1
|
Lyczakowski JJ, Wightman R. Convergent and adaptive evolution drove change of secondary cell wall ultrastructure in extant lineages of seed plants. THE NEW PHYTOLOGIST 2024; 243:2061-2065. [PMID: 39079702 DOI: 10.1111/nph.19983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Accepted: 07/01/2024] [Indexed: 08/23/2024]
Affiliation(s)
- Jan J Lyczakowski
- Department of Plant Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, Krakow, 30-387, Poland
| | - Raymond Wightman
- Microscopy Core Facility, Sainsbury Laboratory Cambridge University, 47 Bateman St., Cambridge, CB2 1LR, UK
| |
Collapse
|
2
|
Muti RM, Barrett CF, Sinn BT. Evolution of Whirly1 in the angiosperms: sequence, splicing, and expression in a clade of early transitional mycoheterotrophic orchids. FRONTIERS IN PLANT SCIENCE 2024; 15:1241515. [PMID: 39006962 PMCID: PMC11239579 DOI: 10.3389/fpls.2024.1241515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 06/07/2024] [Indexed: 07/16/2024]
Abstract
The plastid-targeted transcription factor Whirly1 (WHY1) has been implicated in chloroplast biogenesis, plastid genome stability, and fungal defense response, which together represent characteristics of interest for the study of autotrophic losses across the angiosperms. While gene loss in the plastid and nuclear genomes has been well studied in mycoheterotrophic plants, the evolution of the molecular mechanisms impacting genome stability is completely unknown. Here, we characterize the evolution of WHY1 in four early transitional mycoheterotrophic orchid species in the genus Corallorhiza by synthesizing the results of phylogenetic, transcriptomic, and comparative genomic analyses with WHY1 genomic sequences sampled from 21 orders of angiosperms. We found an increased number of non-canonical WHY1 isoforms assembled from all but the greenest Corallorhiza species, including intron retention in some isoforms. Within Corallorhiza, phylotranscriptomic analyses revealed the presence of tissue-specific differential expression of WHY1 in only the most photosynthetically capable species and a coincident increase in the number of non-canonical WHY1 isoforms assembled from fully mycoheterotrophic species. Gene- and codon-level tests of WHY1 selective regimes did not infer significant signal of either relaxed selection or episodic diversifying selection in Corallorhiza but did so for relaxed selection in the late-stage full mycoheterotrophic orchids Epipogium aphyllum and Gastrodia elata. Additionally, nucleotide substitutions that most likely impact the function of WHY1, such as nonsense mutations, were only observed in late-stage mycoheterotrophs. We propose that our findings suggest that splicing and expression changes may precede the selective shifts we inferred for late-stage mycoheterotrophic species, which therefore does not support a primary role for WHY1 in the transition to mycoheterotrophy in the Orchidaceae. Taken together, this study provides the most comprehensive view of WHY1 evolution across the angiosperms to date.
Collapse
Affiliation(s)
- Rachel M. Muti
- Department of Biology and Earth Science, Otterbein University, Westerville, OH, United States
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA, United States
| | - Craig F. Barrett
- Department of Biology, West Virginia University, Morgantown, WV, United States
| | - Brandon T. Sinn
- Department of Biology and Earth Science, Otterbein University, Westerville, OH, United States
- Faculty of Biology, University of Latvia, Riga, Latvia
| |
Collapse
|
3
|
Tong Y, Lu Y, Tian Z, Yang X, Bai M. Evolutionary radiation strategy revealed in the Scarabaeidae with evidence of continuous spatiotemporal morphology and phylogenesis. Commun Biol 2024; 7:690. [PMID: 38839937 PMCID: PMC11153540 DOI: 10.1038/s42003-024-06250-1] [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: 09/06/2023] [Accepted: 04/26/2024] [Indexed: 06/07/2024] Open
Abstract
Evolutionary biology faces the important challenge of determining how to interpret the relationship between selection pressures and evolutionary radiation. The lack of morphological evidence on cross-species research adds to difficulty of this challenge. We proposed a new paradigm for evaluating the evolution of branches through changes in characters on continuous spatiotemporal scales, for better interpreting the impact of biotic/abiotic drivers on the evolutionary radiation. It reveals a causal link between morphological changes and selective pressures: consistent deformation signals for all tested characters on timeline, which provided strong support for the evolutionary hypothesis of relationship between scarabs and biotic/abiotic drivers; the evolutionary strategies under niche differentiation, which were manifested in the responsiveness degree of functional morphological characters with different selection pressure. This morphological information-driven integrative approach sheds light on the mechanism of macroevolution under different selection pressures and is applicable to more biodiversity research.
Collapse
Affiliation(s)
- Yijie Tong
- Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management (Chinese Academy of Sciences), Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuanyuan Lu
- Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management (Chinese Academy of Sciences), Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhehao Tian
- Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management (Chinese Academy of Sciences), Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- School of Agriculture, Ningxia University, Yinchuan, 750021, China
| | - Xingke Yang
- Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management (Chinese Academy of Sciences), Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, 510260, China
| | - Ming Bai
- Key Laboratory of Animal Biodiversity Conservation and Integrated Pest Management (Chinese Academy of Sciences), Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Plant Protection, Hebei Agricultural University, Baoding, 071001, China.
- Northeast Asia Biodiversity Research Center, Northeast Forestry University, Harbin, 150040, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
4
|
Wang P, Meng F, Yang Y, Ding T, Liu H, Wang F, Li A, Zhang Q, Li K, Fan S, Li B, Ma Z, Zhang T, Zhou Y, Zhao H, Wang X. De novo assembling a high-quality genome sequence of Amur grape ( Vitis amurensis Rupr .) gives insight into Vitis divergence and sex determination. HORTICULTURE RESEARCH 2024; 11:uhae117. [PMID: 38919553 PMCID: PMC11197301 DOI: 10.1093/hr/uhae117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Accepted: 04/09/2024] [Indexed: 06/27/2024]
Abstract
To date, there has been no high-quality sequence for genomes of the East Asian grape species, hindering biological and breeding efforts to improve grape cultivars. This study presents ~522 Mb of the Vitis amurensis (Va) genome sequence containing 27 635 coding genes. Phylogenetic analysis indicated that Vitis riparia (Vr) may have first split from the other two species, Va and Vitis vinifera (Vv). Divergent numbers of duplicated genes reserved among grapes suggests that the core eudicot-common hexaploidy (ECH) and the subsequent genome instability still play a non-negligible role in species divergence and biological innovation. Prominent accumulation of sequence variants might have improved cold resistance in Va, resulting in a more robust network of regulatory cold resistance genes, explaining why it is extremely cold-tolerant compared with Vv and Vr. In contrast, Va has preserved many fewer nucleotide binding site (NBS) disease resistance genes than the other grapes. Notably, multi-omics analysis identified one trans-cinnamate 4-monooxygenase gene positively correlated to the resveratrol accumulated during Va berry development. A selective sweep analysis revealed a hypothetical Va sex-determination region (SDR). Besides, a PPR-containing protein-coding gene in the hypothetical SDR may be related to sex determination in Va. The content and arrangement order of genes in the putative SDR of female Va were similar to those of female Vv. However, the putative SDR of female Va has lost one flavin-containing monooxygenase (FMO) gene and contains one extra protein-coding gene uncharacterized so far. These findings will improve the understanding of Vitis biology and contribute to the improvement of grape breeding.
Collapse
Affiliation(s)
| | - Fanbo Meng
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yiming Yang
- Institute of Special Animal and Plant Sciences of CAAS, Changchun 130000, China
| | | | - Huiping Liu
- Shandong Academy of Grape, Jinan 250100, China
| | | | - Ao Li
- Shandong Academy of Grape, Jinan 250100, China
| | | | - Ke Li
- Shandong Academy of Grape, Jinan 250100, China
| | - Shutian Fan
- Institute of Special Animal and Plant Sciences of CAAS, Changchun 130000, China
| | - Bo Li
- Shandong Academy of Grape, Jinan 250100, China
| | - Zhiyao Ma
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Tianhao Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Yongfeng Zhou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | | | - Xiyin Wang
- North China University of Science and Technology, Tangshan 063000, China
| |
Collapse
|
5
|
Luo L, Fang D, Wang F, Lin Q, Sahu SK, Song Y, Kang J, Guang X, Liu M, Luo S, Hao G, Liu H, Guo X. The chromosome-level genomes of the herbal magnoliids Warburgia ugandensis and Saururus chinensis. Sci Data 2024; 11:554. [PMID: 38816414 PMCID: PMC11139940 DOI: 10.1038/s41597-024-03229-9] [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: 07/27/2023] [Accepted: 04/05/2024] [Indexed: 06/01/2024] Open
Abstract
Warburgia ugandensis and Saururus chinensis are two of the most important medicinal plants in magnoliids and are widely utilized in traditional Kenya and Chinese medicine, respectively. The absence of higher-quality reference genomes has hindered research on the medicinal compound biosynthesis mechanisms of these plants. We report the chromosome-level genome assemblies of W. ugandensis and S. chinensis, and generated 1.13 Gb and 0.53 Gb genomes from 74 and 27 scaffolds, respectively, using BGI-DIPSEQ, Nanopore, and Hi-C sequencing. The scaffold N50 lengths were 82.97 Mb and 48.53 Mb, and the assemblies were anchored to 14 and 11 chromosomes of W. ugandensis and S. chinensis, respectively. In total, 24,739 and 20,561 genes were annotated, and 98.5% and 98% of the BUSCO genes were fully represented, respectively. The chromosome-level genomes of W. ugandensis and S. chinensis will be valuable resources for understanding the genetics of these medicinal plants, studying the evolution of magnoliids and angiosperms and conserving plant genetic resources.
Collapse
Affiliation(s)
- Liuming Luo
- College of Life Science, South China Agricultural University, Guangzhou, 510642, China
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Dongming Fang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Fang Wang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiongqiong Lin
- College of Life Science, South China Agricultural University, Guangzhou, 510642, China
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
- BGI Research, Wuhan, 430074, China
| | - Yali Song
- BGI Research, Beijing, 102601, China
| | | | - Xuanmin Guang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Min Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Shixiao Luo
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
| | - Gang Hao
- College of Life Science, South China Agricultural University, Guangzhou, 510642, China.
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China.
| | - Xing Guo
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China.
- BGI Research, Wuhan, 430074, China.
| |
Collapse
|
6
|
Jiang S, Zou M, Zhang C, Ma W, Xia C, Li Z, Zhao L, Liu Q, Yu F, Huang D, Xia Z. A high-quality haplotype genome of Michelia alba DC reveals differences in methylation patterns and flower characteristics. MOLECULAR HORTICULTURE 2024; 4:23. [PMID: 38807235 PMCID: PMC11134676 DOI: 10.1186/s43897-024-00098-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 04/19/2024] [Indexed: 05/30/2024]
Abstract
Michelia alba DC is a highly valuable ornamental plant of the Magnoliaceae family. This evergreen tropical tree commonly grows in Southeast Asia and is adored for its delightful fragrance. Our study assembled the M. alba haplotype genome MC and MM by utilizing Nanopore ultralong reads, Pacbio Hifi long reads and parental second-generation data. Moreover, the first methylation map of Magnoliaceae was constructed based on the methylation site data obtained using Nanopore data. Metabolomic datasets were generated from the flowers of three different species to assess variations in pigment and volatile compound accumulation. Finally, transcriptome data were generated to link genomic, methylation, and morphological patterns to reveal the reasons underlying the differences between M. alba and its parental lines in petal color, flower shape, and fragrance. We found that the AP1 and AP2 genes are crucial in M. alba petal formation, while the 4CL, PAL, and C4H genes control petal color. The data generated in this study serve as a foundation for future physiological and biochemical research on M. alba, facilitate the targeted improvement of M. alba varieties, and offer a theoretical basis for molecular research on Michelia L.
Collapse
Affiliation(s)
- Sirong Jiang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Meiling Zou
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | | | - Wanfeng Ma
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Chengcai Xia
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Zixuan Li
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | | | - Qi Liu
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Fen Yu
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Dongyi Huang
- College of Tropical Crops, Hainan University, Haikou, China.
| | - Zhiqiang Xia
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, China.
- College of Tropical Crops, Hainan University, Haikou, China.
| |
Collapse
|
7
|
Chen H, Sahu SK, Wang S, Liu J, Yang J, Cheng L, Chiu TY, Liu H. Chromosome-level Alstonia scholaris genome unveils evolutionary insights into biosynthesis of monoterpenoid indole alkaloids. iScience 2024; 27:109599. [PMID: 38646178 PMCID: PMC11033161 DOI: 10.1016/j.isci.2024.109599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 01/25/2024] [Accepted: 03/25/2024] [Indexed: 04/23/2024] Open
Abstract
Alstonia scholaris of the Apocynaceae family is a medicinal plant with a rich source of bioactive monoterpenoid indole alkaloids (MIAs), which possess anti-cancer activity like vinca alkaloids. To gain genomic insights into MIA biosynthesis, we assembled a high-quality chromosome-level genome for A. scholaris using nanopore and Hi-C data. The 444.95 Mb genome contained 35,488 protein-coding genes. A total of 20 chromosomes were assembled with a scaffold N50 of 21.75 Mb. The genome contained a cluster of strictosidine synthases and tryptophan decarboxylases with synteny to other species and a saccharide-terpene cluster involved in the monoterpenoid biosynthesis pathway of the MIA upstream pathway. The multi-omics data of A. scholaris provide a valuable resource for understanding the evolutionary origins of MIAs and for discovering biosynthetic pathways and synthetic biology efforts for producing pharmaceutically useful alkaloids.
