1
|
De novo genome assembly of Oryza granulata reveals rapid genome expansion and adaptive evolution. Commun Biol 2018; 1:84. [PMID: 30271965 PMCID: PMC6123737 DOI: 10.1038/s42003-018-0089-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 06/08/2018] [Indexed: 12/18/2022] Open
Abstract
The wild relatives of rice have adapted to different ecological environments and constitute a useful reservoir of agronomic traits for genetic improvement. Here we present the ~777 Mb de novo assembled genome sequence of Oryza granulata. Recent bursts of long-terminal repeat retrotransposons, especially RIRE2, led to a rapid twofold increase in genome size after O. granulata speciation. Universal centromeric tandem repeats are absent within its centromeres, while gypsy-type LTRs constitute the main centromere-specific repetitive elements. A total of 40,116 protein-coding genes were predicted in O. granulata, which is close to that of Oryza sativa. Both the copy number and function of genes involved in photosynthesis and energy production have undergone positive selection during the evolution of O. granulata, which might have facilitated its adaptation to the low light habitats. Together, our findings reveal the rapid genome expansion, distinctive centromere organization, and adaptive evolution of O. granulata. Zhigang Wu, Dongming Fang, Rui Yang, et al. present the genome assembly of a wild rice species Oryza granulata, revealing critical insights about the rapid genome expansion and evolution observed in the Oryza genus. They find that recent bursts of LTR retrotransposons have led to the rapid increase in O. granulate genome size following speciation.
Collapse
|
2
|
Yang X, Zhao H, Zhang T, Zeng Z, Zhang P, Zhu B, Han Y, Braz GT, Casler MD, Schmutz J, Jiang J. Amplification and adaptation of centromeric repeats in polyploid switchgrass species. THE NEW PHYTOLOGIST 2018; 218:1645-1657. [PMID: 29577299 DOI: 10.1111/nph.15098] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 02/09/2018] [Indexed: 05/24/2023]
Abstract
Centromeres in most higher eukaryotes are composed of long arrays of satellite repeats from a single satellite repeat family. Why centromeres are dominated by a single satellite repeat and how the satellite repeats originate and evolve are among the most intriguing and long-standing questions in centromere biology. We identified eight satellite repeats in the centromeres of tetraploid switchgrass (Panicum virgatum). Seven repeats showed characteristics associated with classical centromeric repeats with monomeric lengths ranging from 166 to 187 bp. Interestingly, these repeats share an 80-bp DNA motif. We demonstrate that this 80-bp motif may dictate translational and rotational phasing of the centromeric repeats with the cenH3 nucleosomes. The sequence of the last centromeric repeat, Pv156, is identical to the 5S ribosomal RNA genes. We demonstrate that a 5S ribosomal RNA gene array was recruited to be the functional centromere for one of the switchgrass chromosomes. Our findings reveal that certain types of satellite repeats, which are associated with unique sequence features and are composed of monomers in mono-nucleosomal length, are favorable for centromeres. Centromeric repeats may undergo dynamic amplification and adaptation before the centromeres in the same species become dominated by the best adapted satellite repeat.
Collapse
Affiliation(s)
- Xueming Yang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Institute of Food Crops, Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Hainan Zhao
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Tao Zhang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province/Key Laboratory of Plant Functional Genomics of Ministry of Education, Yangzhou University, Yangzhou, 225009, China
| | - Zixian Zeng
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Pingdong Zhang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- College of Bioscience and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Bo Zhu
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Yonghua Han
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Guilherme T Braz
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Departmento de Biologia, Universidade Federal de Lavras, Lavras, MG, 37200, Brazil
| | - Michael D Casler
- Dairy Forage Research Center, Agricultural Research Service, USDA, Madison, WI, 53706, USA
| | - Jeremy Schmutz
- Joint Genome Institute, Walnut Creek, CA, 94598, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Jiming Jiang
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| |
Collapse
|