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Kang JS, Yu JG, Xiang QP, Zhang XC. The Possible Earliest Allopolyploidization in Tracheophytes Revealed by Phylotranscriptomics and Morphology of Selaginellaceae. Mol Biol Evol 2024; 41:msae153. [PMID: 39101470 PMCID: PMC11299036 DOI: 10.1093/molbev/msae153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 07/15/2024] [Accepted: 07/19/2024] [Indexed: 08/06/2024] Open
Abstract
Selaginellaceae, originated in the Carboniferous and survived the Permian-Triassic mass extinction, is the largest family of lycophyte, which is sister to other tracheophytes. It stands out from tracheophytes by exhibiting extraordinary habitat diversity and lacking polyploidization. The organelle genome-based phylogenies confirmed the monophyly of Selaginella, with six or seven subgenera grouped into two superclades, but the phylogenetic positions of the enigmatic Selaginella sanguinolenta clade remained problematic. Here, we conducted a phylogenomic study on Selaginellaceae utilizing large-scale nuclear gene data from RNA-seq to elucidate the phylogeny and explore the causes of the phylogenetic incongruence of the S. sanguinolenta clade. Our phylogenetic analyses resolved three different positions of the S. sanguinolenta clade, which were supported by the sorted three nuclear gene sets, respectively. The results from the gene flow test, species network inference, and plastome-based phylogeny congruently suggested a probable hybrid origin of the S. sanguinolenta clade involving each common ancestor of the two superclades in Selaginellaceae. The hybrid hypothesis is corroborated by the evidence from rhizophore morphology and spore micromorphology. The chromosome observation and Ks distributions further suggested hybridization accompanied by polyploidization. Divergence time estimation based on independent datasets from nuclear gene sets and plastid genome data congruently inferred that allopolyploidization occurred in the Early Triassic. To our best knowledge, the allopolyploidization in the Mesozoic reported here represents the earliest record of tracheophytes. Our study revealed a unique triad of phylogenetic positions for a hybrid-originated group with comprehensive evidence and proposed a hypothesis for retaining both parental alleles through gene conversion.
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Affiliation(s)
- Jong-Soo Kang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Ji-Gao Yu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- China National Botanical Garden, Beijing 100093, China
| | - Qiao-Ping Xiang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Xian-Chun Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
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Huang YH, Sun YF, Li H, Li HS, Pang H. PhyloAln: A Convenient Reference-Based Tool to Align Sequences and High-Throughput Reads for Phylogeny and Evolution in the Omic Era. Mol Biol Evol 2024; 41:msae150. [PMID: 39041199 PMCID: PMC11287380 DOI: 10.1093/molbev/msae150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/15/2024] [Accepted: 07/16/2024] [Indexed: 07/24/2024] Open
Abstract
The current trend in phylogenetic and evolutionary analyses predominantly relies on omic data. However, prior to core analyses, traditional methods typically involve intricate and time-consuming procedures, including assembly from high-throughput reads, decontamination, gene prediction, homology search, orthology assignment, multiple sequence alignment, and matrix trimming. Such processes significantly impede the efficiency of research when dealing with extensive data sets. In this study, we develop PhyloAln, a convenient reference-based tool capable of directly aligning high-throughput reads or complete sequences with existing alignments as a reference for phylogenetic and evolutionary analyses. Through testing with simulated data sets of species spanning the tree of life, PhyloAln demonstrates consistently robust performance compared with other reference-based tools across different data types, sequencing technologies, coverages, and species, with percent completeness and identity at least 50 percentage points higher in the alignments. Additionally, we validate the efficacy of PhyloAln in removing a minimum of 90% foreign and 70% cross-contamination issues, which are prevalent in sequencing data but often overlooked by other tools. Moreover, we showcase the broad applicability of PhyloAln by generating alignments (completeness mostly larger than 80%, identity larger than 90%) and reconstructing robust phylogenies using real data sets of transcriptomes of ladybird beetles, plastid genes of peppers, or ultraconserved elements of turtles. With these advantages, PhyloAln is expected to facilitate phylogenetic and evolutionary analyses in the omic era. The tool is accessible at https://github.com/huangyh45/PhyloAln.
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Affiliation(s)
- Yu-Hao Huang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen 518107, China
| | - Yi-Fei Sun
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen 518107, China
| | - Hao Li
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen 518107, China
| | - Hao-Sen Li
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen 518107, China
| | - Hong Pang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen 518107, China
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Contreras MP, Pai H, Thompson R, Marchal C, Claeys J, Adachi H, Kamoun S. The nucleotide-binding domain of NRC-dependent disease resistance proteins is sufficient to activate downstream helper NLR oligomerization and immune signaling. THE NEW PHYTOLOGIST 2024; 243:345-361. [PMID: 38757730 DOI: 10.1111/nph.19818] [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: 12/03/2023] [Accepted: 04/23/2024] [Indexed: 05/18/2024]
Abstract
Nucleotide-binding domain and leucine-rich repeat (NLR) proteins with pathogen sensor activities have evolved to initiate immune signaling by activating helper NLRs. However, the mechanisms underpinning helper NLR activation by sensor NLRs remain poorly understood. Although coiled coil (CC) type sensor NLRs such as the Potato virus X disease resistance protein Rx have been shown to activate the oligomerization of their downstream helpers NRC2, NRC3 and NRC4, the domains involved in sensor-helper signaling are not known. Here, we used Agrobacterium tumefaciens-mediated transient expression in Nicotiana benthamiana to show that the nucleotide-binding (NB) domain within the NB-ARC of Rx is necessary and sufficient for oligomerization and immune signaling of downstream helper NLRs. In addition, the NB domains of the disease resistance proteins Gpa2 (cyst nematode resistance), Rpi-amr1, Rpi-amr3 (oomycete resistance) and Sw-5b (virus resistance) are also sufficient to activate their respective downstream NRC helpers. Using transient expression in the lettuce (Lactuca sativa), we show that Rx (both as full length or as NB domain truncation) and its helper NRC2 form a minimal functional unit that can be transferred from solanaceous plants (lamiids) to Campanulid species. Our results challenge the prevailing paradigm that NLR proteins exclusively signal via their N-terminal domains and reveal a signaling activity for the NB domain of NRC-dependent sensor NLRs. We propose a model in which helper NLRs can perceive the status of the NB domain of their upstream sensors.
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Affiliation(s)
- Mauricio P Contreras
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Hsuan Pai
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Rebecca Thompson
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Clemence Marchal
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Jules Claeys
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Hiroaki Adachi
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Sophien Kamoun
- The Sainsbury Laboratory, University of East Anglia, Norwich Research Park, Norwich, NR4 7UH, UK
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4
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Chen H, Zwaenepoel A, Van de Peer Y. wgd v2: a suite of tools to uncover and date ancient polyploidy and whole-genome duplication. Bioinformatics 2024; 40:btae272. [PMID: 38632086 PMCID: PMC11078771 DOI: 10.1093/bioinformatics/btae272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 03/10/2024] [Accepted: 04/16/2024] [Indexed: 04/19/2024] Open
Abstract
MOTIVATION Major improvements in sequencing technologies and genome sequence assembly have led to a huge increase in the number of available genome sequences. In turn, these genome sequences form an invaluable source for evolutionary, ecological, and comparative studies. One kind of analysis that has become routine is the search for traces of ancient polyploidy, particularly for plant genomes, where whole-genome duplication (WGD) is rampant. RESULTS Here, we present a major update of a previously developed tool wgd, namely wgd v2, to look for remnants of ancient polyploidy, or WGD. We implemented novel and improved previously developed tools to (a) construct KS age distributions for the whole-paranome (collection of all duplicated genes in a genome), (b) unravel intragenomic and intergenomic collinearity resulting from WGDs, (c) fit mixture models to age distributions of gene duplicates, (d) correct substitution rate variation for phylogenetic placement of WGDs, and (e) date ancient WGDs via phylogenetic dating of WGD-retained gene duplicates. The applicability and feasibility of wgd v2 for the identification and the relative and absolute dating of ancient WGDs is demonstrated using different plant genomes. AVAILABILITY AND IMPLEMENTATION wgd v2 is open source and available at https://github.com/heche-psb/wgd.
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Affiliation(s)
- Hengchi Chen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, VIB, Ghent 9052, Belgium
| | - Arthur Zwaenepoel
- UMR 8198, Evo-Eco-Paleo, University of Lille, CNRS, Lille, F-59000, France
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, VIB, Ghent 9052, Belgium
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
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Zhang G, Ma H. Nuclear phylogenomics of angiosperms and insights into their relationships and evolution. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:546-578. [PMID: 38289011 DOI: 10.1111/jipb.13609] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/03/2024] [Indexed: 02/06/2024]
Abstract
Angiosperms (flowering plants) are by far the most diverse land plant group with over 300,000 species. The sudden appearance of diverse angiosperms in the fossil record was referred to by Darwin as the "abominable mystery," hence contributing to the heightened interest in angiosperm evolution. Angiosperms display wide ranges of morphological, physiological, and ecological characters, some of which have probably influenced their species richness. The evolutionary analyses of these characteristics help to address questions of angiosperm diversification and require well resolved phylogeny. Following the great successes of phylogenetic analyses using plastid sequences, dozens to thousands of nuclear genes from next-generation sequencing have been used in angiosperm phylogenomic analyses, providing well resolved phylogenies and new insights into the evolution of angiosperms. In this review we focus on recent nuclear phylogenomic analyses of large angiosperm clades, orders, families, and subdivisions of some families and provide a summarized Nuclear Phylogenetic Tree of Angiosperm Families. The newly established nuclear phylogenetic relationships are highlighted and compared with previous phylogenetic results. The sequenced genomes of Amborella, Nymphaea, Chloranthus, Ceratophyllum, and species of monocots, Magnoliids, and basal eudicots, have facilitated the phylogenomics of relationships among five major angiosperms clades. All but one of the 64 angiosperm orders were included in nuclear phylogenomics with well resolved relationships except the placements of several orders. Most families have been included with robust and highly supported placements, especially for relationships within several large and important orders and families. Additionally, we examine the divergence time estimation and biogeographic analyses of angiosperm on the basis of the nuclear phylogenomic frameworks and discuss the differences compared with previous analyses. Furthermore, we discuss the implications of nuclear phylogenomic analyses on ancestral reconstruction of morphological, physiological, and ecological characters of angiosperm groups, limitations of current nuclear phylogenomic studies, and the taxa that require future attention.
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Affiliation(s)
- Guojin Zhang
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Hong Ma
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
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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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Yu X, Feng Y, Zhang J. Characterization of the Complete Mitochondrial Genome of Wintersweet ( Chimonanthus praecox) and Comparative Analysis within Magnoliids. Life (Basel) 2024; 14:182. [PMID: 38398691 PMCID: PMC10890521 DOI: 10.3390/life14020182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
Mitochondrial genome sequencing is a valuable tool for investigating mitogenome evolution, species phylogeny, and population genetics. Chimonanthus praecox (L.) Link, also known as "La Mei" in Chinese, is a famous ornamental and medical shrub belonging to the order Laurales of the Calycanthaceae family. Although the nuclear genomes and chloroplast genomes of certain Laurales representatives, such as Lindera glauca, Laurus nobilis, and Piper nigrum, have been sequenced, the mitochondrial genome of Laurales members remains unknown. Here, we reported the first complete mitogenome of C. praecox. The mitogenome was 972,347 bp in length and comprised 60 unique coding genes, including 40 protein-coding genes (PCGs), 17 tRNA genes, and three rRNA genes. The skewness of the PCGs showed that the AT skew (-0.0096233) was negative, while the GC skew (0.031656) was positive, indicating higher contents of T's and G's in the mitochondrial genome of C. praecox. The Ka/Ks ratio analysis showed that the Ka/Ks values of most genes were less than one, suggesting that these genes were under purifying selection. Furthermore, there is a substantial abundance of dispersed repeats in C. praecox, constituting 16.98% of the total mitochondrial genome. A total of 731 SSR repeats were identified in the mitogenome, the highest number among the eleven available magnoliids mitogenomes. The mitochondrial phylogenetic analysis based on 29 conserved PCGs placed the C. praecox in Lauraceae, and supported the sister relationship of Laurales with Magnoliales, which was congruent with the nuclear genome evidence. The present study enriches the mitogenome data of C. praecox and promotes further studies on phylogeny and plastid evolution.