Collapse
Affiliation(s)
- Haixia Chen
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Research, Wuhan 430074, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Research, Wuhan 430074, China
| | - Shujie Wang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Jia Liu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Jinlong Yang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Le Cheng
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Tsan-Yu Chiu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| |
Collapse
|
8
|
Chen H, Zwaenepoel A, Van de Peer Y. wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication. Bioinformatics 2024; 40:btae272. [PMID: 38632086 PMCID: PMC11078771 DOI: 10.1093/bioinformatics/btae272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 03/10/2024] [Accepted: 04/16/2024] [Indexed: 04/19/2024] Open
Abstract
MOTIVATION Major improvements in sequencing technologies and genome sequence assembly have led to a huge increase in the number of available genome sequences. In turn, these genome sequences form an invaluable source for evolutionary, ecological, and comparative studies. One kind of analysis that has become routine is the search for traces of ancient polyploidy, particularly for plant genomes, where whole-genome duplication (WGD) is rampant. RESULTS Here, we present a major update of a previously developed tool wgd, namely wgd v2, to look for remnants of ancient polyploidy, or WGD. We implemented novel and improved previously developed tools to (a) construct KS age distributions for the whole-paranome (collection of all duplicated genes in a genome), (b) unravel intragenomic and intergenomic collinearity resulting from WGDs, (c) fit mixture models to age distributions of gene duplicates, (d) correct substitution rate variation for phylogenetic placement of WGDs, and (e) date ancient WGDs via phylogenetic dating of WGD-retained gene duplicates. The applicability and feasibility of wgd v2 for the identification and the relative and absolute dating of ancient WGDs is demonstrated using different plant genomes. AVAILABILITY AND IMPLEMENTATION wgd v2 is open source and available at https://github.com/heche-psb/wgd.
Collapse
Affiliation(s)
- Hengchi Chen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, VIB, Ghent 9052, Belgium
| | - Arthur Zwaenepoel
- UMR 8198, Evo-Eco-Paleo, University of Lille, CNRS, Lille, F-59000, France
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, VIB, Ghent 9052, Belgium
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| |
Collapse
|
9
|
Zuntini AR, Carruthers T, Maurin O, Bailey PC, Leempoel K, Brewer GE, Epitawalage N, Françoso E, Gallego-Paramo B, McGinnie C, Negrão R, Roy SR, Simpson L, Toledo Romero E, Barber VMA, Botigué L, Clarkson JJ, Cowan RS, Dodsworth S, Johnson MG, Kim JT, Pokorny L, Wickett NJ, Antar GM, DeBolt L, Gutierrez K, Hendriks KP, Hoewener A, Hu AQ, Joyce EM, Kikuchi IABS, Larridon I, Larson DA, de Lírio EJ, Liu JX, Malakasi P, Przelomska NAS, Shah T, Viruel J, Allnutt TR, Ameka GK, Andrew RL, Appelhans MS, Arista M, Ariza MJ, Arroyo J, Arthan W, Bachelier JB, Bailey CD, Barnes HF, Barrett MD, Barrett RL, Bayer RJ, Bayly MJ, Biffin E, Biggs N, Birch JL, Bogarín D, Borosova R, Bowles AMC, Boyce PC, Bramley GLC, Briggs M, Broadhurst L, Brown GK, Bruhl JJ, Bruneau A, Buerki S, Burns E, Byrne M, Cable S, Calladine A, Callmander MW, Cano Á, Cantrill DJ, Cardinal-McTeague WM, Carlsen MM, Carruthers AJA, de Castro Mateo A, Chase MW, Chatrou LW, Cheek M, Chen S, Christenhusz MJM, Christin PA, Clements MA, Coffey SC, Conran JG, Cornejo X, Couvreur TLP, Cowie ID, Csiba L, Darbyshire I, Davidse G, Davies NMJ, Davis AP, van Dijk KJ, Downie SR, Duretto MF, Duvall MR, Edwards SL, Eggli U, Erkens RHJ, Escudero M, de la Estrella M, Fabriani F, Fay MF, Ferreira PDL, Ficinski SZ, Fowler RM, Frisby S, Fu L, Fulcher T, Galbany-Casals M, Gardner EM, German DA, Giaretta A, Gibernau M, Gillespie LJ, González CC, Goyder DJ, Graham SW, Grall A, Green L, Gunn BF, Gutiérrez DG, Hackel J, Haevermans T, Haigh A, Hall JC, Hall T, Harrison MJ, Hatt SA, Hidalgo O, Hodkinson TR, Holmes GD, Hopkins HCF, Jackson CJ, James SA, Jobson RW, Kadereit G, Kahandawala IM, Kainulainen K, Kato M, Kellogg EA, King GJ, Klejevskaja B, Klitgaard BB, Klopper RR, Knapp S, Koch MA, Leebens-Mack JH, Lens F, Leon CJ, Léveillé-Bourret É, Lewis GP, Li DZ, Li L, Liede-Schumann S, Livshultz T, Lorence D, Lu M, Lu-Irving P, Luber J, Lucas EJ, Luján M, Lum M, Macfarlane TD, Magdalena C, Mansano VF, Masters LE, Mayo SJ, McColl K, McDonnell AJ, McDougall AE, McLay TGB, McPherson H, Meneses RI, Merckx VSFT, Michelangeli FA, Mitchell JD, Monro AK, Moore MJ, Mueller TL, Mummenhoff K, Munzinger J, Muriel P, Murphy DJ, Nargar K, Nauheimer L, Nge FJ, Nyffeler R, Orejuela A, Ortiz EM, Palazzesi L, Peixoto AL, Pell SK, Pellicer J, Penneys DS, Perez-Escobar OA, Persson C, Pignal M, Pillon Y, Pirani JR, Plunkett GM, Powell RF, Prance GT, Puglisi C, Qin M, Rabeler RK, Rees PEJ, Renner M, Roalson EH, Rodda M, Rogers ZS, Rokni S, Rutishauser R, de Salas MF, Schaefer H, Schley RJ, Schmidt-Lebuhn A, Shapcott A, Al-Shehbaz I, Shepherd KA, Simmons MP, Simões AO, Simões ARG, Siros M, Smidt EC, Smith JF, Snow N, Soltis DE, Soltis PS, Soreng RJ, Sothers CA, Starr JR, Stevens PF, Straub SCK, Struwe L, Taylor JM, Telford IRH, Thornhill AH, Tooth I, Trias-Blasi A, Udovicic F, Utteridge TMA, Del Valle JC, Verboom GA, Vonow HP, Vorontsova MS, de Vos JM, Al-Wattar N, Waycott M, Welker CAD, White AJ, Wieringa JJ, Williamson LT, Wilson TC, Wong SY, Woods LA, Woods R, Worboys S, Xanthos M, Yang Y, Zhang YX, Zhou MY, Zmarzty S, Zuloaga FO, Antonelli A, Bellot S, Crayn DM, Grace OM, Kersey PJ, Leitch IJ, Sauquet H, Smith SA, Eiserhardt WL, Forest F, Baker WJ. Phylogenomics and the rise of the angiosperms. Nature 2024; 629:843-850. [PMID: 38658746 PMCID: PMC11111409 DOI: 10.1038/s41586-024-07324-0] [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: 09/15/2023] [Accepted: 03/15/2024] [Indexed: 04/26/2024]
Abstract
Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins5-7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes8. This 15-fold increase in genus-level sampling relative to comparable nuclear studies9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Elaine Françoso
- Royal Botanic Gardens, Kew, Richmond, UK
- Centre for Ecology, Evolution and Behaviour, Department of Biological Sciences, School of Life Sciences and the Environment, Royal Holloway University of London, London, UK
| | | | | | | | | | - Lalita Simpson
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
| | | | | | - Laura Botigué
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, Spain
| | | | | | - Steven Dodsworth
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | | | - Jan T Kim
- School of Physics, Engineering and Computer Science, University of Hertfordshire, Hatfield, UK
| | - Lisa Pokorny
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Biodiversity and Conservation, Real Jardín Botánico (RJB-CSIC), Madrid, Spain
| | - Norman J Wickett
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Guilherme M Antar
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
- Departamento de Ciências Agrárias e Biológicas, Centro Universitário Norte do Espírito Santo, Universidade Federal do Espírito Santo, São Mateus, Brazil
| | | | | | - Kasper P Hendriks
- Department of Biology, University of Osnabrück, Osnabrück, Germany
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Alina Hoewener
- Plant Biodiversity, Technical University Munich, Freising, Germany
| | - Ai-Qun Hu
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Elizabeth M Joyce
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
- Systematic, Biodiversity and Evolution of Plants, Ludwig Maximilian University of Munich, Munich, Germany
| | - Izai A B S Kikuchi
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Drew A Larson
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Elton John de Lírio
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Jing-Xia Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | | | - Natalia A S Przelomska
- Royal Botanic Gardens, Kew, Richmond, UK
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Toral Shah
- Royal Botanic Gardens, Kew, Richmond, UK
| | | | | | - Gabriel K Ameka
- Department of Plant and Environmental Biology, University of Ghana, Accra, Ghana
| | - Rose L Andrew
- Botany and N.C.W. Beadle Herbarium, University of New England, Armidale, New South Wales, Australia
| | - Marc S Appelhans
- Department of Systematics, Biodiversity and Evolution of Plants, Albrecht-von-Haller Institute of Plant Sciences, University of Göttingen, Göttingen, Germany
| | - Montserrat Arista
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - María Jesús Ariza
- General Research Services, Herbario SEV, CITIUS, Universidad de Sevilla, Seville, Spain
| | - Juan Arroyo
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | | | | | - C Donovan Bailey
- Department of Biology, New Mexico State University, Las Cruces, NM, USA
| | - Helen F Barnes
- Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia
| | - Matthew D Barrett
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
| | - Russell L Barrett
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Randall J Bayer
- Department of Biological Sciences, University of Memphis, Memphis, TN, USA
| | - Michael J Bayly
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Ed Biffin
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Adelaide, South Australia, Australia
| | | | - Joanne L Birch
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Diego Bogarín
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Jardín Botánico Lankester, Universidad de Costa Rica, Cartago, Costa Rica
| | | | | | - Peter C Boyce
- Centro Studi Erbario Tropicale, Dipartimento di Biologia, University of Florence, Florence, Italy
| | | | | | - Linda Broadhurst
- Centre for Australian National Biodiversity Research, National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, Australia
| | - Gillian K Brown
- Queensland Herbarium and Biodiversity Science, Brisbane Botanic Gardens, Toowong, Queensland, Australia
| | - Jeremy J Bruhl
- Botany and N.C.W. Beadle Herbarium, University of New England, Armidale, New South Wales, Australia
| | - Anne Bruneau
- Institut de Recherche en Biologie Végétale and Département de Sciences Biologiques, University of Montreal, Montreal, Quebec, Canada
| | - Sven Buerki
- Department of Biological Sciences, Boise State University, Boise, ID, USA
| | - Edie Burns
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Margaret Byrne
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Government of Western Australia, Kensington, Western Australia, Australia
| | | | - Ainsley Calladine
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Adelaide, South Australia, Australia
| | | | - Ángela Cano
- Cambridge University Botanic Garden, Cambridge, UK
| | | | - Warren M Cardinal-McTeague
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Alejandra de Castro Mateo
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Mark W Chase
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Environment and Agriculture, Curtin University, Bentley, Western Australia, Australia
| | | | | | - Shilin Chen
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, China
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing, China
| | - Maarten J M Christenhusz
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
- Plant Gateway, Den Haag, The Netherlands
| | - Pascal-Antoine Christin
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Mark A Clements
- Centre for Australian National Biodiversity Research, National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, Australia
| | - Skye C Coffey
- Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, Government of Western Australia, Kensington, Western Australia, Australia
| | - John G Conran
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Xavier Cornejo
- Herbario GUAY, Facultad de Ciencias Naturales, Universidad de Guayaquil, Guayaquil, Ecuador
| | | | - Ian D Cowie
- Northern Territory Herbarium Department of Environment Parks & Water Security, Northern Territory Government, Palmerston, Northern Territory, Australia
| | | | | | | | | | | | - Kor-Jent van Dijk
- The University of Adelaide, North Terrace Campus, Adelaide, South Australia, Australia
| | - Stephen R Downie
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Marco F Duretto
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Melvin R Duvall
- Department of Biological Sciences and Institute for the Study of the Environment, Sustainability and Energy, Northern Illinois University, DeKalb, IL, USA
| | | | - Urs Eggli
- Sukkulenten-Sammlung Zürich/ Grün Stadt Zürich, Zürich, Switzerland
| | - Roy H J Erkens
- Naturalis Biodiversity Center, Leiden, The Netherlands
- Maastricht Science Programme, Maastricht University, Maastricht, The Netherlands
- System Earth Science, Maastricht University, Venlo, The Netherlands
| | - Marcial Escudero
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Manuel de la Estrella
- Departamento de Botánica, Ecología y Fisiología Vegetal, Facultad de Ciencias, Universidad de Córdoba, Córdoba, Spain
| | | | | | - Paola de L Ferreira
- Departamento de Biologia, Faculdade de Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, São Paulo, Brazil
- Department of Biology, Aarhus University, Aarhus, Denmark
| | | | - Rachael M Fowler
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Sue Frisby
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Lin Fu
