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Zhang N, Zhao P, Zhang W, Wang H, Wang K, Wang X, Zhang Z, Tan N, Chen L. A chromosome-level genome of Lobelia seguinii provides insights into the evolution of Campanulaceae and the lobeline biosynthesis. Genomics 2024; 117:110979. [PMID: 39675685 DOI: 10.1016/j.ygeno.2024.110979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Revised: 12/04/2024] [Accepted: 12/10/2024] [Indexed: 12/17/2024]
Abstract
Lobelia seguinii is a plant with great ecological and medicinal value and belongs to Campanulaceae. Lobelia contains lobeline, a well-known compound used to treat respiratory diseases. Nevertheless, lobeline biosynthesis needs further exploration. Moreover, whole-genome duplication (WGD) and karyotype evolution within Campanulaceae still need to be better understood. In this study, we obtained a chromosome-level genome of L. seguinii with a size of 1.4 Gb and 38253 protein-coding genes. Analyses revealed two WGDs within Campanulaceae, one at the most recent common ancestor (MRCA) of Campanula and Adenophora, and another at the MRCA of Lobelioideae. Analyses further revealed that the karyotype of Platycodon grandiflorus represents the ancient type within Asterales. We proposed eight enzymes involved in the lobeline biosynthesis pathway of L. seguinii. Molecular cloning and heterologous expression of phenylalanine ammonia-lyase (PAL), a candidate enzyme involved in the first step of lobeline biosynthesis, verified its function to catalyze the deamination of phenylalanine to cinnamic acid. This study sheds light on the evolution of Campanulaceae and lobeline biosynthesis.
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Affiliation(s)
- Na Zhang
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Puguang Zhao
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Wenda Zhang
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
| | - Huiying Wang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 211198, China
| | - Kaixuan Wang
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Xiangyu Wang
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Zhanjing Zhang
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, 530023 Nanning, China.
| | - Ninghua Tan
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China.
| | - Lingyun Chen
- Department of Resources Science of Traditional Chinese Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Medical Botanical Garden, China Pharmaceutical University, Nanjing 211198, China.
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2
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Hu ZC, Majda M, Sun HR, Zhang Y, Ding YN, Yuan Q, Su TB, Lü TF, Gao F, Xu GX, Smith RS, Østergaard L, Dong Y. Evolution of a SHOOTMERISTEMLESS transcription factor binding site promotes fruit shape determination. NATURE PLANTS 2024:10.1038/s41477-024-01854-1. [PMID: 39668212 DOI: 10.1038/s41477-024-01854-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 10/18/2024] [Indexed: 12/14/2024]
Abstract
In animals and plants, organ shape is primarily determined during primordium development by carefully coordinated growth and cell division1-3. Rare examples of post-primordial change in morphology (reshaping) exist that offer tractable systems for the study of mechanisms required for organ shape determination and diversification. One such example is morphogenesis in Capsella fruits whose heart-shaped appearance emerges by reshaping of the ovate spheroid gynoecium upon fertilization4. Here we use whole-organ live-cell imaging and single-cell RNA sequencing (scRNA-seq) analysis to show that Capsella fruit shape determination is based on dynamic changes in cell growth and cell division coupled with local maintenance of meristematic identity. At the molecular level, we reveal an auxin-induced mechanism that is required for morphological alteration and ultimately determined by a single cis-regulatory element. This element resides in the promoter of the Capsella rubella SHOOTMERISTEMLESS5 (CrSTM) gene. The CrSTM meristem identity factor positively regulates its own expression through binding to this element, thereby providing a feed-forward loop at the position and time of protrusion emergence to form the heart. Independent evolution of the STM-binding element in STM promoters across Brassicaceae species correlates with those undergoing a gynoecium-to-fruit shape change. Accordingly, genetic and phenotypic studies show that the STM-binding element is required to facilitate the shape transition and suggest a conserved molecular mechanism for organ morphogenesis.
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Affiliation(s)
- Zhi-Cheng Hu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Mateusz Majda
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
- Computational and Systems Biology Department, John Innes Centre, Norwich, UK
| | - Hao-Ran Sun
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Yao Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Yi-Ning Ding
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Quan Yuan
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Tong-Bing Su
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Tian-Feng Lü
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Feng Gao
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Gui-Xia Xu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Richard S Smith
- Computational and Systems Biology Department, John Innes Centre, Norwich, UK
| | - Lars Østergaard
- Crop Genetics Department, John Innes Centre, Norwich, UK.
- Department of Biology, University of Oxford, Oxford, UK.
| | - Yang Dong
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- China National Botanical Garden, Beijing, China.
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3
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Tyszka AS, Larson DA, Walker JF. Sequencing historical RNA: unrealized potential to increase understanding of the plant tree of life. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00305-4. [PMID: 39613559 DOI: 10.1016/j.tplants.2024.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 10/22/2024] [Accepted: 11/04/2024] [Indexed: 12/01/2024]
Abstract
Recent studies have demonstrated that it is a misconception that transcriptome sequencing requires tissue preserved at ultracold temperatures. Here, we outline the potential origins of this misconception and its possible role in biasing the geographic distribution of published plant transcriptomes. We highlight the importance of ensuring diverse sampling by providing an overview of the questions that transcriptomes can answer about the forces shaping the plant tree of life. We discuss how broadening transcriptome sequencing to include existing specimens will allow the field to grow and more fully utilize biological collections. We hope this article encourages the expansion of the current trend in 'herbariomics' research to include whole-transcriptome sequencing of historical RNA.
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Affiliation(s)
- Alexa S Tyszka
- Department of Biological Sciences, The University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Drew A Larson
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
| | - Joseph F Walker
- Department of Biological Sciences, The University of Illinois at Chicago, Chicago, IL 60607, USA.
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Thomas SK, Hoek KV, Ogoti T, Duong H, Angelovici R, Pires JC, Mendoza-Cozatl D, Washburn J, Schenck CA. Halophytes and heavy metals: A multi-omics approach to understand the role of gene and genome duplication in the abiotic stress tolerance of Cakile maritima. AMERICAN JOURNAL OF BOTANY 2024; 111:e16310. [PMID: 38600732 DOI: 10.1002/ajb2.16310] [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: 12/18/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 04/12/2024]
Abstract
PREMISE The origin of diversity is a fundamental biological question. Gene duplications are one mechanism that provides raw material for the emergence of novel traits, but evolutionary outcomes depend on which genes are retained and how they become functionalized. Yet, following different duplication types (polyploidy and tandem duplication), the events driving gene retention and functionalization remain poorly understood. Here we used Cakile maritima, a species that is tolerant to salt and heavy metals and shares an ancient whole-genome triplication with closely related salt-sensitive mustard crops (Brassica), as a model to explore the evolution of abiotic stress tolerance following polyploidy. METHODS Using a combination of ionomics, free amino acid profiling, and comparative genomics, we characterize aspects of salt stress response in C. maritima and identify retained duplicate genes that have likely enabled adaptation to salt and mild levels of cadmium. RESULTS Cakile maritima is tolerant to both cadmium and salt treatments through uptake of cadmium in the roots. Proline constitutes greater than 30% of the free amino acid pool in C. maritima and likely contributes to abiotic stress tolerance. We find duplicated gene families are enriched in metabolic and transport processes and identify key transport genes that may be involved in C. maritima abiotic stress tolerance. CONCLUSIONS These findings identify pathways and genes that could be used to enhance plant resilience and provide a putative understanding of the roles of duplication types and retention on the evolution of abiotic stress response.
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Affiliation(s)
- Shawn K Thomas
- Division of Biological Sciences, University of Missouri, Columbia, 65211, MO, USA
- Bioinformatics and Analytics Core, University of Missouri, Columbia, 65211, MO, USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, 65211, MO, USA
| | - Kathryn Vanden Hoek
- Department of Biochemistry, University of Missouri, Columbia, 65211, MO, USA
| | - Tasha Ogoti
- Department of Computer Science, University of Missouri, Columbia, 65211, MO, USA
| | - Ha Duong
- Interdisciplinary Plant Group, University of Missouri, Columbia, 65211, MO, USA
- Department of Biochemistry, University of Missouri, Columbia, 65211, MO, USA
| | - Ruthie Angelovici
- Division of Biological Sciences, University of Missouri, Columbia, 65211, MO, USA
- Interdisciplinary Plant Group, University of Missouri, Columbia, 65211, MO, USA
| | - J Chris Pires
- Soil and Crop Sciences, Colorado State University, Fort Collins, 80523-1170, CO, USA
| | - David Mendoza-Cozatl
- Interdisciplinary Plant Group, University of Missouri, Columbia, 65211, MO, USA
- Division of Plant Sciences and Technology, University of Missouri, Columbia, 65211, MO, USA
| | - Jacob Washburn
- Interdisciplinary Plant Group, University of Missouri, Columbia, 65211, MO, USA
- Plant Genetics Research Unit, USDA-ARS, Columbia, 65211, MO, USA
| | - Craig A Schenck
- Interdisciplinary Plant Group, University of Missouri, Columbia, 65211, MO, USA
- Department of Biochemistry, University of Missouri, Columbia, 65211, MO, USA
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5
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McKibben MTW, Finch G, Barker MS. Species-tree topology impacts the inference of ancient whole-genome duplications across the angiosperm phylogeny. AMERICAN JOURNAL OF BOTANY 2024; 111:e16378. [PMID: 39039654 DOI: 10.1002/ajb2.16378] [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: 01/03/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/24/2024]
Abstract
PREMISE The history of angiosperms is marked by repeated rounds of ancient whole-genome duplications (WGDs). Here we used state-of-the-art methods to provide an up-to-date view of the distribution of WGDs in the history of angiosperms that considers both uncertainty introduced by different WGD inference methods and different underlying species-tree hypotheses. METHODS We used the distribution synonymous divergences (Ks) of paralogs and orthologs from transcriptomic and genomic data to infer and place WGDs across two hypothesized angiosperm phylogenies. We further tested these WGD hypotheses with syntenic inferences and Bayesian models of duplicate gene gain and loss. RESULTS The predicted number of WGDs in the history of angiosperms (~170) based on the current taxon sampling is largely similar across different inference methods, but varies in the precise placement of WGDs on the phylogeny. Ks-based methods often yield alternative hypothesized WGD placements due to variation in substitution rates among lineages. Phylogenetic models of duplicate gene gain and loss are more robust to topological variation. However, errors in species-tree inference can still produce spurious WGD hypotheses, regardless of method used. CONCLUSIONS Here we showed that different WGD inference methods largely agree on an average of 3.5 WGD in the history of individual angiosperm species. However, the precise placement of WGDs on the phylogeny is subject to the WGD inference method and tree topology. As researchers continue to test hypotheses regarding the impacts ancient WGDs have on angiosperm evolution, it is important to consider the uncertainty of the phylogeny as well as WGD inference methods.
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Affiliation(s)
- Michael T W McKibben
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Geoffrey Finch
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Michael S Barker
- Department of Ecology & Evolutionary Biology, University of Arizona, Tucson, AZ, USA
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6
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Jeon D, Kim C. Polyploids of Brassicaceae: Genomic Insights and Assembly Strategies. PLANTS (BASEL, SWITZERLAND) 2024; 13:2087. [PMID: 39124204 PMCID: PMC11314605 DOI: 10.3390/plants13152087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Revised: 07/24/2024] [Accepted: 07/26/2024] [Indexed: 08/12/2024]
Abstract
The Brassicaceae family is distinguished by its inclusion of high-value crops such as cabbage, broccoli, mustard, and wasabi, all noted for their glucosinolates. In this family, many polyploidy species are distributed and shaped by numerous whole-genome duplications, independent genome doublings, and hybridization events. The evolutionary trajectory of the family is marked by enhanced diversification and lineage splitting after paleo- and meso-polyploidization, with discernible remnants of whole-genome duplications within their genomes. The recent neopolyploidization events notably increased the proportion of polyploid species within the family. Although sequencing efforts for the Brassicaceae genome have been robust, accurately distinguishing sub-genomes remains a significant challenge, frequently complicating the assembly process. Assembly strategies include comparative analyses with ancestral species and examining k-mers, long terminal repeat retrotransposons, and pollen sequencing. This review comprehensively explores the unique genomic characteristics of the Brassicaceae family, with a particular emphasis on polyploidization events and the latest strategies for sequencing and assembly. This review will significantly improve our understanding of polyploidy in the Brassicaceae family and assist in future genome assembly methods.
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Affiliation(s)
- Donghyun Jeon
- Department of Science in Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Republic of Korea;
| | - Changsoo Kim
- Department of Science in Smart Agriculture Systems, Chungnam National University, Daejeon 34134, Republic of Korea;
- Department of Crop Science, Chungnam National University, Daejeon 34134, Republic of Korea
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7
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Liu J, Zhou SZ, Liu YL, Zhao BY, Yu D, Zhong MC, Jiang XD, Cui WH, Zhao JX, Qiu J, Liu LM, Guo ZH, Li HT, Tan DY, Hu JY, Li DZ. Genomes of Meniocus linifolius and Tetracme quadricornis reveal the ancestral karyotype and genomic features of core Brassicaceae. PLANT COMMUNICATIONS 2024; 5:100878. [PMID: 38475995 PMCID: PMC11287156 DOI: 10.1016/j.xplc.2024.100878] [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: 03/20/2023] [Revised: 03/03/2024] [Accepted: 03/11/2024] [Indexed: 03/14/2024]
Abstract
Brassicaceae represents an important plant family from both a scientific and economic perspective. However, genomic features related to the early diversification of this family have not been fully characterized, especially upon the uplift of the Tibetan Plateau, which was followed by increasing aridity in the Asian interior, intensifying monsoons in Eastern Asia, and significantly fluctuating daily temperatures. Here, we reveal the genomic architecture that accompanied early Brassicaceae diversification by analyzing two high-quality chromosome-level genomes for Meniocus linifolius (Arabodae; clade D) and Tetracme quadricornis (Hesperodae; clade E), together with genomes representing all major Brassicaceae clades and the basal Aethionemeae. We reconstructed an ancestral core Brassicaceae karyotype (CBK) containing 9 pseudochromosomes with 65 conserved syntenic genomic blocks and identified 9702 conserved genes in Brassicaceae. We detected pervasive conflicting phylogenomic signals accompanied by widespread ancient hybridization events, which correlate well with the early divergence of core Brassicaceae. We identified a successive Brassicaceae-specific expansion of the class I TREHALOSE-6-PHOSPHATE SYNTHASE 1 (TPS1) gene family, which encodes enzymes with essential regulatory roles in flowering time and embryo development. The TPS1s were mainly randomly amplified, followed by expression divergence. Our results provide fresh insights into historical genomic features coupled with Brassicaceae evolution and offer a potential model for broad-scale studies of adaptive radiation under an ever-changing environment.
