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Zhang T, Huang W, Zhang L, Li DZ, Qi J, Ma H. Phylogenomic profiles of whole-genome duplications in Poaceae and landscape of differential duplicate retention and losses among major Poaceae lineages. Nat Commun 2024; 15:3305. [PMID: 38632270 PMCID: PMC11024178 DOI: 10.1038/s41467-024-47428-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
Poaceae members shared a whole-genome duplication called rho. However, little is known about the evolutionary pattern of the rho-derived duplicates among Poaceae lineages and implications in adaptive evolution. Here we present phylogenomic/phylotranscriptomic analyses of 363 grasses covering all 12 subfamilies and report nine previously unknown whole-genome duplications. Furthermore, duplications from a single whole-genome duplication were mapped to multiple nodes on the species phylogeny; a whole-genome duplication was likely shared by woody bamboos with possible gene flow from herbaceous bamboos; and recent paralogues of a tetraploid Oryza are implicated in tolerance of seawater submergence. Moreover, rho duplicates showing differential retention among subfamilies include those with functions in environmental adaptations or morphogenesis, including ACOT for aquatic environments (Oryzoideae), CK2β for cold responses (Pooideae), SPIRAL1 for rapid cell elongation (Bambusoideae), and PAI1 for drought/cold responses (Panicoideae). This study presents a Poaceae whole-genome duplication profile with evidence for multiple evolutionary mechanisms that contribute to gene retention and losses.
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Affiliation(s)
- Taikui Zhang
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA, 16802, USA
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Weichen Huang
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA, 16802, USA
| | - Lin Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China
| | - Ji Qi
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Hong Ma
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, State College, PA, 16802, USA.
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Hu H, Scheben A, Wang J, Li F, Li C, Edwards D, Zhao J. Unravelling inversions: Technological advances, challenges, and potential impact on crop breeding. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:544-554. [PMID: 37961986 PMCID: PMC10893937 DOI: 10.1111/pbi.14224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/11/2023] [Accepted: 10/22/2023] [Indexed: 11/15/2023]
Abstract
Inversions, a type of chromosomal structural variation, significantly influence plant adaptation and gene functions by impacting gene expression and recombination rates. However, compared with other structural variations, their roles in functional biology and crop improvement remain largely unexplored. In this review, we highlight technological and methodological advancements that have allowed a comprehensive understanding of inversion variants through the pangenome framework and machine learning algorithms. Genome editing is an efficient method for inducing or reversing inversion mutations in plants, providing an effective mechanism to modify local recombination rates. Given the potential of inversions in crop breeding, we anticipate increasing attention on inversions from the scientific community in future research and breeding applications.
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Affiliation(s)
- Haifei Hu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co‐construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering LaboratoryGuangzhouChina
| | - Armin Scheben
- Simons Center for Quantitative Biology, Cold Spring Harbor LaboratoryCold Spring HarborNew YorkUSA
| | - Jian Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co‐construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering LaboratoryGuangzhouChina
| | - Fangping Li
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro‐BioresourcesSouth China Agricultural UniversityGuangzhouChina
| | - Chengdao Li
- Western Crop Genetics Alliance, Centre for Crop & Food Innovation, Food Futures Institute, College of Science, Health, Engineering and EducationMurdoch UniversityMurdochWestern AustraliaAustralia
| | - David Edwards
- School of Biological SciencesUniversity of Western AustraliaPerthWestern AustraliaAustralia
- Australia & Centre for Applied BioinformaticsUniversity of Western AustraliaPerthWestern AustraliaAustralia
| | - Junliang Zhao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co‐construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering LaboratoryGuangzhouChina
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3
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Vuong TD, Florez-Palacios L, Mozzoni L, Clubb M, Quigley C, Song Q, Kadam S, Yuan Y, Chan TF, Mian MAR, Nguyen HT. Genomic analysis and characterization of new loci associated with seed protein and oil content in soybeans. THE PLANT GENOME 2023; 16:e20400. [PMID: 37940622 DOI: 10.1002/tpg2.20400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 09/30/2023] [Accepted: 10/02/2023] [Indexed: 11/10/2023]
Abstract
Breeding for increased protein without a reduction in oil content in soybeans [Glycine max (L.) Merr.] is a challenge for soybean breeders but an expected goal. Many efforts have been made to develop new soybean varieties with high yield in combination with desirable protein and/or oil traits. An elite line, R05-1415, was reported to be high yielding, high protein, and low oil. Several significant quantitative trait loci (QTL) for protein and oil were reported in this line, but many of them were unstable across environments or genetic backgrounds. Thus, a new study under multiple field environments using the Infinium BARCSoySNP6K BeadChips was conducted to detect and confirm stable genomic loci for these traits. Genetic analyses consistently detected a single major genomic locus conveying these two traits with remarkably high phenotypic variation explained (R2 ), varying between 24.2% and 43.5%. This new genomic locus is located between 25.0 and 26.7 Mb, distant from the previously reported QTL and did not overlap with other commonly reported QTL and the recently cloned gene Glyma.20G085100. Homolog analysis indicated that this QTL did not result from the paracentric chromosome inversion with an adjacent genomic fragment that harbors the reported QTL. The pleiotropic effect of this QTL could be a challenge for improving protein and oil simultaneously; however, a further study of four candidate genes with significant expressions in the seed developmental stages coupled with haplotype analysis may be able to pinpoint causative genes. The functionality and roles of these genes can be determined and characterized, which lay a solid foundation for the improvement of protein and oil content in soybeans.
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Affiliation(s)
- Tri D Vuong
- Division of Plant Science and Technology, University of Missouri, Columbia, Missouri, USA
| | | | - Leandro Mozzoni
- Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas, USA
| | - Michael Clubb
- Division of Plant Science and Technology, the Fisher Delta Research, Extension and Education Center (FDREEC), University of Missouri, Portageville, Missouri, USA
| | - Chuck Quigley
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, Maryland, USA
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, Maryland, USA
| | - Shaila Kadam
- Division of Plant Science and Technology, University of Missouri, Columbia, Missouri, USA
| | - Yuxuan Yuan
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | - Ting Fung Chan
- School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, SAR, China
| | | | - Henry T Nguyen
- Division of Plant Science and Technology, University of Missouri, Columbia, Missouri, USA
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Bapat AR, Moran Lauter AN, Hufford MB, Boerman NA, Scott MP. The Ga1 locus of the genus Zea is associated with novel genome structures derived from multiple, independent nonhomologous recombination events. G3 (BETHESDA, MD.) 2023; 13:jkad196. [PMID: 37652030 PMCID: PMC10627281 DOI: 10.1093/g3journal/jkad196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/11/2023] [Accepted: 08/16/2023] [Indexed: 09/02/2023]
Abstract
The Ga1 locus controls cross-incompatibility between field corn and popcorn. The Ga1-S haplotype contains 2 types of pectin methylesterase (PME) genes, ZmPme3 and several copies of ZmGa1P that are expressed in silk and pollen, respectively. The ga1 haplotype contains nonfunctional tandem repeat sequences related to ZmPme3 and ZmGa1P. This haplotype can cross-pollinate freely and is widely present in field corn. The primary objective of this study is to characterize the repeat sequences from a diverse collection of maize and teosinte lines and use this information to understand the evolution of the Ga1 locus. First, we characterized the complexity of the Ga1 genome region in high-quality maize genome assemblies that led to their categorization into 5 groups based on the number and type of PME-like sequences found at this region. Second, we studied duplication events that led to the ga1 and Ga1-S repeats using maximum likelihood phylogenetic reconstruction. Divergence estimates of the ga1 haplotype suggest that the duplication events occurred more than 600 KYA whereas those in Ga1-S occurred at 3 time points, i.e. >600, ∼260, and ∼100 KYA. These estimates suggest that the ga1 and Ga1-S tandem duplication events occurred independently. Finally, analysis of ZmPme3 and ZmGa1P homologs in Zea and Tripsacum genomes suggests that ga1 and Ga1-S repeats originated from an ancestral pair of PME genes that duplicated and diverged through 2 evolutionary branches prior to the domestication of maize.
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Affiliation(s)
- Amruta R Bapat
- Interdepartmental Genetics and Genomics Program, Iowa State University, Ames, IA 50011, USA
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | | | - Matthew B Hufford
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | | | - M Paul Scott
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011, USA
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Zhao H, Wang W, Yang Y, Wang Z, Sun J, Yuan K, Rabbi SMHA, Khanam M, Kabir MS, Seraj ZI, Rahman MS, Zhang Z. A high-quality chromosome-level wild rice genome of Oryza coarctata. Sci Data 2023; 10:701. [PMID: 37838726 PMCID: PMC10576809 DOI: 10.1038/s41597-023-02594-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/25/2023] [Indexed: 10/16/2023] Open
Abstract
Oryza coarctata (2n = 4X = 48, KKLL) is an allotetraploid, undomesticated relative of rice and the only species in the genus Oryza with tolerance to high salinity and submergence. Therefore, it contains important stress and tolerance genes/factors for rice. The initial draft genome published was limited by data and technical restrictions, leading to an incomplete and highly fragmented assembly. This study reports a new, highly contiguous chromosome-level genome assembly and annotation of O. coarctata. PacBio high-quality HiFi reads generated 460 contigs with a total length of 573.4 Mb and an N50 of 23.1 Mb, which were assembled into scaffolds with Hi-C data, anchoring 96.99% of the assembly onto 24 chromosomes. The genome assembly comprises 45,571 genes, and repetitive content contributes 25.5% of the genome. This study provides the novel identification of the KK and LL genome types of the genus Oryza, leading to valuable insights into rice genome evolution. The chromosome-level genome assembly of O. coarctata is a valuable resource for rice research and molecular breeding.
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Affiliation(s)
- Hang Zhao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Gembloux Agro-Bio Tech, TERRA Teaching and Research Centre, University of Liège, Gembloux, Belgium
| | - Wenzheng Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yirong Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhiwei Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jing Sun
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Kaijun Yuan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Duke university, Durham, USA
| | | | - Munnujan Khanam
- Bangladesh Rice Research Institute, Gazipur, 1701, Bangladesh
| | | | - Zeba I Seraj
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | | | - Zhiguo Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Papon N, Lasserre-Zuber P, Rimbert H, De Oliveira R, Paux E, Choulet F. All families of transposable elements were active in the recent wheat genome evolution and polyploidy had no impact on their activity. THE PLANT GENOME 2023; 16:e20347. [PMID: 37243411 DOI: 10.1002/tpg2.20347] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 05/28/2023]
Abstract
Bread wheat (Triticum aestivum L.) is a major crop and its genome is one of the largest ever assembled at reference-quality level. It is 15 Gb, hexaploid, with 85% of transposable elements (TEs). Wheat genetic diversity was mainly focused on genes and little is known about the extent of genomic variability affecting TEs, transposition rate, and the impact of polyploidy. Multiple chromosome-scale assemblies are now available for bread wheat and for its tetraploid and diploid wild relatives. In this study, we computed base pair-resolved, gene-anchored, whole genome alignments of A, B, and D lineages at different ploidy levels in order to estimate the variability that affects the TE space. We used assembled genomes of 13 T. aestivum cultivars (6x = AABBDD) and a single genome for Triticum durum (4x = AABB), Triticum dicoccoides (4x = AABB), Triticum urartu (2x = AA), and Aegilops tauschii (2x = DD). We show that 5%-34% of the TE fraction is variable, depending on the species divergence. Between 400 and 13,000 novel TE insertions per subgenome were detected. We found lineage-specific insertions for nearly all TE families in di-, tetra-, and hexaploids. No burst of transposition was observed and polyploidization did not trigger any boost of transposition. This study challenges the prevailing idea of wheat TE dynamics and is more in agreement with an equilibrium model of evolution.