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | | | - Mercè Galbany-Casals
- Systematics and Evolution of Vascular Plants (UAB)-Associated Unit to CSIC by IBB, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Elliot M Gardner
- Department of Biology, Case Western Reserve University, Cleveland, OH, USA
| | | | - Augusto Giaretta
- Faculdade de Ciências Biológicas e Ambientais, Universidade Federal da Grande Dourados, Dourados, Brazil
| | - Marc Gibernau
- Laboratoire Sciences Pour l'Environnement, Université de Corse, Ajaccio, France
| | | | - Cynthia C González
- Herbario Trelew, Universidad Nacional de la Patagonia San Juan Bosco, Trelew, Argentina
| | | | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Bee F Gunn
- Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia
| | - Diego G Gutiérrez
- Museo Argentino de Ciencias Naturales (MACN-CONICET), Buenos Aires, Argentina
| | - Jan Hackel
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Biology, Universität Marburg, Marburg, Germany
| | - Thomas Haevermans
- Institut de Systématique, Evolution, Biodiversité, Muséum National d'Histoire Naturelle, Paris, France
| | - Anna Haigh
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Jocelyn C Hall
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Tony Hall
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Melissa J Harrison
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
| | | | - Oriane Hidalgo
- Institut Botànic de Barcelona (IBB CSIC-Ajuntament de Barcelona), Barcelona, Spain
| | - Trevor R Hodkinson
- Botany, School of Natural Sciences, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Gareth D Holmes
- Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia
| | | | | | - Shelley A James
- Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, Government of Western Australia, Kensington, Western Australia, Australia
| | - Richard W Jobson
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Gudrun Kadereit
- Prinzessin Therese von Bayern-Lehrstuhl für Systematik, Biodiversität & Evolution der Pflanzen, Ludwig-Maximilians-Universität München, Botanische Staatssammlung München, Botanischer Garten München-Nymphenburg, Munich, Germany
| | | | | | - Masahiro Kato
- National Museum of Nature and Science, Tsukuba, Japan
| | | | - Graham J King
- Southern Cross University, Lismore, New South Wales, Australia
| | | | | | - Ronell R Klopper
- Foundational Biodiversity Science Division, South African National Biodiversity Institute, Pretoria, South Africa
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | | | - Marcus A Koch
- Centre for Organismal Studies, Biodiversity and Plant Systematics, Heidelberg University, Heidelberg, Germany
| | | | - Frederic Lens
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | | | | | | | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Lan Li
- CSIRO, Canberra, Australian Capital Territory, Australia
| | | | - Tatyana Livshultz
- Department of Biodiversity, Earth and Environmental Sciences, Drexel University, Philadelphia, PA, USA
- Academy of Natural Science, Drexel University, Philadelphia, PA, USA
| | - David Lorence
- National Tropical Botanical Garden, Kalaheo, HI, USA
| | - Meng Lu
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Patricia Lu-Irving
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Jaquelini Luber
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Mabel Lum
- Bioplatforms Australia Ltd, Sydney, New South Wales, Australia
| | - Terry D Macfarlane
- Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, Government of Western Australia, Kensington, Western Australia, Australia
| | | | - Vidal F Mansano
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Kristina McColl
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Angela J McDonnell
- Department of Biological Sciences, Saint Cloud State University, Saint Cloud, MN, USA
| | - Andrew E McDougall
- The University of Adelaide, North Terrace Campus, Adelaide, South Australia, Australia
| | - Todd G B McLay
- Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia
| | - Hannah McPherson
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Rosa I Meneses
- Instituto de Arqueología y Antropología, Universidad Católica del Norte, San Pedro de Atacama, Chile
| | | | | | | | | | | | - Taryn L Mueller
- Department of Ecology, Evolution & Behavior, University of Minnesota, St. Paul, MN, USA
| | - Klaus Mummenhoff
- Department of Biology, University of Osnabrück, Osnabrück, Germany
| | - Jérôme Munzinger
- AMAP Lab, Université Montpellier, IRD, CIRAD, CNRS INRAE, Montpellier, France
| | - Priscilla Muriel
- Laboratorio de Ecofisiología, Escuela de Ciencias Biológicas, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Daniel J Murphy
- Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia
| | - Katharina Nargar
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
- Centre for Australian National Biodiversity Research, National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, Australia
| | - Lars Nauheimer
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
| | - Francis J Nge
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Adelaide, South Australia, Australia
| | - Reto Nyffeler
- Department of Systematic and Evolutionary Botany, University of Zürich, Zürich, Switzerland
| | - Andrés Orejuela
- Royal Botanic Garden Edinburgh, Edinburgh, UK
- Grupo de Investigación en Recursos Naturales Amazónicos, Instituto Tecnológico del Putumayo, Mocoa, Colombia
| | - Edgardo M Ortiz
- Plant Biodiversity, Technical University Munich, Freising, Germany
| | - Luis Palazzesi
- Museo Argentino de Ciencias Naturales (MACN-CONICET), Buenos Aires, Argentina
| | - Ariane Luna Peixoto
- Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Jaume Pellicer
- Institut Botànic de Barcelona (IBB CSIC-Ajuntament de Barcelona), Barcelona, Spain
| | - Darin S Penneys
- Department of Biology and Marine Biology, University of North Carolina Wilmington, Wilmington, NC, USA
| | | | - Claes Persson
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Marc Pignal
- Institut de Systématique, Evolution, Biodiversité, Muséum National d'Histoire Naturelle, Paris, France
| | - Yohan Pillon
- LSTM Université Montpellier, CIRADIRD, Montpellier, France
| | - José R Pirani
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | | | | | | | - Carmen Puglisi
- Royal Botanic Gardens, Kew, Richmond, UK
- Missouri Botanical Garden, St. Louis, MO, USA
| | - Ming Qin
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Richard K Rabeler
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | | | - Matthew Renner
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Eric H Roalson
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Michele Rodda
- National Parks Board, Singapore Botanic Gardens, Singapore, Singapore
| | | | - Saba Rokni
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Rolf Rutishauser
- Department of Systematic and Evolutionary Botany, University of Zürich, Zürich, Switzerland
| | - Miguel F de Salas
- Tasmanian Herbarium, University of Tasmania, Sandy Bay, Tasmania, Australia
| | - Hanno Schaefer
- Plant Biodiversity, Technical University Munich, Freising, Germany
| | | | - Alexander Schmidt-Lebuhn
- Centre for Australian National Biodiversity Research, National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, Australia
| | - Alison Shapcott
- School of Science Technology and Engineering, Center for Bioinnovation, University Sunshine Coast, Sippy Downs, Queensland, Australia
| | | | - Kelly A Shepherd
- Western Australian Herbarium, Department of Biodiversity, Conservation and Attractions, Government of Western Australia, Kensington, Western Australia, Australia
| | - Mark P Simmons
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - André O Simões
- Departamento de Biologia Vegetal, Universidade Estadual de Campinas, Campinas, Brazil
| | | | - Michelle Siros
- Royal Botanic Gardens, Kew, Richmond, UK
- University of California, San Francisco, San Francisco, CA, USA
| | - Eric C Smidt
- Departamento de Botânica, Universidade Federal do Paraná, Curitiba, Brazil
| | - James F Smith
- Department of Biological Sciences, Boise State University, Boise, ID, USA
| | - Neil Snow
- Pittsburg State University, Pittsburg, KS, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | | | | | - Julian R Starr
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | | | | | | | | | - Ian R H Telford
- Botany and N.C.W. Beadle Herbarium, University of New England, Armidale, New South Wales, Australia
| | - Andrew H Thornhill
- Botany and N.C.W. Beadle Herbarium, University of New England, Armidale, New South Wales, Australia
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Adelaide, South Australia, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Ifeanna Tooth
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | | | - Frank Udovicic
- Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia
| | | | - Jose C Del Valle
- Departamento de Biología Vegetal y Ecología, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - G Anthony Verboom
- Department of Biological Sciences and Bolus Herbarium, University of Cape Town, Cape Town, South Africa
| | - Helen P Vonow
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Adelaide, South Australia, Australia
| | | | - Jurriaan M de Vos
- Department of Environmental Sciences-Botany, University of Basel, Basel, Switzerland
| | | | - Michelle Waycott
- State Herbarium of South Australia, Botanic Gardens and State Herbarium, Adelaide, South Australia, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Cassiano A D Welker
- Instituto de Biologia, Universidade Federal de Uberlândia, Uberlândia, Brazil
| | - Adam J White
- Australian National Herbarium, Centre for Australian National Biodiversity Research, National Research Collections Australia, CSIRO, Canberra, Australian Capital Territory, Australia
| | | | - Luis T Williamson
- The University of Adelaide, North Terrace Campus, Adelaide, South Australia, Australia
| | - Trevor C Wilson
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Sin Yeng Wong
- Institute of Biodiversity And Environmental Conservation, Universiti Malaysia Sarawak, Samarahan, Malaysia
| | - Lisa A Woods
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | | | - Stuart Worboys
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
| | | | - Ya Yang
- University of Minnesota-Twin Cities, St. Paul, MN, USA
| | | | - Meng-Yuan Zhou
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | | | | | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Department of Biology, University of Oxford, Oxford, UK
| | | | - Darren M Crayn
- Australian Tropical Herbarium, James Cook University, Smithfield, Queensland, Australia
| | - Olwen M Grace
- Royal Botanic Gardens, Kew, Richmond, UK
- Royal Botanic Garden Edinburgh, Edinburgh, UK
| | | | | | - Hervé Sauquet
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, New South Wales, Australia
| | - Stephen A Smith
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Wolf L Eiserhardt
- Royal Botanic Gardens, Kew, Richmond, UK
- Department of Biology, Aarhus University, Aarhus, Denmark
| | | | - William J Baker
- Royal Botanic Gardens, Kew, Richmond, UK.
- Department of Biology, Aarhus University, Aarhus, Denmark.
| |
Collapse
|
10
|
Jia L, Wang S, Hu J, Miao K, Huang Y, Ji Y. Plastid phylogenomics and fossil evidence provide new insights into the evolutionary complexity of the 'woody clade' in Saxifragales. BMC PLANT BIOLOGY 2024; 24:277. [PMID: 38605351 PMCID: PMC11010409 DOI: 10.1186/s12870-024-04917-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 03/15/2024] [Indexed: 04/13/2024]
Abstract
BACKGROUND The "woody clade" in Saxifragales (WCS), encompassing four woody families (Altingiaceae, Cercidiphyllaceae, Daphniphyllaceae, and Hamamelidaceae), is a phylogenetically recalcitrant node in the angiosperm tree of life, as the interfamilial relationships of the WCS remain contentious. Based on a comprehensive sampling of WCS genera, this study aims to recover a robust maternal backbone phylogeny of the WCS by analyzing plastid genome (plastome) sequence data using Bayesian inference (BI), maximum likelihood (ML), and maximum parsimony (MP) methods, and to explore the possible causes of the phylogenetic recalcitrance with respect to deep relationships within the WCS, in combination with molecular and fossil evidence. RESULTS Although the four WCS families were identically resolved as monophyletic, the MP analysis recovered different tree topologies for the relationships among Altingiaceae, Cercidiphyllaceae, and Daphniphyllaceae from the ML and BI phylogenies. The fossil-calibrated plastome phylogeny showed that the WCS underwent a rapid divergence of crown groups in the early Cretaceous (between 104.79 and 100.23 Ma), leading to the origin of the stem lineage ancestors of Altingiaceae, Cercidiphyllaceae, Daphniphyllaceae, and Hamamelidaceae within a very short time span (∼4.56 Ma). Compared with the tree topology recovered in a previous study based on nuclear genome data, cytonuclear discordance regarding the interfamilial relationships of the WCS was detected. CONCLUSIONS Molecular and fossil evidence imply that the early divergence of the WCS might have experienced radiative diversification of crown groups, extensive extinctions at the genus and species levels around the Cretaceous/Paleocene boundary, and ancient hybridization. Such evolutionarily complex events may introduce biases in topological estimations within the WCS due to incomplete lineage sorting, cytonuclear discordance, and long-branch attraction, potentially impacting the accurate reconstruction of deep relationships.
