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Sedeek K, Mohammed N, Zhou Y, Zuccolo A, Sanikommu K, Kantharajappa S, Al-Bader N, Tashkandi M, Wing RA, Mahfouz MM. Multitrait engineering of Hassawi red rice for sustainable cultivation. Plant Sci 2024; 341:112018. [PMID: 38325660 DOI: 10.1016/j.plantsci.2024.112018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/15/2024] [Accepted: 01/31/2024] [Indexed: 02/09/2024]
Abstract
Sustainable agriculture requires locally adapted varieties that produce nutritious food with limited agricultural inputs. Genome engineering represents a viable approach to develop cultivars that fulfill these criteria. For example, the red Hassawi rice, a native landrace of Saudi Arabia, tolerates local drought and high-salinity conditions and produces grain with diverse health-promoting phytochemicals. However, Hassawi has a long growth cycle, high cultivation costs, low productivity, and susceptibility to lodging. Here, to improve these undesirable traits via genome editing, we established efficient regeneration and Agrobacterium-mediated transformation protocols for Hassawi. In addition, we generated the first high-quality reference genome and targeted the key flowering repressor gene, Hd4, thus shortening the plant's lifecycle and height. Using CRISPR/Cas9 multiplexing, we simultaneously disrupted negative regulators of flowering time (Hd2, Hd4, and Hd5), grain size (GS3), grain number (GN1a), and plant height (Sd1). The resulting homozygous mutant lines flowered extremely early (∼56 days) and had shorter stems (approximately 107 cm), longer grains (by 5.1%), and more grains per plant (by 50.2%), thereby enhancing overall productivity. Furthermore, the awns of grains were 86.4% shorter compared to unedited plants. Moreover, the modified rice grain displayed improved nutritional attributes. As a result, the modified Hassawi rice combines several desirable traits that can incentivize large-scale cultivation and reduce malnutrition.
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Affiliation(s)
- Khalid Sedeek
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Nahed Mohammed
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Yong Zhou
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Andrea Zuccolo
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Crop Science Research Center, Sant'Anna School of Advanced Studies, Piazza Martiri della Libertà 33, 56127 Pisa, Italy
| | - Krishnaveni Sanikommu
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Sunitha Kantharajappa
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Noor Al-Bader
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Manal Tashkandi
- Department of Biological Science, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Rod A Wing
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA; International Rice Research Institute (IRRI), Strategic Innovation, Los Baños, 4031 Laguna, Philippines
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia; Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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Zhou Y, Kathiresan N, Yu Z, Rivera LF, Yang Y, Thimma M, Manickam K, Chebotarov D, Mauleon R, Chougule K, Wei S, Gao T, Green CD, Zuccolo A, Xie W, Ware D, Zhang J, McNally KL, Wing RA. A high-performance computational workflow to accelerate GATK SNP detection across a 25-genome dataset. BMC Biol 2024; 22:13. [PMID: 38273258 PMCID: PMC10809545 DOI: 10.1186/s12915-024-01820-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/09/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Single-nucleotide polymorphisms (SNPs) are the most widely used form of molecular genetic variation studies. As reference genomes and resequencing data sets expand exponentially, tools must be in place to call SNPs at a similar pace. The genome analysis toolkit (GATK) is one of the most widely used SNP calling software tools publicly available, but unfortunately, high-performance computing versions of this tool have yet to become widely available and affordable. RESULTS Here we report an open-source high-performance computing genome variant calling workflow (HPC-GVCW) for GATK that can run on multiple computing platforms from supercomputers to desktop machines. We benchmarked HPC-GVCW on multiple crop species for performance and accuracy with comparable results with previously published reports (using GATK alone). Finally, we used HPC-GVCW in production mode to call SNPs on a "subpopulation aware" 16-genome rice reference panel with ~ 3000 resequenced rice accessions. The entire process took ~ 16 weeks and resulted in the identification of an average of 27.3 M SNPs/genome and the discovery of ~ 2.3 million novel SNPs that were not present in the flagship reference genome for rice (i.e., IRGSP RefSeq). CONCLUSIONS This study developed an open-source pipeline (HPC-GVCW) to run GATK on HPC platforms, which significantly improved the speed at which SNPs can be called. The workflow is widely applicable as demonstrated successfully for four major crop species with genomes ranging in size from 400 Mb to 2.4 Gb. Using HPC-GVCW in production mode to call SNPs on a 25 multi-crop-reference genome data set produced over 1.1 billion SNPs that were publicly released for functional and breeding studies. For rice, many novel SNPs were identified and were found to reside within genes and open chromatin regions that are predicted to have functional consequences. Combined, our results demonstrate the usefulness of combining a high-performance SNP calling architecture solution with a subpopulation-aware reference genome panel for rapid SNP discovery and public deployment.
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Affiliation(s)
- Yong Zhou
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Arizona Genomics Institute (AGI), School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Nagarajan Kathiresan
- KAUST Supercomputing Laboratory (KSL), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Zhichao Yu
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Luis F Rivera
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Yujian Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Manjula Thimma
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Keerthana Manickam
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Dmytro Chebotarov
- International Rice Research Institute (IRRI), Los Baños, Laguna, 4031, Philippines
| | - Ramil Mauleon
- International Rice Research Institute (IRRI), Los Baños, Laguna, 4031, Philippines
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Sharon Wei
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Tingting Gao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Carl D Green
- Information Technology Department, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Andrea Zuccolo
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Crop Science Research Center (CSRC), Scuola Superiore Sant'Anna, Pisa, 56127, Italy
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
- USDA ARS NEA Plant, Soil & Nutrition Laboratory Research Unit, Ithaca, NY, 14853, USA
| | - Jianwei Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Kenneth L McNally
- International Rice Research Institute (IRRI), Los Baños, Laguna, 4031, Philippines
| | - Rod A Wing
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
- Arizona Genomics Institute (AGI), School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.
- International Rice Research Institute (IRRI), Los Baños, Laguna, 4031, Philippines.
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Sedeek K, Zuccolo A, Fornasiero A, Weber AM, Sanikommu K, Sampathkumar S, Rivera LF, Butt H, Mussurova S, Alhabsi A, Nurmansyah N, Ryan EP, Wing RA, Mahfouz MM. Multi-omics resources for targeted agronomic improvement of pigmented rice. Nat Food 2023; 4:366-371. [PMID: 37169820 DOI: 10.1038/s43016-023-00742-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 03/24/2023] [Indexed: 05/13/2023]
Abstract
Pigmented rice (Oryza sativa L.) is a rich source of nutrients, but pigmented lines typically have long life cycles and limited productivity. Here we generated genome assemblies of 5 pigmented rice varieties and evaluated the genetic variation among 51 pigmented rice varieties by resequencing an additional 46 varieties. Phylogenetic analyses divided the pigmented varieties into four varietal groups: Geng-japonica, Xian-indica, circum-Aus and circum-Basmati. Metabolomics and ionomics profiling revealed that black rice varieties are rich in aromatic secondary metabolites. We established a regeneration and transformation system and used CRISPR-Cas9 to knock out three flowering time repressors (Hd2, Hd4 and Hd5) in the black Indonesian rice Cempo Ireng, resulting in an early maturing variety with shorter stature. Our study thus provides a multi-omics resource for understanding and improving Asian pigmented rice.
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Affiliation(s)
- Khalid Sedeek
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Andrea Zuccolo
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Crop Science Research Center, Sant'Anna School of Advanced Studies, Pisa, Italy
| | - Alice Fornasiero
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Annika M Weber
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Krishnaveni Sanikommu
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Sangeetha Sampathkumar
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Luis F Rivera
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Haroon Butt
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Saule Mussurova
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Abdulrahman Alhabsi
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Nurmansyah Nurmansyah
- Department of Agronomy, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Elizabeth P Ryan
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Rod A Wing
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
- International Rice Research Institute, Strategic Innovation, Los Baños, Philippines
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
- Center for Desert Agriculture, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
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Zhou Y, Yu Z, Chebotarov D, Chougule K, Lu Z, Rivera LF, Kathiresan N, Al-Bader N, Mohammed N, Alsantely A, Mussurova S, Santos J, Thimma M, Troukhan M, Fornasiero A, Green CD, Copetti D, Kudrna D, Llaca V, Lorieux M, Zuccolo A, Ware D, McNally K, Zhang J, Wing RA. Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice. Nat Commun 2023; 14:1567. [PMID: 36944612 PMCID: PMC10030860 DOI: 10.1038/s41467-023-37004-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 02/27/2023] [Indexed: 03/23/2023] Open
Abstract
Understanding and exploiting genetic diversity is a key factor for the productive and stable production of rice. Here, we utilize 73 high-quality genomes that encompass the subpopulation structure of Asian rice (Oryza sativa), plus the genomes of two wild relatives (O. rufipogon and O. punctata), to build a pan-genome inversion index of 1769 non-redundant inversions that span an average of ~29% of the O. sativa cv. Nipponbare reference genome sequence. Using this index, we estimate an inversion rate of ~700 inversions per million years in Asian rice, which is 16 to 50 times higher than previously estimated for plants. Detailed analyses of these inversions show evidence of their effects on gene expression, recombination rate, and linkage disequilibrium. Our study uncovers the prevalence and scale of large inversions (≥100 bp) across the pan-genome of Asian rice and hints at their largely unexplored role in functional biology and crop performance.
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Affiliation(s)
- Yong Zhou
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
- Arizona Genomics Institute (AGI), School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Zhichao Yu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Dmytro Chebotarov
- International Rice Research Institute (IRRI), Los Baños, 4031, Laguna, Philippines
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Zhenyuan Lu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA
| | - Luis F Rivera
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Nagarajan Kathiresan
- Supercomputing Core Lab, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Noor Al-Bader
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Nahed Mohammed
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Aseel Alsantely
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Saule Mussurova
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - João Santos
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Manjula Thimma
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | | | - Alice Fornasiero
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Carl D Green
- Information Technology Department, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Dario Copetti
- Arizona Genomics Institute (AGI), School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - David Kudrna
- Arizona Genomics Institute (AGI), School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Victor Llaca
- Research and Development, Corteva Agriscience, Johnston, IA, 50131, USA
| | - Mathias Lorieux
- DIADE, University of Montpellier, CIRAD, IRD, Montpellier, France
| | - Andrea Zuccolo
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
- Crop Science Research Center (CSRC), Scuola Superiore Sant'Anna, Pisa, 56127, Italy.
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
- USDA ARS NEA Plant, Soil & Nutrition Laboratory Research Unit, Ithaca, NY, 14853, USA.
| | - Kenneth McNally
- International Rice Research Institute (IRRI), Los Baños, 4031, Laguna, Philippines.
| | - Jianwei Zhang
- Arizona Genomics Institute (AGI), School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Rod A Wing
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
- Arizona Genomics Institute (AGI), School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, USA.
- International Rice Research Institute (IRRI), Los Baños, 4031, Laguna, Philippines.
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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. J Exp Bot 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Zuccolo A, Mfarrej S, Celii M, Mussurova S, Rivera LF, Llaca V, Mohammed N, Pain A, Alrefaei AF, Alrefaei AF, Wing RA. The gyrfalcon (Falco rusticolus) genome. G3 (Bethesda) 2023; 13:6972330. [PMID: 36611193 PMCID: PMC9997569 DOI: 10.1093/g3journal/jkad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 12/22/2022] [Accepted: 12/26/2022] [Indexed: 01/09/2023]
Abstract
High-quality genome assemblies are characterized by high-sequence contiguity, completeness, and a low error rate, thus providing the basis for a wide array of studies focusing on natural species ecology, conservation, evolution, and population genomics. To provide this valuable resource for conservation projects and comparative genomics studies on gyrfalcon (Falco rusticolus), we sequenced and assembled the genome of this species using third-generation sequencing strategies and optical maps. Here, we describe a highly contiguous and complete genome assembly comprising 20 scaffolds and 13 contigs with a total size of 1.193 Gbp, including 8,064 complete Benchmarking Universal Single-Copy Orthologs (BUSCOs) of the total 8,338 BUSCO groups present in the library aves_odb10. Of these BUSCO genes, 96.7% were complete, 96.1% were present as a single copy, and 0.6% were duplicated. Furthermore, 0.8% of BUSCO genes were fragmented and 2.5% (210) were missing. A de novo search for transposable elements (TEs) identified 5,716 TEs that masked 7.61% of the F. rusticolus genome assembly when combined with publicly available TE collections. Long interspersed nuclear elements, in particular, the element Chicken-repeat 1 (CR1), were the most abundant TEs in the F. rusticolus genome. A de novo first-pass gene annotation was performed using 293,349 PacBio Iso-Seq transcripts and 496,195 transcripts derived from the assembly of 42,429,525 Illumina PE RNA-seq reads. In all, 19,602 putative genes, of which 59.31% were functionally characterized and associated with Gene Ontology terms, were annotated. A comparison of the gyrfalcon genome assembly with the publicly available assemblies of the domestic chicken (Gallus gallus), zebra finch (Taeniopygia guttata), and hummingbird (Calypte anna) revealed several genome rearrangements. In particular, nine putative chromosome fusions were identified in the gyrfalcon genome assembly compared with those in the G. gallus genome assembly. This genome assembly, its annotation for TEs and genes, and the comparative analyses presented, complement and strength the base of high-quality genome assemblies and associated resources available for comparative studies focusing on the evolution, ecology, and conservation of Aves.