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Affiliation(s)
- Xianxian Yu
- College of Urban and Environmental Sciences, Xuchang University, Xuchang 461000, China;
| | - Yanlei Feng
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China;
| | - Jie Zhang
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China
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Dylus D, Altenhoff A, Majidian S, Sedlazeck FJ, Dessimoz C. Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree. Nat Biotechnol 2024; 42:139-147. [PMID: 37081138 PMCID: PMC10791578 DOI: 10.1038/s41587-023-01753-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 03/16/2023] [Indexed: 04/22/2023]
Abstract
Current methods for inference of phylogenetic trees require running complex pipelines at substantial computational and labor costs, with additional constraints in sequencing coverage, assembly and annotation quality, especially for large datasets. To overcome these challenges, we present Read2Tree, which directly processes raw sequencing reads into groups of corresponding genes and bypasses traditional steps in phylogeny inference, such as genome assembly, annotation and all-versus-all sequence comparisons, while retaining accuracy. In a benchmark encompassing a broad variety of datasets, Read2Tree is 10-100 times faster than assembly-based approaches and in most cases more accurate-the exception being when sequencing coverage is high and reference species very distant. Here, to illustrate the broad applicability of the tool, we reconstruct a yeast tree of life of 435 species spanning 590 million years of evolution. We also apply Read2Tree to >10,000 Coronaviridae samples, accurately classifying highly diverse animal samples and near-identical severe acute respiratory syndrome coronavirus 2 sequences on a single tree. The speed, accuracy and versatility of Read2Tree enable comparative genomics at scale.
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Affiliation(s)
- David Dylus
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- F. Hoffmann-La Roche Ltd, Immunology, Infectious Disease, and Ophthalmology (I2O), Roche Pharmaceutical Research and Early Development (pRED), Basel, Switzerland
| | - Adrian Altenhoff
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Computer Science, ETH, Zurich, Switzerland
| | - Sina Majidian
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Computer Science, Rice University, Houston, TX, USA.
| | - Christophe Dessimoz
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Department of Computer Science, University College London, London, UK.
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
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9
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Wang J, Ma X, Hu Y, Feng G, Guo C, Zhang X, Ma H. Regulation of micro- and small-exon retention and other splicing processes by GRP20 for flower development. NATURE PLANTS 2024; 10:66-85. [PMID: 38195906 PMCID: PMC10808074 DOI: 10.1038/s41477-023-01605-8] [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: 11/11/2022] [Accepted: 11/29/2023] [Indexed: 01/11/2024]
Abstract
Pre-mRNA splicing is crucial for gene expression and depends on the spliceosome and splicing factors. Plant exons have an average size of ~180 nucleotides and typically contain motifs for interactions with spliceosome and splicing factors. Micro exons (<51 nucleotides) are found widely in eukaryotes and in genes for plant development and environmental responses. However, little is known about transcript-specific regulation of splicing in plants and about the regulators for micro exon splicing. Here we report that glycine-rich protein 20 (GRP20) is an RNA-binding protein and required for splicing of ~2,100 genes including those functioning in flower development and/or environmental responses. Specifically, GRP20 is required for micro-exon retention in transcripts of floral homeotic genes; these micro exons are conserved across angiosperms. GRP20 is also important for small-exon (51-100 nucleotides) splicing. In addition, GRP20 is required for flower development. Furthermore, GRP20 binds to poly-purine motifs in micro and small exons and a spliceosome component; both RNA binding and spliceosome interaction are important for flower development and micro-exon retention. Our results provide new insights into the mechanisms of micro-exon retention in flower development.
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Affiliation(s)
- Jun Wang
- Department of Biology, Eberly College of Science, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Xinwei Ma
- Department of Biology, Eberly College of Science, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Yi Hu
- Department of Biology, Eberly College of Science, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Guanhua Feng
- Department of Biology, Eberly College of Science, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA
| | - Chunce Guo
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University, Nanchang, China
| | - Xin Zhang
- Department of Chemistry and Department of Biochemistry and Molecular Biology, Eberly College of Science, Pennsylvania State University, University Park, PA, USA
| | - Hong Ma
- Department of Biology, Eberly College of Science, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA.
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10
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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: 4.0] [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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11
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Sha N, Li Z, Sun Q, Han Y, Tian L, Wu Y, Li X, Shi Y, Zhang J, Peng J, Wang L, Dang Z, Liang C. Elucidation of the evolutionary history of Stipa in China using comparative transcriptomic analysis. FRONTIERS IN PLANT SCIENCE 2023; 14:1275018. [PMID: 38148860 PMCID: PMC10751131 DOI: 10.3389/fpls.2023.1275018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/08/2023] [Indexed: 12/28/2023]
Abstract
Phylogenetic analysis provides crucial insights into the evolutionary relationships and diversification patterns within specific taxonomic groups. In this study, we aimed to identify the phylogenetic relationships and explore the evolutionary history of Stipa using transcriptomic data. Samples of 12 Stipa species were collected from the Qinghai-Tibet Plateau and Mongolian Plateau, where they are widely distributed, and transcriptome sequencing was performed using their fresh spikelet tissues. Using bidirectional best BLAST analysis, we identified two sets of one-to-one orthologous genes shared between Brachypodium distachyon and the 12 Stipa species (9397 and 2300 sequences, respectively), as well as 62 single-copy orthologous genes. Concatenation methods were used to construct a robust phylogenetic tree for Stipa, and molecular dating was used to estimate divergence times. Our results indicated that Stipa originated during the Pliocene. In approximately 0.8 million years, it diverged into two major clades each consisting of native species from the Mongolian Plateau and the Qinghai-Tibet Plateau, respectively. The evolution of Stipa was closely associated with the development of northern grassland landscapes. Important external factors such as global cooling during the Pleistocene, changes in monsoonal circulation, and tectonic movements contributed to the diversification of Stipa. This study provided a highly supported phylogenetic framework for understanding the evolution of the Stipa genus in China and insights into its diversification patterns.
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Affiliation(s)
- Na Sha
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, Ministry of Education of China, Collaborative Innovation Center for Grassland Ecological Security, School of Ecology and Environment, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Zhiyong Li
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, Ministry of Education of China, Collaborative Innovation Center for Grassland Ecological Security, School of Ecology and Environment, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Qiang Sun
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, Ministry of Education of China, Collaborative Innovation Center for Grassland Ecological Security, School of Ecology and Environment, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Ying Han
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, Ministry of Education of China, Collaborative Innovation Center for Grassland Ecological Security, School of Ecology and Environment, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Li Tian
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, Ministry of Education of China, Collaborative Innovation Center for Grassland Ecological Security, School of Ecology and Environment, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Yantao Wu
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, Ministry of Education of China, Collaborative Innovation Center for Grassland Ecological Security, School of Ecology and Environment, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Xing Li
- Institute of Landscape and Environment, Inner Mongolia Academy of Forestry Science, Hohhot, Inner Mongolia, China
| | - Yabo Shi
- School of Resources and Environment, Baotou Teachers’ College, Baotou, Inner Mongolia, China
| | - Jinghui Zhang
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, Ministry of Education of China, Collaborative Innovation Center for Grassland Ecological Security, School of Ecology and Environment, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Jiangtao Peng
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, Ministry of Education of China, Collaborative Innovation Center for Grassland Ecological Security, School of Ecology and Environment, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Lixin Wang
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, Ministry of Education of China, Collaborative Innovation Center for Grassland Ecological Security, School of Ecology and Environment, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Zhenhua Dang
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, Ministry of Education of China, Collaborative Innovation Center for Grassland Ecological Security, School of Ecology and Environment, Inner Mongolia University, Hohhot, Inner Mongolia, China
| | - Cunzhu Liang
- Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, Ministry of Education of China, Collaborative Innovation Center for Grassland Ecological Security, School of Ecology and Environment, Inner Mongolia University, Hohhot, Inner Mongolia, China
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12
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Niu Y, Liu L. RNA pseudouridine modification in plants. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6431-6447. [PMID: 37581601 DOI: 10.1093/jxb/erad323] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/11/2023] [Indexed: 08/16/2023]
Abstract
Pseudouridine is one of the well-known chemical modifications in various RNA species. Current advances to detect pseudouridine show that the pseudouridine landscape is dynamic and affects multiple cellular processes. Although our understanding of this post-transcriptional modification mainly depends on yeast and human models, the recent findings provide strong evidence for the critical role of pseudouridine in plants. Here, we review the current knowledge of pseudouridine in plant RNAs, including its synthesis, degradation, regulatory mechanisms, and functions. Moreover, we propose future areas of research on pseudouridine modification in plants.
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Affiliation(s)
- Yanli Niu
- Laboratory of Cell Signal Transduction, School of Basic Medical Sciences, Henan University, Kaifeng 475001, China
| | - Lingyun Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng 475001, China
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13
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Zhang Q, Folk RA, Mo ZQ, Ye H, Zhang ZY, Peng H, Zhao JL, Yang SX, Yu XQ. Phylotranscriptomic analyses reveal deep gene tree discordance in Camellia (Theaceae). Mol Phylogenet Evol 2023; 188:107912. [PMID: 37648181 DOI: 10.1016/j.ympev.2023.107912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 08/09/2023] [Accepted: 08/27/2023] [Indexed: 09/01/2023]
Abstract
Gene tree discordance is a significant legacy of biological evolution. Multiple factors can result in incongruence among genes, such as introgression, incomplete lineage sorting (ILS), gene duplication or loss. Resolving the background of gene tree discordance is a critical way to uncover the process of species diversification. Camellia, the largest genus in Theaceae, has controversial taxonomy and systematics due in part to a complex evolutionary history. We used 60 transcriptomes of 55 species, which represented 15 sections of Camellia to investigate its phylogeny and the possible causes of gene tree discordance. We conducted gene tree discordance analysis based on 1,617 orthologous low-copy nuclear genes, primarily using coalescent species trees and polytomy tests to distinguish hard and soft conflict. A selective pressure analysis was also performed to assess the impact of selection on phylogenetic topology reconstruction. Our results detected different levels of gene tree discordance in the backbone of Camellia, and recovered rapid diversification as one of the possible causes of gene tree discordance. Furthermore, we confirmed that none of the currently proposed sections of Camellia was monophyletic. Comparisons among datasets partitioned under different selective pressure regimes showed that integrating all orthologous genes provided the best phylogenetic resolution of the species tree of Camellia. The findings of this study reveal rapid diversification as a major source of gene tree discordance in Camellia and will facilitate future investigation of reticulate relationships at the species level in this important plant genus.
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Affiliation(s)
- Qiong Zhang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ryan A Folk
- Department of Biological Sciences, Mississippi State University, MS 39762, United States
| | - Zhi-Qiong Mo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Hang Ye
- Guangxi Key Laboratory of Special Non-wood Forest Cultivation and Utilization, Guangxi Forestry Research Institute, Nanning 530002, Guangxi, China
| | - Zhao-Yuan Zhang
- Guangxi Key Laboratory of Special Non-wood Forest Cultivation and Utilization, Guangxi Forestry Research Institute, Nanning 530002, Guangxi, China
| | - Hua Peng
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Jian-Li Zhao
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology and Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming 650091, China.
| | - Shi-Xiong Yang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - Xiang-Qin Yu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
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14
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Renner SS. A time tree for the evolution of insect, vertebrate, wind, and water pollination in the angiosperms. THE NEW PHYTOLOGIST 2023; 240:464-465. [PMID: 37564031 DOI: 10.1111/nph.19201] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
This article is a Commentary on Stephens et al. (2023), 240: 880–891.
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Affiliation(s)
- Susanne S Renner
- Department of Biology, Washington University, St Louis, MO, 63130, USA
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15
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Liu L, Chen M, Folk RA, Wang M, Zhao T, Shang F, Soltis DE, Li P. Phylogenomic and syntenic data demonstrate complex evolutionary processes in early radiation of the rosids. Mol Ecol Resour 2023; 23:1673-1688. [PMID: 37449554 DOI: 10.1111/1755-0998.13833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/16/2023] [Accepted: 06/30/2023] [Indexed: 07/18/2023]
Abstract
Some of the most vexing problems of deep level relationship that remain in angiosperms involve the superrosids. The superrosid clade contains a quarter of all angiosperm species, with 18 orders in three subclades (Vitales, Saxifragales and core rosids) exhibiting remarkable morphological and ecological diversity. To help resolve deep-level relationships, we constructed a high-quality chromosome-level genome assembly for Tiarella polyphylla (Saxifragaceae) thus providing broader genomic representation of Saxifragales. Whole genome microsynteny analysis of superrosids showed that Saxifragales shared more synteny clusters with core rosids than Vitales, further supporting Saxifragales as more closely related with core rosids. To resolve the ordinal phylogeny of superrosids, we screened 122 single copy nuclear genes from genomes of 36 species, representing all 18 superrosid orders. Vitales were recovered as sister to all other superrosids (Saxifragales + core rosids). Our data suggest dramatic differences in relationships compared to earlier studies within core rosids. Fabids should be restricted to the nitrogen-fixing clade, while Picramniales, the Celastrales-Malpighiales (CM) clade, Huerteales, Oxalidales, Sapindales, Malvales and Brassicales formed an "expanded" malvid clade. The Celastrales-Oxalidales-Malpighiales (COM) clade (sensu APG IV) was not monophyletic. Crossosomatales, Geraniales, Myrtales and Zygophyllales did not belong to either of our well-supported malvids or fabids. There is strong discordance between nuclear and plastid phylogenetic hypotheses for superrosid relationships; we show that this is best explained by a combination of incomplete lineage sorting and ancient reticulation.