Collapse
Affiliation(s)
- Linbo Jia
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Shuying Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jinjin Hu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Ke Miao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, 650201, China
| | - Yongjiang Huang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yunheng Ji
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| |
Collapse
|
11
|
Friis EM, Crane PR, Pedersen KR, Marone F. Cretaceous chloranthoids: early prominence, extinct diversity and missing links. ANNALS OF BOTANY 2024; 133:225-260. [PMID: 38597914 PMCID: PMC11005782 DOI: 10.1093/aob/mcad137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 09/07/2023] [Indexed: 04/11/2024]
Abstract
BACKGROUND The Chloranthaceae comprise four extant genera (Hedyosmum, Ascarina, Chloranthus and Sarcandra), all with simple flowers. Molecular phylogenetics indicates that the Chloranthaceae diverged very early in angiosperm evolution, although how they are related to eudicots, magnoliids, monocots and Ceratophyllum is uncertain. Fossil pollen similar to that of Ascarina and Hedyosmum has long been recognized in the Early Cretaceous, but over the last four decades evidence of extinct Chloranthaceae based on other types of fossils has expanded dramatically and contributes significantly to understanding the evolution of the family. SCOPE Studies of fossils from the Cretaceous, especially mesofossils of Early Cretaceous age from Portugal and eastern North America, recognized diverse flowers, fruits, seeds, staminate inflorescences and stamens of extinct chloranthoids. These early chloranthoids include forms related to extant Hedyosmum and also to the Ascarina, Chloranthus and Sarcandra clade. In the Late Cretaceous there are several occurrences of distinctive fossil androecia related to extant Chloranthus. The rich and still expanding Cretaceous record of Chloranthaceae contrasts with a very sparse Cenozoic record, emphasizing that the four extant genera are likely to be relictual, although speciation within the genera might have occurred in relatively recent times. In this study, we describe three new genera of Early Cretaceous chloranthoids and summarize current knowledge on the extinct diversity of the group. CONCLUSIONS The evolutionary lineage that includes extant Chloranthaceae is diverse and abundantly represented in Early Cretaceous mesofossil floras that provide some of the earliest evidence of angiosperm reproductive structures. Extinct chloranthoids, some of which are clearly in the Chloranthaceae crown group, fill some of the morphological gaps that currently separate the extant genera, help to illuminate how some of the unusual features of extant Chloranthaceae evolved and suggest that Chloranthaceae are of disproportionate importance for a more refined understanding of ecology and phylogeny of early angiosperm diversification.
Collapse
Affiliation(s)
- Else Marie Friis
- Department of Geoscience, University of Aarhus, Høegh-Guldbergs Gade 2, DK-8000 Aarhus C, Denmark
- Department of Palaeobiology, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
| | - Peter R Crane
- Oak Spring Garden Foundation, 1776 Loughborough Lane, Upperville, VA 20184, USA
- Yale School of the Environment, Yale University, New Haven, CT 06511, USA
| | - Kaj Raunsgaard Pedersen
- Department of Geoscience, University of Aarhus, Høegh-Guldbergs Gade 2, DK-8000 Aarhus C, Denmark
| | - Federica Marone
- Swiss Light Source, Paul Scherrer Institute, Villigen PSI, Switzerland
| |
Collapse
|
12
|
Dang Z, Xu Y, Zhang X, Mi W, Chi Y, Tian Y, Liu Y, Ren W. Chromosome-level genome assembly provides insights into the genome evolution and functional importance of the phenylpropanoid-flavonoid pathway in Thymus mongolicus. BMC Genomics 2024; 25:291. [PMID: 38504151 PMCID: PMC10949689 DOI: 10.1186/s12864-024-10202-8] [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: 12/02/2023] [Accepted: 03/08/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND Thymus mongolicus (family Lamiaceae) is a Thyme subshrub with strong aroma and remarkable environmental adaptability. Limited genomic information limits the use of this plant. RESULTS Chromosome-level 605.2 Mb genome of T. mongolicus was generated, with 96.28% anchored to 12 pseudochromosomes. The repetitive sequences were dominant, accounting for 70.98%, and 32,593 protein-coding genes were predicted. Synteny analysis revealed that Lamiaceae species generally underwent two rounds of whole genome duplication; moreover, species-specific genome duplication was identified. A recent LTR retrotransposon burst and tandem duplication might play important roles in the formation of the Thymus genome. Using comparative genomic analysis, phylogenetic tree of seven Lamiaceae species was constructed, which revealed that Thyme plants evolved recently in the family. Under the phylogenetic framework, we performed functional enrichment analysis of the genes on nodes that contained the most gene duplication events (> 50% support) and of relevant significant expanded gene families. These genes were highly associated with environmental adaptation and biosynthesis of secondary metabolites. Combined transcriptome and metabolome analyses revealed that Peroxidases, Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferases, and 4-coumarate-CoA ligases genes were the essential regulators of the phenylpropanoid-flavonoid pathway. Their catalytic products (e.g., apigenin, naringenin chalcone, and several apigenin-related compounds) might be responsible for the environmental tolerance and aromatic properties of T. mongolicus. CONCLUSION This study enhanced the understanding of the genomic evolution of T. mongolicus, enabling further exploration of its unique traits and applications, and contributed to the understanding of Lamiaceae genomics and evolutionary biology.
Collapse
Affiliation(s)
- Zhenhua Dang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010070, China
| | - Ying Xu
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010070, China
| | - Xin Zhang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010070, China
| | - Wentao Mi
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010070, China
| | - Yuan Chi
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010070, China
| | - Yunyun Tian
- Ministry of Education Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yaling Liu
- Key Laboratory of Forage Breeding and Seed Production of Inner Mongolia, Inner Mongolia M-Grass Ecology and Environment (Group) Co., National Center of Pratacultural Technology Innovation (under preparation), Ltd, Hohhot, 010060, China
| | - Weibo Ren
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010070, China.
| |
Collapse
|
13
|
Zhang G, Ma H. Nuclear phylogenomics of angiosperms and insights into their relationships and evolution. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:546-578. [PMID: 38289011 DOI: 10.1111/jipb.13609] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/03/2024] [Indexed: 02/06/2024]
Abstract
Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the "abominable mystery," hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological, and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences, dozens to thousands of nuclear genes from next-generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families, and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella, Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families. Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore, we discuss the implications of nuclear phylogenomic analyses on ancestral reconstruction of morphological, physiological, and ecological characters of angiosperm groups, limitations of current nuclear phylogenomic studies, and the taxa that require future attention.
Collapse
Affiliation(s)
- Guojin Zhang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Hong Ma
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| |
Collapse
|
14
|
Xu Y, Wei Y, Zhou Z, Cai X, Boden SA, Umer MJ, Safdar LB, Liu Y, Jin D, Hou Y, Wang Y, Wall SB, Wang K, Yu S, Zhang B, Peng R, Liu F. Widespread incomplete lineage sorting and introgression shaped adaptive radiation in the Gossypium genus. PLANT COMMUNICATIONS 2024; 5:100728. [PMID: 37803827 PMCID: PMC10873890 DOI: 10.1016/j.xplc.2023.100728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 09/14/2023] [Accepted: 10/02/2023] [Indexed: 10/08/2023]
Abstract
Cotton (Gossypium) stands as a crucial economic crop, serving as the primary source of natural fiber for the textile sector. However, the evolutionary mechanisms driving speciation within the Gossypium genus remain unresolved. In this investigation, we leveraged 25 Gossypium genomes and introduced four novel assemblies-G. harknessii, G. gossypioides, G. trilobum, and G. klotzschianum (Gklo)-to delve into the speciation history of this genus. Notably, we encountered intricate phylogenies potentially stemming from introgression. These complexities are further compounded by incomplete lineage sorting (ILS), a factor likely to have been instrumental in shaping the swift diversification of cotton. Our focus subsequently shifted to the rapid radiation episode during a concise period in Gossypium evolution. For a recently diverged lineage comprising G. davidsonii, Gklo, and G. raimondii, we constructed a finely detailed ILS map. Intriguingly, this analysis revealed the non-random distribution of ILS regions across the reference Gklo genome. Moreover, we identified signs of robust natural selection influencing specific ILS regions. Noteworthy variations pertaining to speciation emerged between the closely related sister species Gklo and G. davidsonii. Approximately 15.74% of speciation structural variation genes and 12.04% of speciation-associated genes were estimated to intersect with ILS signatures. These findings enrich our understanding of the role of ILS in adaptive radiation, shedding fresh light on the intricate speciation history of the Gossypium genus.
Collapse
Affiliation(s)
- Yanchao Xu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 40070, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Yangyang Wei
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China
| | - Zhongli Zhou
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xiaoyan Cai
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Scott A Boden
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA 5005, Australia
| | - Muhammad Jawad Umer
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Luqman B Safdar
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA 5005, Australia
| | - Yuling Liu
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China
| | - Dingsha Jin
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya 572000, China
| | - Yuqing Hou
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Yuhong Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Sarah Brooke Wall
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Kunbo Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Shuxun Yu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA.
| | - Renhai Peng
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China.
| | - Fang Liu
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China.
| |
Collapse
|
15
|
Liao B, Xiang YH, Li Y, Yang KY, Shan JX, Ye WW, Dong NQ, Kan Y, Yang YB, Zhao HY, Yu HX, Lu ZQ, Zhao Y, Zhao Q, Guo D, Guo SQ, Lei JJ, Mu XR, Cao YJ, Han B, Lin HX. Dysfunction of duplicated pair rice histone acetyltransferases causes segregation distortion and an interspecific reproductive barrier. Nat Commun 2024; 15:996. [PMID: 38307858 PMCID: PMC10837208 DOI: 10.1038/s41467-024-45377-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 01/21/2024] [Indexed: 02/04/2024] Open
Abstract
Postzygotic reproductive isolation, which results in the irreversible divergence of species, is commonly accompanied by hybrid sterility, necrosis/weakness, or lethality in the F1 or other offspring generations. Here we show that the loss of function of HWS1 and HWS2, a couple of duplicated paralogs, together confer complete interspecific incompatibility between Asian and African rice. Both of these non-Mendelian determinants encode the putative Esa1-associated factor 6 (EAF6) protein, which functions as a characteristic subunit of the histone H4 acetyltransferase complex regulating transcriptional activation via genome-wide histone modification. The proliferating tapetum and inappropriate polar nuclei arrangement cause defective pollen and seeds in F2 hybrid offspring due to the recombinant HWS1/2-mediated misregulation of vitamin (biotin and thiamine) metabolism and lipid synthesis. Evolutionary analysis of HWS1/2 suggests that this gene pair has undergone incomplete lineage sorting (ILS) and multiple gene duplication events during speciation. Our findings have not only uncovered a pair of speciation genes that control hybrid breakdown but also illustrate a passive mechanism that could be scaled up and used in the guidance and optimization of hybrid breeding applications for distant hybridization.
Collapse
Affiliation(s)
- Ben Liao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - You-Huang Xiang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yan Li
- China National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center of Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Kai-Yang Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun-Xiang Shan
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Wang-Wei Ye
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Nai-Qian Dong
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Yi Kan
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Yi-Bing Yang
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Huai-Yu Zhao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong-Xiao Yu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Zi-Qi Lu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Yan Zhao
- China National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center of Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Qiang Zhao
- China National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center of Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Dongling Guo
- China National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center of Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China
| | - Shuang-Qin Guo
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jie-Jie Lei
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Rui Mu
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying-Jie Cao
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Bin Han
- China National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center of Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200233, China.
| | - Hong-Xuan Lin
- National Key Laboratory of Plant Molecular Genetics, CAS Centre for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- University of the Chinese Academy of Sciences, Beijing, 100049, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
| |
Collapse
|
16
|
Yu X, Feng Y, Zhang J. Characterization of the Complete Mitochondrial Genome of Wintersweet ( Chimonanthus praecox) and Comparative Analysis within Magnoliids. Life (Basel) 2024; 14:182. [PMID: 38398691 PMCID: PMC10890521 DOI: 10.3390/life14020182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
Mitochondrial genome sequencing is a valuable tool for investigating mitogenome evolution, species phylogeny, and population genetics. Chimonanthus praecox (L.) Link, also known as "La Mei" in Chinese, is a famous ornamental and medical shrub belonging to the order Laurales of the Calycanthaceae family. Although the nuclear genomes and chloroplast genomes of certain Laurales representatives, such as Lindera glauca, Laurus nobilis, and Piper nigrum, have been sequenced, the mitochondrial genome of Laurales members remains unknown. Here, we reported the first complete mitogenome of C. praecox. The mitogenome was 972,347 bp in length and comprised 60 unique coding genes, including 40 protein-coding genes (PCGs), 17 tRNA genes, and three rRNA genes. The skewness of the PCGs showed that the AT skew (-0.0096233) was negative, while the GC skew (0.031656) was positive, indicating higher contents of T's and G's in the mitochondrial genome of C. praecox. The Ka/Ks ratio analysis showed that the Ka/Ks values of most genes were less than one, suggesting that these genes were under purifying selection. Furthermore, there is a substantial abundance of dispersed repeats in C. praecox, constituting 16.98% of the total mitochondrial genome. A total of 731 SSR repeats were identified in the mitogenome, the highest number among the eleven available magnoliids mitogenomes. The mitochondrial phylogenetic analysis based on 29 conserved PCGs placed the C. praecox in Lauraceae, and supported the sister relationship of Laurales with Magnoliales, which was congruent with the nuclear genome evidence. The present study enriches the mitogenome data of C. praecox and promotes further studies on phylogeny and plastid evolution.