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Affiliation(s)
- Andrea Zuccolo
- Center for Desert Agriculture (CDA), 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, Piazza Martiri della Libertà 33, 56127 Pisa, Italy
| | - Sara Mfarrej
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah 23955-6900, Saudi Arabia
| | - Mirko Celii
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Saule Mussurova
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Luis F Rivera
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Victor Llaca
- Research and Development, Corteva Agriscience, Johnston, IA 50131, USA
| | - Nahed Mohammed
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Arnab Pain
- King Abdullah University of Science and Technology (KAUST), Pathogen Genomics Laboratory, Biological and Environmental Science and Engineering (BESE), Thuwal-Jeddah 23955-6900, Saudi Arabia
| | | | - Abdulwahed Fahad Alrefaei
- Department of Zoology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Rod A Wing
- Center for Desert Agriculture (CDA), Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.,School of Plant Sciences, Arizona Genomics Institute, University of Arizona, 24 Tucson, Arizona 85721, USA
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Ventimiglia M, Marturano G, Vangelisti A, Usai G, Simoni S, Cavallini A, Giordani T, Natali L, Zuccolo A, Mascagni F. Genome-wide identification and characterization of exapted transposable elements in the large genome of sunflower (Helianthus annuus L.). Plant J 2023; 113:734-748. [PMID: 36573648 DOI: 10.1111/tpj.16078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 12/07/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Transposable elements (TEs) are an important source of genome variability, playing many roles in the evolution of eukaryotic species. Besides well-known phenomena, TEs may undergo the exaptation process and generate the so-called exapted transposable element genes (ETEs). Here we present a genome-wide survey of ETEs in the large genome of sunflower (Helianthus annuus L.), in which the massive amount of TEs, provides a significant source for exaptation. A library of sunflower TEs was used to build TE-specific Hidden Markov Model profiles, to search for all available sunflower gene products. In doing so, 20 016 putative ETEs were identified and further investigated for the characteristics that distinguish TEs from genes, leading to the validation of 3530 ETEs. The analysis of ETEs transcription patterns under different stress conditions showed a differential regulation triggered by treatments mimicking biotic and abiotic stress; furthermore, the distribution of functional domains of differentially regulated ETEs revealed a relevant presence of domains involved in many aspects of cellular functions. A comparative genomic investigation was performed including species representative of Asterids and appropriate outgroups: the bulk of ETEs that resulted were specific to the sunflower, while few ETEs presented orthologues in the genome of all analyzed species, making the hypothesis of a conserved function. This study highlights the crucial role played by exaptation, actively contributing to species evolution.
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Affiliation(s)
- Maria Ventimiglia
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Giovanni Marturano
- Crop Science Research Center, Sant'Anna School of Advanced Studies, Piazza Martiri della Libertà 33, 56127, Pisa, Italy
| | - Alberto Vangelisti
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Gabriele Usai
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Samuel Simoni
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Andrea Cavallini
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Tommaso Giordani
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Lucia Natali
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Andrea Zuccolo
- Crop Science Research Center, Sant'Anna School of Advanced Studies, Piazza Martiri della Libertà 33, 56127, Pisa, Italy
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Flavia Mascagni
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
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8
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Niu S, Li J, Bo W, Yang W, Zuccolo A, Giacomello S, Chen X, Han F, Yang J, Song Y, Nie Y, Zhou B, Wang P, Zuo Q, Zhang H, Ma J, Wang J, Wang L, Zhu Q, Zhao H, Liu Z, Zhang X, Liu T, Pei S, Li Z, Hu Y, Yang Y, Li W, Zan Y, Zhou L, Lin J, Yuan T, Li W, Li Y, Wei H, Wu HX. The Chinese pine genome and methylome unveil key features of conifer evolution. Cell 2021; 185:204-217.e14. [PMID: 34965378 DOI: 10.1016/j.cell.2021.12.006] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/23/2021] [Accepted: 12/03/2021] [Indexed: 12/30/2022]
Abstract
Conifers dominate the world's forest ecosystems and are the most widely planted tree species. Their giant and complex genomes present great challenges for assembling a complete reference genome for evolutionary and genomic studies. We present a 25.4-Gb chromosome-level assembly of Chinese pine (Pinus tabuliformis) and revealed that its genome size is mostly attributable to huge intergenic regions and long introns with high transposable element (TE) content. Large genes with long introns exhibited higher expressions levels. Despite a lack of recent whole-genome duplication, 91.2% of genes were duplicated through dispersed duplication, and expanded gene families are mainly related to stress responses, which may underpin conifers' adaptation, particularly in cold and/or arid conditions. The reproductive regulation network is distinct compared with angiosperms. Slow removal of TEs with high-level methylation may have contributed to genomic expansion. This study provides insights into conifer evolution and resources for advancing research on conifer adaptation and development.
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Affiliation(s)
- Shihui Niu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China.
| | - Jiang Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Wenhao Bo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Weifei Yang
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100180, P.R. China
| | - Andrea Zuccolo
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia; Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy
| | - Stefania Giacomello
- SciLife Lab, KTH Royal Institute of Technology, Tomtebodavägen 23, SE-171 65 Stockholm, Sweden
| | - Xi Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Fangxu Han
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Junhe Yang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Yitong Song
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Yumeng Nie
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Biao Zhou
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Peiyi Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Quan Zuo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Hui Zhang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Jingjing Ma
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Jun Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Lvji Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Qianya Zhu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Huanhuan Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Zhanmin Liu
- Qigou State-owned Forest Farm, Pingquan, Hebei Province 067509, P. R. China
| | - Xuemei Zhang
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100180, P.R. China
| | - Tao Liu
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100180, P.R. China
| | - Surui Pei
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100180, P.R. China
| | - Zhimin Li
- Annoroad Gene Technology (Beijing) Co., Ltd, Beijing 100180, P.R. China
| | - Yao Hu
- Alibaba Group, Hangzhou 311121, P.R. China
| | - Yehui Yang
- Alibaba Group, Hangzhou 311121, P.R. China
| | - Wenzhao Li
- Alibaba Group, Hangzhou 311121, P.R. China
| | - Yanjun Zan
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Linnaeus väg 6, 901 83 Umeå, Sweden
| | - Linghua Zhou
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Linnaeus väg 6, 901 83 Umeå, Sweden
| | - Jinxing Lin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Tongqi Yuan
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China; College of Material Science and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Wei Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Yue Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA.
| | - Harry X Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, P.R. China; Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Linnaeus väg 6, 901 83 Umeå, Sweden; CSIRO National Research Collection Australia, Black Mountain Laboratory, Canberra, ACT 2601, Australia.
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9
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Song JM, Xie WZ, Wang S, Guo YX, Koo DH, Kudrna D, Gong C, Huang Y, Feng JW, Zhang W, Zhou Y, Zuccolo A, Long E, Lee S, Talag J, Zhou R, Zhu XT, Yuan D, Udall J, Xie W, Wing RA, Zhang Q, Poland J, Zhang J, Chen LL. Two gap-free reference genomes and a global view of the centromere architecture in rice. Mol Plant 2021; 14:1757-1767. [PMID: 34171480 DOI: 10.1016/j.molp.2021.06.018] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/16/2021] [Accepted: 06/22/2021] [Indexed: 05/04/2023]
Abstract
Rice (Oryza sativa), a major staple throughout the world and a model system for plant genomics and breeding, was the first crop genome sequenced almost two decades ago. However, reference genomes for all higher organisms to date contain gaps and missing sequences. Here, we report the assembly and analysis of gap-free reference genome sequences for two elite O. sativa xian/indica rice varieties, Zhenshan 97 and Minghui 63, which are being used as a model system for studying heterosis and yield. Gap-free reference genomes provide the opportunity for a global view of the structure and function of centromeres. We show that all rice centromeric regions share conserved centromere-specific satellite motifs with different copy numbers and structures. In addition, the similarity of CentO repeats in the same chromosome is higher than across chromosomes, supporting a model of local expansion and homogenization. Both genomes have over 395 non-TE genes located in centromere regions, of which ∼41% are actively transcribed. Two large structural variants at the end of chromosome 11 affect the copy number of resistance genes between the two genomes. The availability of the two gap-free genomes lays a solid foundation for further understanding genome structure and function in plants and breeding climate-resilient varieties.
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Affiliation(s)
- Jia-Ming Song
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Wen-Zhao Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuo Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yi-Xiong Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Dal-Hoe Koo
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Dave Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Chenbo Gong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yicheng Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jia-Wu Feng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Wenhui Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yong Zhou
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - 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
| | - Evan Long
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602, USA
| | - Seunghee Lee
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Jayson Talag
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Run Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xi-Tong Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Daojun Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Joshua Udall
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602, USA
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA; Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; International Rice Research Institute (IRRI), Strategic Innovation, Los Baños, 4031 Laguna, Philippines
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jesse Poland
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, USA.
| | - Jianwei Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
| | - Ling-Ling Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; College of Life Science and Technology, Guangxi University, Nanning 530004, China.
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10
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Lehmann R, Kovařík A, Ocalewicz K, Kirtiklis L, Zuccolo A, Tegner JN, Wanzenböck J, Bernatchez L, Lamatsch DK, Symonová R. DNA Transposon Expansion is Associated with Genome Size Increase in Mudminnows. Genome Biol Evol 2021; 13:6380143. [PMID: 34599322 PMCID: PMC8557787 DOI: 10.1093/gbe/evab228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2021] [Indexed: 12/20/2022] Open
Abstract
Genome sizes of eukaryotic organisms vary substantially, with whole-genome duplications (WGD) and transposable element expansion acting as main drivers for rapid genome size increase. The two North American mudminnows, Umbra limi and Umbra pygmaea, feature genomes about twice the size of their sister lineage Esocidae (e.g., pikes and pickerels). However, it is unknown whether all Umbra species share this genome expansion and which causal mechanisms drive this expansion. Using flow cytometry, we find that the genome of the European mudminnow is expanded similarly to both North American species, ranging between 4.5 and 5.4 pg per diploid nucleus. Observed blocks of interstitially located telomeric repeats in U. limi suggest frequent Robertsonian rearrangements in its history. Comparative analyses of transcriptome and genome assemblies show that the genome expansion in Umbra is driven by the expansion of DNA transposon and unclassified repeat sequences without WGD. Furthermore, we find a substantial ongoing expansion of repeat sequences in the Alaska blackfish Dallia pectoralis, the closest relative to the family Umbridae, which might mark the beginning of a similar genome expansion. Our study suggests that the genome expansion in mudminnows, driven mainly by transposon expansion, but not WGD, occurred before the separation into the American and European lineage.
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Affiliation(s)
- Robert Lehmann
- Division of Biological and Environmental Sciences & Engineering, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Aleš Kovařík
- Laboratory of Molecular Epigenetics, Institute of Biophysics, Czech Academy of Science, Brno, Czech Republic
| | - Konrad Ocalewicz
- Department of Marine Biology and Ecology, Institute of Oceanography, Faculty of Oceanography and Geography, University of Gdansk, Gdansk, Poland
| | - Lech Kirtiklis
- Department of Zoology, Faculty of Biology and Biotechnology, University of Warmia and Mazury, Olsztyn, Poland
| | - Andrea Zuccolo
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.,Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Jesper N Tegner
- Division of Biological and Environmental Sciences & Engineering, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Josef Wanzenböck
- Research Department for Limnology Mondsee, University of Innsbruck, Mondsee, Austria
| | - Louis Bernatchez
- Department of Biology, IBIS (Institut de Biologie Intégrative et des Systèmes), Université Laval, Québec, QC, Canada
| | - Dunja K Lamatsch
- Research Department for Limnology Mondsee, University of Innsbruck, Mondsee, Austria
| | - Radka Symonová
- Department of Bioinformatics, Wissenschaftzentrum Weihenstephan, Technische Universität München, Freising, Germany.,Department of Biology, Faculty of Biology, University of Hradec Kralove, Czech Republic
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11
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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: 165] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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12
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Pinosio S, Marroni F, Zuccolo A, Vitulo N, Mariette S, Sonnante G, Aravanopoulos FA, Ganopoulos I, Palasciano M, Vidotto M, Magris G, Iezzoni A, Vendramin GG, Morgante M. A draft genome of sweet cherry (Prunus avium L.) reveals genome-wide and local effects of domestication. Plant J 2020; 103:1420-1432. [PMID: 32391598 DOI: 10.1111/tpj.14809] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/24/2020] [Accepted: 05/01/2020] [Indexed: 05/26/2023]
Abstract
Sweet cherry (Prunus avium L.) trees are both economically important fruit crops but also important components of natural forest ecosystems in Europe, Asia and Africa. Wild and domesticated trees currently coexist in the same geographic areas with important questions arising on their historical relationships. Little is known about the effects of the domestication process on the evolution of the sweet cherry genome. We assembled and annotated the genome of the cultivated variety "Big Star*" and assessed the genetic diversity among 97 sweet cherry accessions representing three different stages in the domestication and breeding process (wild trees, landraces and modern varieties). The genetic diversity analysis revealed significant genome-wide losses of variation among the three stages and supports a clear distinction between wild and domesticated trees, with only limited gene flow being detected between wild trees and domesticated landraces. We identified 11 domestication sweeps and five breeding sweeps covering, respectively, 11.0 and 2.4 Mb of the P. avium genome. A considerable fraction of the domestication sweeps overlaps with those detected in the related species, Prunus persica (peach), indicating that artificial selection during domestication may have acted independently on the same regions and genes in the two species. We detected 104 candidate genes in sweep regions involved in different processes, such as the determination of fruit texture, the regulation of flowering and fruit ripening and the resistance to pathogens. The signatures of selection identified will enable future evolutionary studies and provide a valuable resource for genetic improvement and conservation programs in sweet cherry.