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Affiliation(s)
- Luxian Liu
- Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng, Henan, China
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Mengzhen Chen
- Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng, Henan, China
| | - Ryan A Folk
- Department of Biological Sciences, Mississippi State University, Starkville, Mississippi, USA
| | - Meizhen Wang
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Tao Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China
| | - Fude Shang
- Laboratory of Plant Germplasm and Genetic Engineering, School of Life Sciences, Henan University, Kaifeng, Henan, China
- Henan Engineering Research Center for Osmanthus Germplasm Innovation and Resource Utilization, Henan Agricultural University, Zhengzhou, Henan, China
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | - Pan Li
- Systematic & Evolutionary Botany and Biodiversity Group, MOE Key Laboratory of Biosystems Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
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16
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Sreedasyam A, Plott C, Hossain MS, Lovell J, Grimwood J, Jenkins J, Daum C, Barry K, Carlson J, Shu S, Phillips J, Amirebrahimi M, Zane M, Wang M, Goodstein D, Haas F, Hiss M, Perroud PF, Jawdy S, Yang Y, Hu R, Johnson J, Kropat J, Gallaher S, Lipzen A, Shakirov E, Weng X, Torres-Jerez I, Weers B, Conde D, Pappas M, Liu L, Muchlinski A, Jiang H, Shyu C, Huang P, Sebastian J, Laiben C, Medlin A, Carey S, Carrell A, Chen JG, Perales M, Swaminathan K, Allona I, Grattapaglia D, Cooper E, Tholl D, Vogel J, Weston DJ, Yang X, Brutnell T, Kellogg E, Baxter I, Udvardi M, Tang Y, Mockler T, Juenger T, Mullet J, Rensing S, Tuskan G, Merchant S, Stacey G, Schmutz J. JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom. Nucleic Acids Res 2023; 51:8383-8401. [PMID: 37526283 PMCID: PMC10484672 DOI: 10.1093/nar/gkad616] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 06/21/2023] [Accepted: 07/11/2023] [Indexed: 08/02/2023] Open
Abstract
Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources to decipher gene function and subsequently provide molecular targets for plant improvement through gene editing. However, biological roles of large proportions of genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, an updateable data resource consisting of transcript abundance assays spanning 18 diverse species. To integrate across these diverse genotypes, we analyzed expression profiles, built gene clusters that exhibited tissue/condition specific expression, and tested for transcriptional response to environmental queues. We discovered extensive phylogenetically constrained and condition-specific expression profiles for genes without any previously documented functional annotation. Such conserved expression patterns and tightly co-expressed gene clusters let us assign expression derived additional biological information to 64 495 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome.jgi.doe.gov/), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.
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Affiliation(s)
| | | | - Md Shakhawat Hossain
- Division of Plant Science and Technology, C.S. Bond Life Science Center, University of Missouri, Columbia, MO, USA
| | - John T Lovell
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jerry W Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Christopher Daum
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kerrie Barry
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Joseph Carlson
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Shengqiang Shu
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jeremy Phillips
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mojgan Amirebrahimi
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Matthew Zane
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mei Wang
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David Goodstein
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Fabian B Haas
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str, Marburg, Germany
| | - Manuel Hiss
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str, Marburg, Germany
| | - Pierre-François Perroud
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str, Marburg, Germany
| | - Sara S Jawdy
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Yongil Yang
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Rongbin Hu
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jenifer Johnson
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Janette Kropat
- Department of Chemistry and Biochemistry and Institute for Genomics and Proteomics, University of California, Los Angeles, CA, USA
| | - Sean D Gallaher
- Department of Chemistry and Biochemistry and Institute for Genomics and Proteomics, University of California, Los Angeles, CA, USA
| | - Anna Lipzen
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Eugene V Shakirov
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Xiaoyu Weng
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | | | - Brock Weers
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Daniel Conde
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Marilia R Pappas
- Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, EPQB Final W5 Norte, Brasília, Brazil
| | - Lifeng Liu
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrew Muchlinski
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Hui Jiang
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Christine Shyu
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Pu Huang
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Jose Sebastian
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Carol Laiben
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Alyssa Medlin
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Sankalpi Carey
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Alyssa A Carrell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Mariano Perales
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | | | - Isabel Allona
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Dario Grattapaglia
- Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, EPQB Final W5 Norte, Brasília, Brazil
| | | | - Dorothea Tholl
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - John P Vogel
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Xiaohan Yang
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | | | - Ivan Baxter
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | | | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - John Mullet
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str, Marburg, Germany
| | - Gerald A Tuskan
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry and Institute for Genomics and Proteomics, University of California, Los Angeles, CA, USA
| | - Gary Stacey
- Division of Plant Science and Technology, C.S. Bond Life Science Center, University of Missouri, Columbia, MO, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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17
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Brazão JM, Foster PG, Cox CJ. Data-specific substitution models improve protein-based phylogenetics. PeerJ 2023; 11:e15716. [PMID: 37576497 PMCID: PMC10416777 DOI: 10.7717/peerj.15716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/16/2023] [Indexed: 08/15/2023] Open
Abstract
Calculating amino-acid substitution models that are specific for individual protein data sets is often difficult due to the computational burden of estimating large numbers of rate parameters. In this study, we tested the computational efficiency and accuracy of five methods used to estimate substitution models, namely Codeml, FastMG, IQ-TREE, P4 (maximum likelihood), and P4 (Bayesian inference). Data-specific substitution models were estimated from simulated alignments (with different lengths) that were generated from a known simulation model and simulation tree. Each of the resulting data-specific substitution models was used to calculate the maximum likelihood score of the simulation tree and simulated data that was used to calculate the model, and compared with the maximum likelihood scores of the known simulation model and simulation tree on the same simulated data. Additionally, the commonly-used empirical models, cpREV and WAG, were assessed similarly. Data-specific models performed better than the empirical models, which under-fitted the simulated alignments, had the highest difference to the simulation model maximum-likelihood score, clustered further from the simulation model in principal component analysis ordination, and inferred less accurate trees. Data-specific models and the simulation model shared statistically indistinguishable maximum-likelihood scores, indicating that the five methods were reasonably accurate at estimating substitution models by this measure. Nevertheless, tree statistics showed differences between optimal maximum likelihood trees. Unlike other model estimating methods, trees inferred using data-specific models generated with IQ-TREE and P4 (maximum likelihood) were not significantly different from the trees derived from the simulation model in each analysis, indicating that these two methods alone were the most accurate at estimating data-specific models. To show the benefits of using data-specific protein models several published data sets were reanalysed using IQ-TREE-estimated models. These newly estimated models were a better fit to the data than the empirical models that were used by the original authors, often inferred longer trees, and resulted in different tree topologies in more than half of the re-analysed data sets. The results of this study show that software availability and high computation burden are not limitations to generating better-fitting data-specific amino-acid substitution models for phylogenetic analyses.
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Affiliation(s)
- João M. Brazão
- Centro de Ciências do Mar, Universidade do Algarve, Faro, Algarve, Portugal
| | - Peter G. Foster
- Department of Life Sciences, Natural History Museum, London, United Kingdom
| | - Cymon J. Cox
- Centro de Ciências do Mar, Universidade do Algarve, Faro, Algarve, Portugal
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18
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Hu J, Qiu S, Wang F, Li Q, Xiang CL, Di P, Wu Z, Jiang R, Li J, Zeng Z, Wang J, Wang X, Zhang Y, Fang S, Qiao Y, Ding J, Jiang Y, Xu Z, Chen J, Chen W. Functional divergence of CYP76AKs shapes the chemodiversity of abietane-type diterpenoids in genus Salvia. Nat Commun 2023; 14:4696. [PMID: 37542034 PMCID: PMC10403556 DOI: 10.1038/s41467-023-40401-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 07/26/2023] [Indexed: 08/06/2023] Open
Abstract
The genus Salvia L. (Lamiaceae) comprises myriad distinct medicinal herbs, with terpenoids as one of their major active chemical groups. Abietane-type diterpenoids (ATDs), such as tanshinones and carnosic acids, are specific to Salvia and exhibit taxonomic chemical diversity among lineages. To elucidate how ATD chemical diversity evolved, we carried out large-scale metabolic and phylogenetic analyses of 71 Salvia species, combined with enzyme function, ancestral sequence and chemical trait reconstruction, and comparative genomics experiments. This integrated approach showed that the lineage-wide ATD diversities in Salvia were induced by differences in the oxidation of the terpenoid skeleton at C-20, which was caused by the functional divergence of the cytochrome P450 subfamily CYP76AK. These findings present a unique pattern of chemical diversity in plants that was shaped by the loss of enzyme activity and associated catalytic pathways.
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Affiliation(s)
- Jiadong Hu
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Department of Pharmacy, Second Affiliated Hospital of Navy Medical University, Shanghai, 200003, China
| | - Shi Qiu
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Feiyan Wang
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Qing Li
- Department of Pharmacy, Second Affiliated Hospital of Navy Medical University, Shanghai, 200003, China
| | - Chun-Lei Xiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Peng Di
- State Local Joint Engineering Research Center of Ginseng Breeding and Application, College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, China
| | - Ziding Wu
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Rui Jiang
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Jinxing Li
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Zhen Zeng
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Jing Wang
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Xingxing Wang
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yuchen Zhang
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Shiyuan Fang
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yuqi Qiao
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Jie Ding
- Urban Horticulture Research and Extension Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yun Jiang
- Urban Horticulture Research and Extension Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Zhichao Xu
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China.
| | - Junfeng Chen
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Wansheng Chen
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
- Department of Pharmacy, Second Affiliated Hospital of Navy Medical University, Shanghai, 200003, China.
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19
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Tai HC, Chang CH, Cai W, Lin JH, Huang SJ, Lin QY, Yuan ECY, Li SL, Lin YCJ, Chan JCC, Tsao CS. Wood cellulose microfibrils have a 24-chain core-shell nanostructure in seed plants. NATURE PLANTS 2023; 9:1154-1168. [PMID: 37349550 DOI: 10.1038/s41477-023-01430-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/08/2023] [Indexed: 06/24/2023]
Abstract
Wood cellulose microfibril (CMF) is the most abundant organic substance on Earth but its nanostructure remains poorly understood. There are controversies regarding the glucan chain number (N) of CMFs during initial synthesis and whether they become fused afterward. Here, we combined small-angle X-ray scattering, solid-state nuclear magnetic resonance and X-ray diffraction analyses to resolve CMF nanostructures in native wood. We developed small-angle X-ray scattering measurement methods for the cross-section aspect ratio and area of the crystalline-ordered CMF core, which has a higher scattering length density than the semidisordered shell zone. The 1:1 aspect ratio suggested that CMFs remain mostly segregated, not fused. The area measurement reflected the chain number in the core zone (Ncore). To measure the ratio of ordered cellulose over total cellulose (Roc) by solid-state nuclear magnetic resonance, we developed a method termed global iterative fitting of T1ρ-edited decay (GIFTED), in addition to the conventional proton spin relaxation editing method. Using the formula N = Ncore/Roc, most wood CMFs were found to contain 24 glucan chains, conserved between gymnosperm and angiosperm trees. The average CMF has a crystalline-ordered core of ~2.2 nm diameter and a semidisordered shell of ~0.5 nm thickness. In naturally and artificially aged wood, we observed only CMF aggregation (contact without crystalline continuity) but not fusion (forming a conjoined crystalline unit). This further argued against the existence of partially fused CMFs in new wood, overturning the recently proposed 18-chain fusion hypothesis. Our findings are important for advancing wood structural knowledge and more efficient use of wood resources in sustainable bio-economies.
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Affiliation(s)
- Hwan-Ching Tai
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, National Innovation Platform for Industry-Education Integration in Vaccine Research, School of Public Health, Xiamen University, Xiamen, People's Republic of China.
| | - Chih-Hui Chang
- Department of Chemistry, National Taiwan University, Taipei, Republic of China
| | - Wenjie Cai
- School of Cultural Industry and Tourism and Cultural Industry Research Center, Fujian Social Science Research Base, Xiamen University of Technology, Xiamen, People's Republic of China
| | - Jer-Horng Lin
- Department of Chemistry, National Taiwan University, Taipei, Republic of China
| | - Shing-Jong Huang
- Instrumentation Center, National Taiwan University, Taipei, Republic of China
| | - Qian-Yan Lin
- Department of Chemistry, National Taiwan University, Taipei, Republic of China
| | | | - Shu-Li Li
- Department of Chemistry, National Taiwan University, Taipei, Republic of China
| | - Ying-Chung Jimmy Lin
- Department of Life Science and Institute of Plant Biology, National Taiwan University, Taipei, Republic of China
| | | | - Cheng-Si Tsao
- Department of Materials Science and Engineering, National Taiwan University, Taipei, Republic of China.