Collapse
Affiliation(s)
- Xianxian Yu
- College of Urban and Environmental Sciences, Xuchang University, Xuchang 461000, China;
| | - Yanlei Feng
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China;
| | - Jie Zhang
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China
| |
Collapse
|
17
|
Luo J, Zhang D, Tang P, Wang N, Zhao S, Kong L. Chemistry and bioactivity of lindenane sesquiterpenoids and their oligomers. Nat Prod Rep 2024; 41:25-58. [PMID: 37791885 DOI: 10.1039/d3np00022b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Covering: 1925 to July 2023Among the sesquiterpenoids with rich structural diversity and potential bioactivities, lindenane sesquiterpenoids (LSs) possess a characteristic cis, trans-3,5,6-carbocyclic skeleton and mainly exist as monomers and diverse oligomers in plants from the Lindera genus and Chloranthaceae family. Since the first identification of lindeneol from Lindera strychnifolia in 1925, 354 natural LSs and their oligomers with anti-inflammatory, antitumor, and anti-infective activities have been discovered. Structurally, two-thirds of LSs exist as oligomers with interesting skeletons through diverse polymeric patterns, especially Diels-Alder [4 + 2] cycloaddition. Fascinated by their diverse bioactivities and intriguing polycyclic architectures, synthetic chemists have engaged in the total synthesis of natural LSs in recent decades. In this review, the research achievements related to LSs from 1925 to July of 2023 are systematically and comprehensively summarized, focusing on the classification of their structures, chemical synthesis, and bioactivities, which will be helpful for further research on LSs and their oligomers.
Collapse
Affiliation(s)
- Jun Luo
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, People's Republic of China.
| | - Danyang Zhang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, People's Republic of China.
| | - Pengfei Tang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, People's Republic of China.
| | - Nan Wang
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, People's Republic of China.
| | - Shuai Zhao
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, People's Republic of China.
| | - Lingyi Kong
- Jiangsu Key Laboratory of Bioactive Natural Product Research and State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 210009, People's Republic of China.
| |
Collapse
|
18
|
Cai L, Liu D, Yang F, Zhang R, Yun Q, Dao Z, Ma Y, Sun W. The chromosome-scale genome of Magnolia sinica (Magnoliaceae) provides insights into the conservation of plant species with extremely small populations (PSESP). Gigascience 2024; 13:giad110. [PMID: 38206588 PMCID: PMC10999834 DOI: 10.1093/gigascience/giad110] [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: 03/06/2023] [Revised: 07/28/2023] [Accepted: 12/04/2023] [Indexed: 01/12/2024] Open
Abstract
Magnolia sinica (Magnoliaceae) is a highly threatened tree endemic to southeast Yunnan, China. In this study, we generated for the first time a high-quality chromosome-scale genome sequence from M. sinica, by combining Illumina and ONT data with Hi-C scaffolding methods. The final assembled genome size of M. sinica was 1.84 Gb, with a contig N50 of ca. 45 Mb and scaffold N50 of 92 Mb. Identified repeats constituted approximately 57% of the genome, and 43,473 protein-coding genes were predicted. Phylogenetic analysis shows that the magnolias form a sister clade with the eudicots and the order Ceratophyllales, while the monocots are sister to the other core angiosperms. In our study, a total of 21 individuals from the 5 remnant populations of M. sinica, as well as 22 specimens belonging to 8 related Magnoliaceae species, were resequenced. The results showed that M. sinica had higher genetic diversity (θw = 0.01126 and θπ = 0.01158) than other related species in the Magnoliaceae. However, population structure analysis suggested that the genetic differentiation among the 5 M. sinica populations was very low. Analyses of the demographic history of the species using different models consistently revealed that 2 bottleneck events occurred. The contemporary effective population size of M. sinica was estimated to be 10.9. The different patterns of genetic loads (inbreeding and numbers of deleterious mutations) suggested constructive strategies for the conservation of these 5 different populations of M. sinica. Overall, this high-quality genome will be a valuable genomic resource for conservation of M. sinica.
Collapse
Affiliation(s)
- Lei Cai
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Detuan Liu
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Fengmao Yang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Rengang Zhang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Quanzheng Yun
- Department of Bioinformatics, Ori (Shandong) Gene Science and Technology Co., Ltd., Weifang, 261000, Shandong, China
| | - Zhiling Dao
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Yongpeng Ma
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Weibang Sun
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| |
Collapse
|
19
|
Yang J, Liu M, Sahu SK, Li R, Wang G, Guo X, Liu J, Cheng L, Jiang H, Zhao F, Wei S, Luo S, Liu H. Chromosome-scale genomes of five Hongmu species in Leguminosae. Sci Data 2023; 10:710. [PMID: 37848504 PMCID: PMC10582184 DOI: 10.1038/s41597-023-02593-2] [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: 04/24/2023] [Accepted: 09/25/2023] [Indexed: 10/19/2023] Open
Abstract
The Legume family (Leguminosae or Fabaceae), is one of the largest and economically important flowering plants. Heartwood, the core of a tree trunk or branch, is a valuable and renewable resource employed for centuries in constructing sturdy and sustainable structures. Hongmu refers to a category of precious timber trees in China, encompassing 29 woody species, primarily from the legume genus. Due to the lack of genome data, detailed studies on their economic and ecological importance are limited. Therefore, this study generates chromosome-scale assemblies of five Hongmu species in Leguminosae: Pterocarpus santalinus, Pterocarpus macrocarpus, Dalbergia cochinchinensis, Dalbergia cultrata, and Senna siamea, using a combination of short-reads, long-read nanopore, and Hi-C data. We obtained 623.86 Mb, 634.58 Mb, 700.60 Mb, 645.98 Mb, and 437.29 Mb of pseudochromosome level assemblies with the scaffold N50 lengths of 63.1 Mb, 63.7 Mb, 70.4 Mb, 61.1 Mb and 32.2 Mb for P. santalinus, P. macrocarpus, D. cochinchinensis, D. cultrata and S. siamea, respectively. These genome data will serve as a valuable resource for studying crucial traits, like wood quality, disease resistance, and environmental adaptation in Hongmu.
Collapse
Affiliation(s)
- Jinlong Yang
- College of Forensic Science, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Min Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Ruirui Li
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guanlong Wang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
- College of Science, South China Agricultural University, Guangzhou, 510642, China
| | - Xing Guo
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Jianmei Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Le Cheng
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Huayan Jiang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Feng Zhao
- Key Laboratory of Ethnic Medical Resources Research and Southeast Asian International Cooperation in Yunnan Province, School of Tea and Coffee & School of Bioinformatics and Engineering, Pu'er University, Puer, 665000, China
| | - Shuguang Wei
- College of Forensic Science, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China.
- Key Laboratory of Ministry of Public Health for Forensic Science, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China.
| | - Shixiao Luo
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong 510650, China.
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China.
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150040, China.
| |
Collapse
|
20
|
Song H, Wang Y, Shao H, Li Z, Hu P, Yap-Chiongco MK, Shi P, Zhang T, Li C, Wang Y, Ma P, Vinther J, Wang H, Kocot KM. Scaphopoda is the sister taxon to Bivalvia: Evidence of ancient incomplete lineage sorting. Proc Natl Acad Sci U S A 2023; 120:e2302361120. [PMID: 37738291 PMCID: PMC10556646 DOI: 10.1073/pnas.2302361120] [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: 02/13/2023] [Accepted: 08/18/2023] [Indexed: 09/24/2023] Open
Abstract
The almost simultaneous emergence of major animal phyla during the early Cambrian shaped modern animal biodiversity. Reconstructing evolutionary relationships among such closely spaced branches in the animal tree of life has proven to be a major challenge, hindering understanding of early animal evolution and the fossil record. This is particularly true in the species-rich and highly varied Mollusca where dramatic inconsistency among paleontological, morphological, and molecular evidence has led to a long-standing debate about the group's phylogeny and the nature of dozens of enigmatic fossil taxa. A critical step needed to overcome this issue is to supplement available genomic data, which is plentiful for well-studied lineages, with genomes from rare but key lineages, such as Scaphopoda. Here, by presenting chromosome-level genomes from both extant scaphopod orders and leveraging complete genomes spanning Mollusca, we provide strong support for Scaphopoda as the sister taxon of Bivalvia, revitalizing the morphology-based Diasoma hypothesis originally proposed 50 years ago. Our molecular clock analysis confidently dates the split between Bivalvia and Scaphopoda at ~520 Ma, prompting a reinterpretation of controversial laterally compressed Early Cambrian fossils, including Anabarella, Watsonella, and Mellopegma, as stem diasomes. Moreover, we show that incongruence in the phylogenetic placement of Scaphopoda in previous phylogenomic studies was due to ancient incomplete lineage sorting (ILS) that occurred during the rapid radiation of Conchifera. Our findings highlight the need to consider ILS as a potential source of error in deep phylogeny reconstruction, especially in the context of the unique nature of the Cambrian Explosion.
Collapse
Affiliation(s)
- Hao Song
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao266237, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Yunan Wang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Haojing Shao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | - Zhuoqing Li
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Pinli Hu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen518000, China
| | | | - Pu Shi
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Tao Zhang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao266237, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Cui Li
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Yiguan Wang
- Institute of Ecology and Evolution, University of Edinburgh, EdinburghEH9 3FL, United Kingdom
| | - Peizhen Ma
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Jakob Vinther
- School of Biological Sciences, University of Bristol, BristolBS8 1TQ, United Kingdom
- School of Earth Sciences, University of Bristol, BristolBS8 1TQ, United Kingdom
| | - Haiyan Wang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao266071, China
- Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao266237, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Kevin M. Kocot
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL35487
- Alabama Museum of Natural History, University of Alabama, Tuscaloosa, AL35487
| |
Collapse
|
21
|
Schoelynck J, De Block P, Van Dyck E, Cooke J. Is there silicon in flowers and what does it tell us? Ecol Evol 2023; 13:e10630. [PMID: 37854315 PMCID: PMC10580012 DOI: 10.1002/ece3.10630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/25/2023] [Accepted: 10/06/2023] [Indexed: 10/20/2023] Open
Abstract
The emergence of flowers marked an important development in plant evolution. Flowers in many species evolved to attract animal pollinators to increase fertilisation chances. In leaves, silicon (Si) discourages herbivores, for example by wearing down mouthparts. Flowers are essentially modified leaves and hence may also have the capacity to accumulate Si. If Si in flowers discourages animal visitors as it does in leaves, Si accumulation may be disadvantageous for pollination. Whether flowers accumulate Si, and what the implications may be, was not known for many species. We analysed leaves and flowers of different taxa, separated into their different anatomical parts. Flowers mostly have low Si concentrations in all parts (mean ± SE of BSi in mg g-1 was 0.22 ± 0.04 in petals, 0.59 ± 0.24 in sepals, 0.14 ± 0.03 in stamens, 0.15 ± 0.04 in styles and stigmas and 0.37 ± 0.19 in ovaries for a subset of 56 species). In most cases, less Si was accumulated in flowers than in leaves (mean ± SE of BSi in mg g-1 was 1.51 ± 0.55 in whole flowers vs. 2.97 ± 0.57 in leaves in 104 species) though intriguing exceptions are found, with some species accumulating more Si in flowers than leaves. The large variation in concentration among flowers across the taxa examined, with a particularly high concentration in grass inflorescences, tantalisingly suggests differences in the use of Si for flowers across plant groups. We conclude that the study of the functions of Si for flowers warrants more attention, with pollination strategy a potential contributing factor.
Collapse
Affiliation(s)
- Jonas Schoelynck
- Department of Biology, ECOSPHERE Research GroupUniversity of AntwerpWilrijkBelgium
| | | | - Eva Van Dyck
- Department of Biology, ECOSPHERE Research GroupUniversity of AntwerpWilrijkBelgium
| | - Julia Cooke
- Earth, Environment and Ecosystem SciencesThe Open UniversityMilton KeynesUK
| |
Collapse
|
22
|
Yang P, Ling XY, Zhou XF, Chen YX, Wang TT, Lin XJ, Zhao YY, Ye YS, Huang LX, Sun YW, Qi YX, Ma DM, Zhan RT, Huang XS, Yang JF. Comparing genomes of Fructus Amomi-producing species reveals genetic basis of volatile terpenoid divergence. PLANT PHYSIOLOGY 2023; 193:1244-1262. [PMID: 37427874 DOI: 10.1093/plphys/kiad400] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/25/2023] [Accepted: 06/13/2023] [Indexed: 07/11/2023]
Abstract
Wurfbainia longiligularis and Wurfbainia villosa are both rich in volatile terpenoids and are 2 primary plant sources of Fructus Amomi used for curing gastrointestinal diseases. Metabolomic profiling has demonstrated that bornyl diphosphate (BPP)-related terpenoids are more abundant in the W. villosa seeds and have a wider tissue distribution in W. longiligularis. To explore the genetic mechanisms underlying the volatile terpenoid divergence, a high-quality chromosome-level genome of W. longiligularis (2.29 Gb, contig N50 of 80.39 Mb) was assembled. Functional characterization of 17 terpene synthases (WlTPSs) revealed that WlBPPS, along with WlTPS 24/26/28 with bornyl diphosphate synthase (BPPS) activity, contributes to the wider tissue distribution of BPP-related terpenoids in W. longiligularis compared to W. villosa. Furthermore, transgenic Nicotiana tabacum showed that the GCN4-motif element positively regulates seed expression of WvBPPS and thus promotes the enrichment of BPP-related terpenoids in W. villosa seeds. Systematic identification and analysis of candidate TPS in 29 monocot plants from 16 families indicated that substantial expansion of TPS-a and TPS-b subfamily genes in Zingiberaceae may have driven increased diversity and production of volatile terpenoids. Evolutionary analysis and functional identification of BPPS genes showed that BPP-related terpenoids may be distributed only in the Zingiberaceae of monocot plants. This research provides valuable genomic resources for breeding and improving Fructus Amomi with medicinal and edible value and sheds light on the evolution of terpenoid biosynthesis in Zingiberaceae.
Collapse
Affiliation(s)
- Peng Yang
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua 418000, China
| | - Xu-Yi Ling
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Xiao-Fan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou 510642, China
| | - Yuan-Xia Chen
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Tian-Tian Wang
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Xiao-Jing Lin
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Yuan-Yuan Zhao
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Yu-Shi Ye
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Lin-Xuan Huang
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Ye-Wen Sun
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Yu-Xin Qi
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua 418000, China
| | - Dong-Ming Ma
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Ruo-Ting Zhan
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Xue-Shuang Huang
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua 418000, China
| | - Jin-Fen Yang
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| |
Collapse
|
23
|
Bai MZ, Guo YY. Bioinformatics Analysis of MSH1 Genes of Green Plants: Multiple Parallel Length Expansions, Intron Gains and Losses, Partial Gene Duplications, and Alternative Splicing. Int J Mol Sci 2023; 24:13620. [PMID: 37686425 PMCID: PMC10487979 DOI: 10.3390/ijms241713620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
MutS homolog 1 (MSH1) is involved in the recombining and repairing of organelle genomes and is essential for maintaining their stability. Previous studies indicated that the length of the gene varied greatly among species and detected species-specific partial gene duplications in Physcomitrella patens. However, there are critical gaps in the understanding of the gene size expansion, and the extent of the partial gene duplication of MSH1 remains unclear. Here, we screened MSH1 genes in 85 selected species with genome sequences representing the main clades of green plants (Viridiplantae). We identified the MSH1 gene in all lineages of green plants, except for nine incomplete species, for bioinformatics analysis. The gene is a singleton gene in most of the selected species with conserved amino acids and protein domains. Gene length varies greatly among the species, ranging from 3234 bp in Ostreococcus tauri to 805,861 bp in Cycas panzhihuaensis. The expansion of MSH1 repeatedly occurred in multiple clades, especially in Gymnosperms, Orchidaceae, and Chloranthus spicatus. MSH1 has exceptionally long introns in certain species due to the gene length expansion, and the longest intron even reaches 101,025 bp. And the gene length is positively correlated with the proportion of the transposable elements (TEs) in the introns. In addition, gene structure analysis indicated that the MSH1 of green plants had undergone parallel intron gains and losses in all major lineages. However, the intron number of seed plants (gymnosperm and angiosperm) is relatively stable. All the selected gymnosperms contain 22 introns except for Gnetum montanum and Welwitschia mirabilis, while all the selected angiosperm species preserve 21 introns except for the ANA grade. Notably, the coding region of MSH1 in algae presents an exceptionally high GC content (47.7% to 75.5%). Moreover, over one-third of the selected species contain species-specific partial gene duplications of MSH1, except for the conserved mosses-specific partial gene duplication. Additionally, we found conserved alternatively spliced MSH1 transcripts in five species. The study of MSH1 sheds light on the evolution of the long genes of green plants.
Collapse
Affiliation(s)
| | - Yan-Yan Guo
- College of Plant Protection, Henan Agricultural University, Zhengzhou 450046, China
| |
Collapse
|
24
|
Sahu SK, Liu M, Li R, Chen Y, Wang G, Fang D, Sahu DN, Wei J, Wang S, Liu H, He C. Chromosome-scale genome of Indian rosewood ( Dalbergia sissoo). FRONTIERS IN PLANT SCIENCE 2023; 14:1218515. [PMID: 37662156 PMCID: PMC10470032 DOI: 10.3389/fpls.2023.1218515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 07/27/2023] [Indexed: 09/05/2023]
Affiliation(s)
- Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, China
| | - Min Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, China
| | - Ruirui Li
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, China
- College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - Yewen Chen
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, China
| | - Guanlong Wang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, China
- College of Science, South China Agricultural University, Guangzhou, China
| | - Dongming Fang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, China
| | - Durgesh Nandini Sahu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, China
| | - Jinpu Wei
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, China
| | - Sibo Wang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, China
| | - Chengzhong He
- Key Laboratory for Forest Genetic & Tree Improvement and Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, China
| |
Collapse
|
25
|
Lan L, Zhao H, Xu S, Kan S, Zhang X, Liu W, Liao X, Tembrock LR, Ren Y, Reeve W, Yang J, Wu Z. A high-quality Bougainvillea genome provides new insights into evolutionary history and pigment biosynthetic pathways in the Caryophyllales. HORTICULTURE RESEARCH 2023; 10:uhad124. [PMID: 37554346 PMCID: PMC10405137 DOI: 10.1093/hr/uhad124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/05/2023] [Indexed: 08/10/2023]
Abstract
Bougainvillea is a perennial ornamental shrub that is highly regarded in ornamental horticulture around the world. However, the absence of genome data limits our understanding of the pathways involved in bract coloration and breeding. Here, we report a chromosome-level assembly of the giga-genome of Bougainvillea × buttiana 'Mrs Butt', a cultivar thought to be the origin of many other Bougainvillea cultivars. The assembled genome is ~5 Gb with a scaffold N50 of 151 756 278 bp and contains 86 572 genes which have undergone recent whole-genome duplication. We confirmed that multiple rounds of whole-genome multiplication have occurred in the evolutionary history of the Caryophyllales, reconstructed the relationship in the Caryophyllales at whole genome level, and found discordance between species and gene trees as the result of complex introgression events. We investigated betalain and anthocyanin biosynthetic pathways and found instances of independent evolutionary innovations in the nine different Caryophyllales species. To explore the potential formation mechanism of diverse bract colors in Bougainvillea, we analyzed the genes involved in betalain and anthocyanin biosynthesis and found extremely low expression of ANS and DFR genes in all cultivars, which may limit anthocyanin biosynthesis. Our findings indicate that the expression pattern of the betalain biosynthetic pathway did not directly correlate with bract color, and a higher expression level in the betalain biosynthetic pathway is required for colored bracts. This improved understanding of the correlation between gene expression and bract color allows plant breeding outcomes to be predicted with greater certainty.
Collapse
Affiliation(s)
- Lan Lan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- School of Medical, Molecularand Forensic Sciences, Murdoch University, 6150, Western Australia, 90 South Street, Murdoch, Australia
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Huiqi Zhao
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, 572025, China
- Institute of Tropical Horticulture Research, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Suxia Xu
- Fujian Key Laboratory of Subtropical Plant Physiology & Biochemistry, Fujian Institute of Subtropical Botany, Xiamen, 361006, China
| | - Shenglong Kan
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xiaoni Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Weichao Liu
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Yonglin Ren
- School of Medical, Molecularand Forensic Sciences, Murdoch University, 6150, Western Australia, 90 South Street, Murdoch, Australia
| | - Wayne Reeve
- School of Medical, Molecularand Forensic Sciences, Murdoch University, 6150, Western Australia, 90 South Street, Murdoch, Australia
| | - Jun Yang
- Sanya Institute, Hainan Academy of Agricultural Sciences, Sanya, 572025, China
- Institute of Tropical Horticulture Research, Hainan Academy of Agricultural Sciences, Haikou, 571100, China
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| |
Collapse
|
26
|
Guo X, Wang F, Fang D, Lin Q, Sahu SK, Luo L, Li J, Chen Y, Dong S, Chen S, Liu Y, Luo S, Guo Y, Liu H. The genome of Acorus deciphers insights into early monocot evolution. Nat Commun 2023; 14:3662. [PMID: 37339966 DOI: 10.1038/s41467-023-38836-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/17/2023] [Indexed: 06/22/2023] Open
Abstract
Acorales is the sister lineage to all the other extant monocot plants. Genomic resource enhancement of this genus can help to reveal early monocot genomic architecture and evolution. Here, we assemble the genome of Acorus gramineus and reveal that it has ~45% fewer genes than the majority of monocots, although they have similar genome size. Phylogenetic analyses based on both chloroplast and nuclear genes consistently support that A. gramineus is the sister to the remaining monocots. In addition, we assemble a 2.2 Mb mitochondrial genome and observe many genes exhibit higher mutation rates than that of most angiosperms, which could be the reason leading to the controversies of nuclear genes- and mitochondrial genes-based phylogenetic trees existing in the literature. Further, Acorales did not experience tau (τ) whole-genome duplication, unlike majority of monocot clades, and no large-scale gene expansion is observed. Moreover, we identify gene contractions and expansions likely linking to plant architecture, stress resistance, light harvesting, and essential oil metabolism. These findings shed light on the evolution of early monocots and genomic footprints of wetland plant adaptations.
Collapse
Affiliation(s)
- Xing Guo
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
| | - Fang Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Dongming Fang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
| | - Qiongqiong Lin
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- College of Life Science, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
| | - Liuming Luo
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- College of Life Science, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
| | - Jiani Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, PR China
| | - Yewen Chen
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Shanshan Dong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, Guangdong, 518004, PR China
| | - Sisi Chen
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, The Chinese Academy of Sciences, South China Botanical Garden, Guangzhou, Guangdong, 510650, PR China
| | - Yang Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, Guangdong, 518004, PR China
| | - Shixiao Luo
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, The Chinese Academy of Sciences, South China Botanical Garden, Guangzhou, Guangdong, 510650, PR China
| | - Yalong Guo
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, PR China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, PR China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China.
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, Heilongjiang, 150040, PR China.
| |
Collapse
|
27
|
Ma L, Liu KW, Li Z, Hsiao YY, Qi Y, Fu T, Tang GD, Zhang D, Sun WH, Liu DK, Li Y, Chen GZ, Liu XD, Liao XY, Jiang YT, Yu X, Hao Y, Huang J, Zhao XW, Ke S, Chen YY, Wu WL, Hsu JL, Lin YF, Huang MD, Li CY, Huang L, Wang ZW, Zhao X, Zhong WY, Peng DH, Ahmad S, Lan S, Zhang JS, Tsai WC, Van de Peer Y, Liu ZJ. Diploid and tetraploid genomes of Acorus and the evolution of monocots. Nat Commun 2023; 14:3661. [PMID: 37339946 DOI: 10.1038/s41467-023-38829-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 05/17/2023] [Indexed: 06/22/2023] Open
Abstract
Monocots are a major taxon within flowering plants, have unique morphological traits, and show an extraordinary diversity in lifestyle. To improve our understanding of monocot origin and evolution, we generate chromosome-level reference genomes of the diploid Acorus gramineus and the tetraploid Ac. calamus, the only two accepted species from the family Acoraceae, which form a sister lineage to all other monocots. Comparing the genomes of Ac. gramineus and Ac. calamus, we suggest that Ac. gramineus is not a potential diploid progenitor of Ac. calamus, and Ac. calamus is an allotetraploid with two subgenomes A, and B, presenting asymmetric evolution and B subgenome dominance. Both the diploid genome of Ac. gramineus and the subgenomes A and B of Ac. calamus show clear evidence of whole-genome duplication (WGD), but Acoraceae does not seem to share an older WGD that is shared by most other monocots. We reconstruct an ancestral monocot karyotype and gene toolkit, and discuss scenarios that explain the complex history of the Acorus genome. Our analyses show that the ancestors of monocots exhibit mosaic genomic features, likely important for that appeared in early monocot evolution, providing fundamental insights into the origin, evolution, and diversification of monocots.
Collapse
Affiliation(s)
- Liang Ma
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ke-Wei Liu
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine, Shenzhen Key Laboratory of Gene and Antibody Therapy, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan City, 701, Taiwan
| | - Yiying Qi
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Tao Fu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Guang-Da Tang
- Henry Fok College of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, China
| | - Diyang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wei-Hong Sun
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ding-Kun Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuanyuan Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Gui-Zhen Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xue-Die Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xing-Yu Liao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yu-Ting Jiang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xia Yu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yang Hao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jie Huang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xue-Wei Zhao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shijie Ke
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - You-Yi Chen
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Wan-Lin Wu
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan
| | - Jui-Ling Hsu
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan
| | - Yu-Fu Lin
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan
| | - Ming-Der Huang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, 80424, Taiwan
| | - Chia-Ying Li
- Department of Applied Chemistry, National Pingtung University, Pingtung City, Pingtung County, 900003, Taiwan
| | - Laiqiang Huang
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine, Shenzhen Key Laboratory of Gene and Antibody Therapy, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | | | | | | | - Dong-Hui Peng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Sagheer Ahmad
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Ji-Sen Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China.
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China.
| | - Wen-Chieh Tsai
- Orchid Research and Development Center, National Cheng Kung University, Tainan City, 701, Taiwan.
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium.
- VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium.
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
- College of Horticulture, Nanjing Agricultural University, Academy for Advanced Interdisciplinary Studies, Nanjing, 210095, China.
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine, Shenzhen Key Laboratory of Gene and Antibody Therapy, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China.
- Institute of Vegetable and Flowers, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, 325005, China.
| |
Collapse
|
28
|
Stull GW, Pham KK, Soltis PS, Soltis DE. Deep reticulation: the long legacy of hybridization in vascular plant evolution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:743-766. [PMID: 36775995 DOI: 10.1111/tpj.16142] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 02/02/2023] [Accepted: 02/07/2023] [Indexed: 05/27/2023]
Abstract
Hybridization has long been recognized as a fundamental evolutionary process in plants but, until recently, our understanding of its phylogenetic distribution and biological significance across deep evolutionary scales has been largely obscure. Over the past decade, genomic and phylogenomic datasets have revealed, perhaps not surprisingly, that hybridization, often associated with polyploidy, has been common throughout the evolutionary history of plants, particularly in various lineages of flowering plants. However, phylogenomic studies have also highlighted the challenges of disentangling signals of ancient hybridization from other sources of genomic conflict (in particular, incomplete lineage sorting). Here, we provide a critical review of ancient hybridization in vascular plants, outlining well-documented cases of ancient hybridization across plant phylogeny, as well as the challenges unique to documenting ancient versus recent hybridization. We provide a definition for ancient hybridization, which, to our knowledge, has not been explicitly attempted before. Further documenting the extent of deep reticulation in plants should remain an important research focus, especially because published examples likely represent the tip of the iceberg in terms of the total extent of ancient hybridization. However, future research should increasingly explore the macroevolutionary significance of this process, in terms of its impact on evolutionary trajectories (e.g. how does hybridization influence trait evolution or the generation of biodiversity over long time scales?), as well as how life history and ecological factors shape, or have shaped, the frequency of hybridization across geologic time and plant phylogeny. Finally, we consider the implications of ubiquitous ancient hybridization for how we conceptualize, analyze, and classify plant phylogeny. Networks, as opposed to bifurcating trees, represent more accurate representations of evolutionary history in many cases, although our ability to infer, visualize, and use networks for comparative analyses is highly limited. Developing improved methods for the generation, visualization, and use of networks represents a critical future direction for plant biology. Current classification systems also do not generally allow for the recognition of reticulate lineages, and our classifications themselves are largely based on evidence from the chloroplast genome. Updating plant classification to better reflect nuclear phylogenies, as well as considering whether and how to recognize hybridization in classification systems, will represent an important challenge for the plant systematics community.
Collapse
Affiliation(s)
- Gregory W Stull
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20013, USA
| | - Kasey K Pham
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| | - Douglas E Soltis
- Department of Biology, University of Florida, Gainesville, FL, 32611, USA
- Florida Museum of Natural History, University of Florida, Gainesville, FL, 32611, USA
| |
Collapse
|
29
|
Yao G, Zhang YQ, Barrett C, Xue B, Bellot S, Baker WJ, Ge XJ. A plastid phylogenomic framework for the palm family (Arecaceae). BMC Biol 2023; 21:50. [PMID: 36882831 PMCID: PMC9993706 DOI: 10.1186/s12915-023-01544-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/14/2023] [Indexed: 03/09/2023] Open
Abstract
BACKGROUND Over the past decade, phylogenomics has greatly advanced our knowledge of angiosperm evolution. However, phylogenomic studies of large angiosperm families with complete species or genus-level sampling are still lacking. The palms, Arecaceae, are a large family with ca. 181 genera and 2600 species and are important components of tropical rainforests bearing great cultural and economic significance. Taxonomy and phylogeny of the family have been extensively investigated by a series of molecular phylogenetic studies in the last two decades. Nevertheless, some phylogenetic relationships within the family are not yet well-resolved, especially at the tribal and generic levels, with consequent impacts for downstream research. RESULTS Plastomes of 182 palm species representing 111 genera were newly sequenced. Combining these with previously published plastid DNA data, we were able to sample 98% of palm genera and conduct a plastid phylogenomic investigation of the family. Maximum likelihood analyses yielded a robustly supported phylogenetic hypothesis. Phylogenetic relationships among all five palm subfamilies and 28 tribes were well-resolved, and most inter-generic phylogenetic relationships were also resolved with strong support. CONCLUSIONS The inclusion of nearly complete generic-level sampling coupled with nearly complete plastid genomes strengthened our understanding of plastid-based relationships of the palms. This comprehensive plastid genome dataset complements a growing body of nuclear genomic data. Together, these datasets form a novel phylogenomic baseline for the palms and an increasingly robust framework for future comparative biological studies of this exceptionally important plant family.
Collapse
Affiliation(s)
- Gang Yao
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Yu-Qu Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Present Address: College of Pharmacy, Shaanxi University of Chinese Medicine, Xi'an, China
| | - Craig Barrett
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Bine Xue
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | | | | | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China. .,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China.
| |
Collapse
|
30
|
Bowles AMC, Williamson CJ, Williams TA, Lenton TM, Donoghue PCJ. The origin and early evolution of plants. TRENDS IN PLANT SCIENCE 2023; 28:312-329. [PMID: 36328872 DOI: 10.1016/j.tplants.2022.09.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 09/23/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Abstract
Plant (archaeplastid) evolution has transformed the biosphere, but we are only now beginning to learn how this took place through comparative genomics, phylogenetics, and the fossil record. This has illuminated the phylogeny of Archaeplastida, Viridiplantae, and Streptophyta, and has resolved the evolution of key characters, genes, and genomes - revealing that many key innovations evolved long before the clades with which they have been casually associated. Molecular clock analyses estimate that Streptophyta and Viridiplantae emerged in the late Mesoproterozoic to late Neoproterozoic, whereas Archaeplastida emerged in the late-mid Palaeoproterozoic. Together, these insights inform on the coevolution of plants and the Earth system that transformed ecology and global biogeochemical cycles, increased weathering, and precipitated snowball Earth events, during which they would have been key to oxygen production and net primary productivity (NPP).
Collapse
Affiliation(s)
- Alexander M C Bowles
- School of Geographical Sciences, University of Bristol, University Road, Bristol BS8 1SS, UK; Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK.
| | | | - Tom A Williams
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK
| | - Timothy M Lenton
- Global Systems Institute, University of Exeter, Laver Building, North Park Road, Exeter EX4 4QE, UK
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Biological Sciences and School of Earth Sciences, Life Sciences Building, University of Bristol, Bristol BS8 1TQ, UK.
| |
Collapse
|
31
|
Xue JY, Li Z, Hu SY, Kao SM, Zhao T, Wang JY, Wang Y, Chen M, Qiu Y, Fan HY, Liu Y, Shao ZQ, Van de Peer Y. The Saururus chinensis genome provides insights into the evolution of pollination strategies and herbaceousness in magnoliids. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:1021-1034. [PMID: 36602036 PMCID: PMC7614262 DOI: 10.1111/tpj.16097] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 01/02/2023] [Indexed: 06/17/2023]
Abstract
Saururus chinensis, an herbaceous magnoliid without perianth, represents a clade of early-diverging angiosperms that have gone through woodiness-herbaceousness transition and pollination obstacles: the characteristic white leaves underneath inflorescence during flowering time are considered a substitute for perianth to attract insect pollinators. Here, using the newly sequenced S. chinensis genome, we revisited the phylogenetic position of magnoliids within mesangiosperms, and recovered a sister relationship for magnoliids and Chloranthales. By considering differentially expressed genes, we identified candidate genes that are involved in the morphogenesis of the white leaves in S. chinensis. Among those genes, we verified - in a transgenic experiment with Arabidopsis - that increasing the expression of the "pseudo-etiolation in light" gene (ScPEL) can inhibit the biosynthesis of chlorophyll. ScPEL is thus likely responsible for the switches between green and white leaves, suggesting that changes in gene expression may underlie the evolution of pollination strategies. Despite being an herbaceous plant, S. chinensis still has vascular cambium and maintains the potential for secondary growth as a woody plant, because the necessary machinery, i.e., the entire gene set involved in lignin biosynthesis, is well preserved. However, similar expression levels of two key genes (CCR and CAD) between the stem and other tissues in the lignin biosynthesis pathway are possibly associated with the herbaceous nature of S. chinensis. In conclusion, the S. chinensis genome provides valuable insights into the adaptive evolution of pollination in Saururaceae and reveals a possible mechanism for the evolution of herbaceousness in magnoliids.
Collapse
Affiliation(s)
- Jia-Yu Xue
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
- Center for Plant Diversity and Systematics, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB-UGent Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Shuai-Ya Hu
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Shu-Min Kao
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB-UGent Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Tao Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Jie-Yu Wang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yue Wang
- Center for Plant Diversity and Systematics, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Min Chen
- Center for Plant Diversity and Systematics, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China
| | - Yichun Qiu
- Max Planck Institute of Molecular Plant Physiology, Potsdam Science Park, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Hai-Yun Fan
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Yang Liu
- Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen 518004, Guangdong, China
| | - Zhu-Qing Shao
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Yves Van de Peer
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB-UGent Center for Plant Systems Biology, B-9052 Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| |
Collapse
|
32
|
Shen Z, Ding X, Cheng J, Wu F, Yin H, Wang M. Phylogenetic studies of magnoliids: Advances and perspectives. FRONTIERS IN PLANT SCIENCE 2023; 13:1100302. [PMID: 36726671 PMCID: PMC9885158 DOI: 10.3389/fpls.2022.1100302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
Magnoliids are the largest flowering plant clades outside of the eudicots and monocots, which are distributed worldwide and have high economic, ornamental and ecological values. Eudicots, monocots and magnoliids are the three major clades of Mesangiospermae, and their phylogenetic relationship is one of the most interesting issues. In recent years, with the continuous accumulation of genomic information, the evolutionary status of magnoliids has become a hot spot in plant phylogenetic research. Although great efforts have been made to study the evolution of magnoliids using molecular data from several representative species such as nuclear genome, plastid genome, mitochondrial genome, and transcriptome, the results of current studies on the phylogenetic status of magnoliids are inconsistent. Here, we systematically describe the current understanding of the molecular research on magnoliid phylogeny and review the differences in the evolutionary state of magnoliids. Understanding the research approaches and limitations of magnoliid phylogeny can guide research strategies to further improve the study of the phylogenetic evolution of magnoliids.
Collapse
Affiliation(s)
- Zhiguo Shen
- National Innovation Alliance of Wintersweet, Henan Academy of Forestry, Zhengzhou, China
| | - Xin Ding
- National Innovation Alliance of Wintersweet, Henan Academy of Forestry, Zhengzhou, China
| | - Jianming Cheng
- Scientific Research Department, Scientific Research Department, Henan Colorful Horticulture Co., Ltd, Zhengzhou, China
| | - Fangfang Wu
- Scientific Research Department, Scientific Research Department, Henan Colorful Horticulture Co., Ltd, Zhengzhou, China
| | - Hengfu Yin
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Minyan Wang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| |
Collapse
|
33
|
Wang ZF, Rouard M, Droc G, Heslop-Harrison P(JS, Ge XJ. Genome assembly of Musa beccarii shows extensive chromosomal rearrangements and genome expansion during evolution of Musaceae genomes. Gigascience 2022; 12:giad005. [PMID: 36807539 PMCID: PMC9941839 DOI: 10.1093/gigascience/giad005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 11/24/2022] [Accepted: 01/27/2023] [Indexed: 02/23/2023] Open
Abstract
BACKGROUND Musa beccarii (Musaceae) is a banana species native to Borneo, sometimes grown as an ornamental plant. The basic chromosome number of Musa species is x = 7, 10, or 11; however, M. beccarii has a basic chromosome number of x = 9 (2n = 2x = 18), which is the same basic chromosome number of species in the sister genera Ensete and Musella. Musa beccarii is in the section Callimusa, which is sister to the section Musa. We generated a high-quality chromosome-scale genome assembly of M. beccarii to better understand the evolution and diversity of genomes within the family Musaceae. FINDINGS The M. beccarii genome was assembled by long-read and Hi-C sequencing, and genes were annotated using both long Iso-seq and short RNA-seq reads. The size of M. beccarii was the largest among all known Musaceae assemblies (∼570 Mbp) due to the expansion of transposable elements and increased 45S ribosomal DNA sites. By synteny analysis, we detected extensive genome-wide chromosome fusions and fissions between M. beccarii and the other Musa and Ensete species, far beyond those expected from differences in chromosome number. Within Musaceae, M. beccarii showed a reduced number of terpenoid synthase genes, which are related to chemical defense, and enrichment in lipid metabolism genes linked to the physical defense of the cell wall. Furthermore, type III polyketide synthase was the most abundant biosynthetic gene cluster (BGC) in M. beccarii. BGCs were not conserved in Musaceae genomes. CONCLUSIONS The genome assembly of M. beccarii is the first chromosome-scale genome assembly in the Callimusa section in Musa, which provides an important genetic resource that aids our understanding of the evolution of Musaceae genomes and enhances our knowledge of the pangenome.
Collapse
Affiliation(s)
- Zheng-Feng Wang
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Key Laboratory of Carbon Sequestration in Terrestrial Ecosystem, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier, France
| | - Gaetan Droc
- CIRAD, UMR AGAP Institut, F-34398 Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Pat (J S) Heslop-Harrison
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Xue-Jun Ge
- Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| |
Collapse
|
34
|
A draft genome of the medicinal plant Cremastra appendiculata (D. Don) provides insights into the colchicine biosynthetic pathway. Commun Biol 2022; 5:1294. [PMID: 36434059 PMCID: PMC9700805 DOI: 10.1038/s42003-022-04229-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 11/07/2022] [Indexed: 11/27/2022] Open
Abstract
Cremastra appendiculata (D. Don) Makino is a rare terrestrial orchid with a high market value as an ornamental and Chinese traditional medicinal herb with a wide range of pharmacological properties. The pseudobulbs of C. appendiculata are one of the primary sources of the famous traditional Chinese medicine "Shancigu", which has been clinically used for treating many diseases, especially, as the main component to treat gout. The lack of genetic research and genome data restricts the modern development and clinical use of C. appendiculata. Here, we report a 2.3 Gb chromosome-level genome of C. appendiculata. We identify a series of candidates of 35 candidate genes responsible for colchicine biosynthesis, among which O-methyltransferase (OMT) gene exhibits an important role in colchicine biosynthesis. Co-expression analysis reveal purple and green-yellow module have close relationships with pseudobulb parts and comprise most of the colchicine pathway genes. Overall, our genome data and the candidate genes reported here set the foundation to decipher the colchicine biosynthesis pathways in medicinal plants.
Collapse
|
35
|
Wang Z, Li Y, Sun P, Zhu M, Wang D, Lu Z, Hu H, Xu R, Zhang J, Ma J, Liu J, Yang Y. A high-quality Buxus austro-yunnanensis (Buxales) genome provides new insights into karyotype evolution in early eudicots. BMC Biol 2022; 20:216. [PMID: 36195948 PMCID: PMC9533543 DOI: 10.1186/s12915-022-01420-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 09/27/2022] [Indexed: 11/21/2022] Open
Abstract
Background Eudicots are the most diverse group of flowering plants that compromise five well-defined lineages: core eudicots, Ranunculales, Proteales, Trochodendrales, and Buxales. However, the phylogenetic relationships between these five lineages and their chromosomal evolutions remain unclear, and a lack of high-quality genome analyses for Buxales has hindered many efforts to address this knowledge gap. Results Here, we present a high-quality chromosome-level genome of Buxus austro-yunnanensis (Buxales). Our phylogenomic analyses revealed that Buxales and Trochodendrales are genetically similar and classified as sisters. Additionally, both are sisters to the core eudicots, while Ranunculales was found to be the first lineage to diverge from these groups. Incomplete lineage sorting and hybridization were identified as the main contributors to phylogenetic discordance (34.33%) between the lineages. In fact, B. austro-yunnanensis underwent only one whole-genome duplication event, and collinear gene phylogeny analyses suggested that separate independent polyploidizations occurred in the five eudicot lineages. Using representative genomes from these five lineages, we reconstructed the ancestral eudicot karyotype (AEK) and generated a nearly gapless karyotype projection for each eudicot species. Within core eudicots, we recovered one common chromosome fusion event in asterids and malvids, respectively. Further, we also found that the previously reported fused AEKs in Aquilegia (Ranunculales) and Vitis (core eudicots) have different fusion positions, which indicates that these two species have different karyotype evolution histories. Conclusions Based on our phylogenomic and karyotype evolution analyses, we revealed the likely relationships and evolutionary histories of early eudicots. Ultimately, our study expands genomic resources for early-diverging eudicots. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01420-1.
Collapse
Affiliation(s)
- Zhenyue Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Ying Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Pengchuan Sun
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics & Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Mingjia Zhu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Dandan Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Zhiqiang Lu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China.,Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
| | - Hongyin Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Renping Xu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jin Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jianxiang Ma
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China. .,Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics & Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China.
| | - Yongzhi Yang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China.
| |
Collapse
|
36
|
Shoot Development in Members of an Ancient Aquatic Angiosperm Lineage, Ceratophyllaceae: A New Interpretation Facilitates Comparisons with Chloranthaceae. Symmetry (Basel) 2022. [DOI: 10.3390/sym14071288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Ceratophyllum is an ancient and phylogenetically isolated angiosperm lineage. Comparisons between Ceratophyllum and other angiosperms are hampered by uncertainty in inferring organ homologies in this genus of specialized aquatics. Interpretation of shoot morphology is especially problematic in Ceratophyllum. Each node has several leaf-like appendages interpreted as verticillate leaves, modified parts of one and the same leaf or parts of two leaves under decussate phyllotaxis. Vegetative branches are axillary, but reproductive units (interpreted as flowers or inflorescences) are commonly viewed as developing from collateral accessory buds. We studied shoot development in Ceratophyllum submersum, C. tanaiticum, and C. demersum using scanning electron microscopy to clarify shoot morphology and branching patterns. Our data support the idea that the phyllotaxis is essentially decussate with appendages of stipular origin resembling leaf blades. We conclude that a leaf axil of Ceratophyllum possesses a complex of two serial buds, the lower one producing a vegetative branch and the upper one developing a reproductive unit. The reproductive unit is congenitally displaced to the subsequent node, a phenomenon known as concaulescence. Either member of the serial bud complex may be absent. There is a theory based on a synthesis of molecular and morphological data that Chloranthaceae are the closest extant relatives of Ceratophyllum. Serial buds and concaulescence are known in Hedyosmum (Chloranthaceae). Our new interpretation facilitates morphological comparisons between Hedyosmum and Ceratophyllum.
Collapse
|
37
|
Sokoloff DD, El ES, Pechenyuk EV, Carrive L, Nadot S, Rudall PJ, Remizowa MV. Refined Interpretation of the Pistillate Flower in Ceratophyllum Sheds Fresh Light on Gynoecium Evolution in Angiosperms. Front Cell Dev Biol 2022; 10:868352. [PMID: 35573671 PMCID: PMC9098228 DOI: 10.3389/fcell.2022.868352] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
Molecular phylogenetic analyses have revealed a superclade of mesangiosperms with five extant lineages: monocots, eudicots, magnoliids, Ceratophyllum and Chloranthaceae. Both Ceratophyllum and Chloranthaceae are ancient lineages with a long fossil record; their precise placement within mesangiosperms is uncertain. Morphological studies have suggested that they form a clade together with some Cretaceous fossils, including Canrightia, Montsechia and Pseudoasterophyllites. Apart from Canrightia, members of this clade share unilocular gynoecia commonly interpreted as monomerous with ascidiate carpels. Alternatively, the gynoecium of Ceratophyllum has also been interpreted as syncarpous with a single fertile carpel (pseudomonomerous). We investigate patterns of morphological, anatomical and developmental variation in gynoecia of three Ceratophyllum species to explore the controversial interpretation of its gynoecium as either monomerous or pseudomonomerous. We use an angiosperm-wide morphological data set and contrasting tree topologies to estimate the ancestral gynoecium type in both Ceratophyllum and mesangiosperms. Gynoecia of all three Ceratophyllum species possess a small (sometimes vestigial) glandular appendage on the abaxial side and an occasionally bifurcating apex. The ovary is usually unilocular with two procambium strands, but sometimes bilocular and/or with three strands in C. demersum. None of the possible phylogenetic placements strongly suggest apocarpy in the stem lineage of Ceratophyllum. Rescoring Ceratophyllum as having two united carpels affects broader-scale reconstructions of the ancestral gynoecium in mesangiosperms. Our interpretation of the glandular appendage as a tepal or staminode homologue makes the Ceratophyllum ovary inferior, thus resembling (semi)inferior ovaries of most Chloranthaceae and potentially related fossils Canrightia and Zlatkocarpus. The entire structure of the flower of Ceratophyllum suggests strong reduction following a long and complex evolutionary history. The widely accepted notion that apocarpy is ancestral in mesangiosperms (and angiosperms) lacks robust support, regardless of which modes of carpel fusion are considered. Our study highlights the crucial importance of incorporating fossils into large-scale analyses to understand character evolution.
Collapse
Affiliation(s)
- Dmitry D Sokoloff
- Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Elena S El
- Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | | | - Laetitia Carrive
- Université Paris-Saclay, CNRS, AgroParisTech, Écologie, Systématique et Évolution, Orsay, France
| | - Sophie Nadot
- Université Paris-Saclay, CNRS, AgroParisTech, Écologie, Systématique et Évolution, Orsay, France
| | | | | |
Collapse
|
38
|
Liu W, Guo W, Chen S, Xu H, Zhao Y, Chen S, You X. A High-Quality Reference Genome Sequence and Genetic Transformation System of Aralia elata. FRONTIERS IN PLANT SCIENCE 2022; 13:822942. [PMID: 35300010 PMCID: PMC8921765 DOI: 10.3389/fpls.2022.822942] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Aralia elata is a perennial woody plant of the genus Aralia in the family Araliaceae. It is rich in saponins and therefore has a wide range of pharmacological effects. Here, we report a high-quality reference genome of A. elata, with a genome size of 1.21 Gb and a contig N50 of 51.34 Mb, produced by PacBio HiFi sequencing technology. This is the first genome assembly for the genus Aralia. Through genome evolutionary analysis, we explored the phylogeny and whole genome duplication (WGD) events in the A. elata genome. The results indicated that a recent WGD event occurred in the A. elata genome. Estimation of the divergence times indicated that the WGD may be shared by Araliaceae. By analyzing the genome sequence of A. elata and combining the transcriptome data from three tissues, we discovered important genes related to triterpene saponins biosynthesis. Furthermore, based on the embryonic callus induction system of A. elata established in our laboratory, we set up the genetic transformation system of this plant. The genomic resources and genetic transformation system obtained in this study provide insights into A. elata and lays the foundation for further exploration of the A. elata regulatory mechanism.
Collapse
Affiliation(s)
- Wenxuan Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Wenhua Guo
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Song Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Honghao Xu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Yue Zhao
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xiangling You
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin, China
| |
Collapse
|
39
|
Yang T, Sahu SK, Yang L, Liu Y, Mu W, Liu X, Strube ML, Liu H, Zhong B. Comparative Analyses of 3,654 Plastid Genomes Unravel Insights Into Evolutionary Dynamics and Phylogenetic Discordance of Green Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:808156. [PMID: 35498716 PMCID: PMC9038950 DOI: 10.3389/fpls.2022.808156] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 03/07/2022] [Indexed: 05/03/2023]
Abstract
The plastid organelle is essential for many vital cellular processes and the growth and development of plants. The availability of a large number of complete plastid genomes could be effectively utilized to understand the evolution of the plastid genomes and phylogenetic relationships among plants. We comprehensively analyzed the plastid genomes of Viridiplantae comprising 3,654 taxa from 298 families and 111 orders and compared the genomic organizations in their plastid genomic DNA among major clades, which include gene gain/loss, gene copy number, GC content, and gene blocks. We discovered that some important genes that exhibit similar functions likely formed gene blocks, such as the psb family presumably showing co-occurrence and forming gene blocks in Viridiplantae. The inverted repeats (IRs) in plastid genomes have doubled in size across land plants, and their GC content is substantially higher than non-IR genes. By employing three different data sets [all nucleotide positions (nt123), only the first and second codon positions (nt12), and amino acids (AA)], our phylogenomic analyses revealed Chlorokybales + Mesostigmatales as the earliest-branching lineage of streptophytes. Hornworts, mosses, and liverworts forming a monophylum were identified as the sister lineage of tracheophytes. Based on nt12 and AA data sets, monocots, Chloranthales and magnoliids are successive sister lineages to the eudicots + Ceratophyllales clade. The comprehensive taxon sampling and analysis of different data sets from plastid genomes recovered well-supported relationships of green plants, thereby contributing to resolving some long-standing uncertainties in the plant phylogeny.
Collapse
Affiliation(s)
- Ting Yang
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Sunil Kumar Sahu
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
- *Correspondence: Sunil Kumar Sahu,
| | - Lingxiao Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yang Liu
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
| | - Weixue Mu
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
| | - Xin Liu
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Huan Liu
- Beijing Genomics Institute Shenzhen, Yantian Beishan Industrial Zone, Shenzhen, China
- State Key Laboratory of Agricultural Genomics, Beijing Genomics Institute Shenzhen, Shenzhen, China
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, China
- Bojian Zhong,
| |
Collapse
|