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Affiliation(s)
- Sara Pinosio
- Institute of Biosciences and Bioresources (IBBR), National Research Council, Via Madonna del Piano 10, Sesto Fiorentino, 50019, Italy
- Istituto di Genomica Applicata (IGA), Via Jacopo Linussio 51, Udine, 33100, Italy
| | - Fabio Marroni
- Istituto di Genomica Applicata (IGA), Via Jacopo Linussio 51, Udine, 33100, Italy
- Dipartimento di Scienze Agro-alimentari Ambientali e Animali (DI4A), Università di Udine, via delle Scienze 206, Udine, 33100, Italy
| | - Andrea Zuccolo
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, 56124, Italy
| | - Nicola Vitulo
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada Le Grazie 15, Verona, 37134, Italy
| | - Stephanie Mariette
- BIOGECO, INRA, University of Bordeaux, route d'Arcachon 69, Cestas, 33612, France
| | - Gabriella Sonnante
- Institute of Biosciences and Bioresources (IBBR), National Research Council, via Amendola 165/A, Bari, 70126, Italy
| | - Filippos A Aravanopoulos
- Faculty of Forestry and Natural Environment, Laboratory of Forest Genetics and Tree Breeding, Aristotle University of Thessaloniki, Thessaloníki, 54124, Greece
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization-DEMETER, Thermi, 57001, Greece
| | - Marino Palasciano
- Dipartimento di Scienze del Suolo, Università degli Studi di Bari Aldo Moro, della Pianta e degli Alimenti, Piazza Umberto I, Bari, 70121, Italy
| | - Michele Vidotto
- Istituto di Genomica Applicata (IGA), Via Jacopo Linussio 51, Udine, 33100, Italy
| | - Gabriele Magris
- Istituto di Genomica Applicata (IGA), Via Jacopo Linussio 51, Udine, 33100, Italy
- Dipartimento di Scienze Agro-alimentari Ambientali e Animali (DI4A), Università di Udine, via delle Scienze 206, Udine, 33100, Italy
| | - Amy Iezzoni
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI, 48824-1325, USA
| | - Giovanni G Vendramin
- Institute of Biosciences and Bioresources (IBBR), National Research Council, Via Madonna del Piano 10, Sesto Fiorentino, 50019, Italy
| | - Michele Morgante
- Istituto di Genomica Applicata (IGA), Via Jacopo Linussio 51, Udine, 33100, Italy
- Dipartimento di Scienze Agro-alimentari Ambientali e Animali (DI4A), Università di Udine, via delle Scienze 206, Udine, 33100, Italy
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13
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Usai G, Mascagni F, Giordani T, Vangelisti A, Bosi E, Zuccolo A, Ceccarelli M, King R, Hassani-Pak K, Zambrano LS, Cavallini A, Natali L. Epigenetic patterns within the haplotype phased fig (Ficus carica L.) genome. Plant J 2020; 102:600-614. [PMID: 31808196 DOI: 10.1111/tpj.14635] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Revised: 11/13/2019] [Accepted: 11/26/2019] [Indexed: 05/22/2023]
Abstract
Due to DNA heterozygosity and repeat content, assembly of non-model plant genomes is challenging. Herein, we report a high-quality genome reference of one of the oldest known domesticated species, fig (Ficus carica L.), using Pacific Biosciences single-molecule, real-time sequencing. The fig genome is ~333 Mbp in size, of which 80% has been anchored to 13 chromosomes. Genome-wide analysis of N6 -methyladenine and N4 -methylcytosine revealed high methylation levels in both genes and transposable elements, and a prevalence of methylated over non-methylated genes. Furthermore, the characterization of N6 -methyladenine sites led to the identification of ANHGA, a species-specific motif, which is prevalent for both genes and transposable elements. Finally, exploiting the contiguity of the 13 pseudomolecules, we identified 13 putative centromeric regions. The high-quality reference genome and the characterization of methylation profiles, provides an important resource for both fig breeding and for fundamental research into the relationship between epigenetic changes and phenotype, using fig as a model species.
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Affiliation(s)
- Gabriele Usai
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Flavia Mascagni
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Tommaso Giordani
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Alberto Vangelisti
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Emanuele Bosi
- Department of Biomedical Experimental and Clinical Sciences, University of Florence, Florence, Italy
| | - Andrea Zuccolo
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Marilena Ceccarelli
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | | | | | - Liceth S Zambrano
- Facultad de Ciencias Zootécnicas, Universidad Técnica de Manabí, Portoviejo, Ecuador
| | - Andrea Cavallini
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Lucia Natali
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
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14
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Zhou Y, Chebotarov D, Kudrna D, Llaca V, Lee S, Rajasekar S, Mohammed N, Al-Bader N, Sobel-Sorenson C, Parakkal P, Arbelaez LJ, Franco N, Alexandrov N, Hamilton NRS, Leung H, Mauleon R, Lorieux M, Zuccolo A, McNally K, Zhang J, Wing RA. A platinum standard pan-genome resource that represents the population structure of Asian rice. Sci Data 2020; 7:113. [PMID: 32265447 PMCID: PMC7138821 DOI: 10.1038/s41597-020-0438-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 03/05/2020] [Indexed: 01/13/2023] Open
Abstract
As the human population grows from 7.8 billion to 10 billion over the next 30 years, breeders must do everything possible to create crops that are highly productive and nutritious, while simultaneously having less of an environmental footprint. Rice will play a critical role in meeting this demand and thus, knowledge of the full repertoire of genetic diversity that exists in germplasm banks across the globe is required. To meet this demand, we describe the generation, validation and preliminary analyses of transposable element and long-range structural variation content of 12 near-gap-free reference genome sequences (RefSeqs) from representatives of 12 of 15 subpopulations of cultivated Asian rice. When combined with 4 existing RefSeqs, that represent the 3 remaining rice subpopulations and the largest admixed population, this collection of 16 Platinum Standard RefSeqs (PSRefSeq) can be used as a template to map resequencing data to detect virtually all standing natural variation that exists in the pan-genome of cultivated Asian rice.
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Affiliation(s)
- Yong Zhou
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Dmytro Chebotarov
- International Rice Research Institute (IRRI), Strategic Innovation, Los Baños, 4031, Laguna, Philippines
| | - Dave Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, 85721, USA
| | - Victor Llaca
- Genomics Technologies, Applied Science and Technology, Corteva AgriscienceTM, Iowa, IA, 50131, USA
| | - Seunghee Lee
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, 85721, USA
| | - Shanmugam Rajasekar
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, 85721, USA
| | - Nahed Mohammed
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Noor Al-Bader
- Center for Desert Agriculture, Biological and Environmental Sciences & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Chandler Sobel-Sorenson
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, 85721, USA
| | - Praveena Parakkal
- Genomics Technologies, Applied Science and Technology, Corteva AgriscienceTM, Iowa, IA, 50131, USA
| | - Lady Johanna Arbelaez
- Rice Genetics and Genomics Lab, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Natalia Franco
- Rice Genetics and Genomics Lab, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Nickolai Alexandrov
- International Rice Research Institute (IRRI), Strategic Innovation, Los Baños, 4031, Laguna, Philippines
| | | | - Hei Leung
- International Rice Research Institute (IRRI), Strategic Innovation, Los Baños, 4031, Laguna, Philippines
| | - Ramil Mauleon
- International Rice Research Institute (IRRI), Strategic Innovation, Los Baños, 4031, Laguna, Philippines
| | - Mathias Lorieux
- Rice Genetics and Genomics Lab, International Center for Tropical Agriculture (CIAT), Cali, Colombia
- University of Montpellier, DIADE, IRD, Montpellier, France
| | - 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, Italy.
| | - Kenneth McNally
- International Rice Research Institute (IRRI), Strategic Innovation, Los Baños, 4031, Laguna, Philippines
| | - Jianwei Zhang
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, 85721, USA.
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - 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.
- International Rice Research Institute (IRRI), Strategic Innovation, Los Baños, 4031, Laguna, Philippines.
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, 85721, USA.
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15
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Mussurova S, Al-Bader N, Zuccolo A, Wing RA. Potential of Platinum Standard Reference Genomes to Exploit Natural Variation in the Wild Relatives of Rice. Front Plant Sci 2020; 11:579980. [PMID: 33072154 PMCID: PMC7539145 DOI: 10.3389/fpls.2020.579980] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/04/2020] [Indexed: 05/14/2023]
Abstract
As the world's population expands from 7.6 billion to 10 billion over the next 30 years, scientists and farmers across the globe must explore every angle necessary to provide a safe, stable and sustainable food supply for generations to come. Rice, and its wild relatives in the genus Oryza, will play a significant role in helping to solve this 10 billion people question due to its place as a staple food for billions. The genus Oryza is composed of 27 species that span 15 million years of evolutionary diversification and have been shown to contain a plethora of untapped adaptive traits, e.g., biotic and abiotic resistances, which can be used to improve cultivated rice. Such traits can be introduced into cultivated rice, in some cases by conventional crossing, and others via genetic transformation and gene editing methods. In cases where traits are too complex to easily transfer to cultivated rice [e.g., quantitative trait loci (QTL)], an alternative strategy is to domesticate the wild relative that already contains the desired adaptive traits - i.e., "neodomestication". To utilize the Oryza genus for crop improvement and neodomestication, we first need a set of genomic resources that can be used to efficiently identify, capture, and guide molecular crop improvement. Here, we introduce the concept of platinum standard reference genome sequences (PSRefSeq) - a new standard by which contiguous near-gap free reference genomes can now be produced. By having a set of PSRefSeqs for every Oryza species we set a new bar for how crop wild relatives can be integrated into crop improvement programs.
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Affiliation(s)
- Saule Mussurova
- Center for Desert Agriculture, Biological and Environmental Sciences Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Noor Al-Bader
- Center for Desert Agriculture, Biological and Environmental Sciences Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Andrea Zuccolo
- Center for Desert Agriculture, Biological and Environmental Sciences Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa, Italy
- *Correspondence: Andrea Zuccolo, ; Rod A. Wing,
| | - Rod A. Wing
- Center for Desert Agriculture, Biological and Environmental Sciences Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- School of Plant Sciences, Arizona Genomics Institute, University of Arizona, Tucson, AZ, United States
- *Correspondence: Andrea Zuccolo, ; Rod A. Wing,
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16
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Cossu RM, Casola C, Giacomello S, Vidalis A, Scofield DG, Zuccolo A. LTR Retrotransposons Show Low Levels of Unequal Recombination and High Rates of Intraelement Gene Conversion in Large Plant Genomes. Genome Biol Evol 2018; 9:3449-3462. [PMID: 29228262 PMCID: PMC5751070 DOI: 10.1093/gbe/evx260] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2017] [Indexed: 12/29/2022] Open
Abstract
The accumulation and removal of transposable elements (TEs) is a major driver of genome size evolution in eukaryotes. In plants, long terminal repeat (LTR) retrotransposons (LTR-RTs) represent the majority of TEs and form most of the nuclear DNA in large genomes. Unequal recombination (UR) between LTRs leads to removal of intervening sequence and formation of solo-LTRs. UR is a major mechanism of LTR-RT removal in many angiosperms, but our understanding of LTR-RT-associated recombination within the large, LTR-RT-rich genomes of conifers is quite limited. We employ a novel read-based methodology to estimate the relative rates of LTR-RT-associated UR within the genomes of four conifer and seven angiosperm species. We found the lowest rates of UR in the largest genomes studied, conifers and the angiosperm maize. Recombination may also resolve as gene conversion, which does not remove sequence, so we analyzed LTR-RT-associated gene conversion events (GCEs) in Norway spruce and six angiosperms. Opposite the trend for UR, we found the highest rates of GCEs in Norway spruce and maize. Unlike previous work in angiosperms, we found no evidence that rates of UR correlate with retroelement structural features in the conifers, suggesting that another process is suppressing UR in these species. Recent results from diverse eukaryotes indicate that heterochromatin affects the resolution of recombination, by favoring gene conversion over crossing-over, similar to our observation of opposed rates of UR and GCEs. Control of LTR-RT proliferation via formation of heterochromatin would be a likely step toward large genomes in eukaryotes carrying high LTR-RT content.
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Affiliation(s)
- Rosa Maria Cossu
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.,Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Claudio Casola
- Department of Ecosystem Science and Management, Texas A&M University
| | - Stefania Giacomello
- Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology, Solna, Sweden.,Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden
| | - Amaryllis Vidalis
- Department of Ecology and Environmental Science, Umeå University, Sweden.,Section of Population Epigenetics and Epigenomics, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Freising, Germany
| | - Douglas G Scofield
- Department of Ecology and Environmental Science, Umeå University, Sweden.,Department of Ecology and Genetics: Evolutionary Biology, Uppsala University, Sweden.,Uppsala Multidisciplinary Center for Advanced Computational Science, Uppsala University, Sweden
| | - Andrea Zuccolo
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.,Istituto di Genomica Applicata, Udine, Italy
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17
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Stein JC, Yu Y, Copetti D, Zwickl DJ, Zhang L, Zhang C, Chougule K, Gao D, Iwata A, Goicoechea JL, Wei S, Wang J, Liao Y, Wang M, Jacquemin J, Becker C, Kudrna D, Zhang J, Londono CEM, Song X, Lee S, Sanchez P, Zuccolo A, Ammiraju JSS, Talag J, Danowitz A, Rivera LF, Gschwend AR, Noutsos C, Wu CC, Kao SM, Zeng JW, Wei FJ, Zhao Q, Feng Q, El Baidouri M, Carpentier MC, Lasserre E, Cooke R, da Rosa Farias D, da Maia LC, Dos Santos RS, Nyberg KG, McNally KL, Mauleon R, Alexandrov N, Schmutz J, Flowers D, Fan C, Weigel D, Jena KK, Wicker T, Chen M, Han B, Henry R, Hsing YIC, Kurata N, de Oliveira AC, Panaud O, Jackson SA, Machado CA, Sanderson MJ, Long M, Ware D, Wing RA. Publisher Correction: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza. Nat Genet 2018; 50:1618. [PMID: 30291357 DOI: 10.1038/s41588-018-0261-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This article was not made open access when initially published online, which was corrected before print publication. In addition, ORCID links were missing for 12 authors and have been added to the HTML and PDF versions of the article.