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Affiliation(s)
- Jie Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shi-Zhao Zhou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yun-Long Liu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Bin-Yan Zhao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongmei Yu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Mi-Cai Zhong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Xiao-Dong Jiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Wei-Hua Cui
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Jiu-Xia Zhao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Juan Qiu
- College of Life Sciences, Xinjiang Agricultural University, Ürümqi 830052, China
| | - Liang-Min Liu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen-Hua Guo
- Germplasm Bank of Wild Species & Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Hong-Tao Li
- Germplasm Bank of Wild Species & Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Dun-Yan Tan
- College of Life Sciences, Xinjiang Agricultural University, Ürümqi 830052, China
| | - Jin-Yong Hu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - De-Zhu Li
- Germplasm Bank of Wild Species & Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
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8
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Waters ER, Bezanilla M, Vierling E. ATAD3 Proteins: Unique Mitochondrial Proteins Essential for Life in Diverse Eukaryotic Lineages. PLANT & CELL PHYSIOLOGY 2024; 65:493-502. [PMID: 37859594 DOI: 10.1093/pcp/pcad122] [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: 08/21/2023] [Revised: 10/05/2023] [Accepted: 10/10/2023] [Indexed: 10/21/2023]
Abstract
ATPase family AAA domain-containing 3 (ATAD3) proteins are unique mitochondrial proteins that arose deep in the eukaryotic lineage but that are surprisingly absent in Fungi and Amoebozoa. These ∼600-amino acid proteins are anchored in the inner mitochondrial membrane and are essential in metazoans and Arabidopsis thaliana. ATAD3s comprise a C-terminal ATPases Associated with a variety of cellular Activities (AAA+) matrix domain and an ATAD3_N domain, which is located primarily in the inner membrane space but potentially extends to the cytosol to interact with the ER. Sequence and structural alignments indicate that ATAD3 proteins are most similar to classic chaperone unfoldases in the AAA+ family, suggesting that they operate in mitochondrial protein quality control. A. thaliana has four ATAD3 genes in two distinct clades that appear first in the seed plants, and both clades are essential for viability. The four genes are generally coordinately expressed, and transcripts are highest in growing apices and imbibed seeds. Plants with disrupted ATAD3 have reduced growth, aberrant mitochondrial morphology, diffuse nucleoids and reduced oxidative phosphorylation complex I. These and other pleiotropic phenotypes are also observed in ATAD3 mutants in metazoans. Here, we discuss the distribution of ATAD3 proteins as they have evolved in the plant kingdom, their unique structure, what we know about their function in plants and the challenges in determining their essential roles in mitochondria.
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Affiliation(s)
- Elizabeth R Waters
- Department of Biology, San Diego State University, 5500 Campanille Dr., San Diego, CA 92182, USA
| | - Magdalena Bezanilla
- Department of Biological Sciences, Dartmouth College, 78 College St., Hanover, NH 03755, USA
| | - Elizabeth Vierling
- Department of Biochemistry & Molecular Biology, University of Massachusetts Amherst, 240 Thatcher Road, Amherst, MA 01003, USA
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9
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Mabry ME, Abrahams RS, Al-Shehbaz IA, Baker WJ, Barak S, Barker MS, Barrett RL, Beric A, Bhattacharya S, Carey SB, Conant GC, Conran JG, Dassanayake M, Edger PP, Hall JC, Hao Y, Hendriks KP, Hibberd JM, King GJ, Kliebenstein DJ, Koch MA, Leitch IJ, Lens F, Lysak MA, McAlvay AC, McKibben MTW, Mercati F, Moore RC, Mummenhoff K, Murphy DJ, Nikolov LA, Pisias M, Roalson EH, Schranz ME, Thomas SK, Yu Q, Yocca A, Pires JC, Harkess AE. Complementing model species with model clades. THE PLANT CELL 2024; 36:1205-1226. [PMID: 37824826 PMCID: PMC11062466 DOI: 10.1093/plcell/koad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/07/2023] [Accepted: 09/22/2023] [Indexed: 10/14/2023]
Abstract
Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant tree of life continues to improve. The intersection of these 2 research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups. Here we promote the utility of the Arabidopsis thaliana model species, especially the ability to connect its genetic and functional resources, to species across the entire Brassicales order. We focus on the utility of using genomics and phylogenomics to bridge the evolution and diversification of several traits across the Brassicales to the resources in Arabidopsis, thereby extending scope from a model species by establishing a "model clade." These Brassicales-wide traits are discussed in the context of both the model species Arabidopsis and the family Brassicaceae. We promote the utility of such a "model clade" and make suggestions for building global networks to support future studies in the model order Brassicales.
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Affiliation(s)
- Makenzie E Mabry
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - R Shawn Abrahams
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN 47906, USA
| | | | | | - Simon Barak
- Ben-Gurion University of the Negev, French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Midreshet Ben-Gurion, 8499000, Israel
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Russell L Barrett
- National Herbarium of New South Wales, Australian Botanic Garden, Locked Bag 6002, Mount Annan, NSW 2567, Australia
| | - Aleksandra Beric
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, St. Louis, MO 63108, USA
| | - Samik Bhattacharya
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
| | - Sarah B Carey
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Gavin C Conant
- Department of Biological Sciences, Bioinformatics Research Center, Program in Genetics, North Carolina State University, Raleigh, NC 27695, USA
| | - John G Conran
- ACEBB and SGC, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI 48864, USA
| | - Jocelyn C Hall
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Yue Hao
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Kasper P Hendriks
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
- Functional Traits, Naturalis Biodiversity Center, PO Box 9517, Leiden 2300 RA, the Netherlands
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | | | - Marcus A Koch
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Frederic Lens
- Functional Traits, Naturalis Biodiversity Center, PO Box 9517, Leiden 2300 RA, the Netherlands
- Institute of Biology Leiden, Plant Sciences, Leiden University, 2333 BE Leiden, the Netherlands
| | - Martin A Lysak
- CEITEC, and NCBR, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Alex C McAlvay
- Institute of Economic Botany, New York Botanical Garden, The Bronx, NY 10458, USA
| | - Michael T W McKibben
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Francesco Mercati
- National Research Council (CNR), Institute of Biosciences and Bioresource (IBBR), Palermo 90129, Italy
| | | | - Klaus Mummenhoff
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
| | - Daniel J Murphy
- Royal Botanic Gardens Victoria, Melbourne, VIC 3004, Australia
| | | | - Michael Pisias
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Eric H Roalson
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, 6708 PB Wageningen, the Netherlands
| | - Shawn K Thomas
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
- Bioinformatics and Analytics Core, University of Missouri, Columbia, MO 65211, USA
| | - Qingyi Yu
- Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Hilo, HI 96720, USA
| | - Alan Yocca
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - J Chris Pires
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523-1170, USA
| | - Alex E Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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10
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Binmöller L, Volkert C, Kiefer C, Zühl L, Slawinska MW, Loreth A, Nauerth BH, Ibberson D, Martinez R, Mandakova TM, Zipper R, Schmidt A. Differential expression and evolutionary diversification of RNA helicases in Boechera sexual and apomictic reproduction. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2451-2469. [PMID: 38263359 DOI: 10.1093/jxb/erae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 01/22/2024] [Indexed: 01/25/2024]
Abstract
In higher plants, sexual reproduction is characterized by meiosis of the first cells of the germlines, and double fertilization of the egg and central cell after gametogenesis. In contrast, in apomicts of the genus Boechera, meiosis is omitted or altered and only the central cell requires fertilization, while the embryo forms parthenogenetically from the egg cell. To deepen the understanding of the transcriptional basis underlying these differences, we applied RNA-seq to compare expression in reproductive tissues of different Boechera accessions. This confirmed previous evidence of an enrichment of RNA helicases in plant germlines. Furthermore, few RNA helicases were differentially expressed in female reproductive ovule tissues harboring mature gametophytes from apomictic and sexual accessions. For some of these genes, we further found evidence for a complex recent evolutionary history. This included a homolog of Arabidopsis thaliana FASCIATED STEM4 (FAS4). In contrast to AtFAS4, which is a single-copy gene, FAS4 is represented by three homologs in Boechera, suggesting a potential for subfunctionalization to modulate reproductive development. To gain first insights into functional roles of FAS4, we studied Arabidopsis lines carrying mutant alleles. This identified the crucial importance of AtFAS4 for reproduction, as we observed developmental defects and arrest during male and female gametogenesis.
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Affiliation(s)
- Laura Binmöller
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
| | - Christopher Volkert
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
| | - Christiane Kiefer
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
| | - Luise Zühl
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
| | - Magdalena W Slawinska
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
| | - Anna Loreth
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
| | - Berit H Nauerth
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
| | - David Ibberson
- Deep Sequencing Core Facility, CellNetworks Excellence Cluster, Heidelberg University, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany
| | - Rafael Martinez
- Centre for Organismal Studies Heidelberg, Department of Developmental Biology, Heidelberg University, Im Neuenheimer Feld 230, D-69120, Heidelberg, Germany
| | - Terezie M Mandakova
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Reinhard Zipper
- Institute of Biology, Plant Evolutionary Biology, University of Hohenheim, Garbenstrasse 30, D-70599 Stuttgart, Germany
| | - Anja Schmidt
- Centre for Organismal Studies Heidelberg, Department of Biodiversity and Plant Systematics, Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
- Institute of Biology, Plant Evolutionary Biology, University of Hohenheim, Garbenstrasse 30, D-70599 Stuttgart, Germany
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11
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Triesch S, Denton AK, Bouvier JW, Buchmann JP, Reichel-Deland V, Guerreiro RNFM, Busch N, Schlüter U, Stich B, Kelly S, Weber APM. Transposable elements contribute to the establishment of the glycine shuttle in Brassicaceae species. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:270-281. [PMID: 38168881 DOI: 10.1111/plb.13601] [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: 09/08/2023] [Accepted: 11/15/2023] [Indexed: 01/05/2024]
Abstract
C3 -C4 intermediate photosynthesis has evolved at least five times convergently in the Brassicaceae, despite this family lacking bona fide C4 species. The establishment of this carbon concentrating mechanism is known to require a complex suite of ultrastructural modifications, as well as changes in spatial expression patterns, which are both thought to be underpinned by a reconfiguration of existing gene-regulatory networks. However, to date, the mechanisms which underpin the reconfiguration of these gene networks are largely unknown. In this study, we used a pan-genomic association approach to identify genomic features that could confer differential gene expression towards the C3 -C4 intermediate state by analysing eight C3 species and seven C3 -C4 species from five independent origins in the Brassicaceae. We found a strong correlation between transposable element (TE) insertions in cis-regulatory regions and C3 -C4 intermediacy. Specifically, our study revealed 113 gene models in which the presence of a TE within a gene correlates with C3 -C4 intermediate photosynthesis. In this set, genes involved in the photorespiratory glycine shuttle are enriched, including the glycine decarboxylase P-protein whose expression domain undergoes a spatial shift during the transition to C3 -C4 photosynthesis. When further interrogating this gene, we discovered independent TE insertions in its upstream region which we conclude to be responsible for causing the spatial shift in GLDP1 gene expression. Our findings hint at a pivotal role of TEs in the evolution of C3 -C4 intermediacy, especially in mediating differential spatial gene expression.
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Affiliation(s)
- S Triesch
- Institute for Plant Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - A K Denton
- Institute for Plant Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - J W Bouvier
- Department of Biology, University of Oxford, Oxford, UK
| | - J P Buchmann
- Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
- Institute for Biological Data Sciences, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - V Reichel-Deland
- Institute for Plant Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - R N F M Guerreiro
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - N Busch
- Institute for Plant Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - U Schlüter
- Institute for Plant Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - B Stich
- Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - S Kelly
- Department of Biology, University of Oxford, Oxford, UK
| | - A P M Weber
- Institute for Plant Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
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12
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Xiao TW, Song F, Vu DQ, Feng Y, Ge XJ. The evolution of ephemeral flora in Xinjiang, China: insights from plastid phylogenomic analyses of Brassicaceae. BMC PLANT BIOLOGY 2024; 24:111. [PMID: 38360561 PMCID: PMC10868009 DOI: 10.1186/s12870-024-04796-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 02/05/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND The ephemeral flora of northern Xinjiang, China, plays an important role in the desert ecosystems. However, the evolutionary history of this flora remains unclear. To gain new insights into its origin and evolutionary dynamics, we comprehensively sampled ephemeral plants of Brassicaceae, one of the essential plant groups of the ephemeral flora. RESULTS We reconstructed a phylogenetic tree using plastid genomes and estimated their divergence times. Our results indicate that ephemeral species began to colonize the arid areas in north Xinjiang during the Early Miocene and there was a greater dispersal of ephemeral species from the surrounding areas into the ephemeral community of north Xinjiang during the Middle and Late Miocene, in contrast to the Early Miocene or Pliocene periods. CONCLUSIONS Our findings, together with previous studies, suggest that the ephemeral flora originated in the Early Miocene, and species assembly became rapid from the Middle Miocene onwards, possibly attributable to global climate changes and regional geological events.
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Affiliation(s)
- Tian-Wen Xiao
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Feng Song
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Duc Quy Vu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Ying Feng
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.
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13
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Xiang Y, Zhang T, Zhao Y, Dong H, Chen H, Hu Y, Huang CH, Xiang J, Ma H. Angiosperm-wide analysis of fruit and ovary evolution aided by a new nuclear phylogeny supports association of the same ovary type with both dry and fleshy fruits. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:228-251. [PMID: 38351714 DOI: 10.1111/jipb.13618] [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: 12/15/2023] [Accepted: 01/11/2024] [Indexed: 02/22/2024]
Abstract
Fruit functions in seed protection and dispersal and belongs to many dry and fleshy types, yet their evolutionary pattern remains unclear in part due to uncertainties in the phylogenetic relationships among several orders and families. Thus we used nuclear genes of 502 angiosperm species representing 231 families to reconstruct a well supported phylogeny, with resolved relationships for orders and families with previously uncertain placements. Using this phylogeny as a framework, molecular dating supports a Triassic origin of the crown angiosperms, followed by the emergence of most orders in the Jurassic and Cretaceous and their rise to ecological dominance during the Cretaceous Terrestrial Revolution. The robust phylogeny allowed an examination of the evolutionary pattern of fruit and ovary types, revealing a trend of parallel carpel fusions during early diversifications in eudicots, monocots, and magnoliids. Moreover, taxa in the same order or family with the same ovary type can develop either dry or fleshy fruits with strong correlations between specific types of dry and fleshy fruits; such associations of ovary, dry and fleshy fruits define several ovary-fruit "modules" each found in multiple families. One of the frequent modules has an ovary containing multiple ovules, capsules and berries, and another with an ovary having one or two ovules, achenes (or other single-seeded dry fruits) and drupes. This new perspective of relationships among fruit types highlights the closeness of specific dry and fleshy fruit types, such as capsule and berry, that develop from the same ovary type and belong to the same module relative to dry and fleshy fruits of other modules (such as achenes and drupes). Further analyses of gene families containing known genes for ovary and fruit development identified phylogenetic nodes with multiple gene duplications, supporting a possible role of whole-genome duplications, in combination with climate changes and animal behaviors, in angiosperm fruit and ovary diversification.