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Affiliation(s)
- Nathan Papon
- INRAE, GDEC, Université Clermont Auvergne, Clermont-Ferrand, France
| | | | - Hélène Rimbert
- INRAE, GDEC, Université Clermont Auvergne, Clermont-Ferrand, France
| | | | - Etienne Paux
- INRAE, GDEC, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Frédéric Choulet
- INRAE, GDEC, Université Clermont Auvergne, Clermont-Ferrand, France
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7
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Kim YK, Jo S, Cheon SH, Hong JR, Kim KJ. Ancient Horizontal Gene Transfers from Plastome to Mitogenome of a Nonphotosynthetic Orchid, Gastrodia pubilabiata (Epidendroideae, Orchidaceae). Int J Mol Sci 2023; 24:11448. [PMID: 37511216 PMCID: PMC10380568 DOI: 10.3390/ijms241411448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/08/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Gastrodia pubilabiata is a nonphotosynthetic and mycoheterotrophic orchid belonging to subfamily Epidendroideae. Compared to other typical angiosperm species, the plastome of G. pubilabiata is dramatically reduced in size to only 30,698 base pairs (bp). This reduction has led to the loss of most photosynthesis-related genes and some housekeeping genes in the plastome, which now only contains 19 protein coding genes, three tRNAs, and three rRNAs. In contrast, the typical orchid species contains 79 protein coding genes, 30 tRNAs, and four rRNAs. This study decoded the entire mitogenome of G. pubilabiata, which consisted of 44 contigs with a total length of 867,349 bp. Its mitogenome contained 38 protein coding genes, nine tRNAs, and three rRNAs. The gene content of G. pubilabiata mitogenome is similar to the typical plant mitogenomes even though the mitogenome size is twice as large as the typical ones. To determine possible gene transfer events between the plastome and the mitogenome individual BLASTN searches were conducted, using all available orchid plastome sequences and flowering plant mitogenome sequences. Plastid rRNA fragments were found at a high frequency in the mitogenome. Seven plastid protein coding gene fragments (ndhC, ndhJ, ndhK, psaA, psbF, rpoB, and rps4) were also identified in the mitogenome of G. pubilabiata. Phylogenetic trees using these seven plastid protein coding gene fragments suggested that horizontal gene transfer (HGT) from plastome to mitogenome occurred before losses of photosynthesis related genes, leading to the lineage of G. pubilabiata. Compared to species phylogeny of the lineage of orchid, it was estimated that HGT might have occurred approximately 30 million years ago.
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Affiliation(s)
- Young-Kee Kim
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Sangjin Jo
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
- International Biological Material Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Se-Hwan Cheon
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Ja-Ram Hong
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Ki-Joong Kim
- Division of Life Sciences, Korea University, Seoul 02841, Republic of Korea
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Abdul Aziz M, Masmoudi K. Insights into the Transcriptomics of Crop Wild Relatives to Unravel the Salinity Stress Adaptive Mechanisms. Int J Mol Sci 2023; 24:9813. [PMID: 37372961 DOI: 10.3390/ijms24129813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 06/29/2023] Open
Abstract
The narrow genomic diversity of modern cultivars is a major bottleneck for enhancing the crop's salinity stress tolerance. The close relatives of modern cultivated plants, crop wild relatives (CWRs), can be a promising and sustainable resource to broaden the diversity of crops. Advances in transcriptomic technologies have revealed the untapped genetic diversity of CWRs that represents a practical gene pool for improving the plant's adaptability to salt stress. Thus, the present study emphasizes the transcriptomics of CWRs for salinity stress tolerance. In this review, the impacts of salt stress on the plant's physiological processes and development are overviewed, and the transcription factors (TFs) regulation of salinity stress tolerance is investigated. In addition to the molecular regulation, a brief discussion on the phytomorphological adaptation of plants under saline environments is provided. The study further highlights the availability and use of transcriptomic resources of CWR and their contribution to pangenome construction. Moreover, the utilization of CWRs' genetic resources in the molecular breeding of crops for salinity stress tolerance is explored. Several studies have shown that cytoplasmic components such as calcium and kinases, and ion transporter genes such as Salt Overly Sensitive 1 (SOS1) and High-affinity Potassium Transporters (HKTs) are involved in the signaling of salt stress, and in mediating the distribution of excess Na+ ions within the plant cells. Recent comparative analyses of transcriptomic profiling through RNA sequencing (RNA-Seq) between the crops and their wild relatives have unraveled several TFs, stress-responsive genes, and regulatory proteins for generating salinity stress tolerance. This review specifies that the use of CWRs transcriptomics in combination with modern breeding experimental approaches such as genomic editing, de novo domestication, and speed breeding can accelerate the CWRs utilization in the breeding programs for enhancing the crop's adaptability to saline conditions. The transcriptomic approaches optimize the crop genomes with the accumulation of favorable alleles that will be indispensable for designing salt-resilient crops.
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Affiliation(s)
- Mughair Abdul Aziz
- Integrative Agriculture Department, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain 15551, United Arab Emirates
| | - Khaled Masmoudi
- Integrative Agriculture Department, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al Ain 15551, United Arab Emirates
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Duan W, Xue B, He Y, Liao S, Li X, Li X, Liang YK. Genome-Wide Identification and Expression Pattern Analysis of Dirigent Members in the Genus Oryza. Int J Mol Sci 2023; 24:ijms24087189. [PMID: 37108350 PMCID: PMC10138954 DOI: 10.3390/ijms24087189] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/10/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Dirigent (DIR) members have been shown to play essential roles in plant growth, development and adaptation to environmental changes. However, to date, there has been no systematic analysis of the DIR members in the genus Oryza. Here, 420 genes were identified from nine rice species to have the conserved DIR domain. Importantly, the cultivated rice species Oryza sativa has more DIR family members than the wild rice species. DIR proteins in rice could be classified into six subfamilies based on phylogeny analysis. Gene duplication event analysis suggests that whole genome/segmental duplication and tandem duplication are the primary drivers for DIR genes' evolution in Oryza, while tandem duplication is the main mechanism of gene family expansion in the DIR-b/d and DIR-c subfamilies. Analysis of the RNA sequencing data indicates that OsjDIR genes respond to a wide range of environmental factors, and most OsjDIR genes have a high expression level in roots. Qualitative reverse transcription PCR assays confirmed the responsiveness of OsjDIR genes to the undersupply of mineral elements, the excess of heavy metals and the infection of Rhizoctonia solani. Furthermore, there exist extensive interactions between DIR family members. Taken together, our results shed light on and provide a research foundation for the further exploration of DIR genes in rice.
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Affiliation(s)
- Wen Duan
- State Key Laboratory of Hybrid Rice, Department of Plant Sciences, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Baoping Xue
- State Key Laboratory of Hybrid Rice, Department of Plant Sciences, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yaqian He
- State Key Laboratory of Hybrid Rice, Department of Plant Sciences, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Shenghao Liao
- State Key Laboratory of Hybrid Rice, Department of Plant Sciences, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xuemei Li
- State Key Laboratory of Hybrid Rice, Department of Plant Sciences, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xueying Li
- State Key Laboratory of Hybrid Rice, Department of Plant Sciences, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yun-Kuan Liang
- State Key Laboratory of Hybrid Rice, Department of Plant Sciences, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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Alsantely A, Gutaker R, Navarrete Rodríguez ME, Arrieta-Espinoza G, Fuchs EJ, Costa de Oliveira A, Tohme J, Zuccolo A, Wing RA, Fornasiero A. The International Oryza Map Alignment Project (IOMAP): the Americas-past achievements and future directions. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:1331-1342. [PMID: 36527431 PMCID: PMC10010607 DOI: 10.1093/jxb/erac490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
The wild relatives of rice hold unexplored genetic diversity that can be employed to feed an estimated population of 10 billion by 2050. The Oryza Map Alignment Project (OMAP) initiated in 2003 has provided comprehensive genomic resources for comparative, evolutionary, and functional characterization of the wild relatives of rice, facilitating the cloning of >600 rice genes, including those for grain width (GW5) and submergence tolerance (SUB1A). Following in the footsteps of the original project, the goal of 'IOMAP: the Americas' is to investigate the present and historic genetic diversity of wild Oryza species endemic to the Americas through the sequencing of herbaria and in situ specimens. The generation of a large diversity panel describing past and current genetic status and potential erosion of genetic variation in the populations will provide useful knowledge for the conservation of the biodiversity in these species. The wild relatives of rice in the Americas present a wide range of resistance traits useful for crop improvement and neodomestication approaches. In the race against time for a sustainable food future, the neodomestication of the first cereal species recently accomplished in O. alta opens the door to the potential neodomestication of the other wild Oryza species in Americas.
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Affiliation(s)
- Aseel Alsantely
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Rafal Gutaker
- Royal Botanic Gardens, Kew, Kew Green, Richmond, Surrey TW9 3AE, UK
| | - María E Navarrete Rodríguez
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Griselda Arrieta-Espinoza
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, Ciudad de la Investigación-C.P., San José 11501-2050, Costa Rica
| | - Eric J Fuchs
- Escuela de Biología, Universidad de Costa Rica, San José 11501-2060, Costa Rica
| | - Antonio Costa de Oliveira
- Plant Genomics and Breeding Center, Eliseu Maciel School of Agronomy, Federal University of Pelotas, Pelotas-RS, Brazil
| | - Joe Tohme
- International Center for Tropical Agriculture (CIAT), Cali 763537, Colombia
| | - Andrea Zuccolo
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Crop Science Research Center, Sant’Anna School of Advanced Studies, Pisa 56127, Italy
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11
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Hu Y, Wang X, Xu Y, Yang H, Tong Z, Tian R, Xu S, Yu L, Guo Y, Shi P, Huang S, Yang G, Shi S, Wei F. Molecular mechanisms of adaptive evolution in wild animals and plants. SCIENCE CHINA. LIFE SCIENCES 2023; 66:453-495. [PMID: 36648611 PMCID: PMC9843154 DOI: 10.1007/s11427-022-2233-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 08/30/2022] [Indexed: 01/18/2023]
Abstract
Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution, an important strategy for species survival and persistence. Uncovering the molecular mechanisms of adaptive evolution is the key to understanding species diversification, phenotypic convergence, and inter-species interaction. As the genome sequences of more and more non-model organisms are becoming available, the focus of studies on molecular mechanisms of adaptive evolution has shifted from the candidate gene method to genetic mapping based on genome-wide scanning. In this study, we reviewed the latest research advances in wild animals and plants, focusing on adaptive traits, convergent evolution, and coevolution. Firstly, we focused on the adaptive evolution of morphological, behavioral, and physiological traits. Secondly, we reviewed the phenotypic convergences of life history traits and responding to environmental pressures, and the underlying molecular convergence mechanisms. Thirdly, we summarized the advances of coevolution, including the four main types: mutualism, parasitism, predation and competition. Overall, these latest advances greatly increase our understanding of the underlying molecular mechanisms for diverse adaptive traits and species interaction, demonstrating that the development of evolutionary biology has been greatly accelerated by multi-omics technologies. Finally, we highlighted the emerging trends and future prospects around the above three aspects of adaptive evolution.
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Affiliation(s)
- Yibo Hu
- CAS Key Lab of Animal Ecology and Conservation Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xiaoping Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Yongchao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hui Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zeyu Tong
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Ran Tian
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Shaohua Xu
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China.
| | - Yalong Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Peng Shi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Shuangquan Huang
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China.
| | - Guang Yang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Fuwen Wei
- CAS Key Lab of Animal Ecology and Conservation Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
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12
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Jayaraman A, Kang J, Antaki JF, Kirby BJ. The roles of sub-micron and microscale roughness on shear-driven thrombosis on titanium alloy surfaces. Artif Organs 2023; 47:490-501. [PMID: 36420933 PMCID: PMC10010941 DOI: 10.1111/aor.14467] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/19/2022] [Accepted: 11/09/2022] [Indexed: 11/27/2022]
Abstract
BACKGROUND Continuous-flow ventricular assist devices (cfVADs) are implanted in patients with end-stage heart failure to assist with blood circulation. However, VAD implantation is associated with dangerous thrombotic complications. Our goal was to determine the impact of micron and sub-micron scale Ti6Al4V surface roughness on adherent platelet aggregate properties under clinically relevant shear rates. METHODS We used fluorescence microscopy to visualize platelets in real time as they adhered to Ti6Al4V coupons of varying degrees of roughness, including a smooth control, in microfluidic channels and quantified deposition using an image processing algorithm. We systematically characterized roughness using spatial frequencies to generalize results for more blood-biomaterial contact applications. RESULTS We observed that on the control and sub-micron rough surfaces, at 1000 s-1 , platelets adhered uniformly on the surface. At 2000 s-1 , we observed small and stably adherent platelet aggregates. At 5500 s-1 , platelet aggregates were large, unstable and interconnected via fibrillar structures. On a surface with micron-scale roughness features, at all three shear rates, platelets deposited in the troughs of the roughened surface, and formed aggregates. Thrombus height at 2000 s-1 and 5500 s-1 was greatest on the roughest surface and lowest on the mirror-finished surface, as indicated by the mean fluorescence intensity. CONCLUSIONS These results demonstrated that at high shear rates, thrombi form regardless of surface topography at the scales applied. At lower shear rates, micron-scale surface features cause thrombus formation, whereas submicron features result in innocuous platelet adhesion. These findings have implications for manufacturing costs and other considerations.
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Affiliation(s)
- Anjana Jayaraman
- Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York, USA
| | - Junhyuk Kang
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York, USA
| | - James F Antaki
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA
| | - Brian J Kirby
- Sibley School of Mechanical and Aerospace Engineering, Cornell University, Ithaca, New York, USA
- Department of Medicine, Division of Hematology and Medical Oncology, Weill-Cornell Medicine, New York, New York, USA
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13
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Chase MW, Samuel R, Leitch AR, Guignard MS, Conran JG, Nollet F, Fletcher P, Jakob A, Cauz-Santos LA, Vignolle G, Dodsworth S, Christenhusz MJM, Buril MT, Paun O. Down, then up: non-parallel genome size changes and a descending chromosome series in a recent radiation of the Australian allotetraploid plant species, Nicotiana section Suaveolentes (Solanaceae). ANNALS OF BOTANY 2023; 131:123-142. [PMID: 35029647 PMCID: PMC9904355 DOI: 10.1093/aob/mcac006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 01/11/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS The extent to which genome size and chromosome numbers evolve in concert is little understood, particularly after polyploidy (whole-genome duplication), when a genome returns to a diploid-like condition (diploidization). We study this phenomenon in 46 species of allotetraploid Nicotiana section Suaveolentes (Solanaceae), which formed <6 million years ago and radiated in the arid centre of Australia. METHODS We analysed newly assessed genome sizes and chromosome numbers within the context of a restriction site-associated nuclear DNA (RADseq) phylogenetic framework. KEY RESULTS RADseq generated a well-supported phylogenetic tree, in which multiple accessions from each species formed unique genetic clusters. Chromosome numbers and genome sizes vary from n = 2x = 15 to 24 and 2.7 to 5.8 pg/1C nucleus, respectively. Decreases in both genome size and chromosome number occur, although neither consistently nor in parallel. Species with the lowest chromosome numbers (n = 15-18) do not possess the smallest genome sizes and, although N. heterantha has retained the ancestral chromosome complement, n = 2x = 24, it nonetheless has the smallest genome size, even smaller than that of the modern representatives of ancestral diploids. CONCLUSIONS The results indicate that decreases in genome size and chromosome number occur in parallel down to a chromosome number threshold, n = 20, below which genome size increases, a phenomenon potentially explained by decreasing rates of recombination over fewer chromosomes. We hypothesize that, more generally in plants, major decreases in genome size post-polyploidization take place while chromosome numbers are still high because in these stages elimination of retrotransposons and other repetitive elements is more efficient. Once such major genome size change has been accomplished, then dysploid chromosome reductions take place to reorganize these smaller genomes, producing species with small genomes and low chromosome numbers such as those observed in many annual angiosperms, including Arabidopsis.
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Affiliation(s)
- Mark W Chase
- Royal Botanic Gardens, Kew, Richmond TW9 3DS, UK
- Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Rosabelle Samuel
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | | | - John G Conran
- ACEBB & SGC, School of Biological Sciences, The University of Adelaide, SA 5005Australia
| | - Felipe Nollet
- Universidade Federal Rural de Pernambuco, Centro de Ciências Biológicas, Departamento de Botânica, Rua Manuel de Medeiros, S/N, Dois Irmãos, 52171-900 Recife, Pernambuco, Brazil
| | - Paul Fletcher
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Aljaž Jakob
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Luiz A Cauz-Santos
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Gabriel Vignolle
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
| | - Steven Dodsworth
- School of Biological Sciences, University of Portsmouth, Portsmouth PO1 2DY, UK
| | - Maarten J M Christenhusz
- Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
| | - Maria Teresa Buril
- ACEBB & SGC, School of Biological Sciences, The University of Adelaide, SA 5005Australia
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, A-1030 Vienna, Austria
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14
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Sun Y, Liu Y, Shi J, Wang L, Liang C, Yang J, Chen J, Chen M. Biased mutations and gene losses underlying diploidization of the tetraploid broomcorn millet genome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:787-801. [PMID: 36575912 DOI: 10.1111/tpj.16085] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/07/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
Broomcorn millet (Panicum miliaceum L.) is one of the earliest domesticated crops, and is a valuable resource to secure food diversity and combat drought stresses under the global warming scenario. However, due to the absence of extant diploid progenitors, the polyploidy genome of broomcorn millet remains poorly understood. Here, we report the chromosome-scale genome assembly of broomcorn millet. We divided the broomcorn millet genome into two subgenomes using the genome sequence of Panicum hallii, a diploid relative of broomcorn millet. Our analyses revealed that the two subgenomes diverged at ~4.8 million years ago (Mya), while the allotetraploidization of broomcorn millet may have occurred about ~0.48 Mya, suggesting that broomcorn millet is a relatively recent allotetraploid. Comparative analyses showed that subgenome B was larger than subgenome A in size, which was caused by the biased accumulation of long terminal repeat retrotransposons in the progenitor of subgenome B before polyploidization. Notably, the accumulation of biased mutations in the transposable element-rich subgenome B led to more gene losses. Although no significant dominance of either subgenome was observed in the expression profiles of broomcorn millet, we found the minimally expressed genes in P. hallii tended to be lost during diploidization of broomcorn millet. These results suggest that broomcorn millet is at the early stage of diploidization and that mutations likely occurred more on genes that were marked with lower expression levels.
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Affiliation(s)
- Yanling Sun
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100039, Beijing, China
| | - Yang Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100039, Beijing, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Jinfeng Shi
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Lun Wang
- Institute of Crop Germplasm Resources, Shanxi Academy of Agricultural Sciences, 030031, Taiyuan, China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100039, Beijing, China
| | - Jun Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, 201602, Shanghai, China
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Jinfeng Chen
- University of Chinese Academy of Sciences, 100039, Beijing, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100039, Beijing, China
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15
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Que Z, Lu Q, Shen C. Chromosome-level genome assembly of Dongxiang wild rice (Oryza rufipogon) provides insights into resistance to disease and freezing. Front Genet 2022; 13:1029879. [DOI: 10.3389/fgene.2022.1029879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 10/31/2022] [Indexed: 11/16/2022] Open
Abstract
Dongxiang wild rice (DXWR, Oryza rufipogon Griff.) belongs to common wild rice O. rufipogon, which is the well-known ancestral progenitor of cultivated rice, possessing important gene resources for rice breeding. However, the distribution of DXWR is decreasing rapidly, and no reference genome has been published to date. In this study, we constructed a chromosome-level reference genome of DXWR by Oxford Nanopore Technology (ONT) and High-through chromosome conformation capture (Hi-C). A total of 58.41 Gb clean data from ONT were de novo assembled into 231 contigs with the total length of 413.46 Mb and N50 length of 5.18 Mb. These contigs were clustered and ordered into 12 pseudo-chromosomes covering about 97.39% assembly with Hi-C data, with a scaffold N50 length of 33.47 Mb. Moreover, 54.10% of the genome sequences were identified as repeat sequences. 33,862 (94.21%) genes were functionally annotated from a total of predicted 35,942 protein-coding sequences. Compared with other species of Oryza genus, the genes related to disease and cold resistance in DXWR had undergone a large-scale expansion, which may be one of the reasons for the stronger disease resistance and cold resistance of DXWR. Comparative transcriptome analysis also determined a list of differentially expressed genes under normal and cold treatment, which supported DXWR as a cold-tolerant variety. The collinearity between DXWR and cultivated rice was high, but there were still some significant structural variations, including a specific inversion on chromosome 11, which may be related to the differentiation of DXWR. The high-quality chromosome-level reference genome of DXWR assembled in this study will become a valuable resource for rice molecular breeding and genetic research in the future.
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16
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Zattera ML, Bruschi DP. Transposable Elements as a Source of Novel Repetitive DNA in the Eukaryote Genome. Cells 2022; 11:cells11213373. [PMID: 36359770 PMCID: PMC9659126 DOI: 10.3390/cells11213373] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 12/02/2022] Open
Abstract
The impact of transposable elements (TEs) on the evolution of the eukaryote genome has been observed in a number of biological processes, such as the recruitment of the host’s gene expression network or the rearrangement of genome structure. However, TEs may also provide a substrate for the emergence of novel repetitive elements, which contribute to the generation of new genomic components during the course of the evolutionary process. In this review, we examine published descriptions of TEs that give rise to tandem sequences in an attempt to comprehend the relationship between TEs and the emergence of de novo satellite DNA families in eukaryotic organisms. We evaluated the intragenomic behavior of the TEs, the role of their molecular structure, and the chromosomal distribution of the paralogous copies that generate arrays of repeats as a substrate for the emergence of new repetitive elements in the genome. We highlight the involvement and importance of TEs in the eukaryote genome and its remodeling processes.