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20
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Carruthers T, Scotland RW. Deconstructing age estimates for angiosperms. Mol Phylogenet Evol 2023:107861. [PMID: 37329931 DOI: 10.1016/j.ympev.2023.107861] [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: 01/16/2023] [Revised: 06/08/2023] [Accepted: 06/13/2023] [Indexed: 06/19/2023]
Abstract
Estimates of the age of angiosperms from molecular phylogenies vary considerably. As in all estimates of evolutionary timescales from phylogenies, generating these estimates requires assumptions about the rate that molecular sequences are evolving (using clock models) and the time duration of the branches in a phylogeny (using fossil calibrations and branching processes). Often, it is difficult to demonstrate that these assumptions reflect current knowledge of molecular evolution or the fossil record. In this study we re-estimate the age of angiosperms using a minimal set of assumptions, therefore avoiding many of the assumptions inherent to other methods. The age estimates we generate are similar for each of the four datasets analysed, ranging from 130 to 400 Ma, but are far less precise than in previous studies. We demonstrate that this reduction in precision results from making less stringent assumptions about both rate and time, and that the analysed molecular dataset has very little effect on age estimates.
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Affiliation(s)
- Tom Carruthers
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA
| | - Robert W Scotland
- Department of Biology, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
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21
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Kong X, Zhang Y, Wang Z, Bao S, Feng Y, Wang J, Yu Z, Long F, Xiao Z, Hao Y, Gao X, Li Y, Ding Y, Wang J, Lei T, Xu C, Wang J. Two-step model of paleohexaploidy, ancestral genome reshuffling and plasticity of heat shock response in Asteraceae. HORTICULTURE RESEARCH 2023; 10:uhad073. [PMID: 37303613 PMCID: PMC10251138 DOI: 10.1093/hr/uhad073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/10/2023] [Indexed: 06/13/2023]
Abstract
An ancient hexaploidization event in the most but not all Asteraceae plants, may have been responsible for shaping the genomes of many horticultural, ornamental, and medicinal plants that promoting the prosperity of the largest angiosperm family on the earth. However, the duplication process of this hexaploidy, as well as the genomic and phenotypic diversity of extant Asteraceae plants caused by paleogenome reorganization, are still poorly understood. We analyzed 11 genomes from 10 genera in Asteraceae, and redated the Asteraceae common hexaploidization (ACH) event ~70.7-78.6 million years ago (Mya) and the Asteroideae specific tetraploidization (AST) event ~41.6-46.2 Mya. Moreover, we identified the genomic homologies generated from the ACH, AST and speciation events, and constructed a multiple genome alignment framework for Asteraceae. Subsequently, we revealed biased fractionations between the paleopolyploidization produced subgenomes, suggesting the ACH and AST both are allopolyplodization events. Interestingly, the paleochromosome reshuffling traces provided clear evidence for the two-step duplications of ACH event in Asteraceae. Furthermore, we reconstructed ancestral Asteraceae karyotype (AAK) that has 9 paleochromosomes, and revealed a highly flexible reshuffling of Asteraceae paleogenome. Of specific significance, we explored the genetic diversity of Heat Shock Transcription Factors (Hsfs) associated with recursive whole-genome polyploidizations, gene duplications, and paleogenome reshuffling, and revealed that the expansion of Hsfs gene families enable heat shock plasticity during the genome evolution of Asteraceae. Our study provides insights on polyploidy and paleogenome remodeling for the successful establishment of Asteraceae, and is helpful for further communication and exploration of the diversification of plant families and phenotypes.
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Affiliation(s)
| | | | | | | | - Yishan Feng
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Jiaqi Wang
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Zijian Yu
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Feng Long
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Zejia Xiao
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Yanan Hao
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Xintong Gao
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Yinfeng Li
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Yue Ding
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Jianyu Wang
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
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22
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Tian XC, Guo JF, Yan XM, Shi TL, Nie S, Zhao SW, Bao YT, Li ZC, Kong L, Su GJ, Mao JF, Lin J. Unique gene duplications and conserved microsynteny potentially associated with resistance to wood decay in the Lauraceae. FRONTIERS IN PLANT SCIENCE 2023; 14:1122549. [PMID: 36968354 PMCID: PMC10030967 DOI: 10.3389/fpls.2023.1122549] [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: 12/13/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Wood decay resistance (WDR) is marking the value of wood utilization. Many trees of the Lauraceae have exceptional WDR, as evidenced by their use in ancient royal palace buildings in China. However, the genetics of WDR remain elusive. Here, through comparative genomics, we revealed the unique characteristics related to the high WDR in Lauraceae trees. We present a 1.27-Gb chromosome-level assembly for Lindera megaphylla (Lauraceae). Comparative genomics integrating major groups of angiosperm revealed Lauraceae species have extensively shared gene microsynteny associated with the biosynthesis of specialized metabolites such as isoquinoline alkaloids, flavonoid, lignins and terpenoid, which play significant roles in WDR. In Lauraceae genomes, tandem and proximal duplications (TD/PD) significantly expanded the coding space of key enzymes of biosynthesis pathways related to WDR, which may enhance the decay resistance of wood by increasing the accumulation of these compounds. Among Lauraceae species, genes of WDR-related biosynthesis pathways showed remarkable expansion by TD/PD and conveyed unique and conserved motifs in their promoter and protein sequences, suggesting conserved gene collinearity, gene expansion and gene regulation supporting the high WDR. Our study thus reveals genomic profiles related to biochemical transitions among major plant groups and the genomic basis of WDR in the Lauraceae.
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Affiliation(s)
- Xue-Chan Tian
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jing-Fang Guo
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xue-Mei Yan
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Tian-Le Shi
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Shuai Nie
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Shi-Wei Zhao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yu-Tao Bao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Zhi-Chao Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Lei Kong
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Guang-Ju Su
- National Tree Breeding Station for Nanmu in Zhuxi, Forest Farm of Zhuxi County, Hubei, China
| | - Jian-Feng Mao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Jinxing Lin
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
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23
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Yao G, Zhang YQ, Barrett C, Xue B, Bellot S, Baker WJ, Ge XJ. A plastid phylogenomic framework for the palm family (Arecaceae). BMC Biol 2023; 21:50. [PMID: 36882831 PMCID: PMC9993706 DOI: 10.1186/s12915-023-01544-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/14/2023] [Indexed: 03/09/2023] Open
Abstract
BACKGROUND Over the past decade, phylogenomics has greatly advanced our knowledge of angiosperm evolution. However, phylogenomic studies of large angiosperm families with complete species or genus-level sampling are still lacking. The palms, Arecaceae, are a large family with ca. 181 genera and 2600 species and are important components of tropical rainforests bearing great cultural and economic significance. Taxonomy and phylogeny of the family have been extensively investigated by a series of molecular phylogenetic studies in the last two decades. Nevertheless, some phylogenetic relationships within the family are not yet well-resolved, especially at the tribal and generic levels, with consequent impacts for downstream research. RESULTS Plastomes of 182 palm species representing 111 genera were newly sequenced. Combining these with previously published plastid DNA data, we were able to sample 98% of palm genera and conduct a plastid phylogenomic investigation of the family. Maximum likelihood analyses yielded a robustly supported phylogenetic hypothesis. Phylogenetic relationships among all five palm subfamilies and 28 tribes were well-resolved, and most inter-generic phylogenetic relationships were also resolved with strong support. CONCLUSIONS The inclusion of nearly complete generic-level sampling coupled with nearly complete plastid genomes strengthened our understanding of plastid-based relationships of the palms. This comprehensive plastid genome dataset complements a growing body of nuclear genomic data. Together, these datasets form a novel phylogenomic baseline for the palms and an increasingly robust framework for future comparative biological studies of this exceptionally important plant family.
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Affiliation(s)
- Gang Yao
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Yu-Qu Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.,Present Address: College of Pharmacy, Shaanxi University of Chinese Medicine, Xi'an, China
| | - Craig Barrett
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Bine Xue
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | | | | | - Xue-Jun Ge
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China. .,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, China.
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24
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Cheng L, Li M, Wang Y, Han Q, Hao Y, Qiao Z, Zhang W, Qiu L, Gong A, Zhang Z, Li T, Luo S, Tang L, Liu D, Yin H, Lu S, Balbuena TS, Zhao Y. Transcriptome-based variations effectively untangling the intraspecific relationships and selection signals in Xinyang Maojian tea population. FRONTIERS IN PLANT SCIENCE 2023; 14:1114284. [PMID: 36890899 PMCID: PMC9986275 DOI: 10.3389/fpls.2023.1114284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
As one of the world's top three popular non-alcoholic beverages, tea is economically and culturally valuable. Xinyang Maojian, this elegant green tea, is one of the top ten famous tea in China and has gained prominence for thousands of years. However, the cultivation history of Xinyang Maojian tea population and selection signals of differentiation from the other major variety Camellia sinensis var. assamica (CSA) remain unclear. We newly generated 94 Camellia sinensis (C. sinensis) transcriptomes including 59 samples in the Xinyang area and 35 samples collected from 13 other major tea planting provinces in China. Comparing the very low resolution of phylogeny inferred from 1785 low-copy nuclear genes with 94 C. sinensis samples, we successfully resolved the phylogeny of C. sinensis samples by 99,115 high-quality SNPs from the coding region. The sources of tea planted in the Xinyang area were extensive and complex. Specifically, Shihe District and Gushi County were the two earliest tea planting areas in Xinyang, reflecting a long history of tea planting. Furthermore, we identified numerous selection sweeps during the differentiation of CSA and CSS and these positive selection genes are involved in many aspects such as regulation of secondary metabolites synthesis, amino acid metabolism, photosynthesis, etc. Numerous specific selective sweeps of modern cultivars were annotated with functions in various different aspects, indicating the CSS and CSA populations possibly underwent independent specific domestication processes. Our study indicated that transcriptome-based SNP-calling is an efficient and cost-effective method in untangling intraspecific phylogenetic relationships. This study provides a significant understanding of the cultivation history of the famous Chinese tea Xinyang Maojian and unravels the genetic basis of physiological and ecological differences between the two major tea subspecies.