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Affiliation(s)
- Yezi Xiang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Department of Biology, Howard Hughes Medical Institute, Duke University, Durham, 27708, NC, USA
| | - Taikui Zhang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, 16802, PA, USA
| | - Yiyong Zhao
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Hongjin Dong
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, China
| | - Hongyi Chen
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, China
| | - Yi Hu
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, 16802, PA, USA
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jun Xiang
- Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization, College of Biology and Agricultural Resources, Huanggang Normal University, Huanggang, 438000, China
| | - Hong Ma
- Department of Biology, the Eberly College of Science, and the Huck Institutes of the Life Sciences, the Pennsylvania State University, University Park, 16802, PA, USA
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14
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Cao F, Guo C, Wang X, Wang X, Yu L, Zhang H, Zhang J. Genome-wide identification, evolution, and expression analysis of the NAC gene family in chestnut ( Castanea mollissima). Front Genet 2024; 15:1337578. [PMID: 38333622 PMCID: PMC10850246 DOI: 10.3389/fgene.2024.1337578] [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: 11/13/2023] [Accepted: 01/18/2024] [Indexed: 02/10/2024] Open
Abstract
The NAC gene family is one of the most important transcription factor families specific to plants, responsible for regulating many biological processes, including development, stress response, and signal transduction. However, it has not yet been characterized in chestnut, an important nut tree species. Here, we identified 115 CmNAC genes in the chestnut genome, which were divided into 16 subgroups based on the phylogenetic analysis. Numerous cis-acting elements related to auxin, gibberellin, and abscisic acid were identified in the promoter region of CmNACs, suggesting that they play an important role in the growth and development of chestnut. The results of the collinear analysis indicated that dispersed duplication and whole-genome-duplication were the main drivers of CmNAC gene expansion. RNA-seq data of developmental stages of chestnut nut, bud, and ovule revealed the expression patterns of CmNAC genes. Additionally, qRT-PCR experiments were used to verify the expression levels of some CmNAC genes. The comprehensive analysis of the above results revealed that some CmNAC members may be related to chestnut bud and nut development, as well as ovule fertility. The systematic analysis of this study will help to increase understanding of the potential functions of the CmNAC genes in chestnut growth and development.
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Affiliation(s)
- Fei Cao
- College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Chunlei Guo
- College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Xiangyu Wang
- The Office of Scientific Research, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Xuan Wang
- College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Liyang Yu
- College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Haie Zhang
- College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
| | - Jingzheng Zhang
- College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
- Engineering Research Center of Chestnut Industry Technology, Ministry of Education, Hebei Normal University of Science and Technology, Qinhuangdao, Hebei, China
- Hebei Collaborative Innovation Center of Chestnut Industry, Qinhuangdao, Hebei, China
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15
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Jo S, Kim J, Yun NR, Lee C, Choi S, Kim SY. Characterization of the complete plastome sequence of Korean endemic, Cardamine glechomifolia H.Lév. (Brassicaceae, Brassicales). Mitochondrial DNA B Resour 2024; 9:133-137. [PMID: 38274850 PMCID: PMC10810622 DOI: 10.1080/23802359.2024.2305394] [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: 08/02/2023] [Accepted: 01/09/2024] [Indexed: 01/27/2024] Open
Abstract
In this study, we report the complete plastome sequence of Cardamine glechomifolia H.Lév. 1913 (NCBI acc. no. OP894664). This plastome shows typical quadripartite structure. The plastome size is 154,307 bp, which consists of 84,015 bp large single-copy (LSC), 17,690 bp small single-copy (SSC), and 26,301 bp inverted repeat (IR) regions. The plastome contains 112 genes, including 78 protein-coding, 30 tRNA, and four rRNA genes. The infA gene is pseudogenized. Sixteen genes contain one intron and two genes (clpP and ycf3) have two introns. The phylogenomic analysis conducted in our study reveals that the genus Cardamine, which encompasses C. glechomifolia, exhibits three distinct clades. In order to elucidate the interrelationship among the three clades, it is imperative to conduct additional investigations by augmenting the number of Cardamine samples.
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Affiliation(s)
- Sangjin Jo
- International Biological Material Research Center (IBMRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Jinki Kim
- Operation Management Team, National Botanic Garden of Korea Native Plant, Gangwon-do, Republic of Korea
| | - Na-Rae Yun
- Department of Botany, Honam National Institute of Biological Resources, Mokpo, Republic of Korea
| | - Changyoung Lee
- International Biological Material Research Center (IBMRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Sangho Choi
- International Biological Material Research Center (IBMRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Soo-Yong Kim
- International Biological Material Research Center (IBMRC), Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
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16
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Liu J, Hu JY, Li DZ. Remarkable mitochondrial genome heterogeneity in Meniocus linifolius (Brassicaceae). PLANT CELL REPORTS 2024; 43:36. [PMID: 38200362 DOI: 10.1007/s00299-023-03102-w] [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: 08/22/2023] [Accepted: 11/06/2023] [Indexed: 01/12/2024]
Abstract
KEY MESSAGE Detailed analyses of 16 genomes identified a remarkable acceleration of mutation rate, hence mitochondrial sequence and structural heterogeneity, in Meniocus linifolius (Brassicaceae). The powerhouse, mitochondria, in plants feature high levels of structural variation, while the encoded genes are normally conserved. However, the substitution rates and spectra of mitochondria DNA within the Brassicaceae, a family with substantial scientific and economic importance, have not been adequately deciphered. Here, by analyzing three newly assembled and 13 known mitochondrial genomes (mitogenomes), we report the highly variable genome structure and mutation rates in Brassicaceae. The genome sizes and GC contents are 196,604 bp and 46.83%, 288,122 bp and 44.79%, and 287,054 bp and 44.93%, for Meniocus linifolius (Mli), Crucihimalaya lasiocarpa (Cla), and Lepidium sativum (Lsa), respectively. In total, 29, 33, and 34 protein-coding genes (PCGs) and 14, 18, and 18 tRNAs are annotated for Mli, Cla, and Lsa, respectively, while all mitogenomes contain one complete circular molecule with three rRNAs and abundant RNA editing sites. The Mli mitogenome features four conformations likely mediated by the two pairs of long repeats, while at the same time seems to have an unusual evolutionary history due to higher GC content, loss of more genes and sequences, but having more repeats and plastid DNA insertions. Corroborating with these, an ambiguous phylogenetic position with long branch length and elevated synonymous substitution rate in nearly all PCGs are observed for Mli. Taken together, our results reveal a high level of mitogenome heterogeneity at the family level and provide valuable resources for further understanding the evolutionary pattern of organelle genomes in Brassicaceae.
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Affiliation(s)
- Jie Liu
- CAS Key Laboratory for Plant Diversity, Biogeography of East Asia, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jin-Yong Hu
- CAS Key Laboratory for Plant Diversity, Biogeography of East Asia, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
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17
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Jia C, Lai Q, Zhu Y, Feng J, Dan X, Zhang Y, Long Z, Wu J, Wang Z, Qumu X, Wang R, Wang J. Intergrative metabolomic and transcriptomic analyses reveal the potential regulatory mechanism of unique dihydroxy fatty acid biosynthesis in the seeds of an industrial oilseed crop Orychophragmus violaceus. BMC Genomics 2024; 25:29. [PMID: 38172664 PMCID: PMC10765717 DOI: 10.1186/s12864-023-09906-0] [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: 11/12/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Orychophragmus violaceus is a potentially important industrial oilseed crop due to the two 24-carbon dihydroxy fatty acids (diOH-FA) that was newly identified from its seed oil via a 'discontinuous elongation' process. Although many research efforts have focused on the diOH-FA biosynthesis mechanism and identified the potential co-expressed diacylglycerol acyltranferase (DGAT) gene associated with triacylglycerol (TAG)-polyestolides biosynthesis, the dynamics of metabolic changes during seed development of O. violaceus as well as its associated regulatory network changes are poorly understood. RESULTS In this study, by combining metabolome and transcriptome analysis, we identified that 1,003 metabolites and 22,479 genes were active across four stages of seed development, which were further divided into three main clusters based on the patterns of metabolite accumulation and/or gene expression. Among which, cluster2 was mostly related to diOH-FA biosynthesis pathway. We thus further constructed transcription factor (TF)-structural genes regulatory map for the genes associated with the flavonoids, fatty acids and diOH-FA biosynthesis pathway in this cluster. In particular, several TF families such as bHLH, B3, HD-ZIP, MYB were found to potentially regulate the metabolism associated with the diOH-FA pathway. Among which, multiple candidate TFs with promising potential for increasing the diOH-FA content were identified, and we further traced the evolutionary history of these key genes among species of Brassicaceae. CONCLUSION Taken together, our study provides new insight into the gene resources and potential relevant regulatory mechanisms of diOH-FA biosynthesis uniquely in seeds of O. violaceus, which will help to promote the downstream breeding efforts of this potential oilseed crop and advance the bio-lubricant industry.
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Affiliation(s)
- Changfu Jia
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Qiang Lai
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yiman Zhu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jiajun Feng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xuming Dan
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yulin Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhiqin Long
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jiali Wu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zeng Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiner Qumu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Rui Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
| | - Jing Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
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18
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Zhang L, Morales-Briones DF, Li Y, Zhang G, Zhang T, Huang CH, Guo P, Zhang K, Wang Y, Wang H, Shang FD, Ma H. Phylogenomics insights into gene evolution, rapid species diversification, and morphological innovation of the apple tribe (Maleae, Rosaceae). THE NEW PHYTOLOGIST 2023; 240:2102-2120. [PMID: 37537712 DOI: 10.1111/nph.19175] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/07/2023] [Indexed: 08/05/2023]
Abstract
Maleae is one of the most widespread tribes of Rosaceae and includes several important fruit crops and ornamental plants. We used nuclear genes from 62 transcriptomes/genomes, including 26 newly generated transcriptomes, to reconstruct a well-supported phylogeny and study the evolution of fruit and leaf morphology and the possible effect of whole genome duplication (WGD). Our phylogeny recovered 11 well-supported clades and supported the monophyly of most genera (except Malus, Sorbus, and Pourthiaea) with at least two sampled species. A WGD was located to the most recent common ancestor (MRCA) of Maleae and dated to c. 54 million years ago (Ma) near the Early Eocene Climatic Optimum, supporting Gillenieae (x = 9) being a parental lineage of Maleae (x = 17) and including duplicate regulatory genes related to the origin of the fleshy pome fruit. Whole genome duplication-derived paralogs that are retained in specific lineages but lost in others are predicted to function in development, metabolism, and other processes. An upshift of diversification and innovations of fruit and leaf morphologies occurred at the MRCA of the Malinae subtribe, coinciding with the Eocene-Oligocene transition (c. 34 Ma), following a lag from the time of the WGD event. Our results provide new insights into the Maleae phylogeny, its rapid diversification, and morphological and molecular evolution.
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Affiliation(s)
- Lin Zhang
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou, 450002, China
- Department of Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, 450002, China
| | - Diego F Morales-Briones
- Princess Therese von Bayern chair of Systematics, Biodiversity and Evolution of Plants, Ludwig-Maximilians-Universität München, Menzinger Str. 67, Munich, 80638, Germany
| | - Yujie Li
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, 450002, China
| | - Guojin Zhang
- Department of Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Taikui Zhang
- Department of Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Chien-Hsun Huang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Peng Guo
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, 450002, China
- College of Life Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Kaiming Zhang
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yihan Wang
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, 450002, China
- College of Life Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hongwei Wang
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, 450002, China
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, China
| | - Fu-De Shang
- College of Landscape Architecture and Art, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, 450002, China
- College of Life Science, Henan Agricultural University, Zhengzhou, 450002, China
| | - Hong Ma
- Department of Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
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19
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Hendriks KP, Kiefer C, Al-Shehbaz IA, Bailey CD, Hooft van Huysduynen A, Nikolov LA, Nauheimer L, Zuntini AR, German DA, Franzke A, Koch MA, Lysak MA, Toro-Núñez Ó, Özüdoğru B, Invernón VR, Walden N, Maurin O, Hay NM, Shushkov P, Mandáková T, Schranz ME, Thulin M, Windham MD, Rešetnik I, Španiel S, Ly E, Pires JC, Harkess A, Neuffer B, Vogt R, Bräuchler C, Rainer H, Janssens SB, Schmull M, Forrest A, Guggisberg A, Zmarzty S, Lepschi BJ, Scarlett N, Stauffer FW, Schönberger I, Heenan P, Baker WJ, Forest F, Mummenhoff K, Lens F. Global Brassicaceae phylogeny based on filtering of 1,000-gene dataset. Curr Biol 2023; 33:4052-4068.e6. [PMID: 37659415 DOI: 10.1016/j.cub.2023.08.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 06/22/2023] [Accepted: 08/08/2023] [Indexed: 09/04/2023]
Abstract
The mustard family (Brassicaceae) is a scientifically and economically important family, containing the model plant Arabidopsis thaliana and numerous crop species that feed billions worldwide. Despite its relevance, most phylogenetic trees of the family are incompletely sampled and often contain poorly supported branches. Here, we present the most complete Brassicaceae genus-level family phylogenies to date (Brassicaceae Tree of Life or BrassiToL) based on nuclear (1,081 genes, 319 of the 349 genera; 57 of the 58 tribes) and plastome (60 genes, 265 genera; all tribes) data. We found cytonuclear discordance between the two, which is likely a result of rampant hybridization among closely and more distantly related lineages. To evaluate the impact of such hybridization on the nuclear phylogeny reconstruction, we performed five different gene sampling routines, which increasingly removed putatively paralog genes. Our cleaned subset of 297 genes revealed high support for the tribes, whereas support for the main lineages (supertribes) was moderate. Calibration based on the 20 most clock-like nuclear genes suggests a late Eocene to late Oligocene origin of the family. Finally, our results strongly support a recently published new family classification, dividing the family into two subfamilies (one with five supertribes), together representing 58 tribes. This includes five recently described or re-established tribes, including Arabidopsideae, a monogeneric tribe accommodating Arabidopsis without any close relatives. With a worldwide community of thousands of researchers working on Brassicaceae and its diverse members, our new genus-level family phylogeny will be an indispensable tool for studies on biodiversity and plant biology.
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Affiliation(s)
- Kasper P Hendriks
- Department of Biology, Botany, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany; Functional Traits Group, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, the Netherlands.
| | - Christiane Kiefer
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | | | - C Donovan Bailey
- Department of Biology, New Mexico State University, PO Box 30001, MSC 3AF, Las Cruces, NM 88003, USA
| | - Alex Hooft van Huysduynen
- Functional Traits Group, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, the Netherlands; Department of Biology, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Lachezar A Nikolov
- Department of Molecular, Cell and Developmental Biology, University of California, 610 Charles E. Young Dr. S., Los Angeles, CA 90095, USA
| | - Lars Nauheimer
- Australian Tropical Herbarium, James Cook University, PO Box 6811, Cairns, QLD 4870, Australia
| | | | - Dmitry A German
- South-Siberian Botanical Garden, Altai State University, Barnaul, Lesosechnaya Ulitsa, 25, Barnaul, Altai Krai, Russia
| | - Andreas Franzke
- Heidelberg Botanic Garden, Heidelberg University, Im Neuenheimer Feld 361, 69120 Heidelberg, Germany
| | - Marcus A Koch
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | - Martin A Lysak
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Óscar Toro-Núñez
- Departamento de Botánica, Universidad de Concepción, Barrio Universitario, Concepción, Chile
| | - Barış Özüdoğru
- Department of Biology, Hacettepe University, Beytepe, Ankara 06800, Türkiye
| | - Vanessa R Invernón
- Sorbonne Université, Muséum National d'Histoire Naturelle, Institut de Systématique, Évolution, Biodiversité (ISYEB), CP 39, 57 rue Cuvier, 75231 Paris Cedex 05, France
| | - Nora Walden
- Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | - Olivier Maurin
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Nikolai M Hay
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Philip Shushkov
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave., Bloomington, IN 47405, USA
| | - Terezie Mandáková
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands
| | - Mats Thulin
- Department of Organismal Biology, Uppsala University, Norbyvägen 18, 752 36 Uppsala, Sweden
| | | | - Ivana Rešetnik
- Department of Biology, University of Zagreb, Marulićev trg 20/II, 10000 Zagreb, Croatia
| | - Stanislav Španiel
- Institute of Botany, Slovak Academy of Sciences, Plant Science and Biodiversity Centre, Dúbravská cesta 9, 845 23 Bratislava, Slovakia
| | - Elfy Ly
- Functional Traits Group, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, the Netherlands; Wetsus, European Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA Leeuwarden, the Netherlands; Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - J Chris Pires
- Soil and Crop Sciences, Colorado State University, 307 University Ave., Fort Collins, CO 80523-1170, USA
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA
| | - Barbara Neuffer
- Department of Biology, Botany, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
| | - Robert Vogt
- Botanischer Garten und Botanisches Museum, Freie Universität Berlin, Königin-Luise-Straße 6-8, 14195 Berlin, Germany
| | - Christian Bräuchler
- Department of Botany, Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
| | - Heimo Rainer
- Department of Botany, Natural History Museum Vienna, Burgring 7, 1010 Vienna, Austria
| | - Steven B Janssens
- Department of Biology, KU Leuven, Kasteelpark Arenberg 31 - box 2435, 3001 Leuven, Belgium; Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium
| | - Michaela Schmull
- Harvard University Herbaria, 22 Divinity Ave., Cambridge, MA 02138, USA
| | - Alan Forrest
- Centre for Middle Eastern Plants, Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh EH3 5LR, UK
| | - Alessia Guggisberg
- ETH Zürich, Institut für Integrative Biologie, Universitätstrasse 16, 8092 Zürich, Switzerland
| | - Sue Zmarzty
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Brendan J Lepschi
- Australian National Herbarium, Centre for Australian National Biodiversity Research, Clunies Ross St, Acton, ACT 2601, Australia
| | - Neville Scarlett
- La Trobe University, Plenty Road and Kingsbury Dr., Bundoora, VIC 3086, Australia
| | - Fred W Stauffer
- Conservatory and Botanic Gardens of Geneva, CP 60, Chambésy, 1292 Geneva, Switzerland
| | - Ines Schönberger
- Manaaki Whenua Landcare Research, Allan Herbarium, PO Box 69040, Lincoln, New Zealand
| | - Peter Heenan
- Manaaki Whenua Landcare Research, Allan Herbarium, PO Box 69040, Lincoln, New Zealand
| | | | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Klaus Mummenhoff
- Department of Biology, Botany, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany.
| | - Frederic Lens
- Functional Traits Group, Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, the Netherlands; Institute of Biology Leiden, Plant Sciences, Leiden University, Sylviusweg 72, 2333 BE Leiden, the Netherlands.
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20
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Clark JW, Hetherington AJ, Morris JL, Pressel S, Duckett JG, Puttick MN, Schneider H, Kenrick P, Wellman CH, Donoghue PCJ. Evolution of phenotypic disparity in the plant kingdom. NATURE PLANTS 2023; 9:1618-1626. [PMID: 37666963 PMCID: PMC10581900 DOI: 10.1038/s41477-023-01513-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 08/07/2023] [Indexed: 09/06/2023]
Abstract
The plant kingdom exhibits diverse bodyplans, from single-celled algae to complex multicellular land plants, but it is unclear how this phenotypic disparity was achieved. Here we show that the living divisions comprise discrete clusters within morphospace, separated largely by reproductive innovations, the extinction of evolutionary intermediates and lineage-specific evolution. Phenotypic complexity correlates not with disparity but with ploidy history, reflecting the role of genome duplication in plant macroevolution. Overall, the plant kingdom exhibits a pattern of episodically increasing disparity throughout its evolutionary history that mirrors the evolutionary floras and reflects ecological expansion facilitated by reproductive innovations. This pattern also parallels that seen in the animal and fungal kingdoms, suggesting a general pattern for the evolution of multicellular bodyplans.
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Affiliation(s)
- James W Clark
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
- School of Biological Sciences, University of Bristol, Bristol, UK.
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK.
| | - Alexander J Hetherington
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
| | - Jennifer L Morris
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | | | | | - Mark N Puttick
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
- Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK
| | - Harald Schneider
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
- The Natural History Museum, London, UK
- Center of Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, China
| | | | | | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
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21
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Huang Y, Guo X, Zhang K, Mandáková T, Cheng F, Lysak MA. The meso-octoploid Heliophila variabilis genome sheds a new light on the impact of polyploidization and diploidization on the diversity of the Cape flora. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:446-466. [PMID: 37428465 DOI: 10.1111/tpj.16383] [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: 02/17/2023] [Revised: 06/05/2023] [Accepted: 07/03/2023] [Indexed: 07/11/2023]
Abstract
Although the South African Cape flora is one of the most remarkable biodiversity hotspots, its high diversity has not been associated with polyploidy. Here, we report the chromosome-scale genome assembly of an ephemeral cruciferous species Heliophila variabilis (~334 Mb, n = 11) adapted to South African semiarid biomes. Two pairs of differently fractionated subgenomes suggest an allo-octoploid origin of the genome at least 12 million years ago. The ancestral octoploid Heliophila genome (2n = 8x = ~60) has probably originated through hybridization between two allotetraploids (2n = 4x = ~30) formed by distant, intertribal, hybridization. Rediploidization of the ancestral genome was marked by extensive reorganization of parental subgenomes, genome downsizing, and speciation events in the genus Heliophila. We found evidence for loss-of-function changes in genes associated with leaf development and early flowering, and over-retention and sub/neofunctionalization of genes involved in pathogen response and chemical defense. The genomic resources of H. variabilis will help elucidate the role of polyploidization and genome diploidization in plant adaptation to hot arid environments and origin of the Cape flora. The sequenced H. variabilis represents the first chromosome-scale genome assembly of a meso-octoploid representative of the mustard family.
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Affiliation(s)
- Yile Huang
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
- National Centre for Biomolecular Research (NCBR), Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Xinyi Guo
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Kang Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Terezie Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
- Department of Experimental Biology, Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
| | - Feng Cheng
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Martin A Lysak
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
- National Centre for Biomolecular Research (NCBR), Masaryk University, Kamenice 5, Brno, 625 00, Czech Republic
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22
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Sharma PP. The Impact of Whole Genome Duplication on the Evolution of the Arachnids. Integr Comp Biol 2023; 63:825-842. [PMID: 37263789 DOI: 10.1093/icb/icad050] [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: 03/01/2023] [Revised: 05/23/2023] [Accepted: 05/26/2023] [Indexed: 06/03/2023] Open
Abstract
The proliferation of genomic resources for Chelicerata in the past 10 years has revealed that the evolution of chelicerate genomes is more dynamic than previously thought, with multiple waves of ancient whole genome duplications affecting separate lineages. Such duplication events are fascinating from the perspective of evolutionary history because the burst of new gene copies associated with genome duplications facilitates the acquisition of new gene functions (neofunctionalization), which may in turn lead to morphological novelties and spur net diversification. While neofunctionalization has been invoked in several contexts with respect to the success and diversity of spiders, the overall impact of whole genome duplications on chelicerate evolution and development remains imperfectly understood. The purpose of this review is to examine critically the role of whole genome duplication on the diversification of the extant arachnid orders, as well as assess functional datasets for evidence of subfunctionalization or neofunctionalization in chelicerates. This examination focuses on functional data from two focal model taxa: the spider Parasteatoda tepidariorum, which exhibits evidence for an ancient duplication, and the harvestman Phalangium opilio, which exhibits an unduplicated genome. I show that there is no evidence that taxa with genome duplications are more successful than taxa with unduplicated genomes. I contend that evidence for sub- or neofunctionalization of duplicated developmental patterning genes in spiders is indirect or fragmentary at present, despite the appeal of this postulate for explaining the success of groups like spiders. Available expression data suggest that the condition of duplicated Hox modules may have played a role in promoting body plan disparity in the posterior tagma of some orders, such as spiders and scorpions, but functional data substantiating this postulate are critically missing. Spatiotemporal dynamics of duplicated transcription factors in spiders may represent cases of developmental system drift, rather than neofunctionalization. Developmental system drift may represent an important, but overlooked, null hypothesis for studies of paralogs in chelicerate developmental biology. To distinguish between subfunctionalization, neofunctionalization, and developmental system drift, concomitant establishment of comparative functional datasets from taxa exhibiting the genome duplication, as well as those that lack the paralogy, is sorely needed.
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Affiliation(s)
- Prashant P Sharma
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
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23
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Gramzow L, Sharma R, Theißen G. Evolutionary Dynamics of FLC-like MADS-Box Genes in Brassicaceae. PLANTS (BASEL, SWITZERLAND) 2023; 12:3281. [PMID: 37765445 PMCID: PMC10536770 DOI: 10.3390/plants12183281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/06/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023]
Abstract
MADS-box genes encode transcription factors that play important roles in the development and evolution of plants. There are more than a dozen clades of MADS-box genes in angiosperms, of which those with functions in the specification of floral organ identity are especially well-known. From what has been elucidated in the model plant Arabidopsis thaliana, the clade of FLC-like MADS-box genes, comprising FLC-like genes sensu strictu and MAF-like genes, are somewhat special among the MADS-box genes of plants since FLC-like genes, especially MAF-like genes, show unusual evolutionary dynamics, in that they generate clusters of tandemly duplicated genes. Here, we make use of the latest genomic data of Brassicaceae to study this remarkable feature of the FLC-like genes in a phylogenetic context. We have identified all FLC-like genes in the genomes of 29 species of Brassicaceae and reconstructed the phylogeny of these genes employing a Maximum Likelihood method. In addition, we conducted selection analyses using PAML. Our results reveal that there are three major clades of FLC-like genes in Brassicaceae that all evolve under purifying selection but with remarkably different strengths. We confirm that the tandem arrangement of MAF-like genes in the genomes of Brassicaceae resulted in a high rate of duplications and losses. Interestingly, MAF-like genes also seem to be prone to transposition. Considering the role of FLC-like genes sensu lato (s.l.) in the timing of floral transition, we hypothesize that this rapid evolution of the MAF-like genes was a main contributor to the successful adaptation of Brassicaceae to different environments.
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Affiliation(s)
- Lydia Gramzow
- Matthias Schleiden Institute/Genetics, Friedrich Schiller University Jena, 07743 Jena, Germany
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24
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Moazzeni H, Mahmoodi M, Jafari M, Schneeweiss GM, Noroozi J. Underestimated diversity in high elevations of a global biodiversity hotspot: two new endemic species of Aethionema (Brassicaceae) from the alpine zone of Iran. FRONTIERS IN PLANT SCIENCE 2023; 14:1182073. [PMID: 37304726 PMCID: PMC10250747 DOI: 10.3389/fpls.2023.1182073] [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: 03/08/2023] [Accepted: 04/13/2023] [Indexed: 06/13/2023]
Abstract
Although the mountains in South-West Asia are a global biodiversity hotspot, our understanding of their biodiversity, especially in the commonly remote alpine and subnival zones, is still limited. This is well exemplified here by Aethionema umbellatum (Brassicaceae), a species considered to have a wide yet disjoint distribution in the Zagros and Yazd-Kerman mountains of western and central Iran. Morphological and molecular phylogenetic data (based on plastid trnL-trnF and nuclear ITS sequences) show that A. umbellatum is restricted to a single mountain range in southwestern Iran (Dena Mts., southern Zagros), whereas populations from central Iran (Yazd-Kerman and central Zagros) and from western Iran (central Zagros) belong to species new to science, A. alpinum and A. zagricum, respectively. Both new species are phylogenetically and morphologically close to A. umbellatum, with which they share unilocular fruits and one-seeded locules. However, they are easily distinguishable by leaf shape, petal size, and fruit characters. This study confirms that the alpine flora of the Irano-Anatolian region is still poorly known. As the proportion of rare and local endemic species in alpine habitats is high, these habitats are of prime interest for conservation efforts.
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Affiliation(s)
- Hamid Moazzeni
- Herbarium, Department of Botany, Research Center for Plant Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Mohammad Mahmoodi
- Herbarium, Research Institute of Forests and Rangelands, Tehran, Iran
| | - Mohammad Jafari
- Herbarium, Department of Botany, Research Center for Plant Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Gerald M. Schneeweiss
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Jalil Noroozi
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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25
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Kusová A, Steinbachová L, Přerovská T, Drábková LZ, Paleček J, Khan A, Rigóová G, Gadiou Z, Jourdain C, Stricker T, Schubert D, Honys D, Schrumpfová PP. Completing the TRB family: newly characterized members show ancient evolutionary origins and distinct localization, yet similar interactions. PLANT MOLECULAR BIOLOGY 2023; 112:61-83. [PMID: 37118559 PMCID: PMC10167121 DOI: 10.1007/s11103-023-01348-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/02/2023] [Indexed: 05/09/2023]
Abstract
Telomere repeat binding proteins (TRBs) belong to a family of proteins possessing a Myb-like domain which binds to telomeric repeats. Three members of this family (TRB1, TRB2, TRB3) from Arabidopsis thaliana have already been described as associated with terminal telomeric repeats (telomeres) or short interstitial telomeric repeats in gene promoters (telo-boxes). They are also known to interact with several protein complexes: telomerase, Polycomb repressive complex 2 (PRC2) E(z) subunits and the PEAT complex (PWOs-EPCRs-ARIDs-TRBs). Here we characterize two novel members of the TRB family (TRB4 and TRB5). Our wide phylogenetic analyses have shown that TRB proteins evolved in the plant kingdom after the transition to a terrestrial habitat in Streptophyta, and consequently TRBs diversified in seed plants. TRB4-5 share common TRB motifs while differing in several others and seem to have an earlier phylogenetic origin than TRB1-3. Their common Myb-like domains bind long arrays of telomeric repeats in vitro, and we have determined the minimal recognition motif of all TRBs as one telo-box. Our data indicate that despite the distinct localization patterns of TRB1-3 and TRB4-5 in situ, all members of TRB family mutually interact and also bind to telomerase/PRC2/PEAT complexes. Additionally, we have detected novel interactions between TRB4-5 and EMF2 and VRN2, which are Su(z)12 subunits of PRC2.
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Affiliation(s)
- Alžbeta Kusová
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Lenka Steinbachová
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tereza Přerovská
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Lenka Záveská Drábková
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
| | - Jan Paleček
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Ahamed Khan
- Institute of Plant Molecular Biology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Gabriela Rigóová
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic
| | - Zuzana Gadiou
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
| | - Claire Jourdain
- Institute of Biology, Freie Universität Berlin, 14195, Berlin, Germany
| | - Tino Stricker
- Institute of Biology, Freie Universität Berlin, 14195, Berlin, Germany
| | - Daniel Schubert
- Institute of Biology, Freie Universität Berlin, 14195, Berlin, Germany
| | - David Honys
- Laboratory of Pollen Biology, Institute of Experimental Botany of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Petra Procházková Schrumpfová
- Laboratory of Functional Genomics and Proteomics, Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic.
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
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26
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Hoang NV, Sogbohossou EOD, Xiong W, Simpson CJC, Singh P, Walden N, van den Bergh E, Becker FFM, Li Z, Zhu XG, Brautigam A, Weber APM, van Haarst JC, Schijlen EGWM, Hendre PS, Van Deynze A, Achigan-Dako EG, Hibberd JM, Schranz ME. The Gynandropsis gynandra genome provides insights into whole-genome duplications and the evolution of C4 photosynthesis in Cleomaceae. THE PLANT CELL 2023; 35:1334-1359. [PMID: 36691724 PMCID: PMC10118270 DOI: 10.1093/plcell/koad018] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/18/2023] [Indexed: 06/17/2023]
Abstract
Gynandropsis gynandra (Cleomaceae) is a cosmopolitan leafy vegetable and medicinal plant, which has also been used as a model to study C4 photosynthesis due to its evolutionary proximity to C3 Arabidopsis (Arabidopsis thaliana). Here, we present the genome sequence of G. gynandra, anchored onto 17 main pseudomolecules with a total length of 740 Mb, an N50 of 42 Mb and 30,933 well-supported gene models. The G. gynandra genome and previously released genomes of C3 relatives in the Cleomaceae and Brassicaceae make an excellent model for studying the role of genome evolution in the transition from C3 to C4 photosynthesis. Our analyses revealed that G. gynandra and its C3 relative Tarenaya hassleriana shared a whole-genome duplication event (Gg-α), then an addition of a third genome (Th-α, +1×) took place in T. hassleriana but not in G. gynandra. Analysis of syntenic copy number of C4 photosynthesis-related gene families indicates that G. gynandra generally retained more duplicated copies of these genes than C3T. hassleriana, and also that the G. gynandra C4 genes might have been under positive selection pressure. Both whole-genome and single-gene duplication were found to contribute to the expansion of the aforementioned gene families in G. gynandra. Collectively, this study enhances our understanding of the polyploidy history, gene duplication and retention, as well as their impact on the evolution of C4 photosynthesis in Cleomaceae.
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Affiliation(s)
| | | | - Wei Xiong
- Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Conor J C Simpson
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Pallavi Singh
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Nora Walden
- Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Erik van den Bergh
- Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Frank F M Becker
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Zheng Li
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Xin-Guang Zhu
- State Key Laboratory for Plant Molecular Genetics, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Andrea Brautigam
- Faculty of Biology, Bielefeld University, 33501 Bielefeld, Germany
| | - Andreas P M Weber
- Cluster of Excellence on Plant Science (CEPLAS), Institute of Plant Biochemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Jan C van Haarst
- Business Unit Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Elio G W M Schijlen
- Business Unit Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Prasad S Hendre
- African Orphan Crops Consortium (AOCC), World Agroforestry (ICRAF), Nairobi 00100, Kenya
| | - Allen Van Deynze
- African Orphan Crops Consortium (AOCC), World Agroforestry (ICRAF), Nairobi 00100, Kenya
- Seed Biotechnology Center, University of California, Davis, California 95616, USA
| | - Enoch G Achigan-Dako
- Laboratory of Genetics, Biotechnology and Seed Science (GbioS), Faculty of Agronomic Sciences, University of Abomey-Calavi, BP 2549 Abomey-Calavi, Republic of Benin
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
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27
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Huang F, Chen P, Tang X, Zhong T, Yang T, Nwafor CC, Yang C, Ge X, An H, Li Z, Cahoon EB, Zhang C. Genome assembly of the Brassicaceae diploid Orychophragmus violaceus reveals complex whole-genome duplication and evolution of dihydroxy fatty acid metabolism. PLANT COMMUNICATIONS 2023; 4:100432. [PMID: 36071666 PMCID: PMC10030321 DOI: 10.1016/j.xplc.2022.100432] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/27/2022] [Accepted: 09/05/2022] [Indexed: 05/04/2023]
Abstract
Orychophragmus violaceus is a Brassicaceae species widely cultivated in China, particularly as a winter cover crop in northern China because of its low-temperature tolerance and low water demand. Recently, O. violaceus has also been cultivated as a potential industrial oilseed crop because of its abundant 24-carbon dihydroxy fatty acids (diOH-FAs), which contribute to superior high-temperature lubricant properties. In this study, we performed de novo assembly of the O. violaceus genome. Whole-genome synteny analysis of the genomes of its relatives demonstrated that O. violaceus is a diploid that has undergone an extra whole-genome duplication (WGD) after the Brassicaceae-specific α-WGD event, with a basic chromosome number of x = 12. Formation of diOH-FAs is hypothesized to have occurred after the WGD event. Based on the genome and the transcriptome data from multiple stages of seed development, we predicted that OvDGAT1-1 and OvDGAT1-2 are candidate genes for the regulation of diOH-FA storage in O. violaceus seeds. These results may greatly facilitate the development of heat-tolerant and eco-friendly plant-based lubricants using O. violaceus seed oil and improve our understanding of the genomic evolution of Brassicaceae.
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Affiliation(s)
- Fan Huang
- National Key Lab of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Peng Chen
- National Key Lab of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xinyu Tang
- National Key Lab of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ting Zhong
- National Key Lab of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Taihua Yang
- National Key Lab of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chinedu Charles Nwafor
- National Key Lab of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chao Yang
- National Key Lab of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xianhong Ge
- National Key Lab of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hong An
- Bioinformatics and Analytics Core, University of Missouri-Columbia, Columbia, MO, USA
| | - Zaiyun Li
- National Key Lab of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Edgar B Cahoon
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA; Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE, USA.
| | - Chunyu Zhang
- National Key Lab of Crop Genetic Improvement and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China.
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28
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German DA, Hendriks KP, Koch MA, Lens F, Lysak MA, Bailey CD, Mummenhoff K, Al-Shehbaz IA. An updated classification of the Brassicaceae (Cruciferae). PHYTOKEYS 2023; 220:127-144. [PMID: 37251613 PMCID: PMC10209616 DOI: 10.3897/phytokeys.220.97724] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/18/2023] [Indexed: 05/31/2023]
Abstract
Based on recent achievements in phylogenetic studies of the Brassicaceae, a novel infrafamilial classification is proposed that includes major improvements at the subfamilial and supertribal levels. Herein, the family is subdivided into two subfamilies, Aethionemoideae (subfam. nov.) and Brassicoideae. The Brassicoideae, with 57 of the 58 tribes of Brassicaceae, are further partitioned into five supertribes, including the previously recognized Brassicodae and the newly established Arabodae, Camelinodae, Heliophilodae, and Hesperodae. Additional tribus-level contributions include descriptions of the newly recognized Arabidopsideae, Asperuginoideae, Hemilophieae, Schrenkielleae, and resurrection of the Chamireae and Subularieae. Further detailed comments on 17 tribes in need of clarifications are provided.
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Affiliation(s)
- Dmitry A. German
- South-Siberian Botanical Garden, Altai State University, Lenin Ave. 61, 656049 Barnaul, RussiaAltai State UniversityBarnaulRussia
| | - Kasper P. Hendriks
- Department of Biology, Botany, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, GermanyUniversity of OsnabrückOsnabrückGermany
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, NetherlandsNaturalis Biodiversity CenterLeidenNetherlands
| | - Marcus A. Koch
- Department of Biodiversity and Plant Systematics, Centre for Organismal Studies (COS), Heidelberg University, Im Neuenheimer Feld 345, D-69120 Heidelberg, GermanyHeidelberg UniversityHeidelbergGermany
| | - Frederic Lens
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR Leiden, NetherlandsNaturalis Biodiversity CenterLeidenNetherlands
- Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE Leiden, NetherlandsLeiden UniversityLeidenNetherlands
| | - Martin A. Lysak
- Central European Institute of Technology (CEITEC) and Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech RepublicMasaryk UniversityBrnoCzech Republic
| | - C. Donovan Bailey
- Department of Biology, New Mexico State University, P.O. Box 30001 MSC 3AF, Las Cruces, NM 88003, USANew Mexico State UniversityLas CrucesUnited States of America
| | - Klaus Mummenhoff
- Department of Biology, Botany, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, GermanyUniversity of OsnabrückOsnabrückGermany
| | - Ihsan A. Al-Shehbaz
- Missouri Botanical Garden, 4344 Shaw Boulevard, St. Louis, Missouri 63110, USAMissouri Botanical GardenSt. LouisUnited States of America
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29
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Walden N, Schranz ME. Synteny Identifies Reliable Orthologs for Phylogenomics and Comparative Genomics of the Brassicaceae. Genome Biol Evol 2023; 15:7059155. [PMID: 36848527 PMCID: PMC10016055 DOI: 10.1093/gbe/evad034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 01/27/2023] [Accepted: 02/17/2023] [Indexed: 03/01/2023] Open
Abstract
Large genomic data sets are becoming the new normal in phylogenetic research, but the identification of true orthologous genes and the exclusion of problematic paralogs is still challenging when applying commonly used sequencing methods such as target enrichment. Here, we compared conventional ortholog detection using OrthoFinder with ortholog detection through genomic synteny in a data set of 11 representative diploid Brassicaceae whole-genome sequences spanning the entire phylogenetic space. Then, we evaluated the resulting gene sets regarding gene number, functional annotation, and gene and species tree resolution. Finally, we used the syntenic gene sets for comparative genomics and ancestral genome analysis. The use of synteny resulted in considerably more orthologs and also allowed us to reliably identify paralogs. Surprisingly, we did not detect notable differences between species trees reconstructed from syntenic orthologs when compared with other gene sets, including the Angiosperms353 set and a Brassicaceae-specific target enrichment gene set. However, the synteny data set comprised a multitude of gene functions, strongly suggesting that this method of marker selection for phylogenomics is suitable for studies that value downstream gene function analysis, gene interaction, and network studies. Finally, we present the first ancestral genome reconstruction for the Core Brassicaceae which predating the Brassicaceae lineage diversification ∼25 million years ago.
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Affiliation(s)
- Nora Walden
- Biosystematics Group, Wageningen University, Wageningen, The Netherlands.,Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
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30
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Huang S, Kang Z, Chen Z, Deng Y. Comparative Analysis of the Chloroplast Genome of Cardamine hupingshanensis and Phylogenetic Study of Cardamine. Genes (Basel) 2022; 13:2116. [PMID: 36421792 PMCID: PMC9690686 DOI: 10.3390/genes13112116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/01/2022] [Accepted: 11/09/2022] [Indexed: 05/04/2024] Open
Abstract
Cardamine hupingshanensis (K. M. Liu, L. B. Chen, H. F. Bai and L. H. Liu) is a perennial herbal species endemic to China with narrow distribution. It is known as an important plant for investigating the metabolism of selenium in plants because of its ability to accumulate selenium. However, the phylogenetic position of this particular species in Cardamine remains unclear. In this study, we reported the chloroplast genome (cp genome) for the species C. hupingshanensis and analyzed its position within Cardamine. The cp genome of C. hupingshanensis is 155,226 bp in length and exhibits a typical quadripartite structure: one large single copy region (LSC, 84,287 bp), one small single copy region (17,943 bp) and a pair of inverted repeat regions (IRs, 26,498 bp). Guanine-Cytosine (GC) content makes up 36.3% of the total content. The cp genome contains 111 unique genes, including 78 protein-coding genes, 29 tRNA genes and 4 rRNA genes. A total of 115 simple sequences repeats (SSRs) and 49 long repeats were identified in the genome. Comparative analyses among 17 Cardamine species identified the five most variable regions (trnH-GUG-psbA, ndhK-ndhC, trnW-CCA-trnP-UGG, rps11-rpl36 and rpl32-trnL-UAG), which could be used as molecular markers for the classification and phylogenetic analyses of various Cardamine species. Phylogenetic analyses based on 79 protein coding genes revealed that the species C. hupingshanensis is more closely related to the species C. circaeoides. This relationship is supported by their shared morphological characteristics.
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Affiliation(s)
- Sunan Huang
- Key Laboratory of Plant Resources Conservation & Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Zujie Kang
- Management Bureau of Hunan Hupingshan National Nature Reserve, Shimen 415300, China
| | - Zhenfa Chen
- Management Bureau of Hunan Hupingshan National Nature Reserve, Shimen 415300, China
| | - Yunfei Deng
- Key Laboratory of Plant Resources Conservation & Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China
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31
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Li J, Wang T, Liu W, Yin D, Lai Z, Zhang G, Zhang K, Ji J, Yin S. A high-quality chromosome-level genome assembly of Pelteobagrus vachelli provides insights into its environmental adaptation and population history. Front Genet 2022; 13:1050192. [DOI: 10.3389/fgene.2022.1050192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/01/2022] [Indexed: 11/16/2022] Open
Abstract
Pelteobagrus vachelli is a freshwater fish with high economic value, but the lack of genome resources has severely restricted its industrial development and population conservation. Here, we constructed the first chromosome-level genome assembly of P. vachelli with a total length of approximately 662.13 Mb and a contig N50 was 14.02 Mb, and scaffolds covering 99.79% of the assembly were anchored to 26 chromosomes. Combining the comparative genome results and transcriptome data under environmental stress (high temperature, hypoxia and Edwardsiella. ictaluri infection), the MAPK signaling pathway, PI3K-Akt signaling pathway and apelin signaling pathway play an important role in environmental adaptation of P. vachelli, and these pathways were interconnected by the ErbB family and involved in cell proliferation, differentiation and apoptosis. Population evolution analysis showed that artificial interventions have affected wild populations of P. vachelli. This study provides a useful genomic information for the genetic breeding of P. vachelli, as well as references for further studies on fish biology and evolution.
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32
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Harris BJ, Clark JW, Schrempf D, Szöllősi GJ, Donoghue PCJ, Hetherington AM, Williams TA. Divergent evolutionary trajectories of bryophytes and tracheophytes from a complex common ancestor of land plants. Nat Ecol Evol 2022; 6:1634-1643. [PMID: 36175544 PMCID: PMC9630106 DOI: 10.1038/s41559-022-01885-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 08/12/2022] [Indexed: 11/16/2022]
Abstract
The origin of plants and their colonization of land fundamentally transformed the terrestrial environment. Here we elucidate the basis of this formative episode in Earth history through patterns of lineage, gene and genome evolution. We use new fossil calibrations, a relative clade age calibration (informed by horizontal gene transfer) and new phylogenomic methods for mapping gene family origins. Distinct rooting strategies resolve tracheophytes (vascular plants) and bryophytes (non-vascular plants) as monophyletic sister groups that diverged during the Cambrian, 515-494 million years ago. The embryophyte stem is characterized by a burst of gene innovation, while bryophytes subsequently experienced an equally dramatic episode of reductive genome evolution in which they lost genes associated with the elaboration of vasculature and the stomatal complex. Overall, our analyses reveal that extant tracheophytes and bryophytes are both highly derived from a more complex ancestral land plant. Understanding the origin of land plants requires tracing character evolution across a diversity of modern lineages.
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Affiliation(s)
- Brogan J Harris
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - James W Clark
- School of Biological Sciences, University of Bristol, Bristol, UK
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | - Dominik Schrempf
- Department of Biological Physics, Eötvös Loránd University, Budapest, Hungary
| | - Gergely J Szöllősi
- Department of Biological Physics, Eötvös Loránd University, Budapest, Hungary
- MTA-ELTE 'Lendület' Evolutionary Genomics Research Group, Budapest, Hungary
- Institute of Evolution, Centre for Ecological Research, Budapest, Hungary
| | - Philip C J Donoghue
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK
| | | | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol, UK.
- Bristol Palaeobiology Group, School of Earth Sciences, University of Bristol, Bristol, UK.
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33
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Ru Y, Mandáková TM, Lysak MA, Koch MA. The evolutionary history of Cardamine bulbifera shows a successful rapid postglacial Eurasian range expansion in the absence of sexual reproduction. ANNALS OF BOTANY 2022; 130:245-263. [PMID: 35789248 PMCID: PMC9445599 DOI: 10.1093/aob/mcac088] [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: 02/01/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND AIMS Sexual reproduction is known to drive plant diversification and adaptation. Here we investigate the evolutionary history and spatiotemporal origin of a dodecaploid (2n = 12x = 96) Eurasian deciduous woodland species, Cardamine bulbifera, which reproduces and spreads via vegetative bulb-like structures only. The species has been among the most successful range-expanding understorey woodland plants in Europe, which raises the question of the genetic architecture of its gene pool, since its hexaploid (2n = 6x = 48) but putatively outcrossing closest relative, C. quinquefolia, displays a smaller distribution range in Eastern Europe towards the Caucasus region. Cardamine bulbifera belongs to a small monophyletic clade of four species comprising also C. abchasica (2n = 2x = 16) and C. bipinnata (unknown ploidy) from the Caucasus region. METHODS We sequenced the genomes of the two polyploids and their two putative ancestors using Illumina short-read sequencing technology (×7-8 coverage). Covering the entire distribution range, genomic data were generated for 67 samples of the two polyploids (51 samples of C. bulbifera, 16 samples of C. quinquefolia) and 6 samples of the putative diploid taxa (4 samples of C. abchasica, 2 samples of C. bipinnata) to unravel the evolutionary origin of the polyploid taxa using phylogenetic reconstructions of biparentally and maternally inherited genetic sequence data. Ploidy levels of C. bulbifera and C. quinquefolia were analysed by comparative chromosome painting. We used genetic assignment analysis (STRUCTURE) and approximate Bayesian computation (ABC) modelling to test whether C. bulbifera represents genetically differentiated lineages and addressed the hypothesis of its hybrid origin. Comparative ecological modelling was applied to unravel possible niche differentiation among the two polyploid species. KEY RESULTS Cardamine bulbifera was shown to be a non-hybridogenous, auto-dodecaploid taxon of early Pleistocene origin, but with a history of past gene flow with its hexaploid sister species C. quinquefolia, likely during the last glacial maximum in shared refuge areas in Eastern Europe towards Western Turkey and the Crimean Peninsula region. The diploid Caucasian endemic C. abchasica is considered an ancestral species, which also provides evidence for the origin of the species complex in the Caucasus region. Cardamine bulbifera successfully expanded its distribution range postglacially towards Central and Western Europe accompanied by a transition to exclusively vegetative propagation. CONCLUSIONS A transition to vegetative propagation in C. bulbifera is hypothesized as the major innovation to rapidly expand its distribution range following postglacially progressing woodland vegetation throughout Europe. Preceding and introgressive gene flow from its sister species C. quinquefolia in the joint refuge area is documented. This transition and ecological differentiation may have been triggered by preceding introgressive gene flow from its sister species in the joint East European refuge areas.
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Affiliation(s)
- Yalu Ru
- Centre for Organismal Studies Heidelberg (COS), Department of Biodiversity and Plant Systematics, Heidelberg University, Heidelberg, Germany
| | - Terezie M Mandáková
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Martin A Lysak
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Brno, Czech Republic
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Liu Z, Li N, Yu T, Wang Z, Wang J, Ren J, He J, Huang Y, Shi K, Yang Q, Wu T, Lin H, Song X. The Brassicaceae genome resource (TBGR): A comprehensive genome platform for Brassicaceae plants. PLANT PHYSIOLOGY 2022; 190:226-237. [PMID: 35670735 PMCID: PMC9434321 DOI: 10.1093/plphys/kiac266] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/03/2022] [Indexed: 06/09/2023]
Abstract
The Brassicaceae is an important plant family. We built a user-friendly, web-based, comparative, and functional genomic database, The Brassicaceae Genome Resource (TBGR, http://www.tbgr.org.cn), based on 82 released genomes from 27 Brassicaceae species. The TBGR database contains a large number of important functional genes, including 4,096 glucosinolate genes, 6,625 auxin genes, 13,805 flowering genes, 36,632 resistance genes, 1,939 anthocyanin genes, and 1,231 m6A genes. A total of 1,174,049 specific guide sequences for clustered regularly interspaced short palindromic repeats and 5,856,479 transposable elements were detected in Brassicaceae. TBGR also provides information on synteny, duplication, and orthologs for 27 Brassicaceae species. The TBGR database contains 1,183,851 gene annotations obtained using the TrEMBL, Swiss-Prot, Nr, GO, and Pfam databases. The BLAST, Synteny, Primer Design, Seq_fetch, and JBrowse tools are provided to help users perform comparative genomic analyses. All the genome assemblies, gene models, annotations, and bioinformatics results can be easily downloaded from the TBGR database. We plan to improve and continuously update the database with newly assembled genomes and comparative genomic studies. We expect the TBGR database to become a key resource for the study of the Brassicaceae.
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Affiliation(s)
- Zhuo Liu
- School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Nan Li
- School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Tong Yu
- School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Zhiyuan Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Jiaqi Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Jun Ren
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jinghua He
- School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Yini Huang
- School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Keqian Shi
- School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Qihang Yang
- School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Tong Wu
- School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Hao Lin
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
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Zuo (左胜) S, Guo (郭新异) X, Mandáková T, Edginton M, Al-Shehbaz IA, Lysak MA. Genome diploidization associates with cladogenesis, trait disparity, and plastid gene evolution. PLANT PHYSIOLOGY 2022; 190:403-420. [PMID: 35670733 PMCID: PMC9434143 DOI: 10.1093/plphys/kiac268] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 05/09/2022] [Indexed: 05/20/2023]
Abstract
Angiosperm genome evolution was marked by many clade-specific whole-genome duplication events. The Microlepidieae is one of the monophyletic clades in the mustard family (Brassicaceae) formed after an ancient allotetraploidization. Postpolyploid cladogenesis has resulted in the extant c. 17 genera and 60 species endemic to Australia and New Zealand (10 species). As postpolyploid genome diploidization is a trial-and-error process under natural selection, it may proceed with different intensity and be associated with speciation events. In Microlepidieae, different extents of homoeologous recombination between the two parental subgenomes generated clades marked by slow ("cold") versus fast ("hot") genome diploidization. To gain a deeper understanding of postpolyploid genome evolution in Microlepidieae, we analyzed phylogenetic relationships in this tribe using complete chloroplast sequences, entire 35S rDNA units, and abundant repetitive sequences. The four recovered intra-tribal clades mirror the varied diploidization of Microlepidieae genomes, suggesting that the intrinsic genomic features underlying the extent of diploidization are shared among genera and species within one clade. Nevertheless, even congeneric species may exert considerable morphological disparity (e.g. in fruit shape), whereas some species within different clades experience extensive morphological convergence despite the different pace of their genome diploidization. We showed that faster genome diploidization is positively associated with mean morphological disparity and evolution of chloroplast genes (plastid-nuclear genome coevolution). Higher speciation rates in perennials than in annual species were observed. Altogether, our results confirm the potential of Microlepidieae as a promising subject for the analysis of postpolyploid genome diploidization in Brassicaceae.
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Affiliation(s)
| | | | - Terezie Mandáková
- CEITEC – Central European Institute of Technology, Masaryk University, Brno, CZ-625 00, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, CZ-625 00, Czech Republic
| | - Mark Edginton
- Queensland Herbarium, Department of Environment and Science, Brisbane Botanic Gardens, Mt Coot-tha Road, Toowong, QLD 4066, Australia
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Schilbert HM, Glover BJ. Analysis of flavonol regulator evolution in the Brassicaceae reveals MYB12, MYB111 and MYB21 duplications and MYB11 and MYB24 gene loss. BMC Genomics 2022; 23:604. [PMID: 35986242 PMCID: PMC9392221 DOI: 10.1186/s12864-022-08819-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 08/03/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Flavonols are the largest subgroup of flavonoids, possessing multiple functions in plants including protection against ultraviolet radiation, antimicrobial activities, and flower pigmentation together with anthocyanins. They are of agronomical and economical importance because the major off-taste component in rapeseed protein isolates is a flavonol derivative, which limits rapeseed protein use for human consumption. Flavonol production in Arabidopsis thaliana is mainly regulated by the subgroup 7 (SG7) R2R3-MYB transcription factors MYB11, MYB12, and MYB111. Recently, the SG19 MYBs MYB21, MYB24, and MYB57 were shown to regulate flavonol accumulation in pollen and stamens. The members of each subgroup are closely related, showing gene redundancy and tissue-specific expression in A. thaliana. However, the evolution of these flavonol regulators inside the Brassicaceae, especially inside the Brassiceae, which include the rapeseed crop species, is not fully understood. RESULTS We studied the SG7 and SG19 MYBs in 44 species, including 31 species of the Brassicaceae, by phylogenetic analyses followed by synteny and gene expression analyses. Thereby we identified a deep MYB12 and MYB111 duplication inside the Brassicaceae, which likely occurred before the divergence of Brassiceae and Thelypodieae. These duplications of SG7 members were followed by the loss of MYB11 after the divergence of Eruca vesicaria from the remaining Brassiceae species. Similarly, MYB21 experienced duplication before the emergence of the Brassiceae tribe, where the gene loss of MYB24 is also proposed to have happened. The members of each subgroup revealed frequent overlapping spatio-temporal expression patterns in the Brassiceae member B. napus, which are assumed to compensate for the loss of MYB11 and MYB24 in the analysed tissues. CONCLUSIONS We identified a duplication of MYB12, MYB111, and MYB21 inside the Brassicaceae and MYB11 and MYB24 gene loss inside the tribe Brassiceae. We propose that polyploidization events have shaped the evolution of the flavonol regulators in the Brassicaceae, especially in the Brassiceae.
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Affiliation(s)
- Hanna M Schilbert
- Department of Plant Sciences, University of Cambridge, Cambridge, UK.
- Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, Bielefeld, Germany.
| | - Beverley J Glover
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
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Dogan M, Mandáková T, Guo X, Lysak MA. Idahoa and Subularia: Hidden polyploid origins of two enigmatic genera of crucifers. AMERICAN JOURNAL OF BOTANY 2022; 109:1273-1289. [PMID: 35912547 DOI: 10.1002/ajb2.16042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 07/10/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
PREMISE The monotypic Idahoa (I. scapigera) and the bispecific Subularia (S. aquatica and S. monticola) belong to Brassicaceae with unclear phylogenetic relationships and no tribal assignment. To fill this knowledge gap, we investigated these species and their closest relatives by combining cytogenomic and phylogenomic methods. METHODS We used whole plastome sequences in maximum likelihood and Bayesian inference analyses. We tested the phylogenetic informativeness of shared genomic repeats. We combined nuclear gene tree reconciliation and comparative chromosome painting (CCP) to examine the occurrence of past whole-genome duplications (WGDs). RESULTS The plastid data set corroborated the sister relationship between Idahoa and Subularia within the crucifer Lineage V but failed to resolve consistent topologies using both inference methods. The shared repetitive sequences provided conflicting pwhylogenetic signals. CCP analysis unexpectedly revealed that Idahoa (2n = 16) has a diploidized mesotetraploid genome, whereas two Subularia species (2n = 28 and 30) have diploidized mesoctoploid genomes. Several ancient allopolyploidy events have also been detected in closely related taxa (Chamira circaeoides, Cremolobeae, Eudemeae, and Notothlaspideae). CONCLUSIONS Our results suggest that the contentious phylogenetic placement of Idahoa and Subularia is best explained by two WGDs involving one or more shared parental genomes. The newly identified mesopolyploid genomes highlight the challenges of studying plant clades with complex polyploidy histories and provide a better framework for understanding genome evolution in the crucifer family.
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Affiliation(s)
- Mert Dogan
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, CZ-625 00, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, CZ-625 00, Czech Republic
| | - Terezie Mandáková
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, CZ-625 00, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, CZ-625 00, Czech Republic
| | - Xinyi Guo
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, CZ-625 00, Czech Republic
| | - Martin A Lysak
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, CZ-625 00, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, CZ-625 00, Czech Republic
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Cheng A, Mohd Hanafiah N, Harikrishna JA, Eem LP, Baisakh N, Mispan MS. A Reappraisal of Polyploidy Events in Grasses (Poaceae) in a Rapidly Changing World. BIOLOGY 2022; 11:biology11050636. [PMID: 35625365 PMCID: PMC9138248 DOI: 10.3390/biology11050636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/14/2022] [Accepted: 04/19/2022] [Indexed: 11/16/2022]
Abstract
Around 80% of megaflora species became extinct at the Cretaceous–Paleogene (K–Pg) boundary. Subsequent polyploidy events drove the survival of thousands of plant species and played a significant historical role in the development of the most successful modern cereal crops. However, current and rapid global temperature change poses an urgent threat to food crops worldwide, including the world’s big three cereals: rice, wheat, and maize, which are members of the grass family, Poaceae. Some minor cereals from the same family (such as teff) have grown in popularity in recent years, but there are important knowledge gaps regarding the similarities and differences between major and minor crops, including how polyploidy affects their biological processes under natural and (a)biotic stress conditions and thus the potential to harness polyploidization attributes for improving crop climate resilience. This review focuses on the impact of polyploidy events on the Poaceae family, which includes the world’s most important food sources, and discusses the past, present, and future of polyploidy research for major and minor crops. The increasing accessibility to genomes of grasses and their wild progenitors together with new tools and interdisciplinary research on polyploidy can support crop improvement for global food security in the face of climate change.
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Affiliation(s)
- Acga Cheng
- Faculty of Science, Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (A.C.); (N.M.H.); (J.A.H.)
| | - Noraikim Mohd Hanafiah
- Faculty of Science, Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (A.C.); (N.M.H.); (J.A.H.)
| | - Jennifer Ann Harikrishna
- Faculty of Science, Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (A.C.); (N.M.H.); (J.A.H.)
- Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Lim Phaik Eem
- Institute of Ocean and Earth Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia;
| | - Niranjan Baisakh
- School of Plant, Environmental, and Soil Science, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
- Correspondence: (N.B.); (M.S.M.)
| | - Muhamad Shakirin Mispan
- Faculty of Science, Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (A.C.); (N.M.H.); (J.A.H.)
- Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, Kuala Lumpur 50603, Malaysia
- Correspondence: (N.B.); (M.S.M.)
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The Phytotoxin Myrigalone A Triggers a Phased Detoxification Programme and Inhibits Lepidium sativum Seed Germination via Multiple Mechanisms including Interference with Auxin Homeostasis. Int J Mol Sci 2022; 23:ijms23094618. [PMID: 35563008 PMCID: PMC9104956 DOI: 10.3390/ijms23094618] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 02/01/2023] Open
Abstract
Molecular responses of plants to natural phytotoxins comprise more general and compound-specific mechanisms. How phytotoxic chalcones and other flavonoids inhibit seedling growth was widely studied, but how they interfere with seed germination is largely unknown. The dihydrochalcone and putative allelochemical myrigalone A (MyA) inhibits seed germination and seedling growth. Transcriptome (RNAseq) and hormone analyses of Lepidium sativum seed responses to MyA were compared to other bioactive and inactive compounds. MyA treatment of imbibed seeds triggered the phased induction of a detoxification programme, altered gibberellin, cis-(+)-12-oxophytodienoic acid and jasmonate metabolism, and affected the expression of hormone transporter genes. The MyA-mediated inhibition involved interference with the antioxidant system, oxidative signalling, aquaporins and water uptake, but not uncoupling of oxidative phosphorylation or p-hydroxyphenylpyruvate dioxygenase expression/activity. MyA specifically affected the expression of auxin-related signalling genes, and various transporter genes, including for auxin transport (PIN7, ABCG37, ABCG4, WAT1). Responses to auxin-specific inhibitors further supported the conclusion that MyA interferes with auxin homeostasis during seed germination. Comparative analysis of MyA and other phytotoxins revealed differences in the specific regulatory mechanisms and auxin transporter genes targeted to interfere with auxin homestasis. We conclude that MyA exerts its phytotoxic activity by multiple auxin-dependent and independent molecular mechanisms.
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Liu SY, Ren ZT, Zhao CY, Hu CX, Wang HC. Hemilophiacardiocarpa (Brassicaceae), a new species from Yunnan, southwest China. PHYTOKEYS 2022; 194:95-103. [PMID: 35586325 PMCID: PMC9038854 DOI: 10.3897/phytokeys.194.82737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/05/2022] [Indexed: 06/15/2023]
Abstract
Hemilophiacardiocarpa (Brassicaceae), the sixth species of the Chinese endemic genus Hemilophia, is described and illustrated. This plant is found in the Jiaozishan Mountains in Dongchuan District, northern Yunnan, southwest China. Morphologically, it shows close relationships with H.rockii and H.pulchella, but differs from it in the leaf shape and size, inflorescence, flower size, shape of fruit and length of its pedicel. An updated key to the taxa of Hemilophia is provided.
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Affiliation(s)
- Shao-Yun Liu
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, Yunnan, ChinaYunnan UniversityKunmingChina
| | - Zheng-Tao Ren
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, Yunnan, ChinaYunnan UniversityKunmingChina
| | - Chang-You Zhao
- Management Bureau of Yunnan Jiaozishan National Natural Reserve, Luquan, 651515, Yunnan, ChinaManagement Bureau of Yunnan Jiaozishan National Natural ReserveLuquanChina
| | - Chun-Xiang Hu
- Management Bureau of Yunnan Jiaozishan National Natural Reserve, Luquan, 651515, Yunnan, ChinaManagement Bureau of Yunnan Jiaozishan National Natural ReserveLuquanChina
| | - Huan-Chong Wang
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, Yunnan, ChinaYunnan UniversityKunmingChina
- Herbarium of Yunnan University, Kunming 650091, Yunnan, ChinaHerbarium of Yunnan UniversityKunmingChina
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41
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Gómez JM, González-Megías A, Narbona E, Navarro L, Perfectti F, Armas C. Phenotypic plasticity guides Moricandia arvensis divergence and convergence across the Brassicaceae floral morphospace. THE NEW PHYTOLOGIST 2022; 233:1479-1493. [PMID: 34657297 DOI: 10.1111/nph.17807] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/10/2021] [Indexed: 06/13/2023]
Abstract
Many flowers exhibit phenotypic plasticity. By inducing the production of several phenotypes, plasticity may favour the rapid exploration of different regions of the floral morphospace. We investigated how plasticity drives Moricandia arvensis, a species displaying within-individual floral polyphenism, across the floral morphospace of the entire Brassicaceae family. We compiled the multidimensional floral phenotype, the phylogenetic relationships, and the pollination niche of over 3000 species to construct a family-wide floral morphospace. We assessed the disparity between the two M. arvensis floral morphs (as the distance between the phenotypic spaces occupied by each morph) and compared it with the family-wide disparity. We measured floral divergence by comparing disparity with the most common ancestor, and estimated the convergence of each floral morph with other species belonging to the same pollination niches. Moricandia arvensis exhibits a plasticity-mediated floral disparity greater than that found between species, genera and tribes. The novel phenotype of M. arvensis moves outside the region occupied by its ancestors and relatives, crosses into a new region where it encounters a different pollination niche, and converges with distant Brassicaceae lineages. Our study suggests that phenotypic plasticity favours floral divergence and rapid appearance of convergent flowers, a process which facilitates the evolution of generalist pollination systems.
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Affiliation(s)
- José M Gómez
- Estación Experimental de Zonas Áridas (EEZA-CSIC), E-04120, Almería, Spain
- Research Unit Modeling Nature, Universidad de Granada, E-18071, Granada, Spain
| | - Adela González-Megías
- Research Unit Modeling Nature, Universidad de Granada, E-18071, Granada, Spain
- Departamento de Zoología, Universidad de Granada, E-18071, Granada, Spain
| | - Eduardo Narbona
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, E-41013, Sevilla, Spain
| | - Luis Navarro
- Departamento de Biología Vegetal y Ciencias del Suelo, Universidad de Vigo, E-36310, Vigo, Spain
| | - Francisco Perfectti
- Research Unit Modeling Nature, Universidad de Granada, E-18071, Granada, Spain
- Departamento de Genética, Universidad de Granada, E-18071, Granada, Spain
| | - Cristina Armas
- Estación Experimental de Zonas Áridas (EEZA-CSIC), E-04120, Almería, Spain
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42
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Chen HL, Al-Shehbaz IA, Qian LS, Zhang JW, Xu B, Zhang TC, Yue JP, Sun H. Pulvinatusia (Brassicaceae), a new cushion genus from China and its systematic position. PHYTOKEYS 2022; 189:9-28. [PMID: 35115879 PMCID: PMC8803735 DOI: 10.3897/phytokeys.189.77926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
The new genus and species Pulvinatusiaxuegulaensis (Brassicaceae) are described and illustrated. The species is a cushion plant collected from Xuegu La, Xizang, China. Its vegetative parts are most similar to those of Arenariabryophylla (Caryophyllaceae) co-occurring in the same region, while its leaves and fruits closely resemble those of Xerodrabapatagonica (Brassicaceae) from Patagonian Argentina and Chile. Family-level phylogenetic analyses based on both nuclear ITS and plastome revealed that it is a member of the tribe Crucihimalayeae, but the infra-/intergeneric relationships within the tribe are yet to be resolved.
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Affiliation(s)
- Hong-Liang Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, ChinaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
- Laboratory of Systematics & Evolutionary Botany and Biodiversity, College of Life Science, Zhejiang University, Hangzhou 310058, Zhejiang, ChinaZhejiang UniversityHangzhouChina
| | - Ihsan A. Al-Shehbaz
- Missouri Botanical Garden, 4344 Shaw Boulevard, St. Louis, Missouri 63110, USAMissouri Botanical GardenSt. LouisUnited States of America
| | - Li-Shen Qian
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, ChinaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
- University of Chinese Academy of Sciences, Beijing 100049, ChinaUniversity of Chinese Academy of SciencesBeijingChina
| | - Jian-Wen Zhang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, ChinaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
| | - Bo Xu
- College of Forestry, Southwest Forestry University, Kunming 650224, Yunnan, ChinaSouthwest Forestry UniversityKunmingChina
| | - Ti-Cao Zhang
- College of Chinese Material Medica, Yunnan University of Chinese Medicine, Kunming 650500, Yunnan, ChinaYunnan University of Chinese MedicineKunmingChina
| | - Ji-Pei Yue
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, ChinaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
| | - Hang Sun
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, ChinaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
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Rempfer C, Wiedemann G, Schween G, Kerres KL, Lucht JM, Horres R, Decker EL, Reski R. Autopolyploidization affects transcript patterns and gene targeting frequencies in Physcomitrella. PLANT CELL REPORTS 2022; 41:153-173. [PMID: 34636965 PMCID: PMC8803787 DOI: 10.1007/s00299-021-02794-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
In Physcomitrella, whole-genome duplications affected the expression of about 3.7% of the protein-encoding genes, some of them relevant for DNA repair, resulting in a massively reduced gene-targeting frequency. Qualitative changes in gene expression after an autopolyploidization event, a pure duplication of the whole genome (WGD), might be relevant for a different regulation of molecular mechanisms between angiosperms growing in a life cycle with a dominant diploid sporophytic stage and the haploid-dominant mosses. Whereas angiosperms repair DNA double-strand breaks (DSB) preferentially via non-homologous end joining (NHEJ), in the moss Physcomitrella homologous recombination (HR) is the main DNA-DSB repair pathway. HR facilitates the precise integration of foreign DNA into the genome via gene targeting (GT). Here, we studied the influence of ploidy on gene expression patterns and GT efficiency in Physcomitrella using haploid plants and autodiploid plants, generated via an artificial WGD. Single cells (protoplasts) were transfected with a GT construct and material from different time-points after transfection was analysed by microarrays and SuperSAGE sequencing. In the SuperSAGE data, we detected 3.7% of the Physcomitrella genes as differentially expressed in response to the WGD event. Among the differentially expressed genes involved in DNA-DSB repair was an upregulated gene encoding the X-ray repair cross-complementing protein 4 (XRCC4), a key player in NHEJ. Analysing the GT efficiency, we observed that autodiploid plants were significantly GT suppressed (p < 0.001) attaining only one third of the expected GT rates. Hence, an alteration of global transcript patterns, including genes related to DNA repair, in autodiploid Physcomitrella plants correlated with a drastic suppression of HR.
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Affiliation(s)
- Christine Rempfer
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104, Freiburg, Germany
| | - Gertrud Wiedemann
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- Department of Hematology and Central Hematology Laboratory, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
| | - Gabriele Schween
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- Corteva Agriscience, Pioneer Hi-Bred Northern Europe, Münstertäler Strasse 26, 79427, Eschbach, Germany
| | - Klaus L Kerres
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Jan M Lucht
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
- Scienceindustries, Nordstrasse 15, 8006, Zurich, Switzerland
| | - Ralf Horres
- GenXPro GmbH, Altenhöferallee 3, 60438, Frankfurt am Main, Germany
| | - Eva L Decker
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, Schaenzlestr. 1, 79104, Freiburg, Germany.
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104, Freiburg, Germany.
- Signalling Research Centres BIOSS and CIBSS, Schaenzlestr. 18, 79104, Freiburg, Germany.
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Wolf E, Gaquerel E, Scharmann M, Yant L, Koch MA. Evolutionary footprints of a cold relic in a rapidly warming world. eLife 2021; 10:e71572. [PMID: 34930524 PMCID: PMC8741218 DOI: 10.7554/elife.71572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
With accelerating global warming, understanding the evolutionary dynamics of plant adaptation to environmental change is increasingly urgent. Here, we reveal the enigmatic history of the genus Cochlearia (Brassicaceae), a Pleistocene relic that originated from a drought-adapted Mediterranean sister genus during the Miocene. Cochlearia rapidly diversified and adapted to circum-Arctic regions and other cold-characterized habitat types during the Pleistocene. This sudden change in ecological preferences was accompanied by a highly complex, reticulate polyploid evolution, which was apparently triggered by the impact of repeated Pleistocene glaciation cycles. Our results illustrate that two early diversified Arctic-alpine diploid gene pools contributed differently to the evolution of this young polyploid genus now captured in a cold-adapted niche. Metabolomics revealed central carbon metabolism responses to cold in diverse species and ecotypes, likely due to continuous connections to cold habitats that may have facilitated widespread adaptation to alpine and subalpine habitats, and which we speculate were coopted from existing drought adaptations. Given the growing scientific interest in the adaptive evolution of temperature-related traits, our results provide much-needed taxonomic and phylogenomic resolution of a model system as well as first insights into the origins of its adaptation to cold.
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Affiliation(s)
- Eva Wolf
- Centre for Organismal Studies, University of HeidelbergHeidelbergGermany
| | - Emmanuel Gaquerel
- Centre for Organismal Studies, University of HeidelbergHeidelbergGermany
| | - Mathias Scharmann
- Department of Ecology and Evolution, University of LausanneLausanneSwitzerland
| | - Levi Yant
- Future Food Beacon and School of Life Sciences, the University of NottinghamNottinghamUnited Kingdom
| | - Marcus A Koch
- Centre for Organismal Studies, University of HeidelbergHeidelbergGermany
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Lu YH, Alam I, Yang YQ, Yu YC, Chi WC, Chen SB, Chalhoub B, Jiang LX. Evolutionary Analysis of the YABBY Gene Family in Brassicaceae. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122700. [PMID: 34961171 PMCID: PMC8704796 DOI: 10.3390/plants10122700] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 06/14/2023]
Abstract
The YABBY gene family is one of the plant transcription factors present in all seed plants. The family members were extensively studied in various plants and shown to play important roles in plant growth and development, such as the polarity establishment in lateral organs, the formation and development of leaves and flowers, and the response to internal plant hormone and external environmental stress signals. In this study, a total of 364 YABBY genes were identified from 37 Brassicaceae genomes, of which 15 were incomplete due to sequence gaps, and nine were imperfect (missing C2C2 zinc-finger or YABBY domain) due to sequence mutations. Phylogenetic analyses resolved these YABBY genes into six compact clades except for a YAB3-like gene identified in Aethionema arabicum. Seventeen Brassicaceae species each contained a complete set of six basic YABBY genes (i.e., 1 FIL, 1 YAB2, 1 YAB3, 1 YAB5, 1 INO and 1 CRC), while 20 others each contained a variable number of YABBY genes (5-25) caused mainly by whole-genome duplication/triplication followed by gene losses, and occasionally by tandem duplications. The fate of duplicate YABBY genes changed considerably according to plant species, as well as to YABBY gene type. These YABBY genes were shown to be syntenically conserved across most of the Brassicaceae species, but their functions might be considerably diverged between species, as well as between paralogous copies, as demonstrated by the promoter and expression analysis of YABBY genes in two Brassica species (B. rapa and B. oleracea). Our study provides valuable insights for understanding the evolutionary story of YABBY genes in Brassicaceae and for further functional characterization of each YABBY gene across the Brassicaceae species.
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Affiliation(s)
- Yun-Hai Lu
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.-C.Y.); (B.C.); (L.-X.J.)
| | - Intikhab Alam
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (I.A.); (Y.-Q.Y.)
| | - Yan-Qing Yang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (I.A.); (Y.-Q.Y.)
| | - Ya-Cen Yu
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.-C.Y.); (B.C.); (L.-X.J.)
| | - Wen-Chao Chi
- Marine and Agricultural Biotechnology Laboratory, Institute of Oceanography, Minjiang University, Fuzhou 350108, China; (W.-C.C.); (S.-B.C.)
| | - Song-Biao Chen
- Marine and Agricultural Biotechnology Laboratory, Institute of Oceanography, Minjiang University, Fuzhou 350108, China; (W.-C.C.); (S.-B.C.)
| | - Boulos Chalhoub
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.-C.Y.); (B.C.); (L.-X.J.)
| | - Li-Xi Jiang
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; (Y.-C.Y.); (B.C.); (L.-X.J.)
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Bayat S, Lysak MA, Mandáková T. Genome structure and evolution in the cruciferous tribe Thlaspideae (Brassicaceae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1768-1785. [PMID: 34661331 DOI: 10.1111/tpj.15542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 09/30/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
Whole-genome duplications (WGDs) and chromosome rearrangements (CRs) play the key role in driving the diversification and evolution of plant lineages. Although the direct link between WGDs and plant diversification is well documented, relatively few studies focus on the evolutionary significance of CRs. The cruciferous tribe Thlaspideae represents an ideal model system to address the role of large-scale chromosome alterations in genome evolution, as most Thlaspideae species share the same diploid chromosome number (2n = 2x = 14). Here we constructed the genome structure in 12 Thlaspideae species, including field pennycress (Thlaspi arvense) and garlic mustard (Alliaria petiolata). We detected and precisely characterized genus- and species-specific CRs, mostly pericentric inversions, as the main genome-diversifying drivers in the tribe. We reconstructed the structure of seven chromosomes of an ancestral Thlaspideae genome, identified evolutionary stable chromosomes versus chromosomes prone to CRs, estimated the rate of CRs, and uncovered an allohexaploid origin of garlic mustard from diploid taxa closely related to A. petiolata and Parlatoria cakiloidea. Furthermore, we performed detailed bioinformatic analysis of the Thlaspideae repeatomes, and identified repetitive elements applicable as unique species- and genus-specific barcodes and chromosome landmarks. This study deepens our general understanding of the evolutionary role of CRs, particularly pericentric inversions, in plant genome diversification, and provides a robust base for follow-up whole-genome sequencing efforts.
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Affiliation(s)
- Soheila Bayat
- CEITEC, Masaryk University, Brno, 62500, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
| | - Martin A Lysak
- CEITEC, Masaryk University, Brno, 62500, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
| | - Terezie Mandáková
- CEITEC, Masaryk University, Brno, 62500, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
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Genome evolution of the psammophyte Pugionium for desert adaptation and further speciation. Proc Natl Acad Sci U S A 2021; 118:2025711118. [PMID: 34649989 PMCID: PMC8545485 DOI: 10.1073/pnas.2025711118] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/22/2021] [Indexed: 12/01/2022] Open
Abstract
Plants’ adaptations to and divergence in arid deserts have long fascinated scientists and the general public. Here, we present a genomic analysis of two congeneric desert plant species that clarifies their evolutionary history and shows that their common ancestor arose from a hybrid polyploidization, which provided genomic foundations for their survival in deserts. The whole-genome duplication was followed by translocation-based rearrangements of the ancestral chromosomes. Rapid evolution of genes in these reshuffled chromosomes contributed greatly to the divergences of the two species in desert microhabitats during which gene flow was continuous. Our results provide insights into plant adaptation in the arid deserts and highlight the significance of polyploidy-driven chromosomal structural variations in species divergence. Deserts exert strong selection pressures on plants, but the underlying genomic drivers of ecological adaptation and subsequent speciation remain largely unknown. Here, we generated de novo genome assemblies and conducted population genomic analyses of the psammophytic genus Pugionium (Brassicaceae). Our results indicated that this bispecific genus had undergone an allopolyploid event, and the two parental genomes were derived from two ancestral lineages with different chromosome numbers and structures. The postpolyploid expansion of gene families related to abiotic stress responses and lignin biosynthesis facilitated environmental adaptations of the genus to desert habitats. Population genomic analyses of both species further revealed their recent divergence with continuous gene flow, and the most divergent regions were found to be centered on three highly structurally reshuffled chromosomes. Genes under selection in these regions, which were mainly located in one of the two subgenomes, contributed greatly to the interspecific divergence in microhabitat adaptation.
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Žerdoner Čalasan A, Hurka H, German DA, Pfanzelt S, Blattner FR, Seidl A, Neuffer B. Pleistocene dynamics of the Eurasian steppe as a driving force of evolution: Phylogenetic history of the genus Capsella (Brassicaceae). Ecol Evol 2021; 11:12697-12713. [PMID: 34594532 PMCID: PMC8462161 DOI: 10.1002/ece3.8015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/06/2021] [Accepted: 07/29/2021] [Indexed: 12/19/2022] Open
Abstract
Capsella is a model plant genus of the Brassicaceae closely related to Arabidopsis. To disentangle its biogeographical history and intrageneric phylogenetic relationships, 282 individuals of all five currently recognized Capsella species were genotyped using a restriction digest-based next-generation sequencing method. Our analysis retrieved two main lineages within Capsella that split c. one million years ago, with western C. grandiflora and C. rubella forming a sister lineage to the eastern lineage consisting of C. orientalis. The split was attributed to continuous latitudinal displacements of the Eurasian steppe belt to the south during Early Pleistocene glacial cycles. During the interglacial cycles of the Late Pleistocene, hybridization of the two lineages took place in the southwestern East European Plain, leading to the allotetraploid C. bursa-pastoris. Extant genetic variation within C. orientalis postdated any extensive glacial events. Ecological niche modeling showed that suitable habitat for C. orientalis existed during the Last Glacial Maximum around the north coast of the Black Sea and in southern Kazakhstan. Such a scenario is also supported by population genomic data that uncovered the highest genetic diversity in the south Kazakhstan cluster, suggesting that C. orientalis originated in continental Asia and migrated north- and possibly eastwards after the last ice age. Post-glacial hybridization events between C. bursa-pastoris and C. grandiflora/rubella in the southwestern East European Plain and the Mediterranean gave rise to C. thracica. Introgression of C. grandiflora/rubella into C. bursa-pastoris resulted in a new Mediterranean cluster within the already existing Eurasian C. bursa-pastoris cluster. This study shows that the continuous displacement and disruption of the Eurasian steppe belt during the Pleistocene was the driving force in the evolution of Capsella.
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Affiliation(s)
| | - Herbert Hurka
- Department 5: Biology/Chemistry, BotanyUniversity of OsnabrückOsnabrückGermany
| | - Dmitry A. German
- South‐Siberian Botanical GardenAltai State UniversityBarnaulRussia
| | - Simon Pfanzelt
- Experimental TaxonomyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)Seeland‐GaterslebenGermany
- Munich Botanical GardenMünchenGermany
| | - Frank R. Blattner
- Experimental TaxonomyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)Seeland‐GaterslebenGermany
| | - Anna Seidl
- Institute of BotanyDepartment of Integrative Biology and Biodiversity ResearchUniversity of Natural Resources and Life SciencesVienna (BOKU)Austria
| | - Barbara Neuffer
- Department 5: Biology/Chemistry, BotanyUniversity of OsnabrückOsnabrückGermany
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Wötzel S, Andrello M, Albani MC, Koch MA, Coupland G, Gugerli F. Arabis alpina: A perennial model plant for ecological genomics and life-history evolution. Mol Ecol Resour 2021; 22:468-486. [PMID: 34415668 PMCID: PMC9293087 DOI: 10.1111/1755-0998.13490] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 07/28/2021] [Accepted: 08/16/2021] [Indexed: 01/03/2023]
Abstract
Many model organisms were chosen and achieved prominence because of an advantageous combination of their life‐history characteristics, genetic properties and also practical considerations. Discoveries made in Arabidopsis thaliana, the most renowned noncrop plant model species, have markedly stimulated studies in other species with different biology. Within the family Brassicaceae, the arctic–alpine Arabis alpina has become a model complementary to Arabidopsis thaliana to study the evolution of life‐history traits, such as perenniality, and ecological genomics in harsh environments. In this review, we provide an overview of the properties that facilitated the rapid emergence of A. alpina as a plant model. We summarize the evolutionary history of A. alpina, including genomic aspects, the diversification of its mating system and demographic properties, and we discuss recent progress in the molecular dissection of developmental traits that are related to its perennial life history and environmental adaptation. From this published knowledge, we derive open questions that might inspire future research in A. alpina, other Brassicaceae species or more distantly related plant families.
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Affiliation(s)
- Stefan Wötzel
- Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt and Senckenberg Biodiversity and Climate Research Centre, Frankfurt (Main), Germany
| | - Marco Andrello
- Institute for the Study of Anthropic Impacts and Sustainability in the Marine Environment, National Research Council, CNR-IAS, Rome, Italy
| | - Maria C Albani
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Marcus A Koch
- Biodiversity and Plant Systematics, Centre for Organismal Studies (COS), Heidelberg University, Heidelberg, Germany
| | - George Coupland
- Department of Plant Development Biology, MPI for Plant Breeding Research, Cologne, Germany
| | - Felix Gugerli
- WSL Swiss Federal Research Institute, Birmensdorf, Switzerland
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50
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Stull GW, Qu XJ, Parins-Fukuchi C, Yang YY, Yang JB, Yang ZY, Hu Y, Ma H, Soltis PS, Soltis DE, Li DZ, Smith SA, Yi TS. Gene duplications and phylogenomic conflict underlie major pulses of phenotypic evolution in gymnosperms. NATURE PLANTS 2021; 7:1015-1025. [PMID: 34282286 DOI: 10.1038/s41477-021-00964-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 06/10/2021] [Indexed: 05/15/2023]
Abstract
Inferring the intrinsic and extrinsic drivers of species diversification and phenotypic disparity across the tree of life is a major challenge in evolutionary biology. In green plants, polyploidy (or whole-genome duplication, WGD) is known to play a major role in microevolution and speciation, but the extent to which WGD has shaped macroevolutionary patterns of diversification and phenotypic innovation across plant phylogeny remains an open question. Here, we examine the relationship of various facets of genomic evolution-including gene and genome duplication, genome size, and chromosome number-with macroevolutionary patterns of phenotypic innovation, species diversification, and climatic occupancy in gymnosperms. We show that genomic changes, such as WGD and genome-size shifts, underlie the origins of most major extant gymnosperm clades, and notably, our results support an ancestral WGD in the gymnosperm lineage. Spikes of gene duplication typically coincide with major spikes of phenotypic innovation, while increased rates of phenotypic evolution are typically found at nodes with high gene-tree conflict, representing historic population-level dynamics during speciation. Most shifts in gymnosperm diversification since the rise of angiosperms are decoupled from putative WGDs and instead are associated with increased rates of climatic occupancy evolution, particularly in cooler and/or more arid climatic conditions, suggesting that ecological opportunity, especially in the later Cenozoic, and environmental heterogeneity have driven a resurgence of gymnosperm diversification. Our study provides critical insight on the processes underlying diversification and phenotypic evolution in gymnosperms, with important broader implications for the major drivers of both micro- and macroevolution in plants.
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Affiliation(s)
- Gregory W Stull
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Xiao-Jian Qu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, China
| | | | - Ying-Ying Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Zhi-Yun Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yi Hu
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Hong Ma
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.
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