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Affiliation(s)
- Michelle Louise Zattera
- Departamento de Genética, Programa de Pós-Graduação em Genética, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba 81530-000, PR, Brazil
| | - Daniel Pacheco Bruschi
- Departamento de Genética, Laboratorio de Citogenética Evolutiva e Conservação Animal, Setor de Ciências Biológicas, Universidade Federal do Paraná, Curitiba 81530-000, PR, Brazil
- Correspondence:
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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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18
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Chromosome-Level Genome Assembly of a Fragrant Japonica Rice Cultivar 'Changxianggeng 1813' Provides Insights into Genomic Variations between Fragrant and Non-Fragrant Japonica Rice. Int J Mol Sci 2022; 23:ijms23179705. [PMID: 36077110 PMCID: PMC9456513 DOI: 10.3390/ijms23179705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/24/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
East Asia has an abundant resource of fragrant japonica rice that is gaining increasing interest among both consumers and producers. However, genomic resources and in particular complete genome sequences currently available for the breeding of fragrant japonica rice are still scarce. Here, integrating Nanopore long-read sequencing, Illumina short-read sequencing, and Hi-C methods, we presented a high-quality chromosome-level genome assembly (~378.78 Mb) for a new fragrant japonica cultivar ‘Changxianggeng 1813’, with 31,671 predicated protein-coding genes. Based on the annotated genome sequence, we demonstrated that it was the badh2-E2 type of deletion (a 7-bp deletion in the second exon) that caused fragrance in ‘Changxianggeng 1813’. Comparative genomic analyses revealed that multiple gene families involved in the abiotic stress response were expanded in the ‘Changxianggeng 1813’ genome, which further supported the previous finding that no generalized loss of abiotic stress tolerance associated with the fragrance phenotype. Although the ‘Changxianggeng 1813’ genome showed high genomic synteny with the genome of the non-fragrant japonica rice cultivar Nipponbare, a total of 289,970 single nucleotide polymorphisms (SNPs), 96,093 small insertion-deletion polymorphisms (InDels), and 8690 large structure variants (SVs, >1000 bp) were identified between them. Together, these genomic resources will be valuable for elucidating the mechanisms underlying economically important traits and have wide-ranging implications for genomics-assisted breeding in fragrant japonica rice.
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Shi T, Huneau C, Zhang Y, Li Y, Chen J, Salse J, Wang Q. The slow-evolving Acorus tatarinowii genome sheds light on ancestral monocot evolution. NATURE PLANTS 2022; 8:764-777. [PMID: 35835857 PMCID: PMC9300462 DOI: 10.1038/s41477-022-01187-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 05/30/2022] [Indexed: 05/03/2023]
Abstract
Monocots are one of the most diverse groups of flowering plants, and tracing the evolution of their ancestral genome into modern species is essential for understanding their evolutionary success. Here, we report a high-quality assembly of the Acorus tatarinowii genome, a species that diverged early from all the other monocots. Genome-wide comparisons with a range of representative monocots characterized Acorus as a slowly evolved genome with one whole-genome duplication. Our inference of the ancestral monocot karyotypes provides new insights into the chromosomal evolutionary history assigned to modern species and reveals the probable molecular functions and processes related to the early adaptation of monocots to wetland or aquatic habitats (that is, low levels of inorganic phosphate, parallel leaf venation and ephemeral primary roots). The evolution of ancestral gene order in monocots is constrained by gene structural and functional features. The newly obtained Acorus genome offers crucial evidence for delineating the origin and diversification of monocots, including grasses.
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Affiliation(s)
- Tao Shi
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Cécile Huneau
- UCA, INRAE, UMR 1095 GDEC (Genetics, Diversity & Ecophysiology of Cereals), Clermont-Ferrand, France
| | - Yue Zhang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Li
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinming Chen
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China.
| | - Jérôme Salse
- UCA, INRAE, UMR 1095 GDEC (Genetics, Diversity & Ecophysiology of Cereals), Clermont-Ferrand, France.
| | - Qingfeng Wang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China.
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, China.
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20
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Chang L, Hu M, Ning J, He W, Gao J, Ndjiondjop MN, Fu Y, Liu F, Sun H, Gu P, Sun C, Zhu Z. The genetic control of glabrous glume during African rice domestication. J Genet Genomics 2022; 49:427-436. [DOI: 10.1016/j.jgg.2022.02.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 11/27/2022]
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21
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Di Marsico M, Paytuvi Gallart A, Sanseverino W, Aiese Cigliano R. GreeNC 2.0: a comprehensive database of plant long non-coding RNAs. Nucleic Acids Res 2022; 50:D1442-D1447. [PMID: 34723326 PMCID: PMC8728176 DOI: 10.1093/nar/gkab1014] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 02/04/2023] Open
Abstract
The Green Non-Coding Database (GreeNC) is one of the reference databases for the study of plant long non-coding RNAs (lncRNAs). Here we present our most recent update where 16 species have been updated, while 78 species have been added, resulting in the annotation of more than 495 000 lncRNAs. Moreover, sequence clustering was applied providing information about sequence conservation and gene families. The current version of the database is available at: http://greenc.sequentiabiotech.com/wiki2/Main_Page.
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Affiliation(s)
- Marco Di Marsico
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Università degli Studi di Perugia, Borgo XX Giugno 74, 06121 Perugia, Italy
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22
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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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Li F, Han Z, Qiao W, Wang J, Song Y, Cui Y, Li J, Ge J, Lou D, Fan W, Li D, Nong B, Zhang Z, Cheng Y, Zhang L, Zheng X, Yang Q. High-Quality Genomes and High-Density Genetic Map Facilitate the Identification of Genes From a Weedy Rice. FRONTIERS IN PLANT SCIENCE 2021; 12:775051. [PMID: 34868173 PMCID: PMC8639688 DOI: 10.3389/fpls.2021.775051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
Genes have been lost or weakened from cultivated rice during rice domestication and breeding. Weedy rice (Oryza sativa f. spontanea) is usually recognized as the progeny between cultivated rice and wild rice and is also known to harbor an gene pool for rice breeding. Therefore, identifying genes from weedy rice germplasms is an important way to break the bottleneck of rice breeding. To discover genes from weedy rice germplasms, we constructed a genetic map based on w-hole-genome sequencing of a F2 population derived from the cross between LM8 and a cultivated rice variety. We further identified 31 QTLs associated with 12 important agronomic traits and revealed that ORUFILM03g000095 gene may play an important role in grain length regulation and participate in grain formation. To clarify the genomic characteristics from weedy rice germplasms of LM8, we generated a high-quality genome assembly using single-molecule sequencing, Bionano optical mapping, and Hi-C technologies. The genome harbored a total size of 375.8 Mb, a scaffold N50 of 24.1 Mb, and originated approximately 0.32 million years ago (Mya) and was more closely related to Oryza sativa ssp. japonica. and contained 672 unique genes. It is related to the formation of grain shape, heading date and tillering. This study generated a high-quality reference genome of weedy rice and high-density genetic map that would benefit the analysis of genome evolution for related species and suggested an effective way to identify genes related to important agronomic traits for further rice breeding.
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Affiliation(s)
- Fei Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhenyun Han
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weihua Qiao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junrui Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning, China
| | - Yue Song
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongxia Cui
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- School of Clinical Medicine, Southwest Medical University, Luzhou, China
| | - Jiaqi Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Little Berry Research Room, Liaoning Institute of Fruit Science, Yingkou, China
| | - Jinyue Ge
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Danjing Lou
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weiya Fan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Danting Li
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Baoxuan Nong
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Zongqiong Zhang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Yunlian Cheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lifang Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoming Zheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qingwen Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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24
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Bohra A, Kilian B, Sivasankar S, Caccamo M, Mba C, McCouch SR, Varshney RK. Reap the crop wild relatives for breeding future crops. Trends Biotechnol 2021; 40:412-431. [PMID: 34629170 DOI: 10.1016/j.tibtech.2021.08.009] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/30/2021] [Accepted: 08/30/2021] [Indexed: 02/07/2023]
Abstract
Crop wild relatives (CWRs) have provided breeders with several 'game-changing' traits or genes that have boosted crop resilience and global agricultural production. Advances in breeding and genomics have accelerated the identification of valuable CWRs for use in crop improvement. The enhanced genetic diversity of breeding pools carrying optimum combinations of favorable alleles for targeted crop-growing regions is crucial to sustain genetic gain. In parallel, growing sequence information on wild genomes in combination with precise gene-editing tools provide a fast-track route to transform CWRs into ideal future crops. Data-informed germplasm collection and management strategies together with adequate policy support will be equally important to improve access to CWRs and their sustainable use to meet food and nutrition security targets.
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Affiliation(s)
- Abhishek Bohra
- ICAR-Indian Institute of Pulses Research (IIPR), 208024 Kanpur, India
| | | | - Shoba Sivasankar
- International Atomic Energy Agency (IAEA), Vienna International Centre, 1400 Vienna, Austria
| | | | - Chikelu Mba
- Food and Agriculture Organization of the United Nations (FAO), Rome 00153, Italy
| | - Susan R McCouch
- Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, Ithaca, NY 14850, USA.
| | - Rajeev K Varshney
- Centre of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA 6150, Australia.
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25
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Białas A, Langner T, Harant A, Contreras MP, Stevenson CEM, Lawson DM, Sklenar J, Kellner R, Moscou MJ, Terauchi R, Banfield MJ, Kamoun S. Two NLR immune receptors acquired high-affinity binding to a fungal effector through convergent evolution of their integrated domain. eLife 2021; 10:e66961. [PMID: 34288868 PMCID: PMC8294853 DOI: 10.7554/elife.66961] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 07/01/2021] [Indexed: 12/17/2022] Open
Abstract
A subset of plant NLR immune receptors carry unconventional integrated domains in addition to their canonical domain architecture. One example is rice Pik-1 that comprises an integrated heavy metal-associated (HMA) domain. Here, we reconstructed the evolutionary history of Pik-1 and its NLR partner, Pik-2, and tested hypotheses about adaptive evolution of the HMA domain. Phylogenetic analyses revealed that the HMA domain integrated into Pik-1 before Oryzinae speciation over 15 million years ago and has been under diversifying selection. Ancestral sequence reconstruction coupled with functional studies showed that two Pik-1 allelic variants independently evolved from a weakly binding ancestral state to high-affinity binding of the blast fungus effector AVR-PikD. We conclude that for most of its evolutionary history the Pik-1 HMA domain did not sense AVR-PikD, and that different Pik-1 receptors have recently evolved through distinct biochemical paths to produce similar phenotypic outcomes. These findings highlight the dynamic nature of the evolutionary mechanisms underpinning NLR adaptation to plant pathogens.
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Affiliation(s)
- Aleksandra Białas
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Thorsten Langner
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Adeline Harant
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Mauricio P Contreras
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Clare EM Stevenson
- Department of Biological Chemistry, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Jan Sklenar
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Ronny Kellner
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Matthew J Moscou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
| | - Ryohei Terauchi
- Division of Genomics and Breeding, Iwate Biotechnology Research CentreIwateJapan
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto UniversityKyotoJapan
| | - Mark J Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich Research ParkNorwichUnited Kingdom
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research ParkNorwichUnited Kingdom
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26
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Białas A, Langner T, Harant A, Contreras MP, Stevenson CE, Lawson DM, Sklenar J, Kellner R, Moscou MJ, Terauchi R, Banfield MJ, Kamoun S. Two NLR immune receptors acquired high-affinity binding to a fungal effector through convergent evolution of their integrated domain. eLife 2021; 10:66961. [PMID: 34288868 DOI: 10.1101/2021.01.26.428286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 07/01/2021] [Indexed: 05/21/2023] Open
Abstract
A subset of plant NLR immune receptors carry unconventional integrated domains in addition to their canonical domain architecture. One example is rice Pik-1 that comprises an integrated heavy metal-associated (HMA) domain. Here, we reconstructed the evolutionary history of Pik-1 and its NLR partner, Pik-2, and tested hypotheses about adaptive evolution of the HMA domain. Phylogenetic analyses revealed that the HMA domain integrated into Pik-1 before Oryzinae speciation over 15 million years ago and has been under diversifying selection. Ancestral sequence reconstruction coupled with functional studies showed that two Pik-1 allelic variants independently evolved from a weakly binding ancestral state to high-affinity binding of the blast fungus effector AVR-PikD. We conclude that for most of its evolutionary history the Pik-1 HMA domain did not sense AVR-PikD, and that different Pik-1 receptors have recently evolved through distinct biochemical paths to produce similar phenotypic outcomes. These findings highlight the dynamic nature of the evolutionary mechanisms underpinning NLR adaptation to plant pathogens.
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Affiliation(s)
- Aleksandra Białas
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Thorsten Langner
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Adeline Harant
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Mauricio P Contreras
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Clare Em Stevenson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - David M Lawson
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Jan Sklenar
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Ronny Kellner
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Matthew J Moscou
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Ryohei Terauchi
- Division of Genomics and Breeding, Iwate Biotechnology Research Centre, Iwate, Japan
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Mark J Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
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27
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Sato Y, Tsuda K, Yamagata Y, Matsusaka H, Kajiya-Kanegae H, Yoshida Y, Agata A, Ta KN, Shimizu-Sato S, Suzuki T, Nosaka-Takahashi M, Kubo T, Kawamoto S, Nonomura KI, Yasui H, Kumamaru T. Collection, preservation and distribution of Oryza genetic resources by the National Bioresource Project RICE (NBRP-RICE). BREEDING SCIENCE 2021; 71:291-298. [PMID: 34776736 PMCID: PMC8573556 DOI: 10.1270/jsbbs.21005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/15/2021] [Indexed: 05/26/2023]
Abstract
Biological resources are the basic infrastructure of bioscience research. Rice (Oryza sativa L.) is a good experimental model for research in cereal crops and monocots and includes important genetic materials used in breeding. The availability of genetic materials, including mutants, is important for rice research. In addition, Oryza species are attractive to researchers for both finding useful genes for breeding and for understanding the mechanism of genome evolution that enables wild plants to adapt to their own habitats. NBRP-RICE contributes to rice research by promoting the usage of genetic materials, especially wild Oryza accessions and mutant lines. Our activity includes collection, preservation and distribution of those materials and the provision of basic information on them, such as morphological and physiological traits and genomic information. In this review paper, we introduce the activities of NBRP-RICE and our database, Oryzabase, which facilitates the access to NBRP-RICE resources and their genomic sequences as well as the current situation of wild Oryza genome sequencing efforts by NBRP-RICE and other institutes.
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Affiliation(s)
- Yutaka Sato
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Katsutoshi Tsuda
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Yoshiyuki Yamagata
- Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku Fukuoka 819-0395, Japan
| | - Hiroaki Matsusaka
- Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku Fukuoka 819-0395, Japan
| | - Hiromi Kajiya-Kanegae
- Research Center for Agricultural Information Technology, National Agriculture and Food Research Organization, Chiyoda-ku, Tokyo 100-0013, Japan
| | - Yuri Yoshida
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Ayumi Agata
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Kim Nhung Ta
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Sae Shimizu-Sato
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Toshiya Suzuki
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Misuzu Nosaka-Takahashi
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Takahiko Kubo
- Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku Fukuoka 819-0395, Japan
| | - Shoko Kawamoto
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Ken-Ichi Nonomura
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Hideshi Yasui
- Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku Fukuoka 819-0395, Japan
| | - Toshihiro Kumamaru
- Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku Fukuoka 819-0395, Japan
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28
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Tian P, Zhang X, Xia R, Liu Y, Wang M, Li B, Liu T, Shi J, Wing RA, Meyers BC, Chen M. Evolution and diversification of reproductive phased small interfering RNAs in Oryza species. THE NEW PHYTOLOGIST 2021; 229:2970-2983. [PMID: 33111313 DOI: 10.1111/nph.17035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 10/12/2020] [Indexed: 05/20/2023]
Abstract
In grasses, two types of phased, small interfering RNAs (phasiRNAs) are expressed largely in young, developing anthers. They are 21 or 24 nucleotides (nt) in length and are triggered by miR2118 or miR2275, respectively. However, most of their functions and activities are not fully understood. We performed comparative genomic analysis of their source loci (PHAS) in five Oryza genomes and combined this with analysis of high-throughput sRNA and degradome datasets. In total, we identified 8216 21-PHAS and 626 24-PHAS loci. Local tandem and segmental duplications mainly contributed to the expansion and supercluster distribution of the 21-PHAS loci. Despite their relatively conserved genomic positions, PHAS sequences diverged rapidly, except for the miR2118/2275 target sites, which were under strong selection for conservation. We found that 21-nt phasiRNAs with a 5'-terminal uridine (U) demonstrated cis-cleavage at PHAS precursors, and these cis-acting sites were also variable among close species. miR2118 could trigger phasiRNA production from its own antisense transcript and the derived phasiRNAs might reversibly regulate miR2118 precursors. We hypothesised that successful initiation of phasiRNA biogenesis is conservatively maintained, while phasiRNA products diverged quickly and are not individually conserved. In particular, phasiRNA production is under the control of multiple reciprocal regulation mechanisms.
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Affiliation(s)
- Peng Tian
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Xuemei Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Yang Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Meijiao Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Bo Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tieyan Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinfeng Shi
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Rod A Wing
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Blake C Meyers
- Division of Plant Sciences, 52 Agriculture Laboratory, University of Missouri, Columbia, Missouri, 65211, USA
- Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO, 63132, USA
| | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
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29
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Yu H, Lin T, Meng X, Du H, Zhang J, Liu G, Chen M, Jing Y, Kou L, Li X, Gao Q, Liang Y, Liu X, Fan Z, Liang Y, Cheng Z, Chen M, Tian Z, Wang Y, Chu C, Zuo J, Wan J, Qian Q, Han B, Zuccolo A, Wing RA, Gao C, Liang C, Li J. A route to de novo domestication of wild allotetraploid rice. Cell 2021; 184:1156-1170.e14. [PMID: 33539781 DOI: 10.1016/j.cell.2021.01.013] [Citation(s) in RCA: 188] [Impact Index Per Article: 62.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 12/02/2020] [Accepted: 01/11/2021] [Indexed: 12/25/2022]
Abstract
Cultivated rice varieties are all diploid, and polyploidization of rice has long been desired because of its advantages in genome buffering, vigorousness, and environmental robustness. However, a workable route remains elusive. Here, we describe a practical strategy, namely de novo domestication of wild allotetraploid rice. By screening allotetraploid wild rice inventory, we identified one genotype of Oryza alta (CCDD), polyploid rice 1 (PPR1), and established two important resources for its de novo domestication: (1) an efficient tissue culture, transformation, and genome editing system and (2) a high-quality genome assembly discriminated into two subgenomes of 12 chromosomes apiece. With these resources, we show that six agronomically important traits could be rapidly improved by editing O. alta homologs of the genes controlling these traits in diploid rice. Our results demonstrate the possibility that de novo domesticated allotetraploid rice can be developed into a new staple cereal to strengthen world food security.
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Affiliation(s)
- Hong Yu
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
| | - Tao Lin
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiangbing Meng
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Huilong Du
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingkun Zhang
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guifu Liu
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Mingjiang Chen
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yanhui Jing
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Liquan Kou
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiuxiu Li
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Gao
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Liang
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiangdong Liu
- Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou 510642, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Zhilan Fan
- National Field Genebank for Wild Rice (Guangzhou), Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Yuntao Liang
- Rice Research Institute, Guangxi Academy of Agricultural Science, Nanning 530007, China
| | - Zhukuan Cheng
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhixi Tian
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yonghong Wang
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chengcai Chu
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianru Zuo
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianmin Wan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Bin Han
- National Center of Plant Gene Research Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences and CAS Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Andrea Zuccolo
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa 56127, Italy
| | - Rod A Wing
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Caixia Gao
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Jiayang Li
- State Key Laboratory of Plant Genomics, and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou 510642, China.
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Zou X, Du Y, Wang X, Wang Q, Zhang B, Chen J, Chen M, Doyle JJ, Ge S. Genome evolution in Oryza allopolyploids of various ages: Insights into the process of diploidization. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:721-735. [PMID: 33145857 DOI: 10.1111/tpj.15066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 09/18/2020] [Accepted: 10/28/2020] [Indexed: 05/20/2023]
Abstract
The prevalence and recurrence of whole-genome duplication in plants and its major role in evolution have been well recognized. Despite great efforts, many aspects of genome evolution, particularly the temporal progression of genomic responses to allopolyploidy and the underlying mechanisms, remain poorly understood. The rice genus Oryza consists of both recently formed and older allopolyploid species, representing an attractive system for studying the genome evolution after allopolyploidy. In this study, through screening BAC libraries and sequencing and annotating the targeted BAC clones, we generated orthologous genomic sequences surrounding the DEP1 locus, a major grain yield QTL in cultivated rice, from four Oryza polyploids of various ages and their likely diploid genome donors or close relatives. Based on sequenced DEP1 region and published data from three other genomic regions, we investigated the temporal evolutionary dynamics of four polyploid genomes at both genetic and expression levels. In the recently formed BBCC polyploid, Oryza minuta, genome dominance was not observed and its short-term responses to allopolyploidy are mainly manifested as a high proportion of homoeologous gene pairs showing unequal expression. This could partly be explained by parental legacy, rewiring of divergent regulatory networks and epigenetic modulation. Moreover, we detected an ongoing diploidization process in this genus, and suggest that the expression divergence driven by changes of selective constraint probably plays a big role in the long-term diploidization. These findings add novel insights into our understanding of genome evolution after allopolyploidy, and could facilitate crop improvements through hybridization and polyploidization.
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Affiliation(s)
- Xinhui Zou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yusu Du
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xin Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qian Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bing Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jinfeng Chen
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Mingsheng Chen
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jeff J Doyle
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York, 14853, USA
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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31
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Wambugu PW, Ndjiondjop MN, Henry R. Genetics and Genomics of African Rice (Oryza glaberrima Steud) Domestication. RICE (NEW YORK, N.Y.) 2021; 14:6. [PMID: 33415579 PMCID: PMC7790969 DOI: 10.1186/s12284-020-00449-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
African rice (Oryza glaberrima Steud) is one of the two independently domesticated rice species, the other one being Asian rice (Oryza sativa L.). Despite major progress being made in understanding the evolutionary and domestication history of African rice, key outstanding issues remain controversial. There appears to be an underlying difficulty in identifying the domestication centre and number of times the crop has been domesticated. Advances in genomics have provided unprecedented opportunities for understanding the genetic architecture of domestication related traits. For most of the domestication traits, the underlying genes and mutations have been identified. Comparative analysis of domestication genes between Asian and African rice has revealed that the two species went through an independent but convergent evolution process. The genetic and developmental basis of some of the domestic traits are conserved not only between Asian and African rice but also with other domesticated crop species. Analysis of genome data and its interpretation is emerging as a major challenge facing studies of domestication in African rice as key studies continue giving contradictory findings and conclusions. Insights obtained on the domestication of this species are vital for guiding crop improvement efforts.
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Affiliation(s)
- Peterson W. Wambugu
- Kenya Agricultural and Livestock Research Organization, Genetic Resources Research Institute, P.O. Box 30148, Nairobi, 00100 Kenya
| | - Marie-Noelle Ndjiondjop
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551 Bouaké 01, Côte d’Ivoire
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072 Australia
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32
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Wang L, Conteh B, Fang L, Xia Q, Nian H. QTL mapping for soybean (Glycine max L.) leaf chlorophyll-content traits in a genotyped RIL population by using RAD-seq based high-density linkage map. BMC Genomics 2020; 21:739. [PMID: 33096992 PMCID: PMC7585201 DOI: 10.1186/s12864-020-07150-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 10/13/2020] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Different soybean (Glycine max L.) leaf chlorophyll-content traits are considered to be significantly linked to soybean yield. To map the quantitative trait loci (QTLs) of soybean leaf chlorophyll-content traits, an advanced recombinant inbred line (RIL, ZH, Zhonghuang 24 × Huaxia 3) population was adopted to phenotypic data acquisitions for the target traits across six distinct environments (seasons and soybean growth stages). Moreover, the restriction site-associated DNA sequencing (RAD-seq) based high-density genetic linkage map of the RIL population was utilized for QTL mapping by carrying out the composite interval mapping (CIM) approach. RESULTS Correlation analyses showed that most traits were correlated with each other under specific chlorophyll assessing method and were regulated both by hereditary and environmental factors. In this study, 78 QTLs for soybean leaf chlorophyll-content traits were identified. Furthermore, 13 major QTLs and five important QTL hotspots were classified and highlighted from the detected QTLs. Finally, Glyma01g15506, Glyma02g08910, Glyma02g11110, Glyma07g15960, Glyma15g19670 and Glyma15g19810 were predicted from the genetic intervals of the major QTLs and important QTL hotspots. CONCLUSIONS The detected QTLs and candidate genes may facilitate to gain a better understanding of the hereditary basis of soybean leaf chlorophyll-content traits and may be valuable to pave the way for the marker-assisted selection (MAS) breeding of the target traits.
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Affiliation(s)
- Liang Wang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095 People’s Republic of China
| | - Brima Conteh
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
| | - Linzhi Fang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
| | - Qiuju Xia
- Beijing Genomics Institute (BGI) Education Center, University of Chinese Academy of Sciences, Shenzhen, 518083 Guangdong People’s Republic of China
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
- Guangdong Provincial Laboratory of Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, 510642 Guangdong People’s Republic of China
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Shen E, Chen T, Zhu X, Fan L, Sun J, Llewellyn DJ, Wilson I, Zhu QH. Expansion of MIR482/2118 by a class-II transposable element in cotton. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:2084-2099. [PMID: 32578284 DOI: 10.1111/tpj.14885] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 05/28/2020] [Accepted: 06/05/2020] [Indexed: 06/11/2023]
Abstract
Some plant microRNA (miRNA) families contain multiple members generating identical or highly similar mature miRNA variants. Mechanisms underlying the expansion of miRNA families remain elusive, although tandem and/or segmental duplications have been proposed. In this study of two tetraploid cottons, Gossypium hirsutum and Gossypium barbadense, and their extant diploid progenitors, Gossypium arboreum and Gossypium raimondii, we investigated the gain and loss of members of the miR482/2118 superfamily, which modulates the expression of nucleotide-binding site leucine-rich repeat (NBS-LRR) disease resistance genes. We found significant expansion of MIR482/2118d in G. barbadense, G. hirsutum and G. raimondii, but not in G. arboreum. Several newly expanded MIR482/2118d loci have mutated to produce different miR482/2118 variants with altered target-gene specificity. Based on detailed analysis of sequences flanking these MIR482/2118 loci, we found that this expansion of MIR482/2118d and its derivatives resulted from an initial capture of an MIR482/2118d by a class-II DNA transposable element (TE) in G. raimondii prior to the tetraploidization event, followed by transposition to new genomic locations in G. barbadense, G. hirsutum and G. raimondii. The 'GosTE' involved in the capture and proliferation of MIR482/2118d and its derivatives belongs to the PIF/Harbinger superfamily, generating a 3-bp target site duplication upon insertion at new locations. All orthologous MIR482/2118 loci in the two diploids were retained in the two tetraploids, but mutation(s) in miR482/2118 were observed across all four species as well as in different cultivars of both G. barbadense and G. hirsutum, suggesting a dynamic co-evolution of miR482/2118 and its NBS-LRR targets. Our results provide fresh insights into the mechanisms contributing to MIRNA proliferation and enrich our knowledge on TEs.
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Affiliation(s)
- Enhui Shen
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- New Rural Development Institute, Zhejiang University, Hangzhou, 310058, China
| | - Tianzi Chen
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Xintian Zhu
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Longjiang Fan
- Institute of Crop Sciences and Institute of Bioinformatics, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jie Sun
- Key Laboratory of Oasis Eco-agriculture, College of Agriculture, Shihezi University, Shihezi, Xinjiang, 832000, China
| | - Danny J Llewellyn
- Black Mountain Laboratories, CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Iain Wilson
- Black Mountain Laboratories, CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Qian-Hao Zhu
- Black Mountain Laboratories, CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
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Evolution of Labdane-Related Diterpene Synthases in Cereals. ACTA ACUST UNITED AC 2020; 61:1850-1859. [DOI: 10.1093/pcp/pcaa106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 08/04/2020] [Indexed: 11/14/2022]
Abstract
Abstract
Gibberellins (GAs) are labdane-related diterpenoid phytohormones that regulate various aspects of higher plant growth. A biosynthetic intermediate of GAs is ent-kaurene, a tetra-cyclic diterpene that is produced through successive cyclization of geranylgeranyl diphosphate catalyzed by the two distinct monofunctional diterpene synthases—ent-copalyl diphosphate synthase (ent-CPS) and ent-kaurene synthase (KS). Various homologous genes of the two diterpene synthases have been identified in cereals, including rice (Oryza sativa), wheat (Triticum aestivum) and maize (Zea mays), and are believed to have been derived from GA biosynthetic ent-CPS and KS genes through duplication and neofunctionalization. They play roles in specialized metabolism, giving rise to diverse labdane-related diterpenoids for defense because a variety of diterpene synthases generate diverse carbon-skeleton structures. This review mainly describes the diterpene synthase homologs that have been identified and characterized in rice, wheat and maize and shows the evolutionary history of various homologs in rice inferred by comparative genomics studies using wild rice species, such as Oryza rufipogon and Oryza brachyantha. In addition, we introduce labdane-related diterpene synthases in bryophytes and gymnosperms to illuminate the macroscopic evolutionary history of diterpene synthases in the plant kingdom—bifunctional enzymes possessing both CPS and KS activities are present in bryophytes; gymnosperms possess monofunctional CPS and KS responsible for GA biosynthesis and also possess bifunctional diterpene synthases facilitating specialized metabolism for defense.
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A chromosome-level genome assembly of the wild rice Oryza rufipogon facilitates tracing the origins of Asian cultivated rice. SCIENCE CHINA-LIFE SCIENCES 2020; 64:282-293. [PMID: 32737856 DOI: 10.1007/s11427-020-1738-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 05/19/2020] [Indexed: 01/15/2023]
Abstract
Oryza rufipogon Griff. is a wild progenitor of the Asian cultivated rice Oryza sativa. To better understand the genomic diversity of the wild rice, high-quality reference genomes of O. rufipogon populations are needed, which also facilitate utilization of the wild genetic resources in rice breeding. In this study, we generated a chromosome-level genome assembly of O. rufipogon using a combination of short-read sequencing, single-molecule sequencing, BioNano and Hi-C platforms. The genome sequence (399.8 Mb) was assembled into 46 scaffolds on the 12 chromosomes, with contig N50 and scaffold N50 of 13.2 Mb and 20.3 Mb, respectively. The genome contains 36,520 protein-coding genes, and 49.37% of the genome consists of repetitive elements. The genome has strong synteny with those of the O. sativa subspecies indica and japonica, but containing some large structural variations. Evolutionary analysis unveiled the polyphyletic origins of O. sativa, in which the japonica and indica genome formations involved different divergent O. rufipogon (including O. nivara) lineages, accompanied by introgression of genomic regions between japonica and indica. This high-quality reference genome provides insight on the genome evolution of the wild rice and the origins of the O. sativa subspecies, and valuable information for basic research and rice breeding.
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36
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Hanscom T, McVey M. Regulation of Error-Prone DNA Double-Strand Break Repair and Its Impact on Genome Evolution. Cells 2020; 9:E1657. [PMID: 32660124 PMCID: PMC7407515 DOI: 10.3390/cells9071657] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 07/06/2020] [Accepted: 07/07/2020] [Indexed: 12/17/2022] Open
Abstract
Double-strand breaks are one of the most deleterious DNA lesions. Their repair via error-prone mechanisms can promote mutagenesis, loss of genetic information, and deregulation of the genome. These detrimental outcomes are significant drivers of human diseases, including many cancers. Mutagenic double-strand break repair also facilitates heritable genetic changes that drive organismal adaptation and evolution. In this review, we discuss the mechanisms of various error-prone DNA double-strand break repair processes and the cellular conditions that regulate them, with a focus on alternative end joining. We provide examples that illustrate how mutagenic double-strand break repair drives genome diversity and evolution. Finally, we discuss how error-prone break repair can be crucial to the induction and progression of diseases such as cancer.
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Affiliation(s)
| | - Mitch McVey
- Department. of Biology, Tufts University, Medford, MA 02155, USA;
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37
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Choi IY, Kwon EC, Kim NS. The C- and G-value paradox with polyploidy, repeatomes, introns, phenomes and cell economy. Genes Genomics 2020; 42:699-714. [DOI: 10.1007/s13258-020-00941-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 05/12/2020] [Indexed: 12/14/2022]
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38
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Shi C, Li W, Zhang QJ, Zhang Y, Tong Y, Li K, Liu YL, Gao LZ. The draft genome sequence of an upland wild rice species, Oryza granulata. Sci Data 2020; 7:131. [PMID: 32350267 PMCID: PMC7190833 DOI: 10.1038/s41597-020-0470-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 03/31/2020] [Indexed: 01/31/2023] Open
Abstract
Exploiting novel gene sources from wild relatives has proven to be an efficient approach to advance crop genetic breeding efforts. Oryza granulata, with the GG genome type, occupies the basal position of the Oryza phylogeny and has the second largest genome (~882 Mb). As an upland wild rice species, it possesses renowned traits that distinguish it from other Oryza species, such as tolerance to shade and drought, immunity to bacterial blight and resistance to the brown planthopper. Here, we generated a 736.66-Mb genome assembly of O. granulata with 40,131 predicted protein-coding genes. With Hi-C data, for the first time, we anchored ~98.2% of the genome assembly to the twelve pseudo-chromosomes. This chromosome-length genome assembly of O. granulata will provide novel insights into rice genome evolution, enhance our efforts to search for new genes for future rice breeding programmes and facilitate the conservation of germplasm of this endangered wild rice species.
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Affiliation(s)
- Cong Shi
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Wei Li
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, 510642, China
| | - Qun-Jie Zhang
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, 510642, China
| | - Yun Zhang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
| | - Yan Tong
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
| | - Kui Li
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, 510642, China
| | - Yun-Long Liu
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China
| | - Li-Zhi Gao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650204, China.
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, 510642, China.
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39
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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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40
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Mao L, Chen M, Chu Q, Jia L, Sultana MH, Wu D, Kong X, Qiu J, Ye CY, Zhu QH, Chen X, Fan L. RiceRelativesGD: a genomic database of rice relatives for rice research. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2019:5574892. [PMID: 31560050 PMCID: PMC6764101 DOI: 10.1093/database/baz110] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 06/25/2019] [Accepted: 08/09/2019] [Indexed: 12/02/2022]
Abstract
Rice (Oryza sativa L.) is one of the most important crops worldwide. Its relatives, including phylogenetically related species of rice and paddy weeds with a similar ecological niche, can provide crucial genetic resources (such as resistance to biotic and abiotic stresses and high photosynthetic efficiency) for rice research. Although many rice genomic databases have been constructed, a database providing large-scale curated genomic data from rice relatives and offering specific gene resources is still lacking. Here, we present RiceRelativesGD, a user-friendly genomic database of rice relatives. RiceRelativesGD integrates large-scale genomic resources from 2 cultivated rice and 11 rice relatives, including 208 321 specific genes and 13 643 genes related to photosynthesis and responsive to external stimuli. Diverse bioinformatics tools are embedded in the database, which allow users to search, visualize and download the information of interest. To our knowledge, this is the first genomic database providing a centralized genetic resource of rice relatives. RiceRelativesGD will serve as a significant and comprehensive knowledgebase for the rice community.
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Affiliation(s)
- Lingfeng Mao
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.,Zhejiang University, Hangzhou 310058, China
| | - Meihong Chen
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Qinjie Chu
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Lei Jia
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.,Zhejiang University, Hangzhou 310058, China
| | - Most Humaira Sultana
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Dongya Wu
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Xiangdong Kong
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Jie Qiu
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China
| | - Chu-Yu Ye
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.,Zhejiang University, Hangzhou 310058, China
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Xi Chen
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.,Zhejiang University, Hangzhou 310058, China
| | - Longjiang Fan
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, Hangzhou 310058, China.,Zhejiang University, Hangzhou 310058, China
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Huang K, Rieseberg LH. Frequency, Origins, and Evolutionary Role of Chromosomal Inversions in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:296. [PMID: 32256515 DOI: 10.3389/fpls.2020.00296/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/27/2020] [Indexed: 05/24/2023]
Abstract
Chromosomal inversions have the potential to play an important role in evolution by reducing recombination between favorable combinations of alleles. Until recently, however, most evidence for their likely importance derived from dipteran flies, whose giant larval salivary chromosomes aided early cytogenetic studies. The widespread application of new genomic technologies has revealed that inversions are ubiquitous across much of the plant and animal kingdoms. Here we review the rapidly accumulating literature on inversions in the plant kingdom and discuss what we have learned about their establishment and likely evolutionary role. We show that inversions are prevalent across a wide range of plant groups. We find that inversions are often associated with locally favored traits, as well as with traits that contribute to assortative mating, suggesting that they may be key to adaptation and speciation in the face of gene flow. We also discuss the role of inversions in sex chromosome formation, and explore possible parallels with inversion establishment on autosomes. The identification of inversion origins, as well as the causal variants within them, will advance our understanding of chromosomal evolution in plants.
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Affiliation(s)
- Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
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42
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Huang K, Rieseberg LH. Frequency, Origins, and Evolutionary Role of Chromosomal Inversions in Plants. FRONTIERS IN PLANT SCIENCE 2020; 11:296. [PMID: 32256515 PMCID: PMC7093584 DOI: 10.3389/fpls.2020.00296] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/27/2020] [Indexed: 05/11/2023]
Abstract
Chromosomal inversions have the potential to play an important role in evolution by reducing recombination between favorable combinations of alleles. Until recently, however, most evidence for their likely importance derived from dipteran flies, whose giant larval salivary chromosomes aided early cytogenetic studies. The widespread application of new genomic technologies has revealed that inversions are ubiquitous across much of the plant and animal kingdoms. Here we review the rapidly accumulating literature on inversions in the plant kingdom and discuss what we have learned about their establishment and likely evolutionary role. We show that inversions are prevalent across a wide range of plant groups. We find that inversions are often associated with locally favored traits, as well as with traits that contribute to assortative mating, suggesting that they may be key to adaptation and speciation in the face of gene flow. We also discuss the role of inversions in sex chromosome formation, and explore possible parallels with inversion establishment on autosomes. The identification of inversion origins, as well as the causal variants within them, will advance our understanding of chromosomal evolution in plants.
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Affiliation(s)
- Kaichi Huang
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - Loren H. Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
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43
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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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Dong X, Wang Z, Tian L, Zhang Y, Qi D, Huo H, Xu J, Li Z, Liao R, Shi M, Wahocho SA, Liu C, Zhang S, Tian Z, Cao Y. De novo assembly of a wild pear (Pyrus betuleafolia) genome. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:581-595. [PMID: 31368610 PMCID: PMC6953202 DOI: 10.1111/pbi.13226] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 06/25/2019] [Accepted: 07/23/2019] [Indexed: 05/18/2023]
Abstract
China is the origin and evolutionary centre of Oriental pears. Pyrus betuleafolia is a wild species native to China and distributed in the northern region, and it is widely used as rootstock. Here, we report the de novo assembly of the genome of P. betuleafolia-Shanxi Duli using an integrated strategy that combines PacBio sequencing, BioNano mapping and chromosome conformation capture (Hi-C) sequencing. The genome assembly size was 532.7 Mb, with a contig N50 of 1.57 Mb. A total of 59 552 protein-coding genes and 247.4 Mb of repetitive sequences were annotated for this genome. The expansion genes in P. betuleafolia were significantly enriched in secondary metabolism, which may account for the organism's considerable environmental adaptability. An alignment analysis of orthologous genes showed that fruit size, sugar metabolism and transport, and photosynthetic efficiency were positively selected in Oriental pear during domestication. A total of 573 nucleotide-binding site (NBS)-type resistance gene analogues (RGAs) were identified in the P. betuleafolia genome, 150 of which are TIR-NBS-LRR (TNL)-type genes, which represented the greatest number of TNL-type genes among the published Rosaceae genomes and explained the strong disease resistance of this wild species. The study of flavour metabolism-related genes showed that the anthocyanidin reductase (ANR) metabolic pathway affected the astringency of pear fruit and that sorbitol transporter (SOT) transmembrane transport may be the main factor affecting the accumulation of soluble organic matter. This high-quality P. betuleafolia genome provides a valuable resource for the utilization of wild pear in fundamental pear studies and breeding.
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Affiliation(s)
- Xingguang Dong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization)Ministry of AgricultureResearch Institute of PomologyChinese Academy of Agricultural SciencesXingchengChina
| | - Zheng Wang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
| | - Luming Tian
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization)Ministry of AgricultureResearch Institute of PomologyChinese Academy of Agricultural SciencesXingchengChina
| | - Ying Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization)Ministry of AgricultureResearch Institute of PomologyChinese Academy of Agricultural SciencesXingchengChina
| | - Dan Qi
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization)Ministry of AgricultureResearch Institute of PomologyChinese Academy of Agricultural SciencesXingchengChina
| | - Hongliang Huo
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization)Ministry of AgricultureResearch Institute of PomologyChinese Academy of Agricultural SciencesXingchengChina
| | - Jiayu Xu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization)Ministry of AgricultureResearch Institute of PomologyChinese Academy of Agricultural SciencesXingchengChina
| | - Zhe Li
- Berry Genomics CorporationBeijingChina
| | - Rui Liao
- Berry Genomics CorporationBeijingChina
| | - Miao Shi
- Berry Genomics CorporationBeijingChina
| | - Safdar Ali Wahocho
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization)Ministry of AgricultureResearch Institute of PomologyChinese Academy of Agricultural SciencesXingchengChina
| | - Chao Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization)Ministry of AgricultureResearch Institute of PomologyChinese Academy of Agricultural SciencesXingchengChina
| | - Simeng Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization)Ministry of AgricultureResearch Institute of PomologyChinese Academy of Agricultural SciencesXingchengChina
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyThe Innovative Academy of Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yufen Cao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization)Ministry of AgricultureResearch Institute of PomologyChinese Academy of Agricultural SciencesXingchengChina
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Read AC, Moscou MJ, Zimin AV, Pertea G, Meyer RS, Purugganan MD, Leach JE, Triplett LR, Salzberg SL, Bogdanove AJ. Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing. PLoS Genet 2020; 16:e1008571. [PMID: 31986137 PMCID: PMC7004385 DOI: 10.1371/journal.pgen.1008571] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 02/06/2020] [Accepted: 12/16/2019] [Indexed: 12/26/2022] Open
Abstract
Long-read sequencing facilitates assembly of complex genomic regions. In plants, loci containing nucleotide-binding, leucine-rich repeat (NLR) disease resistance genes are an important example of such regions. NLR genes constitute one of the largest gene families in plants and are often clustered, evolving via duplication, contraction, and transposition. We recently mapped the Xo1 locus for resistance to bacterial blight and bacterial leaf streak, found in the American heirloom rice variety Carolina Gold Select, to a region that in the Nipponbare reference genome is NLR gene-rich. Here, toward identification of the Xo1 gene, we combined Nanopore and Illumina reads and generated a high-quality Carolina Gold Select genome assembly. We identified 529 complete or partial NLR genes and discovered, relative to Nipponbare, an expansion of NLR genes at the Xo1 locus. One of these has high sequence similarity to the cloned, functionally similar Xa1 gene. Both harbor an integrated zfBED domain, and the repeats within each protein are nearly perfect. Across diverse Oryzeae, we identified two sub-clades of NLR genes with these features, varying in the presence of the zfBED domain and the number of repeats. The Carolina Gold Select genome assembly also uncovered at the Xo1 locus a rice blast resistance gene and a gene encoding a polyphenol oxidase (PPO). PPO activity has been used as a marker for blast resistance at the locus in some varieties; however, the Carolina Gold Select sequence revealed a loss-of-function mutation in the PPO gene that breaks this association. Our results demonstrate that whole genome sequencing combining Nanopore and Illumina reads effectively resolves NLR gene loci. Our identification of an Xo1 candidate is an important step toward mechanistic characterization, including the role(s) of the zfBED domain. Finally, the Carolina Gold Select genome assembly will facilitate identification of other useful traits in this historically important variety. Plants lack adaptive immunity, and instead contain repeat-rich, disease resistance genes that evolve rapidly through duplication, recombination, and transposition. The number, variation, and often clustered arrangement of these genes make them challenging to sequence and catalog. The US heirloom rice variety Carolina Gold Select has resistance to two important bacterial diseases. Toward identifying the responsible gene(s), we combined long- and short-read sequencing technologies to assemble the whole genome and identify the resistance gene repertoire. We previously narrowed the location of the gene(s) to a region on chromosome four. The region in Carolina Gold Select is larger than in the rice reference genome (Nipponbare) and contains twice as many resistance genes. One shares unusual features with a known bacterial disease resistance gene, suggesting that it confers the resistance. Across diverse varieties and related species, we identified two widely-distributed groups of such genes. The results are an important step toward mechanistic characterization and deployment of the bacterial disease resistance. The genome assembly also identified a resistance gene for a fungal disease and predicted a marker phenotype used in breeding for resistance. Thus, the Carolina Gold Select genome assembly can be expected to aid in the identification and deployment of other valuable traits.
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Affiliation(s)
- Andrew C. Read
- Plant Pathology and Plant Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States of America
| | - Matthew J. Moscou
- The Sainsbury Laboratory, University of East Anglia, Norwich, United Kingdom
| | - Aleksey V. Zimin
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, United States of America
| | - Geo Pertea
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, United States of America
| | - Rachel S. Meyer
- Center for Genomics and Systems Biology, New York University, New York, NY, United States of America
| | - Michael D. Purugganan
- Center for Genomics and Systems Biology, New York University, New York, NY, United States of America
- Center for Genomics and Biology, New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates
| | - Jan E. Leach
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States of America
| | - Lindsay R. Triplett
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, United States of America
| | - Steven L. Salzberg
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, United States of America
- Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, MD, United States of America
| | - Adam J. Bogdanove
- Plant Pathology and Plant Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States of America
- * E-mail:
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Huang L, Liu H, Wu J, Zhao R, Li Y, Melaku G, Zhang S, Huang G, Bao Y, Ning M, Chen B, Gong Y, Hu Q, Zhang J, Zhang Y. Evolution of Plant Architecture in Oryza Driven by the PROG1 Locus. FRONTIERS IN PLANT SCIENCE 2020; 11:876. [PMID: 32655603 PMCID: PMC7325765 DOI: 10.3389/fpls.2020.00876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 05/28/2020] [Indexed: 05/20/2023]
Abstract
The genetic control of plant architecture in crops is critical for agriculture and understanding morphological evolution. This study showed that an open reading frame (ORF) of the rice domestication gene PROG1 appeared 3.4-3.9 million years ago (Mya). Subsequently, it acquired a novel protein-coding gene function in the genome of O. rufipogon (~0.3-0.4 Mya). This extremely young gene and its paralogous C2H2 genes located nearby define the prostrate architecture of O. rufipogon and, thus, are of adaptive significance for wild rice in swamp and water areas. However, selection for dense planting and high yield during rice domestication silenced the PROG1 gene and caused the loss of the RPAD locus containing functional C2H2 paralogs; hence, domesticated lines exhibit an erect plant architecture. Analysis of the stepwise origination process of PROG1 and its evolutionary genetics revealed that this zinc-finger coding gene may have rapidly evolved under positive selection and promoted the transition from non- or semi-prostrate growth to prostrate growth. A transgenic assay showed that PROG1 from O. rufipogon exerts a stronger function compared with PROG1 sequences from other Oryza species. However, the analysis of the expression levels of PROG1 in different Oryza species suggests that the transcriptional regulation of PROG1 has played an important role in its evolution. This study provides the first strong case showing how a fundamental morphological trait evolved in Oryza species driven by a gene locus.
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Affiliation(s)
- Liyu Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, China
- *Correspondence: Liyu Huang,
| | - Hui Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Junjie Wu
- College of Agriculture and Biology Science, Dali University, Dali, China
| | - Ruoping Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | | | - Getachew Melaku
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, China
- Agricultural Biotechnology Directorate of the Ethiopian Biotechnology Institute, Addis Ababa, Ethiopia
| | - Shilai Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, China
| | - Guangfu Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, China
| | - Yachong Bao
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, China
| | - Min Ning
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, China
| | - Benjia Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, China
| | - Yurui Gong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, China
| | - Qingyi Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, China
| | - Jing Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center for Perennial Rice Engineering and Technology of Yunnan, School of Agriculture, Yunnan University, Kunming, China
| | - Yesheng Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- BGI-Baoshan, Baoshan, China
- Yesheng Zhang,
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Advances in Molecular Genetics and Genomics of African Rice ( Oryza glaberrima Steud). PLANTS 2019; 8:plants8100376. [PMID: 31561516 PMCID: PMC6843444 DOI: 10.3390/plants8100376] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/23/2019] [Accepted: 09/25/2019] [Indexed: 02/07/2023]
Abstract
African rice (Oryza glaberrima) has a pool of genes for resistance to diverse biotic and abiotic stresses, making it an important genetic resource for rice improvement. African rice has potential for breeding for climate resilience and adapting rice cultivation to climate change. Over the last decade, there have been tremendous technological and analytical advances in genomics that have dramatically altered the landscape of rice research. Here we review the remarkable advances in knowledge that have been witnessed in the last few years in the area of genetics and genomics of African rice. Advances in cheap DNA sequencing technologies have fuelled development of numerous genomic and transcriptomic resources. Genomics has been pivotal in elucidating the genetic architecture of important traits thereby providing a basis for unlocking important trait variation. Whole genome re-sequencing studies have provided great insights on the domestication process, though key studies continue giving conflicting conclusions and theories. However, the genomic resources of African rice appear to be under-utilized as there seems to be little evidence that these vast resources are being productively exploited for example in practical rice improvement programmes. Challenges in deploying African rice genetic resources in rice improvement and the genomics efforts made in addressing them are highlighted.
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Comparative Tyramide-FISH mapping of the genes controlling flavor and bulb color in Allium species revealed an altered gene order. Sci Rep 2019; 9:12007. [PMID: 31427665 PMCID: PMC6700127 DOI: 10.1038/s41598-019-48564-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 08/07/2019] [Indexed: 01/29/2023] Open
Abstract
Evolutionarily related species often share a common order of genes along homeologous chromosomes. Here we report the collinearity disruption of genes located on homeologous chromosome 4 in Allium species. Ultra-sensitive fluorescence in situ hybridization with tyramide signal amplification (tyr-FISH) allowed the visualization of the alliinase multigene family, chalcon synthase gene and EST markers on Allium cepa and Allium fistulosum chromosomes. In A. cepa, bulb alliinase, root alliinase (ALL1) and chalcon synthase (CHS-B) genes were located in the long arm but EST markers (API18 and ACM082) were located in the short arm. In A. fistulosum, all the visualized genes and markers were located in the short arm. Moreover, root alliinase genes (ALL1 and AOB249) showed contrast patterns in number of loci. We suppose that the altered order of the genes/markers is the result of a large pericentric inversion. To get insight into the evolution of the chromosome rearrangement, we mapped the bulb alliinase gene in phylogenetically close and distant species. In the taxonomic clade including A. fistulosum, A. altaicum, A. oschaninii and A. pskemense and in phylogenetically distant species A. roylei and A. nutans, the bulb alliinase gene was located on the short arm of chromosome 4 while, in A. cepa and A. schoenoprasum, the bulb alliinase gene was located on the long arm of chromosome 4. These results have encouraging implications for the further tracing of inverted regions in meiosis of interspecific hybrids and studding chromosome evolution. Also, this finding may have a practical benefit as closely related species are actively used for improving onion crop stock.
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Shameer K, Naika MB, Shafi KM, Sowdhamini R. Decoding systems biology of plant stress for sustainable agriculture development and optimized food production. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 145:19-39. [DOI: 10.1016/j.pbiomolbio.2018.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 10/23/2018] [Accepted: 12/06/2018] [Indexed: 12/13/2022]
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50
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Gao LZ, Liu YL, Zhang D, Li W, Gao J, Liu Y, Li K, Shi C, Zhao Y, Zhao YJ, Jiao JY, Mao SY, Gao CW, Eichler EE. Evolution of Oryza chloroplast genomes promoted adaptation to diverse ecological habitats. Commun Biol 2019; 2:278. [PMID: 31372517 PMCID: PMC6659635 DOI: 10.1038/s42003-019-0531-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/18/2019] [Indexed: 01/05/2023] Open
Abstract
The course, tempo and mode of chloroplast genome evolution remain largely unknown, resulting in limited knowledge about how plant plastome gene and genome evolve during the process of recent plant speciation. Here, we report the complete plastomes of 22 closely related Oryza species in chronologically ordered stages and generate the first precise map of genomic structural variation, to our knowledge. The occurrence rapidity was estimated on average to be ~7 insertions and ~15 deletions per Myr. Relatively fewer deletions than insertions result in an increased repeat density that causes the observed growth of Oryza chloroplast genome sizes. Genome-wide scanning identified 14 positively selected genes that are relevant to photosynthesis system, eight of which were found independently in shade-tolerant or sun-loving rice species. psaA seemed positively selected in both shade-tolerant and sun-loving rice species. The results show that adaptive evolution of chloroplast genes makes rice species adapt to diverse ecological habitats related to sunlight preferences.
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Affiliation(s)
- Li-Zhi Gao
- Plant Germplasm and Genomics Research Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, 650204 Kunming, China
- Institution of Genomics and Bioinformatics, South China Agricultural University, 510642 Guangzhou, China
| | - Yun-Long Liu
- Plant Germplasm and Genomics Research Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, 650204 Kunming, China
| | - Dan Zhang
- Institution of Genomics and Bioinformatics, South China Agricultural University, 510642 Guangzhou, China
| | - Wei Li
- Institution of Genomics and Bioinformatics, South China Agricultural University, 510642 Guangzhou, China
| | - Ju Gao
- Plant Germplasm and Genomics Research Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, 650204 Kunming, China
| | - Yuan Liu
- Plant Germplasm and Genomics Research Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, 650204 Kunming, China
| | - Kui Li
- Plant Germplasm and Genomics Research Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, 650204 Kunming, China
| | - Chao Shi
- Plant Germplasm and Genomics Research Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, 650204 Kunming, China
| | - Yuan Zhao
- The Ministry of Education Key Laboratory for Agricultural Biodiversity and Pest Management, Faculty of Plant Protection, Yunnan Agricultural University, 650204 Kunming, China
| | - You-Jie Zhao
- Southwest China Forestry University, 650224 Kunming, China
| | - Jun-Ying Jiao
- Southwest China Forestry University, 650224 Kunming, China
| | - Shu-Yan Mao
- Plant Germplasm and Genomics Research Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, 650204 Kunming, China
| | - Cheng-Wen Gao
- Plant Germplasm and Genomics Research Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, 650204 Kunming, China
| | - Evan E. Eichler
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195 USA
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