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Affiliation(s)
- Lin Cheng
- Henan International Joint Laboratory of Tea-oil tree Biology and High Value Utilization, Xinyang Normal University, Xinyang, Henan, China
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China
| | - Mengge Li
- Henan International Joint Laboratory of Tea-oil tree Biology and High Value Utilization, Xinyang Normal University, Xinyang, Henan, China
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China
| | - Yachao Wang
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Qunwei Han
- Henan International Joint Laboratory of Tea-oil tree Biology and High Value Utilization, Xinyang Normal University, Xinyang, Henan, China
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China
| | - Yanlin Hao
- Henan International Joint Laboratory of Tea-oil tree Biology and High Value Utilization, Xinyang Normal University, Xinyang, Henan, China
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China
| | - Zhen Qiao
- Henan International Joint Laboratory of Tea-oil tree Biology and High Value Utilization, Xinyang Normal University, Xinyang, Henan, China
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China
| | - Wei Zhang
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China
| | - Lin Qiu
- Institute of Forestry Science, Xinyang Forestry Bureau, Xinyang, Henan, China
| | - Andong Gong
- Henan International Joint Laboratory of Tea-oil tree Biology and High Value Utilization, Xinyang Normal University, Xinyang, Henan, China
- College of Life Sciences, Xinyang Normal University, Xinyang, Henan, China
| | - Zhihan Zhang
- College of Engineering and Technology, Northeast Forestry University, Harbin, China
| | - Tao Li
- College of Agriculture, Guizhou University, Guiyang, China
| | - Shanshan Luo
- College of Agriculture, Guizhou University, Guiyang, China
| | - Linshuang Tang
- College of Agriculture, Guizhou University, Guiyang, China
| | - Daliang Liu
- College of Agriculture, Guizhou University, Guiyang, China
| | - Hao Yin
- College of Agriculture, Guizhou University, Guiyang, China
| | - Song Lu
- College of Agriculture, Guizhou University, Guiyang, China
| | - Tiago Santana Balbuena
- Department of Agricultural, Livestock and Environmental Biotechnology, Sao Paulo State University, Jaboticabal, Brazil
| | - Yiyong Zhao
- College of Agriculture, Guizhou University, Guiyang, China
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25
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Zhao L, Yang YY, Qu XJ, Ma H, Hu Y, Li HT, Yi TS, Li DZ. Phylotranscriptomic analyses reveal multiple whole-genome duplication events, the history of diversification and adaptations in the Araceae. ANNALS OF BOTANY 2023; 131:199-214. [PMID: 35671385 PMCID: PMC9904356 DOI: 10.1093/aob/mcac062] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/13/2022] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS The Araceae are one of the most diverse monocot families with numerous morphological and ecological novelties. Plastid and mitochondrial genes have been used to investigate the phylogeny and to interpret shifts in the pollination biology and biogeography of the Araceae. In contrast, the role of whole-genome duplication (WGD) in the evolution of eight subfamilies remains unclear. METHODS New transcriptomes or low-depth whole-genome sequences of 65 species were generated through Illumina sequencing. We reconstructed the phylogenetic relationships of Araceae using concatenated and species tree methods, and then estimated the age of major clades using TreePL. We inferred the WGD events by Ks and gene tree methods. We investigated the diversification patterns applying time-dependent and trait-dependent models. The expansions of gene families and functional enrichments were analysed using CAFE and InterProScan. KEY RESULTS Gymnostachydoideae was the earliest diverging lineage followed successively by Orontioideae, Lemnoideae and Lasioideae. In turn, they were followed by the clade of 'bisexual climbers' comprised of Pothoideae and Monsteroideae, which was resolved as the sister to the unisexual flowers clade of Zamioculcadoideae and Aroideae. A special WGD event ψ (psi) shared by the True-Araceae clade occurred in the Early Cretaceous. Net diversification rates first declined and then increased through time in the Araceae. The best diversification rate shift along the stem lineage of the True-Araceae clade was detected, and net diversification rates were enhanced following the ψ-WGD. Functional enrichment analyses revealed that some genes, such as those encoding heat shock proteins, glycosyl hydrolase and cytochrome P450, expanded within the True-Araceae clade. CONCLUSIONS Our results improve our understanding of aroid phylogeny using the large number of single-/low-copy nuclear genes. In contrast to the Proto-Araceae group and the lemnoid clade adaption to aquatic environments, our analyses of WGD, diversification and functional enrichment indicated that WGD may play a more important role in the evolution of adaptations to tropical, terrestrial environments in the True-Araceae clade. These insights provide us with new resources to interpret the evolution of the Araceae.
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Affiliation(s)
- Lei Zhao
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Ying-Ying Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Sciences, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Xiao-Jian Qu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Ji’nan, Shandong 250014, China
| | - Hong Ma
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Yi Hu
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Hong-Tao Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
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26
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Habib S, Gong Y, Dong S, Lindstrom A, Stevenson DW, Wu H, Zhang S. Phylotranscriptomics Shed Light on Intrageneric Relationships and Historical Biogeography of Ceratozamia (Cycadales). PLANTS (BASEL, SWITZERLAND) 2023; 12:478. [PMID: 36771563 PMCID: PMC9921377 DOI: 10.3390/plants12030478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/10/2023] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
Ceratozamia Brongn. is one of the species-rich genera of Cycadales comprising 38 species that are mainly distributed in Mexico, with a few species reported from neighboring regions. Phylogenetic relationships within the genus need detailed investigation based on extensive datasets and reliable systematic approaches. Therefore, we used 30 of the known 38 species to reconstruct the phylogeny based on transcriptome data of 3954 single-copy nuclear genes (SCGs) via coalescent and concatenated approaches and three comparative datasets (nt/nt12/aa). Based on all these methods, Ceratozamia is divided into six phylogenetic subclades within three major clades. There were a few discrepancies regarding phylogenetic position of some species within these subclades. Using these phylogenetic trees, biogeographic history and morphological diversity of the genus are explored. Ceratozamia originated from ancestors in southern Mexico since the mid-Miocene. There is a distinct distribution pattern of species through the Trans-Mexican Volcanic Belt (TMVB), that act as a barrier for the species dispersal at TMVB and its southern and northern part. Limited dispersal events occurred during the late Miocene, and maximum diversification happened during the Pliocene epoch. Our study provides a new insight into phylogenetic relationships, the origin and dispersal routes, and morphological diversity of the genus Ceratozamia. We also explain how past climatic changes affected the diversification of this Mesoamerica-native genus.
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Affiliation(s)
- Sadaf Habib
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzhen 518004, China
| | - Yiqing Gong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzhen 518004, China
| | - Shanshan Dong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzhen 518004, China
| | - Anders Lindstrom
- Global Biodiversity Conservancy 144/124 Moo 3, Soi Bua Thong, Bangsalae, Sattahip, Chonburi 20250, Thailand
| | | | - Hong Wu
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Shouzhou Zhang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzhen 518004, China
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27
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Hu H, Sun P, Yang Y, Ma J, Liu J. Genome-scale angiosperm phylogenies based on nuclear, plastome, and mitochondrial datasets. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023. [PMID: 36647606 DOI: 10.1111/jipb.13455] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/16/2023] [Indexed: 06/17/2023]
Abstract
Angiosperms dominate the Earth's ecosystems and provide most of the basic necessities for human life. The major angiosperm clades comprise 64 orders, as recognized by the APG IV classification. However, the phylogenetic relationships of angiosperms remain unclear, as phylogenetic trees with different topologies have been reconstructed depending on the sequence datasets utilized, from targeted genes to transcriptomes. Here, we used currently available de novo genome data to reconstruct the phylogenies of 366 angiosperm species from 241 genera belonging to 97 families across 43 of the 64 orders based on orthologous genes from the nuclear, plastid, and mitochondrial genomes of the same species with compatible datasets. The phylogenetic relationships were largely consistent with previously constructed phylogenies based on sequence variations in each genome type. However, there were major inconsistencies in the phylogenetic relationships of the five Mesangiospermae lineages when different genomes were examined. We discuss ways to address these inconsistencies, which could ultimately lead to the reconstruction of a comprehensive angiosperm tree of life. The angiosperm phylogenies presented here provide a basic framework for further updates and comparisons. These phylogenies can also be used as guides to examine the evolutionary trajectories among the three genome types during lineage radiation.
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Affiliation(s)
- Hongyin Hu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Pengchuan Sun
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Jianxiang Ma
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou, 730000, China
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
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Shen Z, Ding X, Cheng J, Wu F, Yin H, Wang M. Phylogenetic studies of magnoliids: Advances and perspectives. FRONTIERS IN PLANT SCIENCE 2023; 13:1100302. [PMID: 36726671 PMCID: PMC9885158 DOI: 10.3389/fpls.2022.1100302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
Magnoliids are the largest flowering plant clades outside of the eudicots and monocots, which are distributed worldwide and have high economic, ornamental and ecological values. Eudicots, monocots and magnoliids are the three major clades of Mesangiospermae, and their phylogenetic relationship is one of the most interesting issues. In recent years, with the continuous accumulation of genomic information, the evolutionary status of magnoliids has become a hot spot in plant phylogenetic research. Although great efforts have been made to study the evolution of magnoliids using molecular data from several representative species such as nuclear genome, plastid genome, mitochondrial genome, and transcriptome, the results of current studies on the phylogenetic status of magnoliids are inconsistent. Here, we systematically describe the current understanding of the molecular research on magnoliid phylogeny and review the differences in the evolutionary state of magnoliids. Understanding the research approaches and limitations of magnoliid phylogeny can guide research strategies to further improve the study of the phylogenetic evolution of magnoliids.
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Affiliation(s)
- Zhiguo Shen
- National Innovation Alliance of Wintersweet, Henan Academy of Forestry, Zhengzhou, China
| | - Xin Ding
- National Innovation Alliance of Wintersweet, Henan Academy of Forestry, Zhengzhou, China
| | - Jianming Cheng
- Scientific Research Department, Scientific Research Department, Henan Colorful Horticulture Co., Ltd, Zhengzhou, China
| | - Fangfang Wu
- Scientific Research Department, Scientific Research Department, Henan Colorful Horticulture Co., Ltd, Zhengzhou, China
| | - Hengfu Yin
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
| | - Minyan Wang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang, China
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29
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Wang CK, Guo R, Guo CC, Yang GY, Zhang WG. Gelidocalamuszixingensis (Poaceae, Bambusoideae, Arundinarieae), a new species from southern China revealed by morphological and molecular evidence. PHYTOKEYS 2023; 218:29-45. [PMID: 36762271 PMCID: PMC9846285 DOI: 10.3897/phytokeys.218.96849] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/14/2022] [Indexed: 06/18/2023]
Abstract
The genus Gelidocalamus T. H. Wen, endemic to southern China, is a small but taxonomically problematic genus of Arundinarieae (Poaceae, Bambusoideae). During field work, a population of Gelidocalamus from Zixing, Hunan, was discovered, appearing to be distinct from our previously identified collection. Comparisons of the population of Zixing were performed by using scanning electron microscopy (SEM) and a plastid genome-based phylogeny. Morphologically, it was mostly similar to G.multifolius, but differed by culm leaf erect with densely white pubescence, apical branch sheath much longer than the internodes and foliage leaf larger. Phylogenetically, the new species was well-supported as a sister to the clade of G.multifolius + G.tessellatus, and the above three taxa were clustered in the Shibataea clade (IV) of Arundinarieae. Thus, the new species, formally named as Gelidocalamuszixingensis W.G.Zhang, G.Y.Yang & C.K.Wang, was described and illustrated herein.
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Affiliation(s)
- Cheng-Kun Wang
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University, Nanchang 330045, ChinaJiangxi Agricultural UniversityNanchangChina
- Collaborative Innovation Center of Jiangxi Typical Trees Cultivation and Utilization, Nanchang 330045, ChinaCollaborative Innovation Center of Jiangxi Typical Trees Cultivation and UtilizationNanchangChina
| | - Rong Guo
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University, Nanchang 330045, ChinaJiangxi Agricultural UniversityNanchangChina
- Collaborative Innovation Center of Jiangxi Typical Trees Cultivation and Utilization, Nanchang 330045, ChinaCollaborative Innovation Center of Jiangxi Typical Trees Cultivation and UtilizationNanchangChina
| | - Chun-Ce Guo
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University, Nanchang 330045, ChinaJiangxi Agricultural UniversityNanchangChina
- Collaborative Innovation Center of Jiangxi Typical Trees Cultivation and Utilization, Nanchang 330045, ChinaCollaborative Innovation Center of Jiangxi Typical Trees Cultivation and UtilizationNanchangChina
| | - Guang-Yao Yang
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University, Nanchang 330045, ChinaJiangxi Agricultural UniversityNanchangChina
- Collaborative Innovation Center of Jiangxi Typical Trees Cultivation and Utilization, Nanchang 330045, ChinaCollaborative Innovation Center of Jiangxi Typical Trees Cultivation and UtilizationNanchangChina
| | - Wen-Gen Zhang
- Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Forestry College, Jiangxi Agricultural University, Nanchang 330045, ChinaJiangxi Agricultural UniversityNanchangChina
- Collaborative Innovation Center of Jiangxi Typical Trees Cultivation and Utilization, Nanchang 330045, ChinaCollaborative Innovation Center of Jiangxi Typical Trees Cultivation and UtilizationNanchangChina
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30
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Timilsena PR, Barrett CF, Piñeyro-Nelson A, Wafula EK, Ayyampalayam S, McNeal JR, Yukawa T, Givnish TJ, Graham SW, Pires JC, Davis JI, Ané C, Stevenson DW, Leebens-Mack J, Martínez-Salas E, Álvarez-Buylla ER, dePamphilis CW. Phylotranscriptomic Analyses of Mycoheterotrophic Monocots Show a Continuum of Convergent Evolutionary Changes in Expressed Nuclear Genes From Three Independent Nonphotosynthetic Lineages. Genome Biol Evol 2022; 15:6965378. [PMID: 36582124 PMCID: PMC9887272 DOI: 10.1093/gbe/evac183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/13/2022] [Accepted: 12/18/2022] [Indexed: 12/31/2022] Open
Abstract
Mycoheterotrophy is an alternative nutritional strategy whereby plants obtain sugars and other nutrients from soil fungi. Mycoheterotrophy and associated loss of photosynthesis have evolved repeatedly in plants, particularly in monocots. Although reductive evolution of plastomes in mycoheterotrophs is well documented, the dynamics of nuclear genome evolution remains largely unknown. Transcriptome datasets were generated from four mycoheterotrophs in three families (Orchidaceae, Burmanniaceae, Triuridaceae) and related green plants and used for phylogenomic analyses to resolve relationships among the mycoheterotrophs, their relatives, and representatives across the monocots. Phylogenetic trees based on 602 genes were mostly congruent with plastome phylogenies, except for an Asparagales + Liliales clade inferred in the nuclear trees. Reduction and loss of chlorophyll synthesis and photosynthetic gene expression and relaxation of purifying selection on retained genes were progressive, with greater loss in older nonphotosynthetic lineages. One hundred seventy-four of 1375 plant benchmark universally conserved orthologous genes were undetected in any mycoheterotroph transcriptome or the genome of the mycoheterotrophic orchid Gastrodia but were expressed in green relatives, providing evidence for massively convergent gene loss in nonphotosynthetic lineages. We designate this set of deleted or undetected genes Missing in Mycoheterotrophs (MIM). MIM genes encode not only mainly photosynthetic or plastid membrane proteins but also a diverse set of plastid processes, genes of unknown function, mitochondrial, and cellular processes. Transcription of a photosystem II gene (psb29) in all lineages implies a nonphotosynthetic function for this and other genes retained in mycoheterotrophs. Nonphotosynthetic plants enable novel insights into gene function as well as gene expression shifts, gene loss, and convergence in nuclear genomes.
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Affiliation(s)
- Prakash Raj Timilsena
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania
| | - Craig F Barrett
- Department of Biology, West Virginia University, Morgantown, West Virginia
| | - Alma Piñeyro-Nelson
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Mexico City, Mexico,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Eric K Wafula
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania
| | | | - Joel R McNeal
- Department of Ecology, Evolution, and Organismal Biology, Kennesaw State University, Georgia
| | - Tomohisa Yukawa
- Tsukuba Botanical Garden, National Museum of Nature and Science, 1-1, Amakubo 4, Tsukuba, 305-0005, Japan
| | - Thomas J Givnish
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin
| | - Sean W Graham
- Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4Canada
| | - J Chris Pires
- Division of Biological Sciences, University of Missouri–Columbia, Columbia, Missouri
| | - Jerrold I Davis
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, New York, 1485
| | - Cécile Ané
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin,Department of Statistics, University of Wisconsin–Madison, Madison, Wisconsin
| | | | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, Georgia, 3060
| | - Esteban Martínez-Salas
- Departmento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, México
| | - Elena R Álvarez-Buylla
- Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico,Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Mexico City, Mexico
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31
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Morel B, Williams TA, Stamatakis A. Asteroid: a new algorithm to infer species trees from gene trees under high proportions of missing data. Bioinformatics 2022; 39:6964379. [PMID: 36576010 PMCID: PMC9838317 DOI: 10.1093/bioinformatics/btac832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 12/12/2022] [Accepted: 12/26/2022] [Indexed: 12/29/2022] Open
Abstract
MOTIVATION Missing data and incomplete lineage sorting (ILS) are two major obstacles to accurate species tree inference. Gene tree summary methods such as ASTRAL and ASTRID have been developed to account for ILS. However, they can be severely affected by high levels of missing data. RESULTS We present Asteroid, a novel algorithm that infers an unrooted species tree from a set of unrooted gene trees. We show on both empirical and simulated datasets that Asteroid is substantially more accurate than ASTRAL and ASTRID for very high proportions (>80%) of missing data. Asteroid is several orders of magnitude faster than ASTRAL for datasets that contain thousands of genes. It offers advanced features such as parallelization, support value computation and support for multi-copy and multifurcating gene trees. AVAILABILITY AND IMPLEMENTATION Asteroid is freely available at https://github.com/BenoitMorel/Asteroid. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Bristol BS8, UK
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg 69118, Germany,Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe 76131, Germany
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32
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Dylus D, Altenhoff A, Majidian S, Sedlazeck FJ, Dessimoz C. Read2Tree: scalable and accurate phylogenetic trees from raw reads. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.04.18.488678. [PMID: 36561179 PMCID: PMC9774205 DOI: 10.1101/2022.04.18.488678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The inference of phylogenetic trees is foundational to biology. However, state-of-the-art phylogenomics requires running complex pipelines, at significant computational and labour costs, with additional constraints in sequencing coverage, assembly and annotation quality. To overcome these challenges, we present Read2Tree, which directly processes raw sequencing reads into groups of corresponding genes. In a benchmark encompassing a broad variety of datasets, our assembly-free approach was 10-100x faster than conventional approaches, and in most cases more accurate-the exception being when sequencing coverage was high and reference species very distant. To illustrate the broad applicability of the tool, we reconstructed a yeast tree of life of 435 species spanning 590 million years of evolution. Applied to Coronaviridae samples, Read2Tree accurately classified highly diverse animal samples and near-identical SARS-CoV-2 sequences on a single tree-thereby exhibiting remarkable breadth and depth. The speed, accuracy, and versatility of Read2Tree enables comparative genomics at scale.
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Affiliation(s)
- David Dylus
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
- present address: F. Hoffmann-La Roche Ltd, Immunology, Infectious Disease, and Ophthalmology (I2O), Roche Pharmaceutical Research and Early Development (pRED), Basel, 4070, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Adrian Altenhoff
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Department of Computer Science, ETH, 8092 Zurich, Switzerland
| | - Sina Majidian
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Computer Science, Rice University, Houston, TX, 77005, USA
| | - Christophe Dessimoz
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Department of Computer Science, University College London, London WC1E 6BT, UK
- Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London WC1E, UK
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33
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Wang Y, Sun J, Qiao P, Wang J, Wang M, Du Y, Xiong F, Luo J, Yuan Q, Dong W, Huang L, Guo L. Evolutionary history of genus Coptis and its dynamic changes in the potential suitable distribution area. FRONTIERS IN PLANT SCIENCE 2022; 13:1003368. [PMID: 36507390 PMCID: PMC9727247 DOI: 10.3389/fpls.2022.1003368] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 11/07/2022] [Indexed: 06/17/2023]
Abstract
The genus Coptis belongs to the Ranunculaceae family, containing 15 recognized species highly diverse in morphology. It is a conspicuous taxon with special evolutionary position, distribution pattern and medicinal value, which makes it to be of great research and conservation significance. In order to better understand the evolutionary dynamics of Coptis and promote more practical conservation measures, we performed plastome sequencing and used the sequencing data in combination with worldwide occurrence data of Coptis to estimate genetic diversity and divergence times, rebuild biogeographic history and predict its potential suitable distribution area. The average nucleotide diversity of Coptis was 0.0067 and the hotspot regions with the highest hypermutation levels were located in the ycf1 gene. Coptis is most likely to have originated in North America and Japanese archipelago and has a typical Eastern Asian and North American disjunct distribution pattern, while the species diversity center is located in Mid-West China and Japan. The crown age of the genus is estimated at around 8.49 Mya. The most suitable climatic conditions for Coptis were as follows: precipitation of driest quarter > 25.5 mm, annual precipitation > 844.9 mm and annual mean temperature -3.1 to 19 °C. The global and China suitable area shows an upward trend in the future when emission of greenhouse gases is well controlled, but the area, especially in China, decreases significantly without greenhouse gas policy interventions. The results of this study provide a comprehensive insight into the Coptis evolutionary dynamics and will facilitate future conservation efforts.
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Affiliation(s)
- Yiheng Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- Key Laboratory of Biology and Cultivation of Herb Medicine, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Jiahui Sun
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ping Qiao
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Jingyi Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Mengli Wang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yongxi Du
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- Key Laboratory of Biology and Cultivation of Herb Medicine, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Feng Xiong
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- Key Laboratory of Biology and Cultivation of Herb Medicine, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Jun Luo
- Kunming Xishan Forestry and Grassland Comprehensive Service Center, Kunming, China
| | - Qingjun Yuan
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wenpan Dong
- Laboratory of Systematic Evolution and Biogeography of Woody Plants, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lanping Guo
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- Key Laboratory of Biology and Cultivation of Herb Medicine, Ministry of Agriculture and Rural Affairs, Beijing, China
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34
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Timilsena PR, Wafula EK, Barrett CF, Ayyampalayam S, McNeal JR, Rentsch JD, McKain MR, Heyduk K, Harkess A, Villegente M, Conran JG, Illing N, Fogliani B, Ané C, Pires JC, Davis JI, Zomlefer WB, Stevenson DW, Graham SW, Givnish TJ, Leebens-Mack J, dePamphilis CW. Phylogenomic resolution of order- and family-level monocot relationships using 602 single-copy nuclear genes and 1375 BUSCO genes. FRONTIERS IN PLANT SCIENCE 2022; 13:876779. [PMID: 36483967 PMCID: PMC9723157 DOI: 10.3389/fpls.2022.876779] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 09/29/2022] [Indexed: 05/26/2023]
Abstract
We assess relationships among 192 species in all 12 monocot orders and 72 of 77 families, using 602 conserved single-copy (CSC) genes and 1375 benchmarking single-copy ortholog (BUSCO) genes extracted from genomic and transcriptomic datasets. Phylogenomic inferences based on these data, using both coalescent-based and supermatrix analyses, are largely congruent with the most comprehensive plastome-based analysis, and nuclear-gene phylogenomic analyses with less comprehensive taxon sampling. The strongest discordance between the plastome and nuclear gene analyses is the monophyly of a clade comprising Asparagales and Liliales in our nuclear gene analyses, versus the placement of Asparagales and Liliales as successive sister clades to the commelinids in the plastome tree. Within orders, around six of 72 families shifted positions relative to the recent plastome analysis, but four of these involve poorly supported inferred relationships in the plastome-based tree. In Poales, the nuclear data place a clade comprising Ecdeiocoleaceae+Joinvilleaceae as sister to the grasses (Poaceae); Typhaceae, (rather than Bromeliaceae) are resolved as sister to all other Poales. In Commelinales, nuclear data place Philydraceae sister to all other families rather than to a clade comprising Haemodoraceae+Pontederiaceae as seen in the plastome tree. In Liliales, nuclear data place Liliaceae sister to Smilacaceae, and Melanthiaceae are placed sister to all other Liliales except Campynemataceae. Finally, in Alismatales, nuclear data strongly place Tofieldiaceae, rather than Araceae, as sister to all the other families, providing an alternative resolution of what has been the most problematic node to resolve using plastid data, outside of those involving achlorophyllous mycoheterotrophs. As seen in numerous prior studies, the placement of orders Acorales and Alismatales as successive sister lineages to all other extant monocots. Only 21.2% of BUSCO genes were demonstrably single-copy, yet phylogenomic inferences based on BUSCO and CSC genes did not differ, and overall functional annotations of the two sets were very similar. Our analyses also reveal significant gene tree-species tree discordance despite high support values, as expected given incomplete lineage sorting (ILS) related to rapid diversification. Our study advances understanding of monocot relationships and the robustness of phylogenetic inferences based on large numbers of nuclear single-copy genes that can be obtained from transcriptomes and genomes.
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Affiliation(s)
- Prakash Raj Timilsena
- Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Eric K. Wafula
- Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Craig F. Barrett
- Department of Biology, West Virginia University, Morgantown, WV, United States
| | - Saravanaraj Ayyampalayam
- Georgia Advanced Computing Resource Center, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Joel R. McNeal
- Department of Ecology, Evolution, and Organismal Biology, Biology Kennesaw State University, Kennesaw, GA, United States
| | - Jeremy D. Rentsch
- Department of Biology, Francis Marion University, Florence, SC, United States
| | - Michael R. McKain
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL, United States
| | - Karolina Heyduk
- School of Life Sciences, University of Hawai’i at Mānoa, Honolulu, HI, United States
| | - Alex Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Matthieu Villegente
- Institut des Sciences Exactes et Appliquees (ISEA), University of New Caledonia, Noumea, New Caledonia
| | - John G. Conran
- Australian Centre for Evolutionary Biology and Biodiversity & Sprigg Geobiology Centre, School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Nicola Illing
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Bruno Fogliani
- Institut des Sciences Exactes et Appliquees (ISEA), University of New Caledonia, Noumea, New Caledonia
| | - Cécile Ané
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
- Department of Statistics, University of Wisconsin–Madison, Madison, WI, United States
| | - J. Chris Pires
- Division of Biological Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO, United States
| | - Jerrold I. Davis
- School of Integrative Plant Sciences and L.H. Bailey Hortorium, Cornell University, Ithaca, NY, United States
| | - Wendy B. Zomlefer
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | | | | | - Thomas J. Givnish
- Department of Botany, University of Wisconsin-Madison, Madison, WI, United States
| | - James Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Claude W. dePamphilis
- Department of Biology and Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
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Cheng L, Han Q, Chen F, Li M, Balbuena TS, Zhao Y. Phylogenomics as an effective approach to untangle cross-species hybridization event: A case study in the family Nymphaeaceae. Front Genet 2022; 13:1031705. [PMID: 36406110 PMCID: PMC9670182 DOI: 10.3389/fgene.2022.1031705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Hybridization is common and considered as an important evolutionary force to increase intraspecific genetic diversity. Detecting hybridization events is crucial for understanding the evolutionary history of species and further improving molecular breeding. The studies on identifying hybridization events through the phylogenomic approach are still limited. We proposed the conception and method of identifying allopolyploidy events by phylogenomics. The reconciliation and summary of nuclear multi-labeled gene family trees were adopted to untangle hybridization events from next-generation data in our novel phylogenomic approach. Given horticulturalists’ relatively clear cultivated crossbreeding history, the water lily family is a suitable case for examining recent allopolyploidy events. Here, we reconstructed and confirmed the well-resolved nuclear phylogeny for the Nymphaeales family in the context of geological time as a framework for identifying hybridization signals. We successfully identified two possible allopolyploidy events with the parental lineages for the hybrids in the family Nymphaeaceae based on summarization from multi-labeled gene family trees of Nymphaeales. The lineages where species Nymphaea colorata and Nymphaea caerulea are located may be the progenitors of horticultural cultivated species Nymphaea ‘midnight’ and Nymphaea ‘Woods blue goddess’. The proposed hybridization hypothesis is also supported by horticultural breeding records. Our methodology can be widely applied to identify hybridization events and theoretically facilitate the genome breeding design of hybrid plants.
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Affiliation(s)
- Lin Cheng
- Henan International Joint Laboratory of Tea-oil Tree Biology and High-Value Utilization, Xinyang Normal University, Xinyang, Henan, China
| | - Qunwei Han
- Henan International Joint Laboratory of Tea-oil Tree Biology and High-Value Utilization, Xinyang Normal University, Xinyang, Henan, China
| | - Fei Chen
- College of Tropical Crops, Hainan University, Haikou, China
| | - Mengge Li
- Henan International Joint Laboratory of Tea-oil Tree Biology and High-Value Utilization, Xinyang Normal University, Xinyang, Henan, China
| | - Tiago Santana Balbuena
- Department of Agricultural, Livestock and Environmental Biotechnology, UNESP, São Paulo, Brazil
| | - Yiyong Zhao
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
- College of Agriculture, Guizhou University, Guiyang, China
- *Correspondence: Yiyong Zhao, ,
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Genome-Wide Analysis of the Almond AP2/ERF Superfamily and Its Functional Prediction during Dormancy in Response to Freezing Stress. BIOLOGY 2022; 11:biology11101520. [PMID: 36290423 PMCID: PMC9598233 DOI: 10.3390/biology11101520] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022]
Abstract
Simple Summary The ethylene-responsive element (AP2/ERF) is one of the key and conserved transcription factors (TFs) in plants, and it plays a crucial role in regulating plant growth, development, and stress response. The cultivated almond in Xinjiang is often affected by short-term ultralow temperature freezing stress during the winter dormancy period, resulting in the death of large-scale almond plants. In this study, we conducted the first genome-wide analysis of the PdAP2/ERF family in almond, including protein physicochemical properties, phylogenetic relationships, motif types, gene structures, gene replication types, collinearity relationships, and cis-element types in promoter regions. We further analyzed the expression patterns of the PdAP2/ERF gene in different tissues of almond and under freezing stress at different temperatures in annual dormant branches using transcriptome data. In addition, we also analyzed the expression levels of 13 PdAP2/ERF genes in four tissues of almond and in annual dormant branches treated with freezing stress at different temperatures using fluorescence quantitative technology. This study laid the foundation for further exploring the function of the PdAP2/ERF gene in almond. Abstract The AP2/ERF transcription factor family is one of the largest transcription factor families in plants and plays an important role in regulating plant growth and development and the response to biotic and abiotic stresses. However, there is no report on the AP2/ERF gene family in almond (Prunus dulcis). In this study, a total of 136 PdAP2/ERF genes were identified from the almond genome, and their protein physicochemical properties were analyzed. The PdAP2/ERF members were divided into five subgroups: AP2, RAV, ERF, DREB, and Soloist. The PdAP2/ERF members in each subgroup had conserved motif types and exon/intron numbers. PdAP2/ERFS members are distributed on eight chromosomes, with 22 pairs of segmental duplications and 28 pairs of tandem duplications. We further explored the colinear relationship between almond and Arabidopsis thaliana, Oryza sativa, Malus domestica, and Prunus persicaAP2/ERF genes and their evolution. The results of cis-acting elements showed that PdAP2/ERF members are widely involved in various processes, such as growth and development, hormone regulation, and stress response. The results based on transcriptome expression patterns showed that PdAP2/ERF genes had significant tissue-specific expression characteristics and were involved in the response of annual dormant branches of almond to low-temperature freezing stress. In addition, the fluorescence quantitative relative expression results of 13 representative PdAP2/ERF genes in four tissues of ‘Wanfeng’ almond and under six low-temperature freezing treatments of annual dormant branches were consistent with the transcriptome results. It is worth noting that the fluorescence quantitative expression level showed that the PdERF24 gene was extremely significant at −30 °C, suggesting that this gene may play an important role in the response of almond dormancy to ultralow temperature freezing stress. Finally, we identified 7424 and 6971 target genes based on AP2 and ERF/DREB DNA-binding sites, respectively. The GO and KEGG enrichment results showed that these target genes play important roles in protein function and multiple pathways. In summary, we conducted bioinformatics and expression pattern studies on PdAP2/ERF genes, including 13 PdAP2/ERF genes, and performed fluorescence quantitative analysis of annual dormant shoots under different low-temperature freezing stress treatments to understand the tolerance of almond dormancy to freezing stress and suggest future improvements.
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Che X, Lai W, Wang S, Wang X, Hu W, Chen H, Xie X, Tang M. Multiple PHT1 family phosphate transporters are recruited for mycorrhizal symbiosis in Eucalyptus grandis and conserved PHT1;4 is a requirement for the arbuscular mycorrhizal symbiosis. TREE PHYSIOLOGY 2022; 42:2020-2039. [PMID: 35512354 DOI: 10.1093/treephys/tpac050] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 04/24/2022] [Indexed: 06/14/2023]
Abstract
Eucalypts engage in a mutualistic endosymbiosis with arbuscular mycorrhizal (AM) fungi to acquire mineral nutrients from soils, particularly inorganic phosphate (Pi). In return, the host plant provides organic carbons to its fungal partners. However, the mechanism by which the Eucalyptus plants acquire Pi released from the AM fungi has remained elusive. In this study, we investigated the characterization of potential PHOSPHATE TRANSPORTER1 (PHT1) family Pi transporters in AM symbiosis in Eucalyptus grandis W. Hill ex Maiden. We show that multiple PHT1 family Pi transporters were recruited for AM symbiosis in E. grandis. We further report that EgPT4, an E. grandis member of the PHT1 family, is conserved across angiosperms and is exclusively expressed in AM roots with arbuscule-containing cells and localizes to the periarbuscular membrane (PAM). EgPT4 was able to complement a yeast mutant strain defective in all inorganic Pi transporters and mediate Pi uptake. Importantly, EgPT4 is essential for improved E. grandis growth, total phosphorus concentration and arbuscule development during symbiosis. Moreover, silencing of EgPT4 led to the induction of polyphosphate accumulation relevant genes of Rhizophagus irregularis DAOM 197198. Collectively, our results unravel a pivotal role for EgPT4 in symbiotic Pi transport across the PAM required for arbuscule development in E. grandis.
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Affiliation(s)
- Xianrong Che
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Wenzhen Lai
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Sijia Wang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Xinyang Wang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Wentao Hu
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Hui Chen
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Xianan Xie
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, P.R. China
| | - Ming Tang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, P.R. China
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Wang Z, Li Y, Sun P, Zhu M, Wang D, Lu Z, Hu H, Xu R, Zhang J, Ma J, Liu J, Yang Y. A high-quality Buxus austro-yunnanensis (Buxales) genome provides new insights into karyotype evolution in early eudicots. BMC Biol 2022; 20:216. [PMID: 36195948 PMCID: PMC9533543 DOI: 10.1186/s12915-022-01420-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 09/27/2022] [Indexed: 11/21/2022] Open
Abstract
Background Eudicots are the most diverse group of flowering plants that compromise five well-defined lineages: core eudicots, Ranunculales, Proteales, Trochodendrales, and Buxales. However, the phylogenetic relationships between these five lineages and their chromosomal evolutions remain unclear, and a lack of high-quality genome analyses for Buxales has hindered many efforts to address this knowledge gap. Results Here, we present a high-quality chromosome-level genome of Buxus austro-yunnanensis (Buxales). Our phylogenomic analyses revealed that Buxales and Trochodendrales are genetically similar and classified as sisters. Additionally, both are sisters to the core eudicots, while Ranunculales was found to be the first lineage to diverge from these groups. Incomplete lineage sorting and hybridization were identified as the main contributors to phylogenetic discordance (34.33%) between the lineages. In fact, B. austro-yunnanensis underwent only one whole-genome duplication event, and collinear gene phylogeny analyses suggested that separate independent polyploidizations occurred in the five eudicot lineages. Using representative genomes from these five lineages, we reconstructed the ancestral eudicot karyotype (AEK) and generated a nearly gapless karyotype projection for each eudicot species. Within core eudicots, we recovered one common chromosome fusion event in asterids and malvids, respectively. Further, we also found that the previously reported fused AEKs in Aquilegia (Ranunculales) and Vitis (core eudicots) have different fusion positions, which indicates that these two species have different karyotype evolution histories. Conclusions Based on our phylogenomic and karyotype evolution analyses, we revealed the likely relationships and evolutionary histories of early eudicots. Ultimately, our study expands genomic resources for early-diverging eudicots. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01420-1.
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Affiliation(s)
- Zhenyue Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Ying Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Pengchuan Sun
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics & Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China
| | - Mingjia Zhu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Dandan Wang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Zhiqiang Lu
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China.,Center of Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
| | - Hongyin Hu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Renping Xu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jin Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jianxiang Ma
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Jianquan Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China. .,Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education & State Key Laboratory of Hydraulics & Mountain River Engineering, College of Life Sciences, Sichuan University, Chengdu, China.
| | - Yongzhi Yang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China.
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Zhang Y, Zhang L, Xiao Q, Wu C, Zhang J, Xu Q, Yu Z, Bao S, Wang J, Li Y, Wang L, Wang J. Two independent allohexaploidizations and genomic fractionation in Solanales. FRONTIERS IN PLANT SCIENCE 2022; 13:1001402. [PMID: 36212355 PMCID: PMC9538396 DOI: 10.3389/fpls.2022.1001402] [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: 07/23/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Solanales, an order of flowering plants, contains the most economically important vegetables among all plant orders. To date, many Solanales genomes have been sequenced. However, the evolutionary processes of polyploidization events in Solanales and the impact of polyploidy on species diversity remain poorly understood. We compared two representative Solanales genomes (Solanum lycopersicum L. and Ipomoea triloba L.) and the Vitis vinifera L. genome and confirmed two independent polyploidization events. Solanaceae common hexaploidization (SCH) and Convolvulaceae common hexaploidization (CCH) occurred ∼43-49 and ∼40-46 million years ago (Mya), respectively. Moreover, we identified homologous genes related to polyploidization and speciation and constructed multiple genomic alignments with V. vinifera genome, providing a genomic homology framework for future Solanales research. Notably, the three polyploidization-produced subgenomes in both S. lycopersicum and I. triloba showed significant genomic fractionation bias, suggesting the allohexaploid nature of the SCH and CCH events. However, we found that the higher genomic fractionation bias of polyploidization-produced subgenomes in Solanaceae was likely responsible for their more abundant species diversity than that in Convolvulaceae. Furthermore, through genomic fractionation and chromosomal structural variation comparisons, we revealed the allohexaploid natures of SCH and CCH, both of which were formed by two-step duplications. In addition, we found that the second step of two paleohexaploidization events promoted the expansion and diversity of β-amylase (BMY) genes in Solanales. These current efforts provide a solid foundation for future genomic and functional exploration of Solanales.
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Affiliation(s)
- Yan Zhang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Lan Zhang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Qimeng Xiao
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Chunyang Wu
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Jiaqi Zhang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Qiang Xu
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Zijian Yu
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Shoutong Bao
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Jianyu Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Yu Li
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Li Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Jinpeng Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
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Liao Y, Liu Z, Gichira AW, Yang M, Mbichi RW, Meng L, Wan T. Deep evaluation of the evolutionary history of the Heat Shock Factor (HSF) gene family and its expansion pattern in seed plants. PeerJ 2022; 10:e13603. [PMID: 35966928 PMCID: PMC9373977 DOI: 10.7717/peerj.13603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 05/26/2022] [Indexed: 01/17/2023] Open
Abstract
Heat shock factor (HSF) genes are essential in some of the basic developmental pathways in plants. Despite extensive studies on the structure, functional diversification, and evolution of HSF genes, their divergence history and gene duplication pattern remain unknown. To further illustrate the probable divergence patterns in these subfamilies, we analyzed the evolutionary history of HSF genes using phylogenetic reconstruction and genomic syntenic analyses, taking advantage of the increased sampling of genomic data from pteridophytes, gymnosperms and basal angiosperms. We identified a novel clade that includes HSFA2, HSFA6, HSFA7, and HSFA9 with a complex relationship, which is very likely due to orthologous or paralogous genes retained after frequent gene duplication events. We hypothesized that HSFA9 derives from HSFA2 through gene duplication in eudicots at the ancestral state, and then expanded in a lineage-specific way. Our findings indicate that HSFB3 and HSFB5 emerged before the divergence of ancestral angiosperms, but were lost in the most recent common ancestors of monocots. We also presumed that HSFC2 derives from HSFC1 in ancestral monocots. This work proposes that during the radiation of flowering plants, an era during which there was a differentiation of angiosperms, the size of the HSF gene family was also being adjusted with considerable sub- or neo-functionalization. The independent evolution of HSFs in eudicots and monocots, including lineage-specific gene duplication, gave rise to a new gene in ancestral eudicots and monocots, and lineage-specific gene loss in ancestral monocots. Our analyses provide essential insights for studying the evolutionary history of this multigene family.
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Affiliation(s)
- Yiying Liao
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Zhiming Liu
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Andrew W. Gichira
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Min Yang
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Ruth Wambui Mbichi
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Linping Meng
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Science, Shenzhen, China
| | - Tao Wan
- Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China,Sino-Africa Joint Research Centre, Chinese Academy of Sciences, Wuhan, China
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Cheng L, Li M, Han Q, Qiao Z, Hao Y, Balbuena TS, Zhao Y. Phylogenomics Resolves the Phylogeny of Theaceae by Using Low-Copy and Multi-Copy Nuclear Gene Makers and Uncovers a Fast Radiation Event Contributing to Tea Plants Diversity. BIOLOGY 2022; 11:biology11071007. [PMID: 36101388 PMCID: PMC9311850 DOI: 10.3390/biology11071007] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/28/2022] [Accepted: 06/29/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary The Theaceae includes more than 300 species of great morphological diversity and has immense economic, cultural, and ornamental values. However, the evolutionary history of this family remains elusive. We integrated 91 genomes and transcriptome datasets of Theaceae and successfully resolved the phylogeny of Theaceae including relatives of cultivated tea plants from both extensive low-copy and multi-copy nuclear gene markers. Bayes-based molecular dating revealed that the ancestor of the tea family originated slightly earlier than the K-Pg boundary (Mass extinction events including the extinction of dinosaurs) with early diversification of three tribes associated with the Early Eocene Climatic Optimum. Further speciation analysis suggested a sole significant diversification shift rate in the common ancestor of Camellia associated with the Mid-Miocene Climatic Optimum. Collectively, polyploidy events, and key morphological innovation characters, such as pericarp with seed coat hardening, could possibly contribute to the Theaceae species diversity. Abstract Tea is one of the three most popular nonalcoholic beverages globally and has extremely high economic and cultural value. Currently, the classification, taxonomy, and evolutionary history of the tea family are largely elusive, including phylogeny, divergence, speciation, and diversity. For understanding the evolutionary history and dynamics of species diversity in Theaceae, a robust phylogenetic framework based on 1785 low-copy and 79,103 multi-copy nuclear genes from 91 tea plant genomes and transcriptome datasets had been reconstructed. Our results maximumly supported that the tribes Stewartieae and Gordonieae are successive sister groups to the tribe Theeae from both coalescent and super matrix ML tree analyses. Moreover, in the most evolved tribe, Theeae, the monophyletic genera Pyrenaria, Apterosperma, and Polyspora are the successive sister groups of Camellia. We also yield a well-resolved relationship of Camellia, which contains the vast majority of Theaceae species richness. Molecular dating suggests that Theaceae originated in the late L-Cretaceous, with subsequent early radiation under the Early Eocene Climatic Optimal (EECO) for the three tribes. A diversification rate shift was detected in the common ancestors of Camellia with subsequent acceleration in speciation rate under the climate optimum in the early Miocene. These results provide a phylogenetic framework and new insights into factors that likely have contributed to the survival of Theaceae, especially a successful radiation event of genus Camellia members to subtropic/tropic regions. These novel findings will facilitate the efficient conservation and utilization of germplasm resources for breeding cultivated tea and oil-tea. Collectively, these results provide a foundation for further morphological and functional evolutionary analyses across Theaceae.
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Affiliation(s)
- Lin Cheng
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High Value Utilization, Xinyang Normal University, Xinyang 464000, China; (L.C.); (M.L.); (Q.H.); (Z.Q.); (Y.H.)
| | - Mengge Li
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High Value Utilization, Xinyang Normal University, Xinyang 464000, China; (L.C.); (M.L.); (Q.H.); (Z.Q.); (Y.H.)
| | - Qunwei Han
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High Value Utilization, Xinyang Normal University, Xinyang 464000, China; (L.C.); (M.L.); (Q.H.); (Z.Q.); (Y.H.)
| | - Zhen Qiao
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High Value Utilization, Xinyang Normal University, Xinyang 464000, China; (L.C.); (M.L.); (Q.H.); (Z.Q.); (Y.H.)
| | - Yanlin Hao
- Henan International Joint Laboratory of Tea-Oil Tree Biology and High Value Utilization, Xinyang Normal University, Xinyang 464000, China; (L.C.); (M.L.); (Q.H.); (Z.Q.); (Y.H.)
| | - Tiago Santana Balbuena
- Department of Agricultural, Livestock and Environmental Biotechnology, Sao Paulo State University, Jaboticabal 14884-900, Brazil;
| | - Yiyong Zhao
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
- College of Agriculture, Guizhou University, Guiyang 550025, China
- Correspondence:
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Shi T, Huneau C, Zhang Y, Li Y, Chen J, Salse J, Wang Q. The slow-evolving Acorus tatarinowii genome sheds light on ancestral monocot evolution. NATURE PLANTS 2022; 8:764-777. [PMID: 35835857 PMCID: PMC9300462 DOI: 10.1038/s41477-022-01187-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 05/30/2022] [Indexed: 05/03/2023]
Abstract
Monocots are one of the most diverse groups of flowering plants, and tracing the evolution of their ancestral genome into modern species is essential for understanding their evolutionary success. Here, we report a high-quality assembly of the Acorus tatarinowii genome, a species that diverged early from all the other monocots. Genome-wide comparisons with a range of representative monocots characterized Acorus as a slowly evolved genome with one whole-genome duplication. Our inference of the ancestral monocot karyotypes provides new insights into the chromosomal evolutionary history assigned to modern species and reveals the probable molecular functions and processes related to the early adaptation of monocots to wetland or aquatic habitats (that is, low levels of inorganic phosphate, parallel leaf venation and ephemeral primary roots). The evolution of ancestral gene order in monocots is constrained by gene structural and functional features. The newly obtained Acorus genome offers crucial evidence for delineating the origin and diversification of monocots, including grasses.
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Affiliation(s)
- Tao Shi
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
| | - Cécile Huneau
- UCA, INRAE, UMR 1095 GDEC (Genetics, Diversity & Ecophysiology of Cereals), Clermont-Ferrand, France
| | - Yue Zhang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Li
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinming Chen
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China.
| | - Jérôme Salse
- UCA, INRAE, UMR 1095 GDEC (Genetics, Diversity & Ecophysiology of Cereals), Clermont-Ferrand, France.
| | - Qingfeng Wang
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, China.
- Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, China.
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Wu Q, Tong W, Zhao H, Ge R, Li R, Huang J, Li F, Wang Y, Mallano AI, Deng W, Wang W, Wan X, Zhang Z, Xia E. Comparative transcriptomic analysis unveils the deep phylogeny and secondary metabolite evolution of 116 Camellia plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:406-421. [PMID: 35510493 DOI: 10.1111/tpj.15799] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/21/2022] [Accepted: 05/02/2022] [Indexed: 06/14/2023]
Abstract
Camellia plants include more than 200 species of great diversity and immense economic, ornamental, and cultural values. We sequenced the transcriptomes of 116 Camellia plants from almost all sections of the genus Camellia. We constructed a pan-transcriptome of Camellia plants with 89 394 gene families and then resolved the phylogeny of genus Camellia based on 405 high-quality low-copy core genes. Most of the inferred relationships are well supported by multiple nuclear gene trees and morphological traits. We provide strong evidence that Camellia plants shared a recent whole genome duplication event, followed by large expansions of transcription factor families associated with stress resistance and secondary metabolism. Secondary metabolites, particularly those associated with tea quality such as catechins and caffeine, were preferentially heavily accumulated in the Camellia plants from section Thea. We thoroughly examined the expression patterns of hundreds of genes associated with tea quality, and found that some of them exhibited significantly high expression and correlations with secondary metabolite accumulations in Thea species. We also released a web-accessible database for efficient retrieval of Camellia transcriptomes. The reported transcriptome sequences and obtained novel findings will facilitate the efficient conservation and utilization of Camellia germplasm towards a breeding program for cultivated tea, camellia, and oil-tea plants.
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Affiliation(s)
- Qiong Wu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
- Tea Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Wei Tong
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Huijuan Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Ruoheng Ge
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Ruopei Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Jin Huang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Fangdong Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Yanli Wang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Ali Inayat Mallano
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Weiwei Deng
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Wenjie Wang
- Tea Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Xiaochun Wan
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Zhengzhu Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
| | - Enhua Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, 230036, China
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Shoot Development in Members of an Ancient Aquatic Angiosperm Lineage, Ceratophyllaceae: A New Interpretation Facilitates Comparisons with Chloranthaceae. Symmetry (Basel) 2022. [DOI: 10.3390/sym14071288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Ceratophyllum is an ancient and phylogenetically isolated angiosperm lineage. Comparisons between Ceratophyllum and other angiosperms are hampered by uncertainty in inferring organ homologies in this genus of specialized aquatics. Interpretation of shoot morphology is especially problematic in Ceratophyllum. Each node has several leaf-like appendages interpreted as verticillate leaves, modified parts of one and the same leaf or parts of two leaves under decussate phyllotaxis. Vegetative branches are axillary, but reproductive units (interpreted as flowers or inflorescences) are commonly viewed as developing from collateral accessory buds. We studied shoot development in Ceratophyllum submersum, C. tanaiticum, and C. demersum using scanning electron microscopy to clarify shoot morphology and branching patterns. Our data support the idea that the phyllotaxis is essentially decussate with appendages of stipular origin resembling leaf blades. We conclude that a leaf axil of Ceratophyllum possesses a complex of two serial buds, the lower one producing a vegetative branch and the upper one developing a reproductive unit. The reproductive unit is congenitally displaced to the subsequent node, a phenomenon known as concaulescence. Either member of the serial bud complex may be absent. There is a theory based on a synthesis of molecular and morphological data that Chloranthaceae are the closest extant relatives of Ceratophyllum. Serial buds and concaulescence are known in Hedyosmum (Chloranthaceae). Our new interpretation facilitates morphological comparisons between Hedyosmum and Ceratophyllum.
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Mao D, Tao S, Li X, Gao D, Tang M, Liu C, Wu D, Bai L, He Z, Wang X, Yang L, Zhu Y, Zhang D, Zhang W, Chen C. The Harbinger transposon-derived gene PANDA epigenetically coordinates panicle number and grain size in rice. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1154-1166. [PMID: 35239255 PMCID: PMC9129072 DOI: 10.1111/pbi.13799] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/27/2022] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
Transposons significantly contribute to genome fractions in many plants. Although numerous transposon-related mutations have been identified, the evidence regarding transposon-derived genes regulating crop yield and other agronomic traits is very limited. In this study, we characterized a rice Harbinger transposon-derived gene called PANICLE NUMBER AND GRAIN SIZE (PANDA), which epigenetically coordinates panicle number and grain size. Mutation of PANDA caused reduced panicle number but increased grain size in rice, while transgenic plants overexpressing this gene showed the opposite phenotypic change. The PANDA-encoding protein can bind to the core polycomb repressive complex 2 (PRC2) components OsMSI1 and OsFIE2, and regulates the deposition of H3K27me3 in the target genes, thereby epigenetically repressing their expression. Among the target genes, both OsMADS55 and OsEMF1 were negative regulators of panicle number but positive regulators of grain size, partly explaining the involvement of PANDA in balancing panicle number and grain size. Moreover, moderate overexpression of PANDA driven by its own promoter in the indica rice cultivar can increase grain yield. Thus, our findings present a novel insight into the epigenetic control of rice yield traits by a Harbinger transposon-derived gene and provide its potential application for rice yield improvement.
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Affiliation(s)
- Donghai Mao
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
| | - Shentong Tao
- State Key Laboratory for Crop Genetics and Germplