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Wang C, Liu L, Yin M, Liu B, Wu Y, Eller F, Gao Y, Brix H, Wang T, Guo W, Salojärvi J. Chromosome-level genome assemblies reveal genome evolution of an invasive plant Phragmites australis. Commun Biol 2024; 7:1007. [PMID: 39154094 PMCID: PMC11330502 DOI: 10.1038/s42003-024-06660-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 07/30/2024] [Indexed: 08/19/2024] Open
Abstract
Biological invasions pose a significant threat to ecosystems, disrupting local biodiversity and ecosystem functions. The genomic underpinnings of invasiveness, however, are still largely unknown, making it difficult to predict and manage invasive species effectively. The common reed (Phragmites australis) is a dominant grass species in wetland ecosystems and has become particularly invasive when transferred from Europe to North America. Here, we present a high-quality gap-free, telomere-to-telomere genome assembly of Phragmites australis consisting of 24 pseudochromosomes and a B chromosome. Fully phased subgenomes demonstrated considerable subgenome dominance and revealed the divergence of diploid progenitors approximately 30.9 million years ago. Comparative genomics using chromosome-level scaffolds for three other lineages and a previously published draft genome assembly of an invasive lineage revealed that gene family expansions in the form of tandem duplications may have contributed to the invasiveness of the lineage. This study sheds light on the genome evolution of Arundinoideae grasses and suggests that genetic drivers, such as gene family expansions and tandem duplications, may underly the processes of biological invasion in plants. These findings provide a crucial step toward understanding and managing the genetic basis of invasiveness in plant species.
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Affiliation(s)
- Cui Wang
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, Ministry of Natural Resources, School of Life Sciences, Shandong University, Qingdao, PR China
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Lele Liu
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, Ministry of Natural Resources, School of Life Sciences, Shandong University, Qingdao, PR China
| | - Meiqi Yin
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, Ministry of Natural Resources, School of Life Sciences, Shandong University, Qingdao, PR China
| | - Bingbing Liu
- Institute of Loess Plateau, Shanxi University, Taiyuan, China
| | - Yiming Wu
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, Ministry of Natural Resources, School of Life Sciences, Shandong University, Qingdao, PR China
| | | | - Yingqi Gao
- Institute of Loess Plateau, Shanxi University, Taiyuan, China
| | - Hans Brix
- Department of Biology, Aarhus University, Aarhus, Denmark
| | - Tong Wang
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, China
| | - Weihua Guo
- Key Laboratory of Ecological Prewarning, Protection and Restoration of Bohai Sea, Ministry of Natural Resources, School of Life Sciences, Shandong University, Qingdao, PR China.
| | - Jarkko Salojärvi
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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Paritosh K, Rajarammohan S, Yadava SK, Sharma S, Verma R, Mathur S, Mukhopadhyay A, Gupta V, Pradhan AK, Kaur J, Pental D. A chromosome-scale assembly of Brassica carinata (BBCC) accession HC20 containing resistance to multiple pathogens and an early generation assessment of introgressions into B. juncea (AABB). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:762-782. [PMID: 38722594 DOI: 10.1111/tpj.16794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 04/04/2024] [Accepted: 04/22/2024] [Indexed: 07/16/2024]
Abstract
Brassica carinata (BBCC) commonly referred to as Ethiopian mustard is a natural allotetraploid containing the genomes of Brassica nigra (BB) and Brassica oleracea (CC). It is an oilseed crop endemic to the northeastern regions of Africa. Although it is under limited cultivation, B. carinata is valuable as it is resistant/highly tolerant to most of the pathogens affecting widely cultivated Brassica species of the U's triangle. We report a chromosome-scale genome assembly of B. carinata accession HC20 using long-read Oxford Nanopore sequencing and Bionano optical maps. The assembly has a scaffold N50 of ~39.8 Mb and covers ~1.11 Gb of the genome. We compared the long-read genome assemblies of the U's triangle species and found extensive gene collinearity between the diploids and allopolyploids with no evidence of major gene losses. Therefore, B. juncea (AABB), B. napus (AACC), and B. carinata can be regarded as strict allopolyploids. We cataloged the nucleotide-binding and leucine-rich repeat immune receptor (NLR) repertoire of B. carinata and, identified 465 NLRs, and compared these with the NLRs in the other Brassica species. We investigated the extent and nature of early-generation genomic interactions between the constituent genomes of B. carinata and B. juncea in interspecific crosses between the two species. Besides the expected recombination between the constituent B genomes, extensive homoeologous exchanges were observed between the A and C genomes. Interspecific crosses, therefore, can be used for transferring disease resistance from B. carinata to B. juncea and broadening the genetic base of the two allotetraploid species.
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Affiliation(s)
- Kumar Paritosh
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
| | | | - Satish Kumar Yadava
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
| | - Sarita Sharma
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
| | - Rashmi Verma
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
| | - Shikha Mathur
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
| | - Arundhati Mukhopadhyay
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
| | - Vibha Gupta
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
| | - Akshay K Pradhan
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
| | - Jagreet Kaur
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
- Department of Genetics, University of Delhi South Campus, New Delhi, 110021, India
| | - Deepak Pental
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi, 110021, India
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Lyu ZY, Zhou XL, Wang SQ, Yang GM, Sun WG, Zhang JY, Zhang R, Shen SK. The first high-altitude autotetraploid haplotype-resolved genome assembled (Rhododendron nivale subsp. boreale) provides new insights into mountaintop adaptation. Gigascience 2024; 13:giae052. [PMID: 39110622 PMCID: PMC11304948 DOI: 10.1093/gigascience/giae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 04/26/2024] [Accepted: 07/05/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND Rhododendron nivale subsp. boreale Philipson et M. N. Philipson is an alpine woody species with ornamental qualities that serve as the predominant species in mountainous scrub habitats found at an altitude of ∼4,200 m. As a high-altitude woody polyploid, this species may serve as a model to understand how plants adapt to alpine environments. Despite its ecological significance, the lack of genomic resources has hindered a comprehensive understanding of its evolutionary and adaptive characteristics in high-altitude mountainous environments. FINDINGS We sequenced and assembled the genome of R. nivale subsp. boreale, an assembly of the first subgenus Rhododendron and the first high-altitude woody flowering tetraploid, contributing an important genomic resource for alpine woody flora. The assembly included 52 pseudochromosomes (scaffold N50 = 42.93 Mb; BUSCO = 98.8%; QV = 45.51; S-AQI = 98.69), which belonged to 4 haplotypes, harboring 127,810 predicted protein-coding genes. Conjoint k-mer analysis, collinearity assessment, and phylogenetic investigation corroborated autotetraploid identity. Comparative genomic analysis revealed that R. nivale subsp. boreale originated as a neopolyploid of R. nivale and underwent 2 rounds of ancient polyploidy events. Transcriptional expression analysis showed that differences in expression between alleles were common and randomly distributed in the genome. We identified extended gene families and signatures of positive selection that are involved not only in adaptation to the mountaintop ecosystem (response to stress and developmental regulation) but also in autotetraploid reproduction (meiotic stabilization). Additionally, the expression levels of the (group VII ethylene response factor transcription factors) ERF VIIs were significantly higher than the mean global gene expression. We suspect that these changes have enabled the success of this species at high altitudes. CONCLUSIONS We assembled the first high-altitude autopolyploid genome and achieved chromosome-level assembly within the subgenus Rhododendron. In addition, a high-altitude adaptation strategy of R. nivale subsp. boreale was reasonably speculated. This study provides valuable data for the exploration of alpine mountaintop adaptations and the correlation between extreme environments and species polyploidization.