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Affiliation(s)
- Joshua C Stein
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Yeisoo Yu
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.,Phyzen Genomics Institute, Phyzen, Inc., Seoul, South Korea
| | - Dario Copetti
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.,International Rice Research Institute, Los Baños, Philippines
| | - Derrick J Zwickl
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Li Zhang
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Chengjun Zhang
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Kapeel Chougule
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Dongying Gao
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Aiko Iwata
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Jose Luis Goicoechea
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Sharon Wei
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Jun Wang
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Yi Liao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Muhua Wang
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.,Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
| | - Julie Jacquemin
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.,Crop Biodiversity and Breeding Informatics Group, Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
| | - Claude Becker
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Dave Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Jianwei Zhang
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Carlos E M Londono
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Xiang Song
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Seunghee Lee
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Paul Sanchez
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.,Rice Experiment Station, Biggs, CA, USA
| | - Andrea Zuccolo
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.,Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Jetty S S Ammiraju
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.,DuPont-Pioneer, Johnston, IA, USA
| | - Jayson Talag
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Ann Danowitz
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA
| | - Luis F Rivera
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA.,BIOS-Parque Los Yarumos, Manizales, Colombia
| | - Andrea R Gschwend
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | | | - Cheng-Chieh Wu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.,Institute of Botany, National Taiwan University, Taipei, Taiwan
| | - Shu-Min Kao
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.,Department of Plant Systems Biology, VIB and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Jhih-Wun Zeng
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Fu-Jin Wei
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.,Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Tsukuba, Japan
| | - Qiang Zhao
- National Center for Gene Research, Chinese Academy of Sciences, Shanghai, China
| | - Qi Feng
- National Center for Gene Research, Chinese Academy of Sciences, Shanghai, China
| | - Moaine El Baidouri
- Laboratoire Génome et Développement des Plantes, UMR 5096 UPVD/CNRS, Université de Perpignan Via Domitia, Perpignan, France
| | - Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes, UMR 5096 UPVD/CNRS, Université de Perpignan Via Domitia, Perpignan, France
| | - Eric Lasserre
- Laboratoire Génome et Développement des Plantes, UMR 5096 UPVD/CNRS, Université de Perpignan Via Domitia, Perpignan, France
| | - Richard Cooke
- Laboratoire Génome et Développement des Plantes, UMR 5096 UPVD/CNRS, Université de Perpignan Via Domitia, Perpignan, France
| | - Daniel da Rosa Farias
- Plant Genomics and Breeding Center, Universidade Federal de Pelotas, Pelotas, Brazil
| | | | - Railson S Dos Santos
- Plant Genomics and Breeding Center, Universidade Federal de Pelotas, Pelotas, Brazil
| | - Kevin G Nyberg
- Department of Biology, University of Maryland, College Park, MD, USA
| | | | - Ramil Mauleon
- International Rice Research Institute, Los Baños, Philippines
| | | | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Dave Flowers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Chuanzhu Fan
- Department of Biological Sciences, Wayne State University, Detroit, MI, USA
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Kshirod K Jena
- International Rice Research Institute, Los Baños, Philippines
| | - Thomas Wicker
- Institute of Plant Biology, University of Zurich, Zurich, Switzerland
| | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Bin Han
- National Center for Gene Research, Chinese Academy of Sciences, Shanghai, China
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
| | - Yue-Ie C Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Nori Kurata
- National Institute of Genetics, Mishima, Japan
| | | | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes, UMR 5096 UPVD/CNRS, Université de Perpignan Via Domitia, Perpignan, France
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Carlos A Machado
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Michael J Sanderson
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Manyuan Long
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.,Robert W. Holley Center for Agriculture and Health, US Department of Agriculture, Agricultural Research Service, Ithaca, NY, USA
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ, USA. .,International Rice Research Institute, Los Baños, Philippines. .,Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.
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18
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Lwin AK, Bertolini E, Pè ME, Zuccolo A. Genomic skimming for identification of medium/highly abundant transposable elements in Arundo donax and Arundo plinii. Mol Genet Genomics 2016; 292:157-171. [PMID: 27778102 DOI: 10.1007/s00438-016-1263-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 10/17/2016] [Indexed: 11/29/2022]
Abstract
Transposable elements (TEs) are the most abundant genetic material for almost all eukaryotic genomes. Their effects on the host genomes range from an extensive size variation to the regulation of gene expression, altering gene function and creating new genes. Because of TEs pivotal contribute to the host genome structure and regulation, their identification and characterization provide a wealth of useful data for gaining an in-depth understanding of host genome functioning. The giant reed (Arundo donax) is a perennial rhizomatous C3 grass, octadecaploid, with an estimated nuclear genome size of 2744 Mbp. It is a promising feedstock for second-generation biofuels and biomethane production. To identify and characterize the most repetitive TEs in the genomes of A. donax and its ancestral A. plinii species, we carried out low-coverage whole genome shotgun sequencing for both species. Using a de novo repeat identification approach, 33,041 and 28,237 non-redundant repetitive sequences were identified and characterized in A. donax and A. plinii genomes, representing 37.55 and 31.68% of each genome, respectively. Comparative phylogenetic analyses, including the major TE classes identified in A. donax and A. plinii, together with rice and maize TE paralogs, were carried out to understand the evolutionary relationship of the most abundant TE classes. Highly conserved copies of RIRE1-like Ty1-Copia elements were discovered in two Arundo spp. in which they represented nearly 3% of each genomic sequence. We identified and characterized the medium/highly repetitive TEs in two unexplored polyploid genomes, thus generating useful information for the study of the genomic structure, composition, and functioning of these two non-model species. We provided a valuable resource that could be exploited in any effort aimed at sequencing and assembling these two genomes.
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Affiliation(s)
- Aung Kyaw Lwin
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà, 33, 56127, Pisa, Italy.,Sugarcane Research and Seed Farm, Pyinmana, Nay Pyi Taw, Myanmar
| | - Edoardo Bertolini
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà, 33, 56127, Pisa, Italy
| | - Mario Enrico Pè
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà, 33, 56127, Pisa, Italy
| | - Andrea Zuccolo
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà, 33, 56127, Pisa, Italy.
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19
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Wicker T, Yu Y, Haberer G, Mayer KFX, Marri PR, Rounsley S, Chen M, Zuccolo A, Panaud O, Wing RA, Roffler S. DNA transposon activity is associated with increased mutation rates in genes of rice and other grasses. Nat Commun 2016; 7:12790. [PMID: 27599761 PMCID: PMC5023962 DOI: 10.1038/ncomms12790] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 08/02/2016] [Indexed: 12/16/2022] Open
Abstract
DNA (class 2) transposons are mobile genetic elements which move within their ‘host' genome through excising and re-inserting elsewhere. Although the rice genome contains tens of thousands of such elements, their actual role in evolution is still unclear. Analysing over 650 transposon polymorphisms in the rice species Oryza sativa and Oryza glaberrima, we find that DNA repair following transposon excisions is associated with an increased number of mutations in the sequences neighbouring the transposon. Indeed, the 3,000 bp flanking the excised transposons can contain over 10 times more mutations than the genome-wide average. Since DNA transposons preferably insert near genes, this is correlated with increases in mutation rates in coding sequences and regulatory regions. Most importantly, we find this phenomenon also in maize, wheat and barley. Thus, these findings suggest that DNA transposon activity is a major evolutionary force in grasses which provide the basis of most food consumed by humankind. DNA transposons are numerous in plant genomes. Here, Wicker et al. analyse transposon polymorphisms in rice and other grasses and show that sequences flanking excision sites contain up to 10 times more mutations than average, suggesting transposons are a major factor shaping the evolution of grass genomes.
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Affiliation(s)
- Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland
| | - Yeisoo Yu
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA
| | - Georg Haberer
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | | | | | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101 China
| | - Andrea Zuccolo
- Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes, UMR5096 UPVD/CNRS, Université de Perpignan Via Domitia, 66860 Perpignan, France
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona 85721, USA.,International Rice Research Institute, Los Baños, 4031 Laguna, Philippines.,Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
| | - Stefan Roffler
- Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland
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20
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Gebre YG, Bertolini E, Pè ME, Zuccolo A. Identification and characterization of abundant repetitive sequences in Eragrostis tef cv. Enatite genome. BMC Plant Biol 2016; 16:39. [PMID: 26833063 PMCID: PMC4736629 DOI: 10.1186/s12870-016-0725-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 01/28/2016] [Indexed: 06/05/2023]
Abstract
BACKGROUND Eragrostis tef is an allotetraploid (2n = 4 × = 40) annual, C4 grass with an estimated nuclear genome size of 730 Mbp. It is widely grown in Ethiopia, where it provides basic nutrition for more than half of the population. Although a draft assembly of the E. tef genome was made available in 2014, characterization of the repetitive portion of the E. tef genome has not been a subject of a detailed analysis. Repetitive sequences constitute most of the DNA in eukaryotic genomes. Transposable elements are usually the most abundant repetitive component in plant genomes. They contribute to genome size variation, cause mutations, can result in chromosomal rearrangements, and influence gene regulation. An extensive and in depth characterization of the repetitive component is essential in understanding the evolution and function of the genome. RESULTS Using new paired-end sequence data and a de novo repeat identification strategy, we identified the most repetitive elements in the E. tef genome. Putative repeat sequences were annotated based on similarity to known repeat groups in other grasses. Altogether we identified 1,389 medium/highly repetitive sequences that collectively represent about 27% of the teff genome. Phylogenetic analyses of the most important classes of TEs were carried out in a comparative framework including paralog elements from rice and maize. Finally, an abundant tandem repeat accounting for more than 4% of the whole genome was identified and partially characterized. CONCLUSIONS Analyzing a large sample of randomly sheared reads we obtained a library of the repetitive sequences of E. tef. The approach we used was designed to avoid underestimation of repeat contribution; such underestimation is characteristic of whole genome assembly projects. The data collected represent a valuable resource for further analysis of the genome of this important orphan crop.
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Affiliation(s)
- Yohannes Gedamu Gebre
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà, 33-56127, Pisa, Italy.
- Department of Dryland Crop and Horticultural Sciences, College of Dryland Agriculture and Natural Resources, Mekelle University, P.O.Box 231, Mekelle, Ethiopia.
| | - Edoardo Bertolini
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà, 33-56127, Pisa, Italy.
| | - Mario Enrico Pè
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà, 33-56127, Pisa, Italy.
| | - Andrea Zuccolo
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà, 33-56127, Pisa, Italy.
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21
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Cukrov D, Zermiani M, Brizzolara S, Cestaro A, Licausi F, Luchinat C, Santucci C, Tenori L, Van Veen H, Zuccolo A, Ruperti B, Tonutti P. Extreme Hypoxic Conditions Induce Selective Molecular Responses and Metabolic Reset in Detached Apple Fruit. Front Plant Sci 2016; 7:146. [PMID: 26909091 PMCID: PMC4754620 DOI: 10.3389/fpls.2016.00146] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 01/28/2016] [Indexed: 05/05/2023]
Abstract
The ripening physiology of detached fruit is altered by low oxygen conditions with profound effects on quality parameters. To study hypoxia-related processes and regulatory mechanisms, apple (Malus domestica, cv Granny Smith) fruit, harvested at commercial ripening, were kept at 1°C under normoxic (control) and hypoxic (0.4 and 0.8 kPa oxygen) conditions for up to 60 days. NMR analyses of cortex tissue identified eight metabolites showing significantly different accumulations between samples, with ethanol and alanine displaying the most pronounced difference between hypoxic and normoxic treatments. A rapid up-regulation of alcohol dehydrogenase and pyruvate-related metabolism (lactate dehydrogenase, pyruvate decarboxylase, alanine aminotransferase) gene expression was detected under both hypoxic conditions with a more pronounced effect induced by the lowest (0.4 kPa) oxygen concentration. Both hypoxic conditions negatively affected ACC synthase and ACC oxidase transcript accumulation. Analysis of RNA-seq data of samples collected after 24 days of hypoxic treatment identified more than 1000 genes differentially expressed when comparing 0.4 vs. 0.8 kPa oxygen concentration samples. Genes involved in cell-wall, minor and major CHO, amino acid and secondary metabolisms, fermentation and glycolysis as well as genes involved in transport, defense responses, and oxidation-reduction appeared to be selectively affected by treatments. The lowest oxygen concentration induced a higher expression of transcription factors belonging to AUX/IAA, WRKY, HB, Zinc-finger families, while MADS box family genes were more expressed when apples were kept under 0.8 kPa oxygen. Out of the eight group VII ERF members present in apple genome, two genes showed a rapid up-regulation under hypoxia, and western blot analysis showed that apple MdRAP2.12 proteins were differentially accumulated in normoxic and hypoxic samples, with the highest level reached under 0.4 kPa oxygen. These data suggest that ripe apple tissues finely and specifically modulate sensing and regulatory mechanisms in response to different hypoxic stress conditions.
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Affiliation(s)
- Dubravka Cukrov
- Istituto di Scienze della Vita, Scuola Superiore Sant'AnnaPisa, Italy
| | - Monica Zermiani
- Dipartimento di Agronomia Animali Alimenti Risorse Naturali e Ambiente, University of PadovaPadova, Italy
| | | | - Alessandro Cestaro
- Centro Ricerca e Innovazione, Fondazione Edmund Mach di San Michele all'AdigeTrento, Italy
| | - Francesco Licausi
- Istituto di Scienze della Vita, Scuola Superiore Sant'AnnaPisa, Italy
| | | | | | | | - Hans Van Veen
- Istituto di Scienze della Vita, Scuola Superiore Sant'AnnaPisa, Italy
| | - Andrea Zuccolo
- Istituto di Scienze della Vita, Scuola Superiore Sant'AnnaPisa, Italy
| | - Benedetto Ruperti
- Dipartimento di Agronomia Animali Alimenti Risorse Naturali e Ambiente, University of PadovaPadova, Italy
| | - Pietro Tonutti
- Istituto di Scienze della Vita, Scuola Superiore Sant'AnnaPisa, Italy
- *Correspondence: Pietro Tonutti
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22
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Copetti D, Zhang J, El Baidouri M, Gao D, Wang J, Barghini E, Cossu RM, Angelova A, Maldonado L CE, Roffler S, Ohyanagi H, Wicker T, Fan C, Zuccolo A, Chen M, Costa de Oliveira A, Han B, Henry R, Hsing YI, Kurata N, Wang W, Jackson SA, Panaud O, Wing RA. RiTE database: a resource database for genus-wide rice genomics and evolutionary biology. BMC Genomics 2015; 16:538. [PMID: 26194356 PMCID: PMC4508813 DOI: 10.1186/s12864-015-1762-3] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 07/09/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Comparative evolutionary analysis of whole genomes requires not only accurate annotation of gene space, but also proper annotation of the repetitive fraction which is often the largest component of most if not all genomes larger than 50 kb in size. RESULTS Here we present the Rice TE database (RiTE-db)--a genus-wide collection of transposable elements and repeated sequences across 11 diploid species of the genus Oryza and the closely-related out-group Leersia perrieri. The database consists of more than 170,000 entries divided into three main types: (i) a classified and curated set of publicly-available repeated sequences, (ii) a set of consensus assemblies of highly-repetitive sequences obtained from genome sequencing surveys of 12 species; and (iii) a set of full-length TEs, identified and extracted from 12 whole genome assemblies. CONCLUSIONS This is the first report of a repeat dataset that spans the majority of repeat variability within an entire genus, and one that includes complete elements as well as unassembled repeats. The database allows sequence browsing, downloading, and similarity searches. Because of the strategy adopted, the RiTE-db opens a new path to unprecedented direct comparative studies that span the entire nuclear repeat content of 15 million years of Oryza diversity.
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Affiliation(s)
- Dario Copetti
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, United States.
- International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna, Philippines.
| | - Jianwei Zhang
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, United States.
| | - Moaine El Baidouri
- Laboratoire Génome et Développement des Plantes and CNRS and Laboratoire Génome et Développements des Plantes, Université de Perpignan Via Domitia, UMR CNRS/UPVD 5096, 66860, Perpignan, France.
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, United States.
| | - Dongying Gao
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, United States.
| | - Jun Wang
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, United States.
| | - Elena Barghini
- Department of Agriculture, Food, and Environment, University of Pisa, 56124, Pisa, Italy.
| | - Rosa M Cossu
- Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127, Pisa, Italy.
| | - Angelina Angelova
- School of Life Sciences, Heriot-Watt University, Edinburgh, EH14 4AS, Scotland.
| | - Carlos E Maldonado L
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, United States.
| | - Stefan Roffler
- Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland.
| | - Hajime Ohyanagi
- Plant Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.
| | - Thomas Wicker
- Institute of Plant Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland.
| | - Chuanzhu Fan
- Department of Biological Sciences, Wayne State University, Detroit, MI, 48202, United States.
| | - Andrea Zuccolo
- Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127, Pisa, Italy.
| | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology Chinese Academy of Sciences, Beijing, 100101, China.
| | | | - Bin Han
- National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Beijing, 100029, China.
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia.
| | - Yue-Ie Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei, 11529, Taiwan.
| | - Nori Kurata
- Plant Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan.
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences and University of Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, Yunnan, 650223, China.
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, United States.
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes and CNRS and Laboratoire Génome et Développements des Plantes, Université de Perpignan Via Domitia, UMR CNRS/UPVD 5096, 66860, Perpignan, France.
| | - Rod A Wing
- Arizona Genomics Institute, BIO5 Institute and School of Plant Sciences, University of Arizona, Tucson, AZ, 85721, United States.
- International Rice Research Institute, Genetic Resource Center, Los Baños, Laguna, Philippines.
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23
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Zuccolo A, Scofield DG, De Paoli E, Morgante M. The Ty1-copia LTR retroelement family PARTC is highly conserved in conifers over 200 MY of evolution. Gene 2015; 568:89-99. [PMID: 25982862 DOI: 10.1016/j.gene.2015.05.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 04/06/2015] [Accepted: 05/11/2015] [Indexed: 11/26/2022]
Abstract
Long Terminal Repeat retroelements (LTR-RTs) are a major component of many plant genomes. Although well studied and described in angiosperms, their features and dynamics are poorly understood in gymnosperms. Representative complete copies of a Ty1-copia element isolate in Picea abies and named PARTC were identified in six other conifer species (Picea glauca, Pinus sylvestris, Pinus taeda, Abies sibirica, Taxus baccata and Juniperus communis) covering more than 200 million years of evolution. Here we characterized the structure of this element, assessed its abundance across conifers, studied the modes and timing of its amplification, and evaluated the degree of conservation of its extant copies at nucleotide level over distant species. We demonstrated that the element is ancient, abundant, widespread and its paralogous copies are present in the genera Picea, Pinus and Abies as an LTR-RT family. The amplification leading to the extant copies of PARTC occurred over long evolutionary times spanning 10s of MY and mostly took place after the speciation of the conifers analyzed. The level of conservation of PARTC is striking and may be explained by low substitution rates and limited removal mechanisms for LTR-RTs. These PARTC features and dynamics are representative of a more general scenario for LTR-RTs in gymnosperms quite different from that characterizing the vast majority of LTR-RT elements in angiosperms.
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Affiliation(s)
- Andrea Zuccolo
- Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127 Pisa, Italy; Istituto di Genomica Applicata, Via J. Linussio 51, 33100 Udine, Italy.
| | - Douglas G Scofield
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-75236 Uppsala, Sweden
| | - Emanuele De Paoli
- Università degli Studi di Udine, Via delle Scienze 208, 33100 Udine, Italy
| | - Michele Morgante
- Istituto di Genomica Applicata, Via J. Linussio 51, 33100 Udine, Italy; Università degli Studi di Udine, Via delle Scienze 208, 33100 Udine, Italy
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24
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Dell'Acqua M, Zuccolo A, Tuna M, Gianfranceschi L, Pè ME. Targeting environmental adaptation in the monocot model Brachypodium distachyon: a multi-faceted approach. BMC Genomics 2014; 15:801. [PMID: 25236859 PMCID: PMC4177692 DOI: 10.1186/1471-2164-15-801] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 09/04/2014] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The local environment plays a major role in the spatial distribution of plant populations. Natural plant populations have an extremely poor displacing capacity, so their continued survival in a given environment depends on how well they adapt to local pedoclimatic conditions. Genomic tools can be used to identify adaptive traits at a DNA level and to further our understanding of evolutionary processes. Here we report the use of genotyping-by-sequencing on local groups of the sequenced monocot model species Brachypodium distachyon. Exploiting population genetics, landscape genomics and genome wide association studies, we evaluate B. distachyon role as a natural probe for identifying genomic loci involved in environmental adaptation. RESULTS Brachypodium distachyon individuals were sampled in nine locations with different ecologies and characterized with 16,697 SNPs. Variations in sequencing depth showed consistent patterns at 8,072 genomic bins, which were significantly enriched in transposable elements. We investigated the structuration and diversity of this collection, and exploited climatic data to identify loci with adaptive significance through i) two different approaches for genome wide association analyses considering climatic variation, ii) an outlier loci approach, and iii) a canonical correlation analysis on differentially sequenced bins. A linkage disequilibrium-corrected Bonferroni method was applied to filter associations. The two association methods jointly identified a set of 15 genes significantly related to environmental adaptation. The outlier loci approach revealed that 5.7% of the loci analysed were under selection. The canonical correlation analysis showed that the distribution of some differentially sequenced regions was associated to environmental variation. CONCLUSIONS We show that the multi-faceted approach used here targeted different components of B. distachyon adaptive variation, and may lead to the discovery of genes related to environmental adaptation in natural populations. Its application to a model species with a fully sequenced genome is a modular strategy that enables the stratification of biological material and thus improves our knowledge of the functional loci determining adaptation in near-crop species. When coupled with population genetics and measures of genomic structuration, methods coming from genome wide association studies may lead to the exploitation of model species as natural probes to identify loci related to environmental adaptation.
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Affiliation(s)
| | | | | | | | - Mario Enrico Pè
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy.
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25
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Ranade SS, Lin YC, Zuccolo A, Van de Peer Y, García-Gil MDR. Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera. BMC Plant Biol 2014; 14:220. [PMID: 25143005 PMCID: PMC4160553 DOI: 10.1186/s12870-014-0220-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 08/05/2014] [Indexed: 05/24/2023]
Abstract
BACKGROUND Simple Sequence Repeats (SSRs) derived from Expressed Sequence Tags (ESTs) belong to the expressed fraction of the genome and are important for gene regulation, recombination, DNA replication, cell cycle and mismatch repair. Here, we present a comparative analysis of the SSR motif distribution in the 5'UTR, ORF and 3'UTR fractions of ESTs across selected genera of woody trees representing gymnosperms (17 species from seven genera) and angiosperms (40 species from eight genera). RESULTS Our analysis supports a modest contribution of EST-SSR length to genome size in gymnosperms, while EST-SSR density was not associated with genome size in neither angiosperms nor gymnosperms. Multiple factors seem to have contributed to the lower abundance of EST-SSRs in gymnosperms that has resulted in a non-linear relationship with genome size diversity. The AG/CT motif was found to be the most abundant in SSRs of both angiosperms and gymnosperms, with a relative increase in AT/AT in the latter. Our data also reveals a higher abundance of hexamers across the gymnosperm genera. CONCLUSIONS Our analysis provides the foundation for future comparative studies at the species level to unravel the evolutionary processes that control the SSR genesis and divergence between angiosperm and gymnosperm tree species.
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Affiliation(s)
- Sonali Sachin Ranade
- />Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901-83 Umeå, Sweden
| | - Yao-Cheng Lin
- />Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Andrea Zuccolo
- />Istituto di Genomica Applicata, Via J. Linussio 51, 33100 Udine, Italy
- />Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127 Pisa, Italy
| | - Yves Van de Peer
- />Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
- />Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria, 0028 South Africa
| | - María del Rosario García-Gil
- />Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901-83 Umeå, Sweden
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Wang M, Yu Y, Haberer G, Marri PR, Fan C, Goicoechea JL, Zuccolo A, Song X, Kudrna D, Ammiraju JSS, Cossu RM, Maldonado C, Chen J, Lee S, Sisneros N, de Baynast K, Golser W, Wissotski M, Kim W, Sanchez P, Ndjiondjop MN, Sanni K, Long M, Carney J, Panaud O, Wicker T, Machado CA, Chen M, Mayer KFX, Rounsley S, Wing RA. The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nat Genet 2014; 46:982-8. [PMID: 25064006 PMCID: PMC7036042 DOI: 10.1038/ng.3044] [Citation(s) in RCA: 282] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Accepted: 06/30/2014] [Indexed: 12/19/2022]
Abstract
Mingsheng Chen, Klaus Mayer, Steve Rounsley, Rod Wing and colleagues report the genome sequence of African rice (Oryza glaberrima), a different species than Asian rice. The authors resequenced 20 O. glaberrima accessions and 94 Oryza barthii accessions (the putative progenitor species of O. glaberrima), and their analyses support the hypothesis that O. glaberrima was domesticated in a single region along the upper Niger river. The cultivation of rice in Africa dates back more than 3,000 years. Interestingly, African rice is not of the same origin as Asian rice (Oryza sativa L.) but rather is an entirely different species (i.e., Oryza glaberrima Steud.). Here we present a high-quality assembly and annotation of the O. glaberrima genome and detailed analyses of its evolutionary history of domestication and selection. Population genomics analyses of 20 O. glaberrima and 94 Oryza barthii accessions support the hypothesis that O. glaberrima was domesticated in a single region along the Niger river as opposed to noncentric domestication events across Africa. We detected evidence for artificial selection at a genome-wide scale, as well as with a set of O. glaberrima genes orthologous to O. sativa genes that are known to be associated with domestication, thus indicating convergent yet independent selection of a common set of genes during two geographically and culturally distinct domestication processes.
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Affiliation(s)
- Muhua Wang
- 1] Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA. [2]
| | - Yeisoo Yu
- 1] Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA. [2]
| | - Georg Haberer
- 1] Plant Genome and Systems Biology, Helmholtz Center Munich, Neuherberg, Germany. [2]
| | | | - Chuanzhu Fan
- 1] Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA. [2] Department of Biological Sciences, Wayne State University, Detroit, Michigan, USA
| | - Jose Luis Goicoechea
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Andrea Zuccolo
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Xiang Song
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Dave Kudrna
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Jetty S S Ammiraju
- 1] Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA. [2] DuPont Pioneer, Johnston, Iowa, USA
| | - Rosa Maria Cossu
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Carlos Maldonado
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Jinfeng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Seunghee Lee
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Nick Sisneros
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Kristi de Baynast
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Wolfgang Golser
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Marina Wissotski
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Woojin Kim
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
| | - Paul Sanchez
- 1] Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA. [2] US Arid Land Agricultural Research Center, Maricopa, Arizona, USA
| | | | | | - Manyuan Long
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, USA
| | - Judith Carney
- Department of Geography, Institute of the Environment and Sustainability, University of California, Los Angeles, California, USA
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes, UMR CNRS/Institut de Recherche pour le Développement/l'Université de Perpignan Via Domitia, Université de Perpignan, Perpignan, France
| | - Thomas Wicker
- Institute of Plant Biology, University of Zurich, Zurich, Switzerland
| | - Carlos A Machado
- Department of Biology, University of Maryland, College Park, Maryland, USA
| | - Mingsheng Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Klaus F X Mayer
- Plant Genome and Systems Biology, Helmholtz Center Munich, Neuherberg, Germany
| | | | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, Arizona, USA
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Wu GA, Prochnik S, Jenkins J, Salse J, Hellsten U, Murat F, Perrier X, Ruiz M, Scalabrin S, Terol J, Takita MA, Labadie K, Poulain J, Couloux A, Jabbari K, Cattonaro F, Del Fabbro C, Pinosio S, Zuccolo A, Chapman J, Grimwood J, Tadeo FR, Estornell LH, Muñoz-Sanz JV, Ibanez V, Herrero-Ortega A, Aleza P, Pérez-Pérez J, Ramón D, Brunel D, Luro F, Chen C, Farmerie WG, Desany B, Kodira C, Mohiuddin M, Harkins T, Fredrikson K, Burns P, Lomsadze A, Borodovsky M, Reforgiato G, Freitas-Astúa J, Quetier F, Navarro L, Roose M, Wincker P, Schmutz J, Morgante M, Machado MA, Talon M, Jaillon O, Ollitrault P, Gmitter F, Rokhsar D. Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication. Nat Biotechnol 2014; 32:656-62. [PMID: 24908277 PMCID: PMC4113729 DOI: 10.1038/nbt.2906] [Citation(s) in RCA: 320] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 04/14/2014] [Indexed: 01/21/2023]
Abstract
Cultivated citrus are selections from, or hybrids of, wild progenitor species whose identities and contributions to citrus domestication remain controversial. Here we sequence and compare citrus genomes--a high-quality reference haploid clementine genome and mandarin, pummelo, sweet-orange and sour-orange genomes--and show that cultivated types derive from two progenitor species. Although cultivated pummelos represent selections from one progenitor species, Citrus maxima, cultivated mandarins are introgressions of C. maxima into the ancestral mandarin species Citrus reticulata. The most widely cultivated citrus, sweet orange, is the offspring of previously admixed individuals, but sour orange is an F1 hybrid of pure C. maxima and C. reticulata parents, thus implying that wild mandarins were part of the early breeding germplasm. A Chinese wild 'mandarin' diverges substantially from C. reticulata, thus suggesting the possibility of other unrecognized wild citrus species. Understanding citrus phylogeny through genome analysis clarifies taxonomic relationships and facilitates sequence-directed genetic improvement.
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Affiliation(s)
- G. Albert Wu
- US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Simon Prochnik
- US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Jerry Jenkins
- HudsonAlpha Biotechnology Institute, Huntsville, AL, USA
| | - Jerome Salse
- INRA/UBP UMR 1095 GDEC, Clermont Ferrand, France
| | - Uffe Hellsten
- US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | | | | | | | | | - Javier Terol
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | | | - Karine Labadie
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Julie Poulain
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Arnaud Couloux
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | - Kamel Jabbari
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
| | | | | | | | - Andrea Zuccolo
- Istituto di Genomica Applicata, Udine, Italy
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Jarrod Chapman
- US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Jane Grimwood
- HudsonAlpha Biotechnology Institute, Huntsville, AL, USA
| | - Francisco R. Tadeo
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Leandro H. Estornell
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Juan V. Muñoz-Sanz
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Victoria Ibanez
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Amparo Herrero-Ortega
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Pablo Aleza
- Centro de Protección Vegetal y Biotecnología-IVIA, Moncada, Valencia, Spain
| | | | | | - Dominique Brunel
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
- INRA, US EPGV_1279, Evry, France
| | | | - Chunxian Chen
- Citrus Research and Education Center (CREC), Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, USA
| | - William G. Farmerie
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Brian Desany
- 454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA
| | - Chinnappa Kodira
- 454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA
| | - Mohammed Mohiuddin
- 454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA
| | - Tim Harkins
- 454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA
| | - Karin Fredrikson
- 454 Life Sciences, A Roche Company, 15 Commercial Street, Branford CT, USA
| | - Paul Burns
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- School of Computational Science & Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Alexandre Lomsadze
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- School of Computational Science & Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Mark Borodovsky
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- School of Computational Science & Engineering, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Giuseppe Reforgiato
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura (CRA-ACM), Acireale, Italy
| | - Juliana Freitas-Astúa
- Centro de Citricultura Sylvio Moreira, IAC, Cordeirópolis, SP, Brazil
- Embrapa Cassava and Fruits, Cruz das Almas, BA, Brazil
| | - Francis Quetier
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
- Département de Biologie, Université d’Evry, Evry, France
| | - Luis Navarro
- Centro de Protección Vegetal y Biotecnología-IVIA, Moncada, Valencia, Spain
| | - Mikeal Roose
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Patrick Wincker
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
- Département de Biologie, Université d’Evry, Evry, France
- Centre National de Recherche Scientifique (CNRS), Evry, France
| | - Jeremy Schmutz
- HudsonAlpha Biotechnology Institute, Huntsville, AL, USA
| | - Michele Morgante
- Istituto di Genomica Applicata, Udine, Italy
- Department of Agriculture and Environmental Sciences, University of Udine, Udine, Italy
| | | | - Manuel Talon
- Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Valencia, Spain
| | - Olivier Jaillon
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, France
- Département de Biologie, Université d’Evry, Evry, France
- Centre National de Recherche Scientifique (CNRS), Evry, France
| | | | - Frederick Gmitter
- Citrus Research and Education Center (CREC), Institute of Food and Agricultural Sciences (IFAS), University of Florida, Lake Alfred, FL, USA
| | - Daniel Rokhsar
- US-Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
- Division of Genetics, Genomics, and Development, University of California, Berkeley, CA, USA
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28
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Stival Sena J, Giguère I, Boyle B, Rigault P, Birol I, Zuccolo A, Ritland K, Ritland C, Bohlmann J, Jones S, Bousquet J, Mackay J. Evolution of gene structure in the conifer Picea glauca: a comparative analysis of the impact of intron size. BMC Plant Biol 2014; 14:95. [PMID: 24734980 PMCID: PMC4108047 DOI: 10.1186/1471-2229-14-95] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 04/09/2014] [Indexed: 05/04/2023]
Abstract
BACKGROUND A positive relationship between genome size and intron length is observed across eukaryotes including Angiosperms plants, indicating a co-evolution of genome size and gene structure. Conifers have very large genomes and longer introns on average than most plants, but impacts of their large genome and longer introns on gene structure has not be described. RESULTS Gene structure was analyzed for 35 genes of Picea glauca obtained from BAC sequencing and genome assembly, including comparisons with A. thaliana, P. trichocarpa and Z. mays. We aimed to develop an understanding of impact of long introns on the structure of individual genes. The number and length of exons was well conserved among the species compared but on average, P. glauca introns were longer and genes had four times more intronic sequence than Arabidopsis, and 2 times more than poplar and maize. However, pairwise comparisons of individual genes gave variable results and not all contrasts were statistically significant. Genes generally accumulated one or a few longer introns in species with larger genomes but the position of long introns was variable between plant lineages. In P. glauca, highly expressed genes generally had more intronic sequence than tissue preferential genes. Comparisons with the Pinus taeda BACs and genome scaffolds showed a high conservation for position of long introns and for sequence of short introns. A survey of 1836 P. glauca genes obtained by sequence capture mostly containing introns <1 Kbp showed that repeated sequences were 10× more abundant in introns than in exons. CONCLUSION Conifers have large amounts of intronic sequence per gene for seed plants due to the presence of few long introns and repetitive element sequences are ubiquitous in their introns. Results indicate a complex landscape of intron sizes and distribution across taxa and between genes with different expression profiles.
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Affiliation(s)
- Juliana Stival Sena
- Center for Forest Research and Institute for Systems and Integrative Biology, 1030 rue de la Médecine, Université Laval, Québec, QC G1V 0A6, Canada
| | - Isabelle Giguère
- Center for Forest Research and Institute for Systems and Integrative Biology, 1030 rue de la Médecine, Université Laval, Québec, QC G1V 0A6, Canada
| | - Brian Boyle
- Center for Forest Research and Institute for Systems and Integrative Biology, 1030 rue de la Médecine, Université Laval, Québec, QC G1V 0A6, Canada
| | | | - Inanc Birol
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Andrea Zuccolo
- Applied Genomics Institute, Udine 33100, Italy
- Institute of Life Sciences, Scuola Superiore Sant’Anna, Pisa 56127, Italy
| | - Kermit Ritland
- Department of Forest Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Carol Ritland
- Department of Forest Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Steven Jones
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jean Bousquet
- Center for Forest Research and Institute for Systems and Integrative Biology, 1030 rue de la Médecine, Université Laval, Québec, QC G1V 0A6, Canada
- Canada Research Chair in Forest Genomics, Université Laval, Québec, QC G1V 0A6, Canada
| | - John Mackay
- Center for Forest Research and Institute for Systems and Integrative Biology, 1030 rue de la Médecine, Université Laval, Québec, QC G1V 0A6, Canada
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29
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Verde I, Abbott AG, Scalabrin S, Jung S, Shu S, Marroni F, Zhebentyayeva T, Dettori MT, Grimwood J, Cattonaro F, Zuccolo A, Rossini L, Jenkins J, Vendramin E, Meisel LA, Decroocq V, Sosinski B, Prochnik S, Mitros T, Policriti A, Cipriani G, Dondini L, Ficklin S, Goodstein DM, Xuan P, Del Fabbro C, Aramini V, Copetti D, Gonzalez S, Horner DS, Falchi R, Lucas S, Mica E, Maldonado J, Lazzari B, Bielenberg D, Pirona R, Miculan M, Barakat A, Testolin R, Stella A, Tartarini S, Tonutti P, Arús P, Orellana A, Wells C, Main D, Vizzotto G, Silva H, Salamini F, Schmutz J, Morgante M, Rokhsar DS. The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nat Genet 2013; 45:487-94. [PMID: 23525075 DOI: 10.1038/ng.2586] [Citation(s) in RCA: 578] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 02/22/2013] [Indexed: 11/09/2022]
Abstract
Rosaceae is the most important fruit-producing clade, and its key commercially relevant genera (Fragaria, Rosa, Rubus and Prunus) show broadly diverse growth habits, fruit types and compact diploid genomes. Peach, a diploid Prunus species, is one of the best genetically characterized deciduous trees. Here we describe the high-quality genome sequence of peach obtained from a completely homozygous genotype. We obtained a complete chromosome-scale assembly using Sanger whole-genome shotgun methods. We predicted 27,852 protein-coding genes, as well as noncoding RNAs. We investigated the path of peach domestication through whole-genome resequencing of 14 Prunus accessions. The analyses suggest major genetic bottlenecks that have substantially shaped peach genome diversity. Furthermore, comparative analyses showed that peach has not undergone recent whole-genome duplication, and even though the ancestral triplicated blocks in peach are fragmentary compared to those in grape, all seven paleosets of paralogs from the putative paleoancestor are detectable.
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Affiliation(s)
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- Consiglio per la Ricerca e la Sperimentazione in Agricoltura (CRA)-Centro di Ricerca per la Frutticoltura, Rome, Italy.
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30
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Cooper KK, Cooper MA, Zuccolo A, Joens LA. Re-sequencing of a virulent strain of Campylobacter jejuni NCTC11168 reveals potential virulence factors. Res Microbiol 2012; 164:6-11. [PMID: 23046762 DOI: 10.1016/j.resmic.2012.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 09/12/2012] [Indexed: 11/25/2022]
Abstract
In vitro passage of Campylobacter jejuni strains results in phenotypic changes and a general loss of virulence, as is the case with the genome-sequenced strain C. jejuni NCTC11168. Re-sequencing of a virulent strain of NCTC11168 identified 41 SNPs or indels involving 20 genes, four intergenic regions and three pseudogenes. The genes include six motility genes, two chemotaxis genes, three hypothetical genes and a capsule biosynthesis gene, which might have a critical role in C. jejuni virulence. Additionally, we found an insertion in both Cj0676 and Cj1470c, pseudogenes in avirulent NCTC11168, but functional proteins in virulent NCTC11168.
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Affiliation(s)
- Kerry K Cooper
- Department of Veterinary Science and Microbiology, University of Arizona, Tucson, AZ 85721, USA.
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31
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Zuccolo A, Bowers JE, Estill JC, Xiong Z, Luo M, Sebastian A, Goicoechea JL, Collura K, Yu Y, Jiao Y, Duarte J, Tang H, Ayyampalayam S, Rounsley S, Kudrna D, Paterson AH, Pires JC, Chanderbali A, Soltis DE, Chamala S, Barbazuk B, Soltis PS, Albert VA, Ma H, Mandoli D, Banks J, Carlson JE, Tomkins J, dePamphilis CW, Wing RA, Leebens-Mack J. A physical map for the Amborella trichopoda genome sheds light on the evolution of angiosperm genome structure. Genome Biol 2011; 12:R48. [PMID: 21619600 PMCID: PMC3219971 DOI: 10.1186/gb-2011-12-5-r48] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2010] [Revised: 05/19/2011] [Accepted: 05/27/2011] [Indexed: 01/19/2023] Open
Abstract
Background Recent phylogenetic analyses have identified Amborella trichopoda, an understory tree species endemic to the forests of New Caledonia, as sister to a clade including all other known flowering plant species. The Amborella genome is a unique reference for understanding the evolution of angiosperm genomes because it can serve as an outgroup to root comparative analyses. A physical map, BAC end sequences and sample shotgun sequences provide a first view of the 870 Mbp Amborella genome. Results Analysis of Amborella BAC ends sequenced from each contig suggests that the density of long terminal repeat retrotransposons is negatively correlated with that of protein coding genes. Syntenic, presumably ancestral, gene blocks were identified in comparisons of the Amborella BAC contigs and the sequenced Arabidopsis thaliana, Populus trichocarpa, Vitis vinifera and Oryza sativa genomes. Parsimony mapping of the loss of synteny corroborates previous analyses suggesting that the rate of structural change has been more rapid on lineages leading to Arabidopsis and Oryza compared with lineages leading to Populus and Vitis. The gamma paleohexiploidy event identified in the Arabidopsis, Populus and Vitis genomes is shown to have occurred after the divergence of all other known angiosperms from the lineage leading to Amborella. Conclusions When placed in the context of a physical map, BAC end sequences representing just 5.4% of the Amborella genome have facilitated reconstruction of gene blocks that existed in the last common ancestor of all flowering plants. The Amborella genome is an invaluable reference for inferences concerning the ancestral angiosperm and subsequent genome evolution.
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Affiliation(s)
- Andrea Zuccolo
- Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, 1657 East Helen Street, Tucson, AZ 85721, USA
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32
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Hurwitz BL, Kudrna D, Yu Y, Sebastian A, Zuccolo A, Jackson SA, Ware D, Wing RA, Stein L. Rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza. Plant J 2010; 63:990-1003. [PMID: 20626650 DOI: 10.1111/j.1365-313x.2010.04293.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Rapid progress in comparative genomics among the grasses has revealed similar gene content and order despite exceptional differences in chromosome size and number. Large- and small-scale genomic variations are of particular interest, especially among cultivated and wild species, as they encode rapidly evolving features that may be important in adaptation to particular environments. We present a genome-wide study of intermediate-sized structural variation (SV) among rice (Oryza sativa) and three of its closest relatives in the genus Oryza (Oryza nivara, Oryza rufipogon and Oryza glaberrima). We computationally identified regional expansions, contractions and inversions in the Oryza species genomes relative to O. sativa by combining data from paired-end clone alignments to the O. sativa reference genome and physical maps. A subset of the computational predictions was validated using a new approach for BAC size determination. The result was a confirmed catalog of 674 expansions (25-38 Mb) and 611 (4-19 Mb) contractions, and 140 putative inversions (14-19 Mb) between the three Oryza species and O. sativa. In the expanded regions unique to O. sativa we found enrichment in transposable elements (TEs): long terminal repeats (LTRs) were randomly located across the chromosomes, and their insertion times corresponded to the date of the A genome radiation. Also, rice-expanded regions contained an over-representation of single-copy genes related to defense factors in the environment. This catalog of confirmed SV in reference to O. sativa provides an entry point for future research in genome evolution, speciation, domestication and novel gene discovery.
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Affiliation(s)
- Bonnie L Hurwitz
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
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Lin L, Pierce GJ, Bowers JE, Estill JC, Compton RO, Rainville LK, Kim C, Lemke C, Rong J, Tang H, Wang X, Braidotti M, Chen AH, Chicola K, Collura K, Epps E, Golser W, Grover C, Ingles J, Karunakaran S, Kudrna D, Olive J, Tabassum N, Um E, Wissotski M, Yu Y, Zuccolo A, ur Rahman M, Peterson DG, Wing RA, Wendel JF, Paterson AH. A draft physical map of a D-genome cotton species (Gossypium raimondii). BMC Genomics 2010; 11:395. [PMID: 20569427 PMCID: PMC2996926 DOI: 10.1186/1471-2164-11-395] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Accepted: 06/22/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genetically anchored physical maps of large eukaryotic genomes have proven useful both for their intrinsic merit and as an adjunct to genome sequencing. Cultivated tetraploid cottons, Gossypium hirsutum and G. barbadense, share a common ancestor formed by a merger of the A and D genomes about 1-2 million years ago. Toward the long-term goal of characterizing the spectrum of diversity among cotton genomes, the worldwide cotton community has prioritized the D genome progenitor Gossypium raimondii for complete sequencing. RESULTS A whole genome physical map of G. raimondii, the putative D genome ancestral species of tetraploid cottons was assembled, integrating genetically-anchored overgo hybridization probes, agarose based fingerprints and 'high information content fingerprinting' (HICF). A total of 13,662 BAC-end sequences and 2,828 DNA probes were used in genetically anchoring 1585 contigs to a cotton consensus genetic map, and 370 and 438 contigs, respectively to Arabidopsis thaliana (AT) and Vitis vinifera (VV) whole genome sequences. CONCLUSION Several lines of evidence suggest that the G. raimondii genome is comprised of two qualitatively different components. Much of the gene rich component is aligned to the Arabidopsis and Vitis vinifera genomes and shows promise for utilizing translational genomic approaches in understanding this important genome and its resident genes. The integrated genetic-physical map is of value both in assembling and validating a planned reference sequence.
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Affiliation(s)
- Lifeng Lin
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Gary J Pierce
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - John E Bowers
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - James C Estill
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Rosana O Compton
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Lisa K Rainville
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Changsoo Kim
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Cornelia Lemke
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Junkang Rong
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
- School of Agriculture and Food Sciences, Zhejiang Forestry University, Lin'an, Hangzhou, Zhejiang, 311300, China
| | - Haibao Tang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
- Department of Plant and Microbiology, College of Natural Resources, University of California, Berkeley, CA, USA
| | - Xiyin Wang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Michele Braidotti
- Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, Tucson, AZ 85721, USA
| | - Amy H Chen
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Kristen Chicola
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Kristi Collura
- Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, Tucson, AZ 85721, USA
| | - Ethan Epps
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Wolfgang Golser
- Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, Tucson, AZ 85721, USA
| | - Corrinne Grover
- Department of Ecology, Evolution, & Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Jennifer Ingles
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | | | - Dave Kudrna
- Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, Tucson, AZ 85721, USA
| | - Jaime Olive
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Nabila Tabassum
- National Institute for Biotechnology & Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Eareana Um
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
| | - Marina Wissotski
- Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, Tucson, AZ 85721, USA
| | - Yeisoo Yu
- Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, Tucson, AZ 85721, USA
| | - Andrea Zuccolo
- Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, Tucson, AZ 85721, USA
| | - Mehboob ur Rahman
- National Institute for Biotechnology & Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Daniel G Peterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
- Life Sciences & Biotechnology Institute, Mississippi State University, Mississippi State, MS 39762 USA
| | - Rod A Wing
- Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, Tucson, AZ 85721, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, & Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, 30605, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
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Cavallini A, Natali L, Zuccolo A, Giordani T, Jurman I, Ferrillo V, Vitacolonna N, Sarri V, Cattonaro F, Ceccarelli M, Cionini PG, Morgante M. Analysis of transposons and repeat composition of the sunflower (Helianthus annuus L.) genome. Theor Appl Genet 2010; 120:491-508. [PMID: 19826774 DOI: 10.1007/s00122-009-1170-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2009] [Accepted: 09/27/2009] [Indexed: 05/25/2023]
Abstract
A sample-sequencing strategy combined with slot-blot hybridization and FISH was used to study the composition of the repetitive component of the sunflower genome. One thousand six hundred thirty-eight sequences for a total of 954,517 bp were analyzed. The fraction of sequences that can be classified as repetitive using computational and hybridization approaches amounts to 62% in total. Almost two thirds remain as yet uncharacterized in nature. Of those characterized, most belong to the gypsy superfamily of LTR-retrotransposons. Unlike in other species, where single families can account for large fractions of the genome, it appears that no transposon family has been amplified to very high levels in sunflower. All other known classes of transposable elements were also found. One family of unknown nature (contig 61) was the most repeated in the sunflower genome. The evolution of the repetitive component in the Helianthus genus and in other Asteraceae was studied by comparative analysis of the hybridization of total genomic DNAs from these species to the sunflower small-insert library and compared to gene-based phylogeny. Very little similarity is observed between Helianthus species and two related Asteraceae species outside of the genus. Most repetitive elements are similar in annual and perennial Helianthus species indicating that sequence amplification largely predates such divergence. Gypsy-like elements are more represented in the annuals than in the perennials, while copia-like elements are similarly represented, attesting a different amplification history of the two superfamilies of LTR-retrotransposons in the Helianthus genus.
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Affiliation(s)
- Andrea Cavallini
- Genetics Section, Department of Crop Plant Biology, University of Pisa, Pisa, Italy
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35
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Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh CT, Emrich SJ, Jia Y, Kalyanaraman A, Hsia AP, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia JM, Deragon JM, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK. The B73 Maize Genome: Complexity, Diversity, and Dynamics. Science 2009; 326:1112-5. [PMID: 19965430 DOI: 10.1126/science.1178534] [Citation(s) in RCA: 2467] [Impact Index Per Article: 164.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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36
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Natali L, Ceccarelli M, Giordani T, Sarri V, Zuccolo A, Jurman I, Morgante M, Cavallini A, Cionini PG. Phylogenetic relationships between annual and perennial species of Helianthus: evolution of a tandem repeated DNA sequence and cytological hybridization experiments. Genome 2008; 51:1047-53. [PMID: 19088818 DOI: 10.1139/g08-089] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The amplification and chromosomal localization of tandem repeated DNA sequences from Helianthus annuus (clone HAG004N15) and the physical organization of ribosomal DNA were studied in annual and perennial species of Helianthus. HAG004N15-related sequences, which did not show amplification in other Asteraceae except for Viguiera multiflora, were redundant in all the Helianthus species tested, but their frequency was significantly higher in perennials than in annuals. These sequences were located at the ends and intercalary regions of all chromosome pairs of annual species. A similar pattern was found in the perennials, but a metacentric pair in their complement was not labelled. Ribosomal cistrons were carried on two chromosome pairs in perennials and on three pairs in annuals except for H. annuus, where rDNA loci were on four pairs. No difference was observed between cultivated H. annuus and its wild accessions in the hybridization pattern of the HAG004N15 and ribosomal probes. These findings support the hypothesis that the separation between annual and perennial Helianthus species occurred through interspecific hybridization involving at least one different parent. However, GISH in H. annuus using genomic DNA from the perennial Helianthus giganteus as blocking DNA failed to reveal different genomic assets in annual and perennial species.
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Affiliation(s)
- L Natali
- Dipartimento di Biologia delle Piante Agrarie, Sezione di Genetica, Universita di Pisa, Via del Borghetto 80, 56124 Pisa, Italy
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37
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Ammiraju JSS, Lu F, Sanyal A, Yu Y, Song X, Jiang N, Pontaroli AC, Rambo T, Currie J, Collura K, Talag J, Fan C, Goicoechea JL, Zuccolo A, Chen J, Bennetzen JL, Chen M, Jackson S, Wing RA. Dynamic evolution of oryza genomes is revealed by comparative genomic analysis of a genus-wide vertical data set. Plant Cell 2008; 20:3191-209. [PMID: 19098269 PMCID: PMC2630430 DOI: 10.1105/tpc.108.063727] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2008] [Revised: 12/01/2008] [Accepted: 12/06/2008] [Indexed: 05/18/2023]
Abstract
Oryza (23 species; 10 genome types) contains the world's most important food crop - rice. Although the rice genome serves as an essential tool for biological research, little is known about the evolution of the other Oryza genome types. They contain a historical record of genomic changes that led to diversification of this genus around the world as well as an untapped reservoir of agriculturally important traits. To investigate the evolution of the collective Oryza genome, we sequenced and compared nine orthologous genomic regions encompassing the Adh1-Adh2 genes (from six diploid genome types) with the rice reference sequence. Our analysis revealed the architectural complexities and dynamic evolution of this region that have occurred over the past approximately 15 million years. Of the 46 intact genes and four pseudogenes in the japonica genome, 38 (76%) fell into eight multigene families. Analysis of the evolutionary history of each family revealed independent and lineage-specific gain and loss of gene family members as frequent causes of synteny disruption. Transposable elements were shown to mediate massive replacement of intergenic space (>95%), gene disruption, and gene/gene fragment movement. Three cases of long-range structural variation (inversions/deletions) spanning several hundred kilobases were identified that contributed significantly to genome diversification.
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Affiliation(s)
- Jetty S S Ammiraju
- Arizona Genomics Institute, Department of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, Arizona 85721, USA
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38
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Sarri V, Minelli S, Panara F, Morgante M, Jurman I, Zuccolo A, Cionini PG. Characterization and chromosomal organization of satellite DNA sequences in Picea abies. Genome 2008; 51:705-13. [PMID: 18772948 DOI: 10.1139/g08-048] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Three clones containing satellite DNA sequences were selected from a randomly sheared genomic DNA library of Picea abies (clones PAF1, PAG004P22F (2F), and PAG004E03C (3C)). PAF1 contained 7 repeats that were 37-55 bp in length and had 68.9%-91.9% nucleotide sequence similarity. Two 2F repeats were 305-306 bp in length and had 83% sequence similarity. Two 3C repeats were 193-226 bp in length and had a sequence similarity of 78.6%. The copy number per 1C DNA of PAF1, 2F, and 3C repeats was 2.7 x 10(6), 2.9 x 10(5), and 2.9 x 10(4), respectively. In situ hybridization showed centromeric localization of these sequences in two chromosome pairs with PAF1, all pairs but one with 2F, and three pairs with 3C. Moreover, PAF1 sequences hybridized at secondary constrictions in six pairs, while 2F-related sequences were found at these chromosome regions only in four pairs. These hybridization patterns allow all chromosome pairs to be distinguished. PAF1-related repeats were contained in the intergenic spacer (IGS) of ribosomal cistrons in all six nucleolar organizers of the complement, while sequences related to 2F were found on only one side of the rDNA arrays in four pairs, showing structural diversity between rDNA regions of different chromosomes.
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Affiliation(s)
- V Sarri
- Dipartimento di Biologia Cellulare e Ambientale, Sezione di Biologia Cellulare e Molecolare, Universita di Perugia, Via Elce di Sotto, 06123 Perugia, Italy
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39
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Soltis DE, Albert VA, Leebens-Mack J, Palmer JD, Wing RA, dePamphilis CW, Ma H, Carlson JE, Altman N, Kim S, Wall PK, Zuccolo A, Soltis PS. The Amborella genome: an evolutionary reference for plant biology. Genome Biol 2008; 9:402. [PMID: 18341710 PMCID: PMC2397498 DOI: 10.1186/gb-2008-9-3-402] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The nuclear genome sequence of Amborella trichopoda, the sister species to all other extant angiosperms, will be an exceptional resource for plant genomics. The nuclear genome sequence of Amborella trichopoda, the sister species to all other extant angiosperms, will be an exceptional resource for plant genomics.
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Affiliation(s)
- Douglas E Soltis
- Department of Botany and the Genetics Institute, University of Florida, Gainesville, FL 32611, USA
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40
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Tanaka T, Antonio BA, Kikuchi S, Matsumoto T, Nagamura Y, Numa H, Sakai H, Wu J, Itoh T, Sasaki T, Aono R, Fujii Y, Habara T, Harada E, Kanno M, Kawahara Y, Kawashima H, Kubooka H, Matsuya A, Nakaoka H, Saichi N, Sanbonmatsu R, Sato Y, Shinso Y, Suzuki M, Takeda JI, Tanino M, Todokoro F, Yamaguchi K, Yamamoto N, Yamasaki C, Imanishi T, Okido T, Tada M, Ikeo K, Tateno Y, Gojobori T, Lin YC, Wei FJ, Hsing YI, Zhao Q, Han B, Kramer MR, McCombie RW, Lonsdale D, O'Donovan CC, Whitfield EJ, Apweiler R, Koyanagi KO, Khurana JP, Raghuvanshi S, Singh NK, Tyagi AK, Haberer G, Fujisawa M, Hosokawa S, Ito Y, Ikawa H, Shibata M, Yamamoto M, Bruskiewich RM, Hoen DR, Bureau TE, Namiki N, Ohyanagi H, Sakai Y, Nobushima S, Sakata K, Barrero RA, Sato Y, Souvorov A, Smith-White B, Tatusova T, An S, An G, OOta S, Fuks G, Fuks G, Messing J, Christie KR, Lieberherr D, Kim H, Zuccolo A, Wing RA, Nobuta K, Green PJ, Lu C, Meyers BC, Chaparro C, Piegu B, Panaud O, Echeverria M. The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res 2007; 36:D1028-33. [PMID: 18089549 PMCID: PMC2238920 DOI: 10.1093/nar/gkm978] [Citation(s) in RCA: 210] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. Since the last publication of the RAP-DB, the IRGSP genome has been revised and reassembled. In addition, a large number of rice-expressed sequence tags have been released, and functional genomics resources have been produced worldwide. Thus, we have thoroughly updated our genome annotation by manual curation of all the functional descriptions of rice genes. The latest version of the RAP-DB contains a variety of annotation data as follows: clone positions, structures and functions of 31 439 genes validated by cDNAs, RNA genes detected by massively parallel signature sequencing (MPSS) technology and sequence similarity, flanking sequences of mutant lines, transposable elements, etc. Other annotation data such as Gnomon can be displayed along with those of RAP for comparison. We have also developed a new keyword search system to allow the user to access useful information. The RAP-DB is available at: http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/.
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Affiliation(s)
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- National Institute of Agrobiological Sciences, Ibaraki 305-8602, Japan
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Ceccarelli M, Sarri V, Natali L, Giordani T, Cavallini A, Zuccolo A, Jurman I, Morgante M, Cionini PG. Characterization of the chromosome complement of Helianthus annuus by in situ hybridization of a tandemly repeated DNA sequence. Genome 2007; 50:429-34. [PMID: 17612611 DOI: 10.1139/g07-019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A tandemly repeated sequence isolated from a clone (HAG004N15) of a nebulized genomic DNA library of sunflower (Helianthus annuus L., 2n = 34) was characterized and used to study the chromosome complement of sunflower. HAG004N15 repeat units (368 bp in length) were found to be highly methylated, and their copy number per haploid (1C) genome was estimated to be 7800. After in situ hybridization of HAG004N15 repeats onto chromosome spreads, signals were observed at the end of both chromosome arms in 4 pairs and at the end of only one arm in 8 other pairs. Signals were also observed at the intercalary (mostly subtelomeric) regions in all pairs, in both arms in 8 pairs, and in only one arm in the other 9 pairs. The short arm of 1 pair was labelled entirely. The chromosomal location of ribosomal DNA was also studied by hybridizing the wheat ribosomal probe pTa71. Four chromosome pairs contained ribosomal cistrons at the end of their shorter arm, but a satellite was seen in only 3 pairs. These hybridization patterns were the same in the 3 sunflower lines studied (HA89, RA20031, and HOR). The chromosomal localization of HAG004N15-related sequences allowed all of the chromosome pairs to be distinguished from each other, in spite of small size and similar morphology.
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Affiliation(s)
- M Ceccarelli
- Dipartimento di Biologia Cellulare e Ambientale, Sezione di Biologia Cellulare e Molecolare, Universitá di Perugia, Via Elce di Sotto, Perugia, Italy
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42
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Ammiraju JSS, Zuccolo A, Yu Y, Song X, Piegu B, Chevalier F, Walling JG, Ma J, Talag J, Brar DS, SanMiguel PJ, Jiang N, Jackson SA, Panaud O, Wing RA. Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza. Plant J 2007; 52:342-51. [PMID: 17764506 DOI: 10.1111/j.1365-313x.2007.03242.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Long terminal repeat (LTR) retrotransposons constitute a significant portion of most eukaryote genomes and can dramatically change genome size and organization. Although LTR retrotransposon content variation is well documented, the dynamics of genomic flux caused by their activity are poorly understood on an evolutionary time scale. This is primarily because of the lack of an experimental system composed of closely related species whose divergence times are within the limits of the ability to detect ancestrally related retrotransposons. The genus Oryza, with 24 species, ten genome types, different ploidy levels and over threefold genome size variation, constitutes an ideal experimental system to explore genus-level transposon dynamics. Here we present data on the discovery and characterization of an LTR retrotransposon family named RWG in the genus Oryza. Comparative analysis of transposon content (approximately 20 to 27,000 copies) and transpositional history of this family across the genus revealed a broad spectrum of independent and lineage-specific changes that have implications for the evolution of genome size and organization. In particular, we provide evidence that the basal GG genome of Oryza (O. granulata) has expanded by nearly 25% by a burst of the RWG lineage Gran3 subsequent to speciation. Finally we describe the recent evolutionary origin of Dasheng, a large retrotransposon derivative of the RWG family, specifically found in the A, B and C genome lineages of Oryza.
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Affiliation(s)
- Jetty S S Ammiraju
- Arizona Genomics Institute, Department of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
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Zuccolo A, Sebastian A, Talag J, Yu Y, Kim H, Collura K, Kudrna D, Wing RA. Transposable element distribution, abundance and role in genome size variation in the genus Oryza. BMC Evol Biol 2007; 7:152. [PMID: 17727727 PMCID: PMC2041954 DOI: 10.1186/1471-2148-7-152] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2007] [Accepted: 08/29/2007] [Indexed: 12/13/2022] Open
Abstract
Background The genus Oryza is composed of 10 distinct genome types, 6 diploid and 4 polyploid, and includes the world's most important food crop – rice (Oryza sativa [AA]). Genome size variation in the Oryza is more than 3-fold and ranges from 357 Mbp in Oryza glaberrima [AA] to 1283 Mbp in the polyploid Oryza ridleyi [HHJJ]. Because repetitive elements are known to play a significant role in genome size variation, we constructed random sheared small insert genomic libraries from 12 representative Oryza species and conducted a comprehensive study of the repetitive element composition, distribution and phylogeny in this genus. Particular attention was paid to the role played by the most important classes of transposable elements (Long Terminal Repeats Retrotransposons, Long interspersed Nuclear Elements, helitrons, DNA transposable elements) in shaping these genomes and in their contributing to genome size variation. Results We identified the elements primarily responsible for the most strikingly genome size variation in Oryza. We demonstrated how Long Terminal Repeat retrotransposons belonging to the same families have proliferated to very different extents in various species. We also showed that the pool of Long Terminal Repeat Retrotransposons is substantially conserved and ubiquitous throughout the Oryza and so its origin is ancient and its existence predates the speciation events that originated the genus. Finally we described the peculiar behavior of repeats in the species Oryza coarctata [HHKK] whose placement in the Oryza genus is controversial. Conclusion Long Terminal Repeat retrotransposons are the major component of the Oryza genomes analyzed and, along with polyploidization, are the most important contributors to the genome size variation across the Oryza genus. Two families of Ty3-gypsy elements (RIRE2 and Atlantys) account for a significant portion of the genome size variations present in the Oryza genus.
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Affiliation(s)
- Andrea Zuccolo
- Arizona Genomics Institute, Department of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Aswathy Sebastian
- Arizona Genomics Institute, Department of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Jayson Talag
- Arizona Genomics Institute, Department of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Yeisoo Yu
- Arizona Genomics Institute, Department of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - HyeRan Kim
- Arizona Genomics Institute, Department of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Kristi Collura
- Arizona Genomics Institute, Department of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Dave Kudrna
- Arizona Genomics Institute, Department of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Rod A Wing
- Arizona Genomics Institute, Department of Plant Sciences, BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
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Abstract
Long terminal repeat (LTR)-retrotransposons comprise a significant portion of the rice genome. Their complete characterization is thus necessary if the sequenced genome is to be annotated correctly. In addition, because LTR-retrotransposons can influence the expression of neighboring genes, the complete identification of these elements in the rice genome is essential in order to study their putative functional interactions with the plant genes. The aims of the database are to (i) Assemble a comprehensive dataset of LTR-retrotransposons that includes not only abundant elements, but also low copy number elements. (ii) Provide an interface to efficiently access the resources stored in the database. This interface should also allow the community to annotate these elements. (iii) Provide a means for identifying LTR-retrotransposons inserted near genes. Here we present the results, where 242 complete LTR-retrotransposons have been structurally and functionally annotated. A web interface to the database has been made available (http://www.retroryza.org/), through which the user can annotate a sequence or search for LTR-retrotransposons in the neighborhood of a gene of interest.
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Affiliation(s)
| | | | - Andrea Zuccolo
- Department of Plant Sciences, Arizona Genomics Institute, University of ArizonaTucson, AZ 85721, USA
| | | | - Olivier Panaud
- To whom correspondence should be addressed. Tel: +33 468 661773; Fax: +33 468 668499;
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Luo M, Kim H, Kudrna D, Sisneros NB, Lee SJ, Mueller C, Collura K, Zuccolo A, Buckingham EB, Grim SM, Yanagiya K, Inoko H, Shiina T, Flajnik MF, Wing RA, Ohta Y. Construction of a nurse shark (Ginglymostoma cirratum) bacterial artificial chromosome (BAC) library and a preliminary genome survey. BMC Genomics 2006; 7:106. [PMID: 16672057 PMCID: PMC1513397 DOI: 10.1186/1471-2164-7-106] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2005] [Accepted: 05/03/2006] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Sharks are members of the taxonomic class Chondrichthyes, the oldest living jawed vertebrates. Genomic studies of this group, in comparison to representative species in other vertebrate taxa, will allow us to theorize about the fundamental genetic, developmental, and functional characteristics in the common ancestor of all jawed vertebrates. AIMS In order to obtain mapping and sequencing data for comparative genomics, we constructed a bacterial artificial chromosome (BAC) library for the nurse shark, Ginglymostoma cirratum. RESULTS The BAC library consists of 313,344 clones with an average insert size of 144 kb, covering ~4.5 x 1010 bp and thus providing an 11-fold coverage of the haploid genome. BAC end sequence analyses revealed, in addition to LINEs and SINEs commonly found in other animal and plant genomes, two new groups of nurse shark-specific repetitive elements, NSRE1 and NSRE2 that seem to be major components of the nurse shark genome. Screening the library with single-copy or multi-copy gene probes showed 6-28 primary positive clones per probe of which 50-90% were true positives, demonstrating that the BAC library is representative of the different regions of the nurse shark genome. Furthermore, some BAC clones contained multiple genes, making physical mapping feasible. CONCLUSION We have constructed a deep-coverage, high-quality, large insert, and publicly available BAC library for a cartilaginous fish. It will be very useful to the scientific community interested in shark genomic structure, comparative genomics, and functional studies. We found two new groups of repetitive elements specific to the nurse shark genome, which may contribute to the architecture and evolution of the nurse shark genome.
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Affiliation(s)
- Meizhong Luo
- Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
- College of Life Sciences and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - HyeRan Kim
- Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Dave Kudrna
- Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Nicholas B Sisneros
- Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - So-Jeong Lee
- Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Christopher Mueller
- Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Kristi Collura
- Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Andrea Zuccolo
- Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - E Bryan Buckingham
- University of Maryland, Department of Microbiology and Immunology, 655 West Baltimore Street, BRB3-052, Baltimore, MD 21201, USA
| | - Suzanne M Grim
- University of Maryland, Department of Microbiology and Immunology, 655 West Baltimore Street, BRB3-052, Baltimore, MD 21201, USA
| | - Kazuyo Yanagiya
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1143, Japan
| | - Hidetoshi Inoko
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1143, Japan
| | - Takashi Shiina
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1143, Japan
| | - Martin F Flajnik
- University of Maryland, Department of Microbiology and Immunology, 655 West Baltimore Street, BRB3-052, Baltimore, MD 21201, USA
| | - Rod A Wing
- Arizona Genomics Institute, Department of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Yuko Ohta
- University of Maryland, Department of Microbiology and Immunology, 655 West Baltimore Street, BRB3-052, Baltimore, MD 21201, USA
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Abstract
In this paper, we describe an algorithm for the localization of structured models, i.e. sequences of (simple) motifs and distance constraints. It basically combines standard pattern matching procedures with a constraint satisfaction solver, and it has the ability, not present in similar tools, to search for partial matches. A significant feature of our approach, especially in terms of efficiency for the application context, is that the (potentially) exponentially many solutions to the considered problem are represented in compact form as a graph. Moreover, the time and space necessary to build the graph are linear in the number of occurrences of the component patterns.
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Affiliation(s)
- Michele Morgante
- Department of Crop Sciences and Agricultural Engineering, via delle Scienze 206, 33100 Udine, Italy
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Morgante M, Brunner S, Pea G, Fengler K, Zuccolo A, Rafalski A. Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nat Genet 2005; 37:997-1002. [PMID: 16056225 DOI: 10.1038/ng1615] [Citation(s) in RCA: 333] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2005] [Accepted: 06/27/2005] [Indexed: 12/19/2022]
Abstract
We report a whole-genome comparison of gene content in allelic BAC contigs from two maize inbred lines. Genic content polymorphisms involve as many as 10,000 sequences and are mainly generated by DNA insertions. The termini of eight of the nine genic insertions that we analyzed shared the structural hallmarks of helitron rolling-circle transposons. DNA segments defined by helitron termini contained multiple gene-derived fragments and had a structure typical of nonautonomous helitron-like transposons. Closely related insertions were found in multiple genomic locations. Some of these produced transcripts containing segments of different genes, supporting the idea that these transposition events have a role in exon shuffling and the evolution of new proteins. We identified putative autonomous helitron elements and found evidence for their transcription. Helitrons in maize seem to continually produce new nonautonomous elements responsible for the duplicative insertion of gene segments into new locations and for the unprecedented genic diversity. The maize genome is in constant flux, as transposable elements continue to change both the genic and nongenic fractions of the genome, profoundly affecting genetic diversity.
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Affiliation(s)
- Michele Morgante
- Dipartimento di Scienze Agrarie ed Ambientali, Universita' di Udine, Via delle Scienze 208, 33100 Udine, Italy.
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Catanzaro OL, Vila SB, Zuccolo A, Seeber AM. Effect of furosemide on the rat submandibular gland kallikrein secretion. Adv Exp Med Biol 1986; 198 Pt A:279-82. [PMID: 3544715 DOI: 10.1007/978-1-4684-5143-6_38] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The effects of furosemide and Captopril were studied in normals and nephrectomized rats. Different doses of furosemide (5 to 50 mg/kg) increased the saliva kallikrein activity of submaxillary gland perfused with pilocarpine. Rats injected with captopril (10 mg) increased the blood flow of the gland, but did not modify the blood pressure. After furosemide (50 mg/kg) and captopril (10 mg), a decrease in arterial blood pressure was observed. The results suggest a release of glandular kallikrein which is secreted from the gland directly into the vascular compartment. On the other hand, rats sialodectomized showed no alterations in blood pressure in response to both drugs. These data suggest that submaxillary gland kallikrein play a role in regulating blood flow of the gland and blood pressure, at least in our experimental conditions.
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