the diversification of Fabaceae. Among them, dozens of genes are candidates for new genes that have evolved from intergenic regions and are thus regarded as de novo-originated genes. They differ significantly from established genes in coding sequence length, exon number, guanine-cytosine content, and expression patterns among tissues. Functional analysis revealed that many new genes are related to asparagine metabolism. This study represents an important advance in understanding the evolutionary pattern of new genes in legumes and provides a valuable resource for plant phylogenomic studies.
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Affiliation(s)
- Jinglong Li
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Jingting Shen
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Rui Wang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Yamao Chen
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Taikui Zhang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Haifeng Wang
- College of Agriculture, Guangxi University, Nanning 530004, China
| | - Chunce Guo
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University, Nanchang 330045, China
| | - Ji Qi
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China.
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3
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Ahmad M. Genomics and transcriptomics to protect rice ( Oryza sativa. L.) from abiotic stressors: -pathways to achieving zero hunger. FRONTIERS IN PLANT SCIENCE 2022; 13:1002596. [PMID: 36340401 PMCID: PMC9630331 DOI: 10.3389/fpls.2022.1002596] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
More over half of the world's population depends on rice as a major food crop. Rice (Oryza sativa L.) is vulnerable to abiotic challenges including drought, cold, and salinity since it grown in semi-aquatic, tropical, or subtropical settings. Abiotic stress resistance has bred into rice plants since the earliest rice cultivation techniques. Prior to the discovery of the genome, abiotic stress-related genes were identified using forward genetic methods, and abiotic stress-tolerant lines have developed using traditional breeding methods. Dynamic transcriptome expression represents the degree of gene expression in a specific cell, tissue, or organ of an individual organism at a specific point in its growth and development. Transcriptomics can reveal the expression at the entire genome level during stressful conditions from the entire transcriptional level, which can be helpful in understanding the intricate regulatory network relating to the stress tolerance and adaptability of plants. Rice (Oryza sativa L.) gene families found comparatively using the reference genome sequences of other plant species, allowing for genome-wide identification. Transcriptomics via gene expression profiling which have recently dominated by RNA-seq complements genomic techniques. The identification of numerous important qtl,s genes, promoter elements, transcription factors and miRNAs involved in rice response to abiotic stress was made possible by all of these genomic and transcriptomic techniques. The use of several genomes and transcriptome methodologies to comprehend rice (Oryza sativa, L.) ability to withstand abiotic stress have been discussed in this review.
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Affiliation(s)
- Mushtaq Ahmad
- Visiting Scientist Plant Sciences, University of Nebraska, Lincoln, NE, United States
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4
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Riehl K, Riccio C, Miska EA, Hemberg M. TransposonUltimate: software for transposon classification, annotation and detection. Nucleic Acids Res 2022; 50:e64. [PMID: 35234904 PMCID: PMC9226531 DOI: 10.1093/nar/gkac136] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 02/09/2022] [Accepted: 02/14/2022] [Indexed: 12/17/2022] Open
Abstract
Most genomes harbor a large number of transposons, and they play an important role in evolution and gene regulation. They are also of interest to clinicians as they are involved in several diseases, including cancer and neurodegeneration. Although several methods for transposon identification are available, they are often highly specialised towards specific tasks or classes of transposons, and they lack common standards such as a unified taxonomy scheme and output file format. We present TransposonUltimate, a powerful bundle of three modules for transposon classification, annotation, and detection of transposition events. TransposonUltimate comes as a Conda package under the GPL-3.0 licence, is well documented and it is easy to install through https://github.com/DerKevinRiehl/TransposonUltimate. We benchmark the classification module on the large TransposonDB covering 891,051 sequences to demonstrate that it outperforms the currently best existing solutions. The annotation and detection modules combine sixteen existing softwares, and we illustrate its use by annotating Caenorhabditis elegans, Rhizophagus irregularis and Oryza sativa subs. japonica genomes. Finally, we use the detection module to discover 29 554 transposition events in the genomes of 20 wild type strains of C. elegans. Databases, assemblies, annotations and further findings can be downloaded from (https://doi.org/10.5281/zenodo.5518085).
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Affiliation(s)
- Kevin Riehl
- Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Cristian Riccio
- Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Eric A Miska
- Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Martin Hemberg
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
- Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women’s Hospital, 75 Francis Street, Boston, MA 02215, USA
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5
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Meijer A, De Meyer T, Vandepoele K, Kyndt T. Spatiotemporal expression profile of novel and known small RNAs throughout rice plant development focussing on seed tissues. BMC Genomics 2022; 23:44. [PMID: 35012466 PMCID: PMC8750796 DOI: 10.1186/s12864-021-08264-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/13/2021] [Indexed: 02/10/2023] Open
Abstract
Background Small RNAs (sRNAs) regulate numerous plant processes directly related to yield, such as disease resistance and plant growth. To exploit this yield-regulating potential of sRNAs, the sRNA profile of one of the world’s most important staple crops – rice – was investigated throughout plant development using next-generation sequencing. Results Root and leaves were investigated at both the vegetative and generative phase, and early-life sRNA expression was characterized in the embryo and endosperm. This led to the identification of 49,505 novel sRNAs and 5581 tRNA-derived sRNAs (tsRNAs). In all tissues, 24 nt small interfering RNAs (siRNAs) were highly expressed and associated with euchromatic, but not heterochromatic transposable elements. Twenty-one nt siRNAs deriving from genic regions in the endosperm were exceptionally highly expressed, mimicking previously reported expression levels of 24 nt siRNAs in younger endosperm samples. In rice embryos, sRNA content was highly diverse while tsRNAs were underrepresented, possibly due to snoRNA activity. Publicly available mRNA expression and DNA methylation profiles were used to identify putative siRNA targets in embryo and endosperm. These include multiple genes related to the plant hormones gibberellic acid and ethylene, and to seed phytoalexin and iron content. Conclusions This work introduces multiple sRNAs as potential regulators of rice yield and quality, identifying them as possible targets for the continuous search to optimize rice production. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08264-z.
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Affiliation(s)
- Anikó Meijer
- Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Tim De Meyer
- Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. .,VIB Center for Plant Systems Biology, Ghent, Belgium. .,Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium.
| | - Tina Kyndt
- Department of Biotechnology, Ghent University, Ghent, Belgium.
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6
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Dai SF, Zhu XG, Hutang GR, Li JY, Tian JQ, Jiang XH, Zhang D, Gao LZ. Genome Size Variation and Evolution Driven by Transposable Elements in the Genus Oryza. FRONTIERS IN PLANT SCIENCE 2022; 13:921937. [PMID: 35874017 PMCID: PMC9301470 DOI: 10.3389/fpls.2022.921937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 05/16/2022] [Indexed: 05/08/2023]
Abstract
Genome size variation and evolutionary forces behind have been long pursued in flowering plants. The genus Oryza, consisting of approximately 25 wild species and two cultivated rice, harbors eleven extant genome types, six of which are diploid (AA, BB, CC, EE, FF, and GG) and five of which are tetraploid (BBCC, CCDD, HHJJ, HHKK, and KKLL). To obtain the most comprehensive knowledge of genome size variation in the genus Oryza, we performed flow cytometry experiments and estimated genome sizes of 166 accessions belonging to 16 non-AA genome Oryza species. k-mer analyses were followed to verify the experimental results of the two accessions for each species. Our results showed that genome sizes largely varied fourfold in the genus Oryza, ranging from 279 Mb in Oryza brachyantha (FF) to 1,203 Mb in Oryza ridleyi (HHJJ). There was a 2-fold variation (ranging from 570 to 1,203 Mb) in genome size among the tetraploid species, while the diploid species had 3-fold variation, ranging from 279 Mb in Oryza brachyantha (FF) to 905 Mb in Oryza australiensis (EE). The genome sizes of the tetraploid species were not always two times larger than those of the diploid species, and some diploid species even had larger genome sizes than those of tetraploids. Nevertheless, we found that genome sizes of newly formed allotetraploids (BBCC-) were almost equal to totaling genome sizes of their parental progenitors. Our results showed that the species belonging to the same genome types had similar genome sizes, while genome sizes exhibited a gradually decreased trend during the evolutionary process in the clade with AA, BB, CC, and EE genome types. Comparative genomic analyses further showed that the species with different rice genome types may had experienced dissimilar amplification histories of retrotransposons, resulting in remarkably different genome sizes. On the other hand, the closely related rice species may have experienced similar amplification history. We observed that the contents of transposable elements, long terminal repeats (LTR) retrotransposons, and particularly LTR/Gypsy retrotransposons varied largely but were significantly correlated with genome sizes. Therefore, this study demonstrated that LTR retrotransposons act as an active driver of genome size variation in the genus Oryza.
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Affiliation(s)
- Shuang-feng Dai
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
| | - Xun-ge Zhu
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Ge-rang Hutang
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jia-yue Li
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
| | - Jia-qi Tian
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
| | - Xian-hui Jiang
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
| | - Dan Zhang
- College of Tropical Crops, Hainan University, Haikou, China
| | - Li-zhi Gao
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
- Plant Germplasm and Genomics Center, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- College of Tropical Crops, Hainan University, Haikou, China
- *Correspondence: Li-zhi Gao,
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7
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Li K, Jiang W, Hui Y, Kong M, Feng LY, Gao LZ, Li P, Lu S. Gapless indica rice genome reveals synergistic contributions of active transposable elements and segmental duplications to rice genome evolution. MOLECULAR PLANT 2021; 14:1745-1756. [PMID: 34171481 DOI: 10.1016/j.molp.2021.06.017] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/18/2021] [Accepted: 06/22/2021] [Indexed: 05/04/2023]
Abstract
The ultimate goal of genome assembly is a high-accuracy gapless genome. Here, we report a new assembly pipeline that is used to produce a gapless genome for the indica rice cultivar Minghui 63. The resulting 397.71-Mb final assembly is composed of 12 contigs with a contig N50 size of 31.93 Mb. Each chromosome is represented by a single contig and the genomic sequences of all chromosomes are gapless. Quality evaluation of this gapless genome assembly showed that gene regions in our assembly have the highest completeness compared with the other 15 reported high-quality rice genomes. Further comparison with the japonica rice genome revealed that the gapless indica genome assembly contains more transposable elements (TEs) and segmental duplications (SDs), the latter of which produce many duplicated genes that can affect agronomic traits through dose effect or sub-/neo-functionalization. The insertion of TEs can also affect the expression of duplicated genes, which may drive the evolution of these genes. Furthermore, we found the expansion of nucleotide-binding site with leucine-rich repeat disease-resistance genes and cis-zeatin-O-glucosyltransferase growth-related genes in SDs in the gapless indica genome assembly, suggesting that SDs contribute to the adaptive evolution of rice disease resistance and developmental processes. Collectively, our findings suggest that active TEs and SDs synergistically contribute to rice genome evolution.
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Affiliation(s)
- Kui Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Wenkai Jiang
- Novogene Bioinformatics Institute, Building 301, Zone A10 Jiuxianqiao North Road, Chaoyang District, Beijing 100083, China
| | - Yuanyuan Hui
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Mengjuan Kong
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Li-Ying Feng
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China
| | - Li-Zhi Gao
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China.
| | - Pengfu Li
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China.
| | - Shan Lu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China; Shenzhen Research Institute of Nanjing University, Shenzhen 518000, China.
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8
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Martin GT, Seymour DK, Gaut BS. CHH Methylation Islands: A Nonconserved Feature of Grass Genomes That Is Positively Associated with Transposable Elements but Negatively Associated with Gene-Body Methylation. Genome Biol Evol 2021; 13:evab144. [PMID: 34146109 PMCID: PMC8374106 DOI: 10.1093/gbe/evab144] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2021] [Indexed: 12/28/2022] Open
Abstract
Methylated CHH (mCHH) islands are peaks of CHH methylation that occur primarily upstream to genes. These regions are actively targeted by the methylation machinery, occur at boundaries between heterochromatin and euchromatin, and tend to be near highly expressed genes. Here we took an evolutionary perspective by studying upstream mCHH islands across a sample of eight grass species. Using a statistical approach to define mCHH islands as regions that differ from genome-wide background CHH methylation levels, we demonstrated that mCHH islands are common and associate with 39% of genes, on average. We hypothesized that islands should be more frequent in genomes of large size, because they have more heterochromatin and hence more need for defined boundaries. We found, however, that smaller genomes tended to have a higher proportion of genes associated with 5' mCHH islands. Consistent with previous work suggesting that islands reflect the silencing of the edge of transposable elements (TEs), genes with nearby TEs were more likely to have mCHH islands. However, the presence of mCHH islands was not a function solely of TEs, both because the underlying sequences of islands were often not homologous to TEs and because genic properties also predicted the presence of 5' mCHH islands. These genic properties included length and gene-body methylation (gbM); in fact, in three of eight species, the absence of gbM was a stronger predictor of a 5' mCHH island than TE proximity. In contrast, gene expression level was a positive but weak predictor of the presence of an island. Finally, we assessed whether mCHH islands were evolutionarily conserved by focusing on a set of 2,720 orthologs across the eight species. They were generally not conserved across evolutionary time. Overall, our data establish additional genic properties that are associated with mCHH islands and suggest that they are not just a consequence of the TE silencing machinery.
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Affiliation(s)
- Galen T Martin
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
| | - Danelle K Seymour
- Department of Botany and Plant Sciences, University of California, Riverside, California, USA
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, California, USA
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9
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Verstraeten B, Atighi MR, Ruiz-Ferrer V, Escobar C, De Meyer T, Kyndt T. Non-coding RNAs in the interaction between rice and Meloidogyne graminicola. BMC Genomics 2021; 22:560. [PMID: 34284724 PMCID: PMC8293575 DOI: 10.1186/s12864-021-07735-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/17/2021] [Indexed: 12/12/2022] Open
Abstract
Background Root knot nematodes (RKN) are plant parasitic nematodes causing major yield losses of widely consumed food crops such as rice (Oryza sativa). Because non-coding RNAs, including small interfering RNAs (siRNA), microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), are key regulators of various plant processes, elucidating their regulation during this interaction may lead to new strategies to improve crop protection. In this study, we aimed to identify and characterize rice siRNAs, miRNAs and lncRNAs responsive to early infection with RKN Meloidogyne graminicola (Mg), based on sequencing of small RNA, degradome and total RNA libraries from rice gall tissues compared with uninfected root tissues. Results We found 425 lncRNAs, 3739 siRNAs and 16 miRNAs to be differentially expressed between both tissues, of which a subset was independently validated with RT-qPCR. Functional prediction of the lncRNAs indicates that a large part of their potential target genes code for serine/threonine protein kinases and transcription factors. Differentially expressed siRNAs have a predominant size of 24 nts, suggesting a role in DNA methylation. Differentially expressed miRNAs are generally downregulated and target transcription factors, which show reduced degradation according to the degradome data. Conclusions To our knowledge, this work is the first to focus on small and long non-coding RNAs in the interaction between rice and Mg, and provides an overview of rice non-coding RNAs with the potential to be used as a resource for the development of new crop protection strategies. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07735-7.
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Affiliation(s)
| | | | - Virginia Ruiz-Ferrer
- Department of Environmental Science, University of Castilla-La Mancha, Toledo, Spain
| | - Carolina Escobar
- Department of Environmental Science, University of Castilla-La Mancha, Toledo, Spain
| | - Tim De Meyer
- Department of Data Analysis & Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Tina Kyndt
- Department of Biotechnology, Ghent University, Ghent, Belgium.
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10
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Shenton M, Kobayashi M, Terashima S, Ohyanagi H, Copetti D, Hernández-Hernández T, Zhang J, Ohmido N, Fujita M, Toyoda A, Ikawa H, Fujiyama A, Furuumi H, Miyabayashi T, Kubo T, Kudrna D, Wing R, Yano K, Nonomura KI, Sato Y, Kurata N. Evolution and Diversity of the Wild Rice Oryza officinalis Complex, across Continents, Genome Types, and Ploidy Levels. Genome Biol Evol 2021; 12:413-428. [PMID: 32125373 PMCID: PMC7531200 DOI: 10.1093/gbe/evaa037] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2020] [Indexed: 12/15/2022] Open
Abstract
The Oryza officinalis complex is the largest species group in
Oryza, with more than nine species from four continents, and is a
tertiary gene pool that can be exploited in breeding programs for the improvement of
cultivated rice. Most diploid and tetraploid members of this group have a C genome. Using
a new reference C genome for the diploid species O. officinalis, and
draft genomes for two other C genome diploid species Oryza eichingeri and
Oryza rhizomatis, we examine the influence of transposable elements on
genome structure and provide a detailed phylogeny and evolutionary history of the
Oryza C genomes. The O. officinalis genome is 1.6
times larger than the A genome of cultivated Oryza sativa, mostly due to
proliferation of Gypsy type long-terminal repeat transposable elements,
but overall syntenic relationships are maintained with other Oryza
genomes (A, B, and F). Draft genome assemblies of the two other C genome diploid species,
Oryza eichingeri and Oryza rhizomatis, and short-read
resequencing of a series of other C genome species and accessions reveal that after the
divergence of the C genome progenitor, there was still a substantial degree of variation
within the C genome species through proliferation and loss of both DNA and long-terminal
repeat transposable elements. We provide a detailed phylogeny and evolutionary history of
the Oryza C genomes and a genomic resource for the exploitation of the
Oryza tertiary gene pool.
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Affiliation(s)
| | | | | | - Hajime Ohyanagi
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Dario Copetti
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona.,T.T. Chang Genetic Resources Center, International Rice Research Institute, Los Baños, Philippines
| | | | - Jianwei Zhang
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona
| | - Nobuko Ohmido
- Division of the Living Environment, Kobe University, Japan
| | | | | | | | | | | | | | - Takahiko Kubo
- National Institute of Genetics, Mishima, Japan.,Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - David Kudrna
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona
| | - Rod Wing
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona.,T.T. Chang Genetic Resources Center, International Rice Research Institute, Los Baños, Philippines.,Biological and Environment Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - Kentaro Yano
- School of Agriculture, Meiji University, Tokyo, Japan
| | | | - Yutaka Sato
- National Institute of Genetics, Mishima, Japan
| | - Nori Kurata
- National Institute of Genetics, Mishima, Japan
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11
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Khong GN, Le NT, Pham MT, Adam H, Gauron C, Le HQ, Pham DT, Colonges K, Pham XH, Do VN, Lebrun M, Jouannic S. A cluster of Ankyrin and Ankyrin-TPR repeat genes is associated with panicle branching diversity in rice. PLoS Genet 2021; 17:e1009594. [PMID: 34097698 PMCID: PMC8211194 DOI: 10.1371/journal.pgen.1009594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/17/2021] [Accepted: 05/10/2021] [Indexed: 12/13/2022] Open
Abstract
The number of grains per panicle is an important yield-related trait in cereals which depends in part on panicle branching complexity. One component of this complexity is the number of secondary branches per panicle. Previously, a GWAS site associated with secondary branch and spikelet numbers per panicle in rice was identified. Here we combined gene capture, bi-parental genetic population analysis, expression profiling and transgenic approaches in order to investigate the functional significance of a cluster of 6 ANK and ANK-TPR genes within the QTL. Four of the ANK and ANK-TPR genes present a differential expression associated with panicle secondary branch number in contrasted accessions. These differential expression patterns correlate in the different alleles of these genes with specific deletions of potential cis-regulatory sequences in their promoters. Two of these genes were confirmed through functional analysis as playing a role in the control of panicle architecture. Our findings indicate that secondary branching diversity in the rice panicle is governed in part by differentially expressed genes within this cluster encoding ANK and ANK-TPR domain proteins that may act as positive or negative regulators of panicle meristem’s identity transition from indeterminate to determinate state. Grain yield is one of the most important indexes in rice breeding, which is controlled in part by panicle branching complexity. A new QTL with co-location of spikelet number (SpN) and secondary branch number (SBN) traits was identified by genome-wide association study in a Vietnamese rice landrace panel. A set of four Ankyrin and Tetratricopeptide repeat domain-encoding genes was identified from this QTL based on their difference of expression levels between two contrasted haplotypes for the SpN and SBN traits. The differential expression is correlated with deletions in the promoter regions of these genes. Two of the genes act as negative regulators of the panicle meristem’s identity transition from indeterminate to determinate state while the other two act as positive regulators of this meristem fate transition. Based on the different phenotypes between overexpressed and mutant plants, two of these genes were confirmed as playing a role in the control of panicle architecture. These findings can be directly used to assist selection for grain yield improvement.
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Affiliation(s)
- Giang Ngan Khong
- LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
- * E-mail: (GNK); (SJ)
| | - Nhu Thi Le
- LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | - Mai Thi Pham
- LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | - Helene Adam
- UMR DIADE, University of Montpellier, IRD, Montpellier, France
| | - Carole Gauron
- UMR DIADE, University of Montpellier, IRD, Montpellier, France
| | - Hoa Quang Le
- School of Biotechnology and Food Technology, Hanoi University of Science and Technology, Hanoi, Vietnam
| | - Dung Tien Pham
- School of Biotechnology and Food Technology, Hanoi University of Science and Technology, Hanoi, Vietnam
| | - Kelly Colonges
- LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | - Xuan Hoi Pham
- LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | - Vinh Nang Do
- LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
| | - Michel Lebrun
- LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
- UMR LSTM, University of Montpellier, IRD, CIRAD, INRAE, SupAgro, Montpellier, France
| | - Stefan Jouannic
- LMI RICE, National Key Laboratory for Plant Cell Biotechnology, Agronomical Genetics Institute, Hanoi, Vietnam
- UMR DIADE, University of Montpellier, IRD, Montpellier, France
- * E-mail: (GNK); (SJ)
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12
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Wang C, Chen S, Feng A, Su J, Wang W, Feng J, Chen B, Zhang M, Yang J, Zeng L, Zhu X. Xa7, a Small Orphan Gene Harboring Promoter Trap for AvrXa7, Leads to the Durable Resistance to Xanthomonas oryzae Pv. oryzae. RICE (NEW YORK, N.Y.) 2021; 14:48. [PMID: 34056673 PMCID: PMC8165051 DOI: 10.1186/s12284-021-00490-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 05/10/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND The rice (Oryza sativa) gene Xa7 has been hypothesized to be a typical executor resistance gene against Xanthomonas oryzae pv. oryzae (Xoo), and has conferred durable resistance in the field for decades. Its identity and the molecular mechanisms underlying this resistance remain elusive. RESULTS Here, we filled in gaps of genome in Xa7 mapping locus via BAC library construction, revealing the presence of a 100-kb non-collinear sequence in the line IRBB7 compared with Nipponbare reference genomes. Complementary transformation with sequentially overlapping subclones of the BACs demonstrated that Xa7 is an orphan gene, encoding a small novel protein distinct from any other resistance proteins reported. A 27-bp effector binding element (EBE) in the Xa7 promoter is essential for AvrXa7-inducing expression model. XA7 is anchored in the endoplasmic reticulum membrane and triggers programmed cell death in rice and tobacco (Nicotiana benthamiana). The Xa7 gene is absent in most cultivars, landraces, and wild rice accessions, but highly homologs of XA7 were identified in Leersia perrieri, the nearest outgroup of the genus Oryza. CONCLUSIONS Xa7 acts as a trap to perceive AvrXa7 via EBEAvrXa7 in its promoter, leading to the initiation of resistant reaction. Since EBEAvrXa7 is ubiquitous in promoter of rice susceptible gene SWEET14, the elevated expression of which is conducive to the proliferation of Xoo, that lends a great benefit for the Xoo strains retaining AvrXa7. As a result, varieties harboring Xa7 would show more durable resistance in the field. Xa7 alleles analysis suggests that the discovery of new resistance genes could be extended beyond wild rice, to include wild grasses such as Leersia species.
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Affiliation(s)
- Congying Wang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Shen Chen
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Aiqing Feng
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jing Su
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Wenjuan Wang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jinqi Feng
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Bing Chen
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Meiying Zhang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jianyuan Yang
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Liexian Zeng
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Xiaoyuan Zhu
- Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
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13
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de Freitas KEJ, dos Santos RS, Busanello C, de Carvalho Victoria F, Lopes JL, Wing RA, de Oliveira AC. Starch Synthesis-Related Genes (SSRG) Evolution in the Genus Oryza. PLANTS 2021; 10:plants10061057. [PMID: 34070565 PMCID: PMC8229393 DOI: 10.3390/plants10061057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/14/2021] [Accepted: 04/14/2021] [Indexed: 11/18/2022]
Abstract
Cooking quality is an important attribute in Common/Asian rice (Oryzasativa L.) varieties, being highly dependent on grain starch composition. This composition is known to be highly dependent on a cultivar’s genetics, but the way in which their genes express different phenotypes is not well understood. Further analysis of variation of grain quality genes using new information obtained from the wild relatives of rice should provide important insights into the evolution and potential use of these genetic resources. All analyses were conducted using bioinformatics approaches. The analysis of the protein sequences of grain quality genes across the Oryza suggest that the deletion/mutation of amino acids in active sites result in variations that can negatively affect specific steps of starch biosynthesis in the endosperm. On the other hand, the complete deletion of some genes in the wild species may not affect the amylose content. Here we present new insights for Starch Synthesis-Related Genes (SSRGs) evolution from starch-specific rice phenotypes.
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Affiliation(s)
- Karine E. Janner de Freitas
- Centro de desenvolvimento Tecnológico—CDTec, Graduate Program in biotechnology, Capão do Leão Campus, Federal de Pelotas, Pelotas 96160, Brazil; (K.E.J.d.F.); (C.B.); (J.L.L.)
| | | | - Carlos Busanello
- Centro de desenvolvimento Tecnológico—CDTec, Graduate Program in biotechnology, Capão do Leão Campus, Federal de Pelotas, Pelotas 96160, Brazil; (K.E.J.d.F.); (C.B.); (J.L.L.)
| | - Filipe de Carvalho Victoria
- Núcleo de Estudos da Vegetação Antártica—NEVA, Campus São Gabriel Federal do Pampa (UNIPAMPA), São Gabriel 97030, Brazil;
| | - Jennifer Luz Lopes
- Centro de desenvolvimento Tecnológico—CDTec, Graduate Program in biotechnology, Capão do Leão Campus, Federal de Pelotas, Pelotas 96160, Brazil; (K.E.J.d.F.); (C.B.); (J.L.L.)
| | - Rod A. Wing
- The School of Plant Sciences, Ecology & Evolutionary Biology, Arizona Genomics Institute, Tucson, AZ 97030, USA;
- Center for Desert Agriculture, King Abdullah University of Science & Technology, Thuwal 23955, Saudi Arabia
| | - Antonio Costa de Oliveira
- Centro de desenvolvimento Tecnológico—CDTec, Graduate Program in biotechnology, Capão do Leão Campus, Federal de Pelotas, Pelotas 96160, Brazil; (K.E.J.d.F.); (C.B.); (J.L.L.)
- Correspondence:
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14
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Luo D, Huguet-Tapia JC, Raborn RT, White FF, Brendel VP, Yang B. The Xa7 resistance gene guards the rice susceptibility gene SWEET14 against exploitation by the bacterial blight pathogen. PLANT COMMUNICATIONS 2021; 2:100164. [PMID: 34027391 PMCID: PMC8132128 DOI: 10.1016/j.xplc.2021.100164] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 05/03/2023]
Abstract
Many plant disease resistance (R) genes function specifically in reaction to the presence of cognate effectors from a pathogen. Xanthomonas oryzae pathovar oryzae (Xoo) uses transcription activator-like effectors (TALes) to target specific rice genes for expression, thereby promoting host susceptibility to bacterial blight. Here, we report the molecular characterization of Xa7, the cognate R gene to the TALes AvrXa7 and PthXo3, which target the rice major susceptibility gene SWEET14. Xa7 was mapped to a unique 74-kb region. Gene expression analysis of the region revealed a candidate gene that contained a putative AvrXa7 effector binding element (EBE) in its promoter and encoded a 113-amino-acid peptide of unknown function. Genome editing at the Xa7 locus rendered the plants susceptible to avrXa7-carrying Xoo strains. Both AvrXa7 and PthXo3 activated a GUS reporter gene fused with the EBE-containing Xa7 promoter in Nicotiana benthamiana. The EBE of Xa7 is a close mimic of the EBE of SWEET14 for TALe-induced disease susceptibility. Ectopic expression of Xa7 triggers cell death in N. benthamiana. Xa7 is prevalent in indica rice accessions from 3000 rice genomes. Xa7 appears to be an adaptation that protects against pathogen exploitation of SWEET14 and disease susceptibility.
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Affiliation(s)
- Dangping Luo
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Jose C. Huguet-Tapia
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - R. Taylor Raborn
- Department of Biology, Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
- Current address: Biodesign Institute Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85281, USA
| | - Frank F. White
- Department of Plant Pathology, University of Florida, Gainesville, FL 32611, USA
| | - Volker P. Brendel
- Department of Biology, Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
| | - Bing Yang
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
- Corresponding author
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15
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Vaughn JN, Korani W, Stein JC, Edwards JD, Peterson DG, Simpson SA, Youngblood RC, Grimwood J, Chougule K, Ware DH, McClung AM, Scheffler BE. Gene disruption by structural mutations drives selection in US rice breeding over the last century. PLoS Genet 2021; 17:e1009389. [PMID: 33735256 PMCID: PMC7971508 DOI: 10.1371/journal.pgen.1009389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 01/28/2021] [Indexed: 12/30/2022] Open
Abstract
The genetic basis of general plant vigor is of major interest to food producers, yet the trait is recalcitrant to genetic mapping because of the number of loci involved, their small effects, and linkage. Observations of heterosis in many crops suggests that recessive, malfunctioning versions of genes are a major cause of poor performance, yet we have little information on the mutational spectrum underlying these disruptions. To address this question, we generated a long-read assembly of a tropical japonica rice (Oryza sativa) variety, Carolina Gold, which allowed us to identify structural mutations (>50 bp) and orient them with respect to their ancestral state using the outgroup, Oryza glaberrima. Supporting prior work, we find substantial genome expansion in the sativa branch. While transposable elements (TEs) account for the largest share of size variation, the majority of events are not directly TE-mediated. Tandem duplications are the most common source of insertions and are highly enriched among 50-200bp mutations. To explore the relative impact of various mutational classes on crop fitness, we then track these structural events over the last century of US rice improvement using 101 resequenced varieties. Within this material, a pattern of temporary hybridization between medium and long-grain varieties was followed by recent divergence. During this long-term selection, structural mutations that impact gene exons have been removed at a greater rate than intronic indels and single-nucleotide mutations. These results support the use of ab initio estimates of mutational burden, based on structural data, as an orthogonal predictor in genomic selection. Some crop varieties have superior performance across years and environments. In hybrids, harmful mutations in one parent are masked by the ancestral alleles in the other parent, resulting in increased vigor. Unfortunately, these mutations are very difficult to identify precisely because, individually, they only have a small effect. In this study, we use long-read sequencing to characterize the entire mutational spectrum between two rice varieties. We then track these mutations through the last century of rice breeding. We show that large structural mutations in exons are selected against at a greater rate than any other mutational class. These findings illuminate the nature of deleterious alleles and will guide attempts to predict variety vigor based solely on genomic information.
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Affiliation(s)
- Justin N. Vaughn
- USDA-ARS, Genomics and Bioinformatics Research Unit, Stoneville, Mississippi, United States of America
- University of Georgia, Athens, Institute of Plant Breeding, Genetics, and Genomics, Athens, Georgia, United States of America
- * E-mail: (JNV); (BES)
| | - Walid Korani
- University of Georgia, Athens, Institute of Plant Breeding, Genetics, and Genomics, Athens, Georgia, United States of America
| | - Joshua C. Stein
- Cold Spring Harbor Laboratory, Cold Springs Harbor, New York, United States of America
| | - Jeremy D. Edwards
- USDA-ARS, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas, United States of America
| | - Daniel G. Peterson
- Mississippi State University, Institute for Genomics, Biocomputing & Biotechnology, Starkville, Mississippi, United States of America
| | - Sheron A. Simpson
- USDA-ARS, Genomics and Bioinformatics Research Unit, Stoneville, Mississippi, United States of America
| | - Ramey C. Youngblood
- Mississippi State University, Institute for Genomics, Biocomputing & Biotechnology, Starkville, Mississippi, United States of America
| | - Jane Grimwood
- Hudson-Alpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, Cold Springs Harbor, New York, United States of America
| | - Doreen H. Ware
- Cold Spring Harbor Laboratory, Cold Springs Harbor, New York, United States of America
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, New York, United States of America
| | - Anna M. McClung
- USDA-ARS, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas, United States of America
| | - Brian E. Scheffler
- USDA-ARS, Genomics and Bioinformatics Research Unit, Stoneville, Mississippi, United States of America
- * E-mail: (JNV); (BES)
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16
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Wanichthanarak K, Thitisaksakul M. ThRSDB: a database of Thai rice starch composition, molecular structure and functionality. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:6013757. [PMID: 33258964 PMCID: PMC7706180 DOI: 10.1093/database/baaa068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 07/14/2020] [Accepted: 07/29/2020] [Indexed: 11/12/2022]
Abstract
As starch properties can affect end product quality in many ways, rice starch from Thai domesticated cultivars and landraces has been the focus of increasing research interest. Increasing knowledge in this area creates a high demand from the research community for better organized information. The Thai Rice Starch Database (ThRSDB) is an online database containing data extensively curated from original research articles on Thai rice starch composition, molecular structure and functionality. The key aim of the ThRSDB is to facilitate accessibility to dispersed rice starch information for, but not limited to, both research and industrial users. Currently, 373 samples from 191 different Thai rice cultivars have been collected from 39 published articles. The ThRSDB includes the search functions necessary for accessing data together with a user-friendly web interface and interactive visualization tools. We have also demonstrated how the collected data can be efficiently used to observe the relationships between starch parameters and rice cultivars through correlation analysis and Partial Least Squares Discriminant Analysis. Database URL: http://thairicestarch.kku.ac.th
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Affiliation(s)
- Kwanjeera Wanichthanarak
- Siriraj Metabolomics and Phenomics Center, Faculty of Medicine Siriraj Hospital, Mahidol University, 2 Wanglang Road, Bangkok Noi, Bangkok 10700, Thailand
| | - Maysaya Thitisaksakul
- Department of Biochemistry, Faculty of Science, Khon Kaen University, 123 Moo 16 Mittraphap Road, Nai-Muang, Muang District, Khon Kaen 40002, Thailand
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17
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do Amaral MN, Auler PA, Rossatto T, Barros PM, Oliveira MM, Braga EJB. Long-term somatic memory of salinity unveiled from physiological, biochemical and epigenetic responses in two contrasting rice genotypes. PHYSIOLOGIA PLANTARUM 2020; 170:248-268. [PMID: 32515828 DOI: 10.1111/ppl.13149] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/30/2020] [Accepted: 06/04/2020] [Indexed: 06/11/2023]
Abstract
Plants are constantly exposed to environmental fluctuations, that may occur in a single day or over longer periods. In many cases, abiotic stresses are transient and recurrent, impacting how plants respond in subsequent adverse conditions. Adaptation mechanisms may occur at the physiological, biochemical and molecular level, modifying transcriptional response, regulatory proteins, epigenetic marks or metabolites. Here, we aimed to uncover the different strategies that rice uses to respond to recurrent stress. We tested varieties with contrasting behavior towards salinity (tolerance or sensitivity) and imposed salt stress (150 mM NaCl) during 48 h at vegetative and/or reproductive stages. After 48 h of stress in reproductive stage, leaves and roots were harvested separately or otherwise the plants were submitted to a 24 h recovery, prior to sample harvesting. Plants submitted to a recurrent stress responded differently from those suffering a single stress event. In the case of the sensitive genotype, recurrent stress led to lower Na/K ratio in roots and lower hydrogen peroxide accumulation and lipid peroxidation in leaves, but maintenance of global DNA methylation levels. In the tolerant genotype, recurrent stress did neither affect the Na/K ratio nor the stomatal conductance, although the levels of superoxide anion and hydrogen peroxide accumulation were lower, as also observed for global levels of DNA methylation. Our work shows that a short pre-exposure to salt stress may improve rice tolerance to subsequent stress, trough biochemical, physiological and epigenetic processes, with more significant changes visible in the tolerant genotype.
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Affiliation(s)
| | - Priscila Ariane Auler
- Department of Botany, Biology Institute, Federal University of Pelotas, Pelotas, RS, Brazil
| | - Tatiana Rossatto
- Department of Botany, Biology Institute, Federal University of Pelotas, Pelotas, RS, Brazil
| | - Pedro M Barros
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress - Plant Functional Genomics Lab, Av. da República, Oeiras, 2780-157, Portugal
| | - Maria Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress - Plant Functional Genomics Lab, Av. da República, Oeiras, 2780-157, Portugal
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18
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da Cruz MHP, Domingues DS, Saito PTM, Paschoal AR, Bugatti PH. TERL: classification of transposable elements by convolutional neural networks. Brief Bioinform 2020; 22:5900933. [PMID: 34020551 DOI: 10.1093/bib/bbaa185] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/07/2020] [Accepted: 07/20/2020] [Indexed: 11/12/2022] Open
Abstract
Transposable elements (TEs) are the most represented sequences occurring in eukaryotic genomes. Few methods provide the classification of these sequences into deeper levels, such as superfamily level, which could provide useful and detailed information about these sequences. Most methods that classify TE sequences use handcrafted features such as k-mers and homology-based search, which could be inefficient for classifying non-homologous sequences. Here we propose an approach, called transposable elements pepresentation learner (TERL), that preprocesses and transforms one-dimensional sequences into two-dimensional space data (i.e., image-like data of the sequences) and apply it to deep convolutional neural networks. This classification method tries to learn the best representation of the input data to classify it correctly. We have conducted six experiments to test the performance of TERL against other methods. Our approach obtained macro mean accuracies and F1-score of 96.4% and 85.8% for superfamilies and 95.7% and 91.5% for the order sequences from RepBase, respectively. We have also obtained macro mean accuracies and F1-score of 95.0% and 70.6% for sequences from seven databases into superfamily level and 89.3% and 73.9% for the order level, respectively. We surpassed accuracy, recall and specificity obtained by other methods on the experiment with the classification of order level sequences from seven databases and surpassed by far the time elapsed of any other method for all experiments. Therefore, TERL can learn how to predict any hierarchical level of the TEs classification system and is about 20 times and three orders of magnitude faster than TEclass and PASTEC, respectively https://github.com/muriloHoracio/TERL. Contact:murilocruz@alunos.utfpr.edu.br.
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Affiliation(s)
- Murilo Horacio Pereira da Cruz
- Federal University of Technology - Parana (UTFPR), Brazil.,Bioinformatics Graduation Program (PPGBIOINFO), Department of Computer Science, Federal University of Technology - Parana (UTFPR), Brazil
| | - Douglas Silva Domingues
- São Paulo State University at Botucatu, Brazil.,University of São Paulo, Brazil.,Department of Biodiversity, São Paulo State University at Rio Claro, Brazil
| | - Priscila Tiemi Maeda Saito
- Euripides Soares da Rocha University of Marilia, Brazil.,University of São Paulo (ICMC-USP), Brazil.,University of Campinas (IC-UNICAMP), Brazil.,Department of Computing, Federal University of Technology - Parana (UTFPR), Brazil
| | | | - Pedro Henrique Bugatti
- Euripides Soares da Rocha University of Marilia, Brazil.,University of São Paulo (ICMC-USP), Brazil.,Department of Computing, Federal University of Technology - Parana (UTFPR), Brazil
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19
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Zavallo D, Crescente JM, Gantuz M, Leone M, Vanzetti LS, Masuelli RW, Asurmendi S. Genomic re-assessment of the transposable element landscape of the potato genome. PLANT CELL REPORTS 2020; 39:1161-1174. [PMID: 32435866 DOI: 10.1007/s00299-020-02554-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/07/2020] [Indexed: 05/14/2023]
Abstract
We provide a comprehensive and reliable potato TE landscape, based on a wide variety of identification tools and integrative approaches, producing clear and ready-to-use outputs for the scientific community. Transposable elements (TEs) are DNA sequences with the ability to autoreplicate and move throughout the host genome. TEs are major drivers in stress response and genome evolution. Given their significance, the development of clear and efficient TE annotation pipelines has become essential for many species. The latest de novo TE discovery tools, along with available TEs from Repbase and sRNA-seq data, allowed us to perform a reliable potato TEs detection, classification and annotation through an open-source and freely available pipeline ( https://github.com/DiegoZavallo/TE_Discovery ). Using a variety of tools, approaches and rules, we were able to provide a clearly annotated of characterized TEs landscape. Additionally, we described the distribution of the different types of TEs across the genome, where LTRs and MITEs present a clear clustering pattern in pericentromeric and subtelomeric/telomeric regions respectively. Finally, we analyzed the insertion age and distribution of LTR retrotransposon families which display a distinct pattern between the two major superfamilies. While older Gypsy elements concentrated around heterochromatic regions, younger Copia elements located predominantly on euchromatic regions. Overall, we delivered not only a reliable, ready-to-use potato TE annotation files, but also all the necessary steps to perform de novo detection for other species.
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Affiliation(s)
- Diego Zavallo
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Los Reseros y Nicolas Repeto, Hurlingham, Argentina.
| | - Juan Manuel Crescente
- Grupo Biotecnologia y Recursos Genéticos, EEA INTA Marcos Juárez, Ruta 12 Km 3, 2580, Marcos Juárez, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Magdalena Gantuz
- Instituto de Biología Agrícola de Mendoza (IBAM), Facultad de Ciencias Agrarias (FCA), CONICET-UNCuyo, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Melisa Leone
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Los Reseros y Nicolas Repeto, Hurlingham, Argentina
- Agencia Nacional de Promocion Científica y Tecnológica (ANPCyT), Buenos Aires, Argentina
| | - Leonardo Sebastian Vanzetti
- Grupo Biotecnologia y Recursos Genéticos, EEA INTA Marcos Juárez, Ruta 12 Km 3, 2580, Marcos Juárez, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Ricardo Williams Masuelli
- Instituto de Biología Agrícola de Mendoza (IBAM), Facultad de Ciencias Agrarias (FCA), CONICET-UNCuyo, Almirante Brown 500, M5528AHB, Chacras de Coria, Mendoza, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Sebastian Asurmendi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Los Reseros y Nicolas Repeto, Hurlingham, Argentina.
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20
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Atighi MR, Verstraeten B, De Meyer T, Kyndt T. Genome-wide DNA hypomethylation shapes nematode pattern-triggered immunity in plants. THE NEW PHYTOLOGIST 2020; 227:545-558. [PMID: 32162327 PMCID: PMC7317725 DOI: 10.1111/nph.16532] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 02/26/2020] [Indexed: 05/22/2023]
Abstract
A role for DNA hypomethylation has recently been suggested in the interaction between bacteria and plants; it is unclear whether this phenomenon reflects a conserved response. Treatment of plants of monocot rice and dicot tomato with nematode-associated molecular patterns from different nematode species or bacterial pathogen-associated molecular pattern flg22 revealed global DNA hypomethylation. A similar hypomethylation response was observed during early gall induction by Meloidogyne graminicola in rice. Evidence for the causal impact of hypomethylation on immunity was revealed by a significantly reduced plant susceptibility upon treatment with DNA methylation inhibitor 5-azacytidine. Whole-genome bisulphite sequencing of young galls revealed massive hypomethylation in the CHH context, while not for CG or CHG nucleotide contexts. Further, CHH hypomethylated regions were predominantly associated with gene promoter regions, which was not correlated with activated gene expression at the same time point but, rather, was correlated with a delayed transcriptional gene activation. Finally, the relevance of CHH hypomethylation in plant defence was confirmed in rice mutants of the RNA-directed DNA methylation pathway and DECREASED DNA METHYLATION 1. We demonstrated that DNA hypomethylation is associated with reduced susceptibility in rice towards root-parasitic nematodes and is likely to be part of the basal pattern-triggered immunity response in plants.
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Affiliation(s)
| | | | - Tim De Meyer
- Department of Data Analysis & Mathematical ModellingGhent UniversityB‐9000GhentBelgium
| | - Tina Kyndt
- Department of BiotechnologyGhent UniversityB‐9000GhentBelgium
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21
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Li W, Zhang Q, Zhu T, Tong Y, Li K, Shi C, Zhang Y, Liu Y, Jiang J, Liu Y, Xia E, Huang H, Zhang L, Zhang D, Shi C, Jiang W, Zhao Y, Mao S, Jiao J, Xu P, Yang L, Gao L. Draft genomes of two outcrossing wild rice, Oryza rufipogon and O. longistaminata, reveal genomic features associated with mating-system evolution. PLANT DIRECT 2020; 4:e00232. [PMID: 32537559 PMCID: PMC7287411 DOI: 10.1002/pld3.232] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 05/07/2020] [Accepted: 05/15/2020] [Indexed: 05/04/2023]
Abstract
Oryza rufipogon and O. longistaminata are important wild relatives of cultivated rice, harboring a promising source of novel genes for rice breeding programs. Here, we present de novo assembled draft genomes and annotation of O. rufipogon and O. longistaminata. Our analysis reveals a considerable number of lineage-specific gene families associated with the self-incompatibility (SI) and formation of reproductive separation. We show how lineage-specific expansion or contraction of gene families with functional enrichment of the recognition of pollen, thus enlightening their reproductive diversification. We documented a large number of lineage-specific gene families enriched in salt stress, antifungal response, and disease resistance. Our comparative analysis further shows a genome-wide expansion of genes encoding NBS-LRR proteins in these two outcrossing wild species in contrast to six other selfing rice species. Conserved noncoding sequences (CNSs) in the two wild rice genomes rapidly evolve relative to selfing rice species, resulting in the reduction of genomic variation owing to shifts of mating systems. We find that numerous genes related to these rapidly evolving CNSs are enriched in reproductive structure development, flower development, and postembryonic development, which may associate with SI in O. rufipogon and O. longistaminata.
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Affiliation(s)
- Wei Li
- Institution of Genomics and BioinformaticsSouth China Agricultural UniversityGuangzhouChina
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Qun‐Jie Zhang
- Institution of Genomics and BioinformaticsSouth China Agricultural UniversityGuangzhouChina
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Ting Zhu
- Institution of Genomics and BioinformaticsSouth China Agricultural UniversityGuangzhouChina
- College of Life ScienceLiaoning Normal UniversityDalianChina
| | - Yan Tong
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Kui Li
- Institution of Genomics and BioinformaticsSouth China Agricultural UniversityGuangzhouChina
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Cong Shi
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
- University of the Chinese Academy of SciencesBeijingChina
| | - Yun Zhang
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Yun‐Long Liu
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Jian‐Jun Jiang
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Yuan Liu
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - En‐Hua Xia
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Hui Huang
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Li‐Ping Zhang
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Dan Zhang
- Institution of Genomics and BioinformaticsSouth China Agricultural UniversityGuangzhouChina
| | - Chao Shi
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Wen‐Kai Jiang
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - You‐Jie Zhao
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Shu‐Yan Mao
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Jun‐ying Jiao
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Ping‐Zhen Xu
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Li‐Li Yang
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
| | - Li‐Zhi Gao
- Institution of Genomics and BioinformaticsSouth China Agricultural UniversityGuangzhouChina
- Plant Germplasm and Genomics CenterGermplasm Bank of Wild Species in Southwestern China Kunming Institute of Botany Chinese Academy of SciencesKunmingChina
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22
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Akakpo R, Carpentier MC, Ie Hsing Y, Panaud O. The impact of transposable elements on the structure, evolution and function of the rice genome. THE NEW PHYTOLOGIST 2020; 226:44-49. [PMID: 31797393 DOI: 10.1111/nph.16356] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/05/2019] [Indexed: 06/10/2023]
Abstract
Transposable elements (TEs) are ubiquitous in plants and are the primary genomic component of the majority of taxa. Knowledge of their impact on the structure, function and evolution of plant genomes is therefore a priority in the field of genomics. Rice, as one of the most prevalent crops for food security worldwide, has been subjected to intense research efforts over recent decades. Consequently, a considerable amount of genomic resources has been generated and made freely available to the scientific community. These can be exploited both to improve our understanding of some basic aspects of genome biology of this species and to develop new concepts for crop improvement. In this review, we describe the current knowledge on how TEs have shaped rice chromosomes and propose a new strategy based on a genome-wide association study (GWAS) to address the important question of their functional impact on this crop.
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Affiliation(s)
- Roland Akakpo
- Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS/UPVD, Université de Perpignan, Via Domitia, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
| | - Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS/UPVD, Université de Perpignan, Via Domitia, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
| | - Yue Ie Hsing
- Institute of Plant and Microbial Biology, Acadeia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, 115, Taipei, Taiwan
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS/UPVD, Université de Perpignan, Via Domitia, 52 Avenue Paul Alduy, 66860, Perpignan Cedex, France
- Institut Universitaire de France, 1 Rue Descartes, 75231, Paris Cedex 05, France
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23
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Kamboj R, Singh B, Mondal TK, Bisht DS. Current status of genomic resources on wild relatives of rice. BREEDING SCIENCE 2020; 70:135-144. [PMID: 32523396 PMCID: PMC7272243 DOI: 10.1270/jsbbs.19064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 09/26/2019] [Indexed: 06/02/2023]
Abstract
Rice is a food crop of global importance, cultivated in diverse agro-climatic zones of the world. However, in the process of domestication many beneficial alleles have been eroded from the gene pool of the rice cultivated globally and eventually has made it vulnerable to a plethora of stresses. In contrast, the wild relatives of rice, despite being agronomically inferior, have inherited a potential of surviving in a range of geographical habitats. These adaptations enrich them with novel traits that upon introgression to modern cultivated varieties offer tremendous potential of increasing yield and adaptability. But, due to the unavailability of their genetic as well as genomic resources, identification and characterisation of these novel beneficial alleles has been a challenging task. Nevertheless, with the unprecedented surge in the area of conservation genomics, researchers have now shifted their focus towards these natural repositories of beneficial traits. Presently, there are several generic and specialized databases harboring genome-wide information on wild species of rice, and are acting as a useful resource for identification of novel genes and alleles, designing of molecular markers, comparative analysis and evolutionary biology studies. In this review, we introduce the key features of these databases focusing on their utility in rice breeding programs.
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Affiliation(s)
- Richa Kamboj
- National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India
| | - Balwant Singh
- National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India
| | - Tapan Kumar Mondal
- National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India
| | - Deepak Singh Bisht
- National Institute for Plant Biotechnology, LBS Building, Pusa Campus, New Delhi 110012, India
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24
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Low Long Terminal Repeat (LTR)-Retrotransposon Expression in Leaves of the Marine Phanerogam Posidonia Oceanica L. Life (Basel) 2020; 10:life10030030. [PMID: 32213979 PMCID: PMC7151569 DOI: 10.3390/life10030030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/14/2020] [Accepted: 03/21/2020] [Indexed: 12/29/2022] Open
Abstract
Seagrasses as Posidonia oceanica reproduce mostly by vegetative propagation, which can reduce genetic variability within populations. Since, in clonally propagated species, insurgence of genetic variability can be determined by the activity of transposable elements, we have estimated the activity of such repeat elements by measuring their expression level in the leaves of plants from a Mediterranean site, for which Illumina complementary DNA (cDNA) sequence reads (produced from RNAs isolated by leaves of plants from deep and shallow meadows) were publicly available. Firstly, we produced a collection of retrotransposon-related sequences and then mapped Illumina cDNA reads onto these sequences. With this approach, it was evident that Posidonia retrotransposons are, in general, barely expressed; only nine elements resulted transcribed at levels comparable with those of reference genes encoding tubulins and actins. Differences in transcript abundance were observed according to the superfamily and the lineage to which the retrotransposons belonged. Only small differences were observed between retrotransposon expression levels in leaves of shallow and deep Posidonia meadow stands, whereas one TAR/Tork element resulted differentially expressed in deep plants exposed to heat. It can be concluded that, in P. oceanica, the contribution of retrotransposon activity to genetic variability is reduced, although the nine specific active elements could actually produce new structural variations.
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25
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Choi JY, Lye ZN, Groen SC, Dai X, Rughani P, Zaaijer S, Harrington ED, Juul S, Purugganan MD. Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice. Genome Biol 2020; 21:21. [PMID: 32019604 PMCID: PMC7001208 DOI: 10.1186/s13059-020-1938-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 01/17/2020] [Indexed: 01/23/2023] Open
Abstract
Background The circum-basmati group of cultivated Asian rice (Oryza sativa) contains many iconic varieties and is widespread in the Indian subcontinent. Despite its economic and cultural importance, a high-quality reference genome is currently lacking, and the group’s evolutionary history is not fully resolved. To address these gaps, we use long-read nanopore sequencing and assemble the genomes of two circum-basmati rice varieties. Results We generate two high-quality, chromosome-level reference genomes that represent the 12 chromosomes of Oryza. The assemblies show a contig N50 of 6.32 Mb and 10.53 Mb for Basmati 334 and Dom Sufid, respectively. Using our highly contiguous assemblies, we characterize structural variations segregating across circum-basmati genomes. We discover repeat expansions not observed in japonica—the rice group most closely related to circum-basmati—as well as the presence and absence variants of over 20 Mb, one of which is a circum-basmati-specific deletion of a gene regulating awn length. We further detect strong evidence of admixture between the circum-basmati and circum-aus groups. This gene flow has its greatest effect on chromosome 10, causing both structural variation and single-nucleotide polymorphism to deviate from genome-wide history. Lastly, population genomic analysis of 78 circum-basmati varieties shows three major geographically structured genetic groups: Bhutan/Nepal, India/Bangladesh/Myanmar, and Iran/Pakistan. Conclusion The availability of high-quality reference genomes allows functional and evolutionary genomic analyses providing genome-wide evidence for gene flow between circum-aus and circum-basmati, describes the nature of circum-basmati structural variation, and reveals the presence/absence variation in this important and iconic rice variety group.
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Affiliation(s)
- Jae Young Choi
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA.
| | - Zoe N Lye
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Simon C Groen
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | | | | | | | | | - Sissel Juul
- Oxford Nanopore Technologies, New York, NY, USA
| | - Michael D Purugganan
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA. .,Center for Genomics and Systems Biology, NYU Abu Dhabi Research Institute, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
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26
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Ou S, Su W, Liao Y, Chougule K, Agda JRA, Hellinga AJ, Lugo CSB, Elliott TA, Ware D, Peterson T, Jiang N, Hirsch CN, Hufford MB. Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biol 2019. [PMID: 31843001 DOI: 10.1101/657890v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Sequencing technology and assembly algorithms have matured to the point that high-quality de novo assembly is possible for large, repetitive genomes. Current assemblies traverse transposable elements (TEs) and provide an opportunity for comprehensive annotation of TEs. Numerous methods exist for annotation of each class of TEs, but their relative performances have not been systematically compared. Moreover, a comprehensive pipeline is needed to produce a non-redundant library of TEs for species lacking this resource to generate whole-genome TE annotations. RESULTS We benchmark existing programs based on a carefully curated library of rice TEs. We evaluate the performance of methods annotating long terminal repeat (LTR) retrotransposons, terminal inverted repeat (TIR) transposons, short TIR transposons known as miniature inverted transposable elements (MITEs), and Helitrons. Performance metrics include sensitivity, specificity, accuracy, precision, FDR, and F1. Using the most robust programs, we create a comprehensive pipeline called Extensive de-novo TE Annotator (EDTA) that produces a filtered non-redundant TE library for annotation of structurally intact and fragmented elements. EDTA also deconvolutes nested TE insertions frequently found in highly repetitive genomic regions. Using other model species with curated TE libraries (maize and Drosophila), EDTA is shown to be robust across both plant and animal species. CONCLUSIONS The benchmarking results and pipeline developed here will greatly facilitate TE annotation in eukaryotic genomes. These annotations will promote a much more in-depth understanding of the diversity and evolution of TEs at both intra- and inter-species levels. EDTA is open-source and freely available: https://github.com/oushujun/EDTA.
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Affiliation(s)
- Shujun Ou
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
| | - Weija Su
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Yi Liao
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Jireh R A Agda
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Adam J Hellinga
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | | | - Tyler A Elliott
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- USDA-ARS NEA Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY, 14853, USA
| | - Thomas Peterson
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Ning Jiang
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA.
| | - Candice N Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA.
| | - Matthew B Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA.
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27
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Ou S, Su W, Liao Y, Chougule K, Agda JRA, Hellinga AJ, Lugo CSB, Elliott TA, Ware D, Peterson T, Jiang N, Hirsch CN, Hufford MB. Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biol 2019; 20:275. [PMID: 31843001 PMCID: PMC6913007 DOI: 10.1186/s13059-019-1905-y] [Citation(s) in RCA: 491] [Impact Index Per Article: 98.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 11/28/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sequencing technology and assembly algorithms have matured to the point that high-quality de novo assembly is possible for large, repetitive genomes. Current assemblies traverse transposable elements (TEs) and provide an opportunity for comprehensive annotation of TEs. Numerous methods exist for annotation of each class of TEs, but their relative performances have not been systematically compared. Moreover, a comprehensive pipeline is needed to produce a non-redundant library of TEs for species lacking this resource to generate whole-genome TE annotations. RESULTS We benchmark existing programs based on a carefully curated library of rice TEs. We evaluate the performance of methods annotating long terminal repeat (LTR) retrotransposons, terminal inverted repeat (TIR) transposons, short TIR transposons known as miniature inverted transposable elements (MITEs), and Helitrons. Performance metrics include sensitivity, specificity, accuracy, precision, FDR, and F1. Using the most robust programs, we create a comprehensive pipeline called Extensive de-novo TE Annotator (EDTA) that produces a filtered non-redundant TE library for annotation of structurally intact and fragmented elements. EDTA also deconvolutes nested TE insertions frequently found in highly repetitive genomic regions. Using other model species with curated TE libraries (maize and Drosophila), EDTA is shown to be robust across both plant and animal species. CONCLUSIONS The benchmarking results and pipeline developed here will greatly facilitate TE annotation in eukaryotic genomes. These annotations will promote a much more in-depth understanding of the diversity and evolution of TEs at both intra- and inter-species levels. EDTA is open-source and freely available: https://github.com/oushujun/EDTA.
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Affiliation(s)
- Shujun Ou
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011 USA
| | - Weija Su
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011 USA
| | - Yi Liao
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 USA
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724 USA
| | - Jireh R. A. Agda
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario N1G 2W1 Canada
| | - Adam J. Hellinga
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario N1G 2W1 Canada
| | | | - Tyler A. Elliott
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario N1G 2W1 Canada
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724 USA
- USDA-ARS NEA Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY 14853 USA
| | - Thomas Peterson
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA 50011 USA
| | - Ning Jiang
- Department of Horticulture, Michigan State University, East Lansing, MI 48824 USA
| | - Candice N. Hirsch
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108 USA
| | - Matthew B. Hufford
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011 USA
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28
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Jain R, Jenkins J, Shu S, Chern M, Martin JA, Copetti D, Duong PQ, Pham NT, Kudrna DA, Talag J, Schackwitz WS, Lipzen AM, Dilworth D, Bauer D, Grimwood J, Nelson CR, Xing F, Xie W, Barry KW, Wing RA, Schmutz J, Li G, Ronald PC. Genome sequence of the model rice variety KitaakeX. BMC Genomics 2019; 20:905. [PMID: 31775618 PMCID: PMC6882167 DOI: 10.1186/s12864-019-6262-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 11/05/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The availability of thousands of complete rice genome sequences from diverse varieties and accessions has laid the foundation for in-depth exploration of the rice genome. One drawback to these collections is that most of these rice varieties have long life cycles, and/or low transformation efficiencies, which limits their usefulness as model organisms for functional genomics studies. In contrast, the rice variety Kitaake has a rapid life cycle (9 weeks seed to seed) and is easy to transform and propagate. For these reasons, Kitaake has emerged as a model for studies of diverse monocotyledonous species. RESULTS Here, we report the de novo genome sequencing and analysis of Oryza sativa ssp. japonica variety KitaakeX, a Kitaake plant carrying the rice XA21 immune receptor. Our KitaakeX sequence assembly contains 377.6 Mb, consisting of 33 scaffolds (476 contigs) with a contig N50 of 1.4 Mb. Complementing the assembly are detailed gene annotations of 35,594 protein coding genes. We identified 331,335 genomic variations between KitaakeX and Nipponbare (ssp. japonica), and 2,785,991 variations between KitaakeX and Zhenshan97 (ssp. indica). We also compared Kitaake resequencing reads to the KitaakeX assembly and identified 219 small variations. The high-quality genome of the model rice plant KitaakeX will accelerate rice functional genomics. CONCLUSIONS The high quality, de novo assembly of the KitaakeX genome will serve as a useful reference genome for rice and will accelerate functional genomics studies of rice and other species.
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Affiliation(s)
- Rashmi Jain
- Department of Plant Pathology and the Genome Center, University of California, One Shields Avenue, Davis, CA, 95616, USA.,Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jerry Jenkins
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Shengqiang Shu
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Mawsheng Chern
- Department of Plant Pathology and the Genome Center, University of California, One Shields Avenue, Davis, CA, 95616, USA.,Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Joel A Martin
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Dario Copetti
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.,Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, 8092, Zurich, Switzerland.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Phat Q Duong
- Department of Plant Pathology and the Genome Center, University of California, One Shields Avenue, Davis, CA, 95616, USA.,Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Nikki T Pham
- Department of Plant Pathology and the Genome Center, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - David A Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.,BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Jayson Talag
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.,BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Wendy S Schackwitz
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Anna M Lipzen
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - David Dilworth
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Diane Bauer
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jane Grimwood
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Catherine R Nelson
- Department of Plant Pathology and the Genome Center, University of California, One Shields Avenue, Davis, CA, 95616, USA
| | - Feng Xing
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Kerrie W Barry
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.,BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.,International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna, Philippines
| | - Jeremy Schmutz
- U.S. Department of Energy, Joint Genome Institute, Walnut Creek, CA, 94598, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Guotian Li
- Department of Plant Pathology and the Genome Center, University of California, One Shields Avenue, Davis, CA, 95616, USA. .,Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. .,The Provincial Key Lab of Plant Pathology of Hubei Province and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Pamela C Ronald
- Department of Plant Pathology and the Genome Center, University of California, One Shields Avenue, Davis, CA, 95616, USA. .,Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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29
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Genome-wide association mapping of date palm fruit traits. Nat Commun 2019; 10:4680. [PMID: 31615981 PMCID: PMC6794320 DOI: 10.1038/s41467-019-12604-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 09/19/2019] [Indexed: 12/30/2022] Open
Abstract
Date palms (Phoenix dactylifera) are an important fruit crop of arid regions of the Middle East and North Africa. Despite its importance, few genomic resources exist for date palms, hampering evolutionary genomic studies of this perennial species. Here we report an improved long-read genome assembly for P. dactylifera that is 772.3 Mb in length, with contig N50 of 897.2 Kb, and use this to perform genome-wide association studies (GWAS) of the sex determining region and 21 fruit traits. We find a fruit color GWAS at the R2R3-MYB transcription factor VIRESCENS gene and identify functional alleles that include a retrotransposon insertion and start codon mutation. We also find a GWAS peak for sugar composition spanning deletion polymorphisms in multiple linked invertase genes. MYB transcription factors and invertase are implicated in fruit color and sugar composition in other crops, demonstrating the importance of parallel evolution in the evolutionary diversification of domesticated species. Date palm is an important fruit crop in the Middle East and North Africa. Here, the authors report an improved genome assembly of this species and perform GWAS mapping of sex determining region and 21 fruit traits using high density SNP data generated from re-sequencing of the mapping population.
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Lang JM, Pérez-Quintero AL, Koebnik R, DuCharme E, Sarra S, Doucoure H, Keita I, Ziegle J, Jacobs JM, Oliva R, Koita O, Szurek B, Verdier V, Leach JE. A Pathovar of Xanthomonas oryzae Infecting Wild Grasses Provides Insight Into the Evolution of Pathogenicity in Rice Agroecosystems. FRONTIERS IN PLANT SCIENCE 2019; 10:507. [PMID: 31114597 PMCID: PMC6503118 DOI: 10.3389/fpls.2019.00507] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 04/02/2019] [Indexed: 05/21/2023]
Abstract
Xanthomonas oryzae (Xo) are globally important rice pathogens. Virulent lineages from Africa and Asia and less virulent strains from the United States have been well characterized. Xanthomonas campestris pv. leersiae (Xcl), first described in 1957, causes bacterial streak on the perennial grass, Leersia hexandra, and is a close relative of Xo. L. hexandra, a member of the Poaceae, is highly similar to rice phylogenetically, is globally ubiquitous around rice paddies, and is a reservoir of pathogenic Xo. We used long read, single molecule real time (SMRT) genome sequences of five strains of Xcl from Burkina Faso, China, Mali, and Uganda to determine the genetic relatedness of this organism with Xo. Novel transcription activator-like effectors (TALEs) were discovered in all five strains of Xcl. Predicted TALE target sequences were identified in the Leersia perrieri genome and compared to rice susceptibility gene homologs. Pathogenicity screening on L. hexandra and diverse rice cultivars confirmed that Xcl are able to colonize rice and produce weak but not progressive symptoms. Overall, based on average nucleotide identity (ANI), type III (T3) effector repertoires, and disease phenotype, we propose to rename Xcl to X. oryzae pv. leersiae (Xol) and use this parallel system to improve understanding of the evolution of bacterial pathogenicity in rice agroecosystems.
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Affiliation(s)
- Jillian M. Lang
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
| | - Alvaro L. Pérez-Quintero
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
| | - Ralf Koebnik
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
| | - Elysa DuCharme
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
| | - Soungalo Sarra
- Centre Régional de Recherche Agronomique de Niono, Institut d’Economie Rural, Bamako, Mali
| | - Hinda Doucoure
- Laboratoire de Biologie Moléculaire Appliquée, Université des Sciences Techniques et Technologiques de Bamako, Bamako, Mali
| | - Ibrahim Keita
- Laboratoire de Biologie Moléculaire Appliquée, Université des Sciences Techniques et Technologiques de Bamako, Bamako, Mali
| | - Janet Ziegle
- Pacific Biosciences, Menlo Park, CA, United States
| | - Jonathan M. Jacobs
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
- Department of Plant Pathology, Infectious Disease Institute, Ohio State University, Columbus, OH, United States
| | - Ricardo Oliva
- International Rice Research Institute, Los Baños, Philippines
| | - Ousmane Koita
- Laboratoire de Biologie Moléculaire Appliquée, Université des Sciences Techniques et Technologiques de Bamako, Bamako, Mali
| | - Boris Szurek
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
| | - Valérie Verdier
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
- IRD, Cirad, Univ. Montpellier, IPME, Montpellier, France
| | - Jan E. Leach
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States
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31
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Fuentes RR, Chebotarov D, Duitama J, Smith S, De la Hoz JF, Mohiyuddin M, Wing RA, McNally KL, Tatarinova T, Grigoriev A, Mauleon R, Alexandrov N. Structural variants in 3000 rice genomes. Genome Res 2019; 29:870-880. [PMID: 30992303 PMCID: PMC6499320 DOI: 10.1101/gr.241240.118] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 03/11/2019] [Indexed: 12/24/2022]
Abstract
Investigation of large structural variants (SVs) is a challenging yet important task in understanding trait differences in highly repetitive genomes. Combining different bioinformatic approaches for SV detection, we analyzed whole-genome sequencing data from 3000 rice genomes and identified 63 million individual SV calls that grouped into 1.5 million allelic variants. We found enrichment of long SVs in promoters and an excess of shorter variants in 5′ UTRs. Across the rice genomes, we identified regions of high SV frequency enriched in stress response genes. We demonstrated how SVs may help in finding causative variants in genome-wide association analysis. These new insights into rice genome biology are valuable for understanding the effects SVs have on gene function, with the prospect of identifying novel agronomically important alleles that can be utilized to improve cultivated rice.
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Affiliation(s)
- Roven Rommel Fuentes
- International Rice Research Institute, Laguna 4031, Philippines.,Bioinformatics Group, Wageningen University and Research, 6708 PB Wageningen, the Netherlands
| | | | - Jorge Duitama
- Systems and Computing Engineering Department, Universidad de Los Andes, Bogotá 111711, Colombia.,Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali 6713, Colombia
| | - Sean Smith
- Biology Department, Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey 08102, USA
| | - Juan Fernando De la Hoz
- Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali 6713, Colombia
| | | | - Rod A Wing
- International Rice Research Institute, Laguna 4031, Philippines.,Arizona Genomics Institute, University of Arizona, Tucson, Arizona 85721, USA.,King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia
| | | | - Tatiana Tatarinova
- Department of Biology, University of La Verne, La Verne, California 91750, USA.,Vavilov Institute of General Genetics, Moscow 119333, Russia.,A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow 127051, Russia.,Laboratory of Forest Genomics, Siberian Federal University, Krasnoyarsk 660041, Russia
| | - Andrey Grigoriev
- Biology Department, Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey 08102, USA
| | - Ramil Mauleon
- International Rice Research Institute, Laguna 4031, Philippines
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32
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Choi JY, Purugganan MD. Evolutionary Epigenomics of Retrotransposon-Mediated Methylation Spreading in Rice. Mol Biol Evol 2019; 35:365-382. [PMID: 29126199 PMCID: PMC5850837 DOI: 10.1093/molbev/msx284] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Plant genomes contain numerous transposable elements (TEs), and many hypotheses on the evolutionary drivers that restrict TE activity have been postulated. Few models, however, have focused on the evolutionary epigenomic interaction between the plant host and its TE. The host genome recruits epigenetic factors, such as methylation, to silence TEs but methylation can spread beyond the TE sequence and influence the expression of nearby host genes. In this study, we investigated this epigenetic trade-off between TE and proximal host gene silencing by studying the epigenomic regulation of repressing long terminal repeat (LTR) retrotransposons (RTs) in Oryza sativa. Results showed significant evidence of methylation spreading originating from the LTR-RT sequences, and the extent of spreading was dependent on five factors: 1) LTR-RT family, 2) time since the LTR-RT insertion, 3) recombination rate of the LTR-RT region, 4) level of LTR-RT sequence methylation, and 5) chromosomal location. Methylation spreading had negative effects by reducing host gene expression, but only on host genes with LTR-RT inserted in its introns. Our results also suggested high levels of LTR-RT methylation might have a role in suppressing TE-mediated deleterious ectopic recombination. In the end, despite the methylation spreading, no strong epigenetic trade-off was detected and majority of LTR-RT may have only minor epigenetic effects on nearby host genes.
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Affiliation(s)
- Jae Young Choi
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY
| | - Michael D Purugganan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY.,Center for Genomics and Systems Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
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33
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Tonnessen BW, Bossa-Castro AM, Mauleon R, Alexandrov N, Leach JE. Shared cis-regulatory architecture identified across defense response genes is associated with broad-spectrum quantitative resistance in rice. Sci Rep 2019; 9:1536. [PMID: 30733489 PMCID: PMC6367480 DOI: 10.1038/s41598-018-38195-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 12/18/2018] [Indexed: 12/30/2022] Open
Abstract
Plant disease resistance that is durable and effective against diverse pathogens (broad-spectrum) is essential to stabilize crop production. Such resistance is frequently controlled by Quantitative Trait Loci (QTL), and often involves differential regulation of Defense Response (DR) genes. In this study, we sought to understand how expression of DR genes is orchestrated, with the long-term goal of enabling genome-wide breeding for more effective and durable resistance. We identified short sequence motifs in rice promoters that are shared across Broad-Spectrum DR (BS-DR) genes co-expressed after challenge with three major rice pathogens (Magnaporthe oryzae, Rhizoctonia solani, and Xanthomonas oryzae pv. oryzae) and several chemical elicitors. Specific groupings of these BS-DR-associated motifs, called cis-Regulatory Modules (CRMs), are enriched in DR gene promoters, and the CRMs include cis-elements known to be involved in disease resistance. Polymorphisms in CRMs occur in promoters of genes in resistant relative to susceptible BS-DR haplotypes providing evidence that these CRMs have a predictive role in the contribution of other BS-DR genes to resistance. Therefore, we predict that a CRM signature within BS-DR gene promoters can be used as a marker for future breeding practices to enrich for the most responsive and effective BS-DR genes across the genome.
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Affiliation(s)
| | | | - Ramil Mauleon
- International Rice Research Institute, Manila, Philippines
| | | | - Jan E Leach
- Colorado State University, Fort Collins, CO, USA.
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34
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Carpentier MC, Manfroi E, Wei FJ, Wu HP, Lasserre E, Llauro C, Debladis E, Akakpo R, Hsing YI, Panaud O. Retrotranspositional landscape of Asian rice revealed by 3000 genomes. Nat Commun 2019; 10:24. [PMID: 30604755 PMCID: PMC6318337 DOI: 10.1038/s41467-018-07974-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 12/05/2018] [Indexed: 12/21/2022] Open
Abstract
The recent release of genomic sequences for 3000 rice varieties provides access to the genetic diversity at species level for this crop. We take advantage of this resource to unravel some features of the retrotranspositional landscape of rice. We develop software TRACKPOSON specifically for the detection of transposable elements insertion polymorphisms (TIPs) from large datasets. We apply this tool to 32 families of retrotransposons and identify more than 50,000 TIPs in the 3000 rice genomes. Most polymorphisms are found at very low frequency, suggesting that they may have occurred recently in agro. A genome-wide association study shows that these activations in rice may be triggered by external stimuli, rather than by the alteration of genetic factors involved in transposable element silencing pathways. Finally, the TIPs dataset is used to trace the origin of rice domestication. Our results suggest that rice originated from three distinct domestication events.
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Affiliation(s)
- Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France
| | - Ernandes Manfroi
- Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 90040-060, Brazil
| | - Fu-Jin Wei
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, 115, Taipei, Taiwan
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, 1 Matsunosato, Tsukuba, 305-8687, Ibaraki, Japan
| | - Hshin-Ping Wu
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, 115, Taipei, Taiwan
| | - Eric Lasserre
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France
| | - Christel Llauro
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France
| | - Emilie Debladis
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France
| | - Roland Akakpo
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France
| | - Yue-Ie Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, 128, Section 2, Yien-chu-yuan Road, Nankang, 115, Taipei, Taiwan
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes, UMR CNRS/UPVD 5096, Université de Perpignan Via Domitia, 52 Avenue Paul Alduy., 66860, Perpignan Cedex, France.
- Institut Universitaire de France, 1 rue Descartes, 75231, Paris Cedex 05, France.
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35
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da Cruz MHP, Saito PTM, Paschoal AR, Bugatti PH. Classification of Transposable Elements by Convolutional Neural Networks. ARTIFICIAL INTELLIGENCE AND SOFT COMPUTING 2019. [DOI: 10.1007/978-3-030-20915-5_15] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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36
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37
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Valdes Franco JA, Wang Y, Huo N, Ponciano G, Colvin HA, McMahan CM, Gu YQ, Belknap WR. Modular assembly of transposable element arrays by microsatellite targeting in the guayule and rice genomes. BMC Genomics 2018; 19:271. [PMID: 29673330 PMCID: PMC5907723 DOI: 10.1186/s12864-018-4653-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 04/10/2018] [Indexed: 12/30/2022] Open
Abstract
Background Guayule (Parthenium argentatum A. Gray) is a rubber-producing desert shrub native to Mexico and the United States. Guayule represents an alternative to Hevea brasiliensis as a source for commercial natural rubber. The efficient application of modern molecular/genetic tools to guayule improvement requires characterization of its genome. Results The 1.6 Gb guayule genome was sequenced, assembled and annotated. The final 1.5 Gb assembly, while fragmented (N50 = 22 kb), maps > 95% of the shotgun reads and is essentially complete. Approximately 40,000 transcribed, protein encoding genes were annotated on the assembly. Further characterization of this genome revealed 15 families of small, microsatellite-associated, transposable elements (TEs) with unexpected chromosomal distribution profiles. These SaTar (Satellite Targeted) elements, which are non-autonomous Mu-like elements (MULEs), were frequently observed in multimeric linear arrays of unrelated individual elements within which no individual element is interrupted by another. This uniformly non-nested TE multimer architecture has not been previously described in either eukaryotic or prokaryotic genomes. Five families of similarly distributed non-autonomous MULEs (microsatellite associated, modularly assembled) were characterized in the rice genome. Families of TEs with similar structures and distribution profiles were identified in sorghum and citrus. Conclusion The sequencing and assembly of the guayule genome provides a foundation for application of current crop improvement technologies to this plant. In addition, characterization of this genome revealed SaTar elements with distribution profiles unique among TEs. Satar targeting appears based on an alternative MULE recombination mechanism with the potential to impact gene evolution. Electronic supplementary material The online version of this article (10.1186/s12864-018-4653-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- José A Valdes Franco
- Universidad Autónoma de Nuevo León, Monterrey, NL, Mexico.,Present Address: Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Yi Wang
- USDA-Agricultural Research Service, Western Regional Research Center, Albany, CA, USA
| | - Naxin Huo
- USDA-Agricultural Research Service, Western Regional Research Center, Albany, CA, USA
| | - Grisel Ponciano
- USDA-Agricultural Research Service, Western Regional Research Center, Albany, CA, USA
| | | | - Colleen M McMahan
- USDA-Agricultural Research Service, Western Regional Research Center, Albany, CA, USA
| | - Yong Q Gu
- USDA-Agricultural Research Service, Western Regional Research Center, Albany, CA, USA.
| | - William R Belknap
- USDA-Agricultural Research Service, Western Regional Research Center, Albany, CA, USA
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38
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Bailey PC, Schudoma C, Jackson W, Baggs E, Dagdas G, Haerty W, Moscou M, Krasileva KV. Dominant integration locus drives continuous diversification of plant immune receptors with exogenous domain fusions. Genome Biol 2018; 19:23. [PMID: 29458393 PMCID: PMC5819176 DOI: 10.1186/s13059-018-1392-6] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Accepted: 01/16/2018] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The plant immune system is innate and encoded in the germline. Using it efficiently, plants are capable of recognizing a diverse range of rapidly evolving pathogens. A recently described phenomenon shows that plant immune receptors are able to recognize pathogen effectors through the acquisition of exogenous protein domains from other plant genes. RESULTS We show that plant immune receptors with integrated domains are distributed unevenly across their phylogeny in grasses. Using phylogenetic analysis, we uncover a major integration clade, whose members underwent repeated independent integration events producing diverse fusions. This clade is ancestral in grasses with members often found on syntenic chromosomes. Analyses of these fusion events reveals that homologous receptors can be fused to diverse domains. Furthermore, we discover a 43 amino acid long motif associated with this dominant integration clade which is located immediately upstream of the fusion site. Sequence analysis reveals that DNA transposition and/or ectopic recombination are the most likely mechanisms of formation for nucleotide binding leucine rich repeat proteins with integrated domains. CONCLUSIONS The identification of this subclass of plant immune receptors that is naturally adapted to new domain integration will inform biotechnological approaches for generating synthetic receptors with novel pathogen "baits."
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Affiliation(s)
- Paul C Bailey
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | | | - William Jackson
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Erin Baggs
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Gulay Dagdas
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Wilfried Haerty
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Matthew Moscou
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Ksenia V Krasileva
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK.
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.
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39
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Sperotto RA, de Araújo Junior AT, Adamski JM, Cargnelutti D, Ricachenevsky FK, de Oliveira BHN, da Cruz RP, Dos Santos RP, da Silva LP, Fett JP. Deep RNAseq indicates protective mechanisms of cold-tolerant indica rice plants during early vegetative stage. PLANT CELL REPORTS 2018; 37:347-375. [PMID: 29151156 DOI: 10.1007/s00299-017-2234-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 11/08/2017] [Indexed: 05/13/2023]
Abstract
Cold-tolerance in rice may be related to increased cellulose deposition in the cell wall, membrane fatty acids unsaturation and differential expression of several newly identified genes. Low temperature exposure during early vegetative stages limits rice plant's growth and development. Most genes previously related to cold tolerance in rice are from the japonica subspecies. To help clarify the mechanisms that regulate cold tolerance in young indica rice plants, comparative transcriptome analysis of 6 h cold-treated (10 °C) leaves from two genotypes, cold-tolerant (CT) and cold-sensitive (CS), was performed. Differentially expressed genes were identified: 831 and 357 sequences more expressed in the tolerant and in the sensitive genotype, respectively. The genes with higher expression in the CT genotype were used in systems biology analyses to identify protein-protein interaction (PPI) networks and nodes (proteins) that are hubs and bottlenecks in the PPI. From the genes more expressed in the tolerant plants, 60% were reported as affected by cold in previous transcriptome experiments and 27% are located within QTLs related to cold tolerance during the vegetative stage. Novel cold-responsive genes were identified. Quantitative RT-PCR confirmed the high-quality of RNAseq libraries. Several genes related to cell wall assembly or reinforcement are cold-induced or constitutively highly expressed in the tolerant genotype. Cold-tolerant plants have increased cellulose deposition under cold. Genes related to lipid metabolism are more expressed in the tolerant genotype, which has higher membrane fatty acids unsaturation, with increasing levels of linoleic acid under cold. The CT genotype seems to have higher photosynthetic efficiency and antioxidant capacity, as well as more effective ethylene, Ca2+ and hormone signaling than the CS. These genes could be useful in future biotechnological approaches aiming to increase cold tolerance in rice.
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Affiliation(s)
- Raul Antonio Sperotto
- Centro de Ciências Biológicas e da Saúde (CCBS), Programa de Pós-Graduação em Biotecnologia (PPGBiotec), Universidade do Vale do Taquari-UNIVATES, Lajeado, RS, Brazil.
| | | | - Janete Mariza Adamski
- Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Denise Cargnelutti
- Departamento de Agronomia, Universidade Federal da Fronteira Sul (UFFS), Erechim, RS, Brazil
| | | | - Ben-Hur Neves de Oliveira
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Renata Pereira da Cruz
- Departamento de Plantas de Lavoura, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Rinaldo Pires Dos Santos
- Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Leila Picolli da Silva
- Departamento de Zootecnia, Universidade Federal de Santa Maria (UFSM), Santa Maria, RS, Brazil
| | - Janette Palma Fett
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
- Departamento de Botânica, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
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Kiegle EA, Garden A, Lacchini E, Kater MM. A Genomic View of Alternative Splicing of Long Non-coding RNAs during Rice Seed Development Reveals Extensive Splicing and lncRNA Gene Families. FRONTIERS IN PLANT SCIENCE 2018; 9:115. [PMID: 29467783 PMCID: PMC5808331 DOI: 10.3389/fpls.2018.00115] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/22/2018] [Indexed: 05/08/2023]
Abstract
Alternative splicing (AS) is a key modulator of development in many eukaryotic organisms. In plants, alternative splice forms of non-coding RNAs (ncRNAs) are known to modulate flowering time in Arabidopsis and fertility in rice. Here we demonstrate that alternative splicing of coding and long non-coding RNAs occurs during rice seed development by comparing AS in immature seeds vs. embryo and endosperm of mature seeds. Based on computational predictions of AS events determined from a Bayesian analysis of junction counts of RNA-seq datasets, differential splicing of protein-coding, and non-coding RNAs was determined. In contrast to roots, leaves, flowers, buds, and reproductive meristems, developing seeds had 5.8-57 times more predicted AS. Primers designed to span introns and exons were used to detect AS events predicted by rMATs in cDNA derived from early (milk) seed, embryo, and endosperm. Comparing milk seed vs. mature embryo and endosperm, AS of MORC7 (a gene implicated in epigenetic gene silencing), was markedly different. Long non-coding RNAs (lncRNAs) also underwent AS during the transition from milk seed to mature embryo and endosperm, with a complex gene structure, and were more extensively processed than predicted by current genome annotation. Exon retention of lncRNAs was enhanced in embryos. Searching all 5,515 lncRNAs in the NCBI genome annotation uncovered gene families based on highly conserved regions shared by groups of 3-35 lncRNAs. The homologies to other lncRNAs, as well as homologies to coding sequences, and the genomic context of lncRNAs provide inroads for functional analysis of multi-exonic lncRNAs that can be extensively processed during seed development.
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Haritha G, Malathi S, Divya B, Swamy BPM, Mangrauthia SK, Sarla N. Oryza nivara Sharma et Shastry. COMPENDIUM OF PLANT GENOMES 2018. [DOI: 10.1007/978-3-319-71997-9_20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Copetti D, Búrquez A, Bustamante E, Charboneau JLM, Childs KL, Eguiarte LE, Lee S, Liu TL, McMahon MM, Whiteman NK, Wing RA, Wojciechowski MF, Sanderson MJ. Extensive gene tree discordance and hemiplasy shaped the genomes of North American columnar cacti. Proc Natl Acad Sci U S A 2017; 114:12003-12008. [PMID: 29078296 PMCID: PMC5692538 DOI: 10.1073/pnas.1706367114] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Few clades of plants have proven as difficult to classify as cacti. One explanation may be an unusually high level of convergent and parallel evolution (homoplasy). To evaluate support for this phylogenetic hypothesis at the molecular level, we sequenced the genomes of four cacti in the especially problematic tribe Pachycereeae, which contains most of the large columnar cacti of Mexico and adjacent areas, including the iconic saguaro cactus (Carnegiea gigantea) of the Sonoran Desert. We assembled a high-coverage draft genome for saguaro and lower coverage genomes for three other genera of tribe Pachycereeae (Pachycereus, Lophocereus, and Stenocereus) and a more distant outgroup cactus, Pereskia We used these to construct 4,436 orthologous gene alignments. Species tree inference consistently returned the same phylogeny, but gene tree discordance was high: 37% of gene trees having at least 90% bootstrap support conflicted with the species tree. Evidently, discordance is a product of long generation times and moderately large effective population sizes, leading to extensive incomplete lineage sorting (ILS). In the best supported gene trees, 58% of apparent homoplasy at amino sites in the species tree is due to gene tree-species tree discordance rather than parallel substitutions in the gene trees themselves, a phenomenon termed "hemiplasy." The high rate of genomic hemiplasy may contribute to apparent parallelisms in phenotypic traits, which could confound understanding of species relationships and character evolution in cacti.
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Affiliation(s)
- Dario Copetti
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721
- International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Alberto Búrquez
- Instituto de Ecología, Unidad Hermosillo, Universidad Nacional Autónoma de México, Hermosillo, Sonora, Mexico
| | - Enriquena Bustamante
- Instituto de Ecología, Unidad Hermosillo, Universidad Nacional Autónoma de México, Hermosillo, Sonora, Mexico
| | - Joseph L M Charboneau
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721
| | - Kevin L Childs
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Seunghee Lee
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721
| | - Tiffany L Liu
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824
| | | | - Noah K Whiteman
- Department of Integrative Biology, University of California, Berkeley, CA 94720
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721
- International Rice Research Institute, Los Baños, Laguna, Philippines
| | | | - Michael J Sanderson
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721;
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Brozynska M, Copetti D, Furtado A, Wing RA, Crayn D, Fox G, Ishikawa R, Henry RJ. Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:765-774. [PMID: 27889940 PMCID: PMC5425390 DOI: 10.1111/pbi.12674] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 10/10/2016] [Accepted: 11/23/2016] [Indexed: 05/04/2023]
Abstract
The related A genome species of the Oryza genus are the effective gene pool for rice. Here, we report draft genomes for two Australian wild A genome taxa: O. rufipogon-like population, referred to as Taxon A, and O. meridionalis-like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short- and long-read next-generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here, we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A has a sequence that is much closer to that of domesticated rice (O. sativa) than to the other Australian wild populations. Analysis of 4643 genes in the A genome clade showed that the Australian annual, O. meridionalis, and related perennial taxa have the most divergent (around 3 million years) genome sequences relative to domesticated rice. A test for admixture showed possible introgression into the Australian Taxon A (diverged around 1.6 million years ago) especially from the wild indica/O. nivara clade in Asia. These results demonstrate that northern Australia may be the centre of diversity of the A genome Oryza and suggest the possibility that this might also be the centre of origin of this group and represent an important resource for rice improvement.
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Affiliation(s)
- Marta Brozynska
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbaneQLDAustralia
| | - Dario Copetti
- Arizona Genomics InstituteSchool of Plant SciencesUniversity of ArizonaTucsonAZUSA
- International Rice Research InstituteT.T. Chang Genetic Resources CenterLos BañosLagunaPhilippines
| | - Agnelo Furtado
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbaneQLDAustralia
| | - Rod A. Wing
- Arizona Genomics InstituteSchool of Plant SciencesUniversity of ArizonaTucsonAZUSA
- International Rice Research InstituteT.T. Chang Genetic Resources CenterLos BañosLagunaPhilippines
| | - Darren Crayn
- Australian Tropical HerbariumJames Cook UniversityCairnsQLDAustralia
| | - Glen Fox
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandToowoombaQLDAustralia
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life ScienceHirosaki UniversityHirosakiAomoriJapan
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food InnovationUniversity of QueenslandBrisbaneQLDAustralia
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Song X, Cao X. Transposon-mediated epigenetic regulation contributes to phenotypic diversity and environmental adaptation in rice. CURRENT OPINION IN PLANT BIOLOGY 2017; 36:111-118. [PMID: 28273484 DOI: 10.1016/j.pbi.2017.02.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 02/03/2017] [Accepted: 02/06/2017] [Indexed: 05/19/2023]
Abstract
Transposable elements (TEs) have long been regarded as 'selfish DNA', and are generally silenced by epigenetic mechanisms. However, work in the past decade has identified positive roles for TEs in generating genomic novelty and diversity in plants. In particular, recent studies suggested that TE-induced epigenetic alterations and modification of gene expression contribute to phenotypic variation and adaptation to geography or stress. These findings have led many to regard TEs, not as junk DNA, but as sources of control elements and genomic diversity. As a staple food crop and model system for genomic research on monocot plants, rice (Oryza sativa) has a modest-sized genome that harbors massive numbers of DNA transposons (class II transposable elements) scattered across the genome, which may make TE regulation of genes more prevalent. In this review, we summarize recent progress in research on the functions of rice TEs in modulating gene expression and creating new genes. We also examine the contributions of TEs to phenotypic diversity and adaptation to environmental conditions.
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Affiliation(s)
- Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
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Copetti D, Wing RA. The Dark Side of the Genome: Revealing the Native Transposable Element/Repeat Content of Eukaryotic Genomes. MOLECULAR PLANT 2016; 9:1664-1666. [PMID: 27693675 DOI: 10.1016/j.molp.2016.09.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 09/12/2016] [Accepted: 09/22/2016] [Indexed: 06/06/2023]
Affiliation(s)
- Dario Copetti
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA; International Rice Research Institute, T.T. Chang Genetic Resources Center, Los Baños, Laguna 63108, Philippines
| | - Rod A Wing
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA; International Rice Research Institute, T.T. Chang Genetic Resources Center, Los Baños, Laguna 63108, Philippines.
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Identification and characterisation of Short Interspersed Nuclear Elements in the olive tree (Olea europaea L.) genome. Mol Genet Genomics 2016; 292:53-61. [PMID: 27714457 DOI: 10.1007/s00438-016-1255-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 10/03/2016] [Indexed: 10/20/2022]
Abstract
Short Interspersed Nuclear Elements (SINEs) are nonautonomous retrotransposons in the genome of most eukaryotic species. While SINEs have been intensively investigated in humans and other animal systems, SINE identification has been carried out only in a limited number of plant species. This lack of information is apparent especially in non-model plants whose genome has not been sequenced yet. The aim of this work was to produce a specific bioinformatics pipeline for analysing second generation sequence reads of a non-model species and identifying SINEs. We have identified, for the first time, 227 putative SINEs of the olive tree (Olea europaea), that constitute one of the few sets of such sequences in dicotyledonous species. The identified SINEs ranged from 140 to 362 bp in length and were characterised with regard to the occurrence of the tRNA domain in their sequence. The majority of identified elements resulted in single copy or very lowly repeated, often in association with genic sequences. Analysis of sequence similarity allowed us to identify two major groups of SINEs showing different abundances in the olive tree genome, the former with sequence similarity to SINEs of Scrophulariaceae and Solanaceae and the latter to SINEs of Salicaceae. A comparison of sequence conservation between olive SINEs and LTR retrotransposon families suggested that SINE expansion in the genome occurred especially in very ancient times, before LTR retrotransposon expansion, and presumably before the separation of the rosids (to which Oleaceae belong) from the Asterids. Besides providing data on olive SINEs, our results demonstrate the suitability of the pipeline employed for SINE identification. Applying this pipeline will favour further structural and functional analyses on these relatively unknown elements to be performed also in other plant species, even in the absence of a reference genome, and will allow establishing general evolutionary patterns for this kind of repeats in plants.
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Zhu L, Zhang YH, Su F, Chen L, Huang T, Cai YD. A Shortest-Path-Based Method for the Analysis and Prediction of Fruit-Related Genes in Arabidopsis thaliana. PLoS One 2016; 11:e0159519. [PMID: 27434024 PMCID: PMC4951011 DOI: 10.1371/journal.pone.0159519] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 07/05/2016] [Indexed: 12/11/2022] Open
Abstract
Biologically, fruits are defined as seed-bearing reproductive structures in angiosperms that develop from the ovary. The fertilization, development and maturation of fruits are crucial for plant reproduction and are precisely regulated by intrinsic genetic regulatory factors. In this study, we used Arabidopsis thaliana as a model organism and attempted to identify novel genes related to fruit-associated biological processes. Specifically, using validated genes, we applied a shortest-path-based method to identify several novel genes in a large network constructed using the protein-protein interactions observed in Arabidopsis thaliana. The described analyses indicate that several of the discovered genes are associated with fruit fertilization, development and maturation in Arabidopsis thaliana.
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Affiliation(s)
- Liucun Zhu
- School of Life Sciences, Shanghai University, Shanghai, People’s Republic of China
| | - Yu-Hang Zhang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Fangchu Su
- School of Life Sciences, Shanghai University, Shanghai, People’s Republic of China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, People’s Republic of China
| | - Tao Huang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People’s Republic of China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, People’s Republic of China
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Wang J, Yu Y, Tao F, Zhang J, Copetti D, Kudrna D, Talag J, Lee S, Wing RA, Fan C. DNA methylation changes facilitated evolution of genes derived from Mutator-like transposable elements. Genome Biol 2016; 17:92. [PMID: 27154274 PMCID: PMC4858842 DOI: 10.1186/s13059-016-0954-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 04/14/2016] [Indexed: 01/17/2023] Open
Abstract
Background Mutator-like transposable elements, a class of DNA transposons, exist pervasively in both prokaryotic and eukaryotic genomes, with more than 10,000 copies identified in the rice genome. These elements can capture ectopic genomic sequences that lead to the formation of new gene structures. Here, based on whole-genome comparative analyses, we comprehensively investigated processes and mechanisms of the evolution of putative genes derived from Mutator-like transposable elements in ten Oryza species and the outgroup Leersia perieri, bridging ~20 million years of evolutionary history. Results Our analysis identified thousands of putative genes in each of the Oryza species, a large proportion of which have evidence of expression and contain chimeric structures. Consistent with previous reports, we observe that the putative Mutator-like transposable element-derived genes are generally GC-rich and mainly derive from GC-rich parental sequences. Furthermore, we determine that Mutator-like transposable elements capture parental sequences preferentially from genomic regions with low methylation levels and high recombination rates. We explicitly show that methylation levels in the internal and terminated inverted repeat regions of these elements, which might be directed by the 24-nucleotide small RNA-mediated pathway, are different and change dynamically over evolutionary time. Lastly, we demonstrate that putative genes derived from Mutator-like transposable elements tend to be expressed in mature pollen, which have undergone de-methylation programming, thereby providing a permissive expression environment for newly formed/transposable element-derived genes. Conclusions Our results suggest that DNA methylation may be a primary mechanism to facilitate the origination, survival, and regulation of genes derived from Mutator-like transposable elements, thus contributing to the evolution of gene innovation and novelty in plant genomes. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-0954-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jun Wang
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA
| | - Yeisoo Yu
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Feng Tao
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA
| | - Jianwei Zhang
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Dario Copetti
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Dave Kudrna
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Jayson Talag
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Seunghee Lee
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Rod A Wing
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.,T.T. Chang Genetics Resources Center, International Rice Research Institute, Los Baños, Laguna, 4031, Philippines
| | - Chuanzhu Fan
- Department of Biological Sciences, Wayne State University, 5047 Gullen Mall, Detroit, MI, 48202, USA.
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Barghini E, Mascagni F, Natali L, Giordani T, Cavallini A. Analysis of the repetitive component and retrotransposon population in the genome of a marine angiosperm, Posidonia oceanica (L.) Delile. Mar Genomics 2015; 24 Pt 3:397-404. [PMID: 26472701 DOI: 10.1016/j.margen.2015.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2015] [Revised: 09/24/2015] [Accepted: 10/08/2015] [Indexed: 10/22/2022]
Abstract
Posidonia oceanica is a monocotyledonous marine plant that plays a crucial role in maintaining the Mediterranean environment. Despite its ecological importance, basic knowledge of the functional and structural genomics of this species is still limited, as it is for the other seagrasses. Here, for the first time, we report data on the repetitive component of the genome of this seagrass using a low coverage of Illumina sequences and different assembly approaches. A dataset of 19,760 assembled sequences, mostly belonging to the repetitive fraction of the genome, was produced and annotated. Based on mapping Illumina reads onto this dataset, the genome structure of P. oceanica and its repetitive component was inferred. A very large proportion of the genome is represented by long-terminal-repeat (LTR) retrotransposons of both the Copia and Gypsy superfamilies. Posidonia LTR-retrotransposons were classified and their sequences analysed. Gypsy elements belong to three main lineages, while Copia ones belong to seven lineages. Gypsy elements were more represented than Copia ones in the set of assembled sequences and in the genome. Analysis of sequence variability indicated that Gypsy lineages have experienced amplification in more recent times compared to Copia ones.
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Affiliation(s)
- Elena Barghini
- Department of Agriculture, Food, and Environment, University of Pisa, Via del Borghetto, 80, I-56124 Pisa, Italy
| | - Flavia Mascagni
- Department of Agriculture, Food, and Environment, University of Pisa, Via del Borghetto, 80, I-56124 Pisa, Italy
| | - Lucia Natali
- Department of Agriculture, Food, and Environment, University of Pisa, Via del Borghetto, 80, I-56124 Pisa, Italy
| | - Tommaso Giordani
- Department of Agriculture, Food, and Environment, University of Pisa, Via del Borghetto, 80, I-56124 Pisa, Italy
| | - Andrea Cavallini
- Department of Agriculture, Food, and Environment, University of Pisa, Via del Borghetto, 80, I-56124 Pisa, Italy.
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