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Affiliation(s)
- Zhen-Yu Lyu
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650504 Yunnan, China
| | - Xiong-Li Zhou
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650504 Yunnan, China
| | - Si-Qi Wang
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650504 Yunnan, China
| | - Gao-Ming Yang
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650504 Yunnan, China
| | - Wen-Guang Sun
- School of Life Sciences, Yunnan Normal University, Kunming 650500 Yunnan, China
| | - Jie-Yu Zhang
- School of Life Sciences, Yunnan Normal University, Kunming 650500 Yunnan, China
| | - Rui Zhang
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650504 Yunnan, China
| | - Shi-Kang Shen
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650504 Yunnan, China
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Zhou W, Zhang L, He J, Chen W, Zhao F, Fu C, Li M. Transcriptome Shock in Developing Embryos of a Brassica napus and Brassica rapa Hybrid. Int J Mol Sci 2023; 24:16238. [PMID: 38003428 PMCID: PMC10671433 DOI: 10.3390/ijms242216238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Interspecific crosses that fuse the genomes of two different species may result in overall gene expression changes in the hybrid progeny, called 'transcriptome shock'. To better understand the expression pattern after genome merging during the early stages of allopolyploid formation, we performed RNA sequencing analysis on developing embryos of Brassica rapa, B. napus, and their synthesized allotriploid hybrids. Here, we show that the transcriptome shock occurs in the developing seeds of the hybrids. Of the homoeologous gene pairs, 17.1% exhibit expression bias, with an overall expression bias toward B. rapa. The expression level dominance also biases toward B. rapa, mainly induced by the expression change in homoeologous genes from B. napus. Functional enrichment analysis revealed significant differences in differentially expressed genes (DEGs) related to photosynthesis, hormone synthesis, and other pathways. Further study showed that significant changes in the expression levels of the key transcription factors (TFs) could regulate the overall interaction network in the developing embryo, which might be an essential cause of phenotype change. In conclusion, the present results have revealed the global changes in gene expression patterns in developing seeds of the hybrid between B. rapa and B. napus, and provided novel insights into the occurrence of transcriptome shock for harnessing heterosis.
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Affiliation(s)
- Weixian Zhou
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (W.Z.); (L.Z.); (J.H.); (W.C.); (F.Z.); (C.F.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Libin Zhang
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (W.Z.); (L.Z.); (J.H.); (W.C.); (F.Z.); (C.F.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Jianjie He
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (W.Z.); (L.Z.); (J.H.); (W.C.); (F.Z.); (C.F.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Wang Chen
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (W.Z.); (L.Z.); (J.H.); (W.C.); (F.Z.); (C.F.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Feifan Zhao
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (W.Z.); (L.Z.); (J.H.); (W.C.); (F.Z.); (C.F.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Chunhua Fu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (W.Z.); (L.Z.); (J.H.); (W.C.); (F.Z.); (C.F.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
| | - Maoteng Li
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (W.Z.); (L.Z.); (J.H.); (W.C.); (F.Z.); (C.F.)
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Wuhan 430074, China
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Wang J, Yuan M, Feng Y, Zhang Y, Bao S, Hao Y, Ding Y, Gao X, Yu Z, Xu Q, Zhao J, Zhu Q, Wang P, Wu C, Wang J, Li Y, Xu C, Wang J. A common whole-genome paleotetraploidization in Cucurbitales. PLANT PHYSIOLOGY 2022; 190:2430-2448. [PMID: 36053177 PMCID: PMC9706448 DOI: 10.1093/plphys/kiac410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/10/2022] [Indexed: 06/01/2023]
Abstract
Cucurbitales are an important order of flowering plants known for encompassing edible plants of economic and medicinal value and numerous ornamental plants of horticultural value. By reanalyzing the genomes of two representative families (Cucurbitaceae and Begoniaceae) in Cucurbitales, we found that the previously identified Cucurbitaceae common paleotetraploidization that occurred shortly after the core-eudicot-common hexaploidization event is shared by Cucurbitales, including Begoniaceae. We built a multigenome alignment framework for Cucurbitales by identifying orthologs and paralogs and systematically redating key evolutionary events in Cucurbitales. Notably, characterizing the gene retention levels and genomic fractionation patterns between subgenomes generated from different polyploidizations in Cucurbitales suggested the autopolyploid nature of the Begoniaceae common tetraploidization and the allopolyploid nature of the Cucurbitales common tetraploidization and the Cucurbita-specific tetraploidization. Moreover, we constructed the ancestral Cucurbitales karyotype comprising 17 proto-chromosomes, confirming that the most recent common ancestor of Cucurbitaceae contained 15 proto-chromosomes and rejecting the previous hypothesis for an ancestral Cucurbitaceae karyotype with 12 proto-chromosomes. In addition, we found that the polyploidization and tandem duplication events promoted the expansion of gene families involved in the cucurbitacin biosynthesis pathway; however, gene loss and chromosomal rearrangements likely limited the expansion of these gene families.
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Affiliation(s)
- Jiaqi Wang
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Min Yuan
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Yishan Feng
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Yan Zhang
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Shoutong Bao
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Yanan Hao
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Yue Ding
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Xintong Gao
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Zijian Yu
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Qiang Xu
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Junxin Zhao
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Qianwen Zhu
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Ping Wang
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Chunyang Wu
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Jianyu Wang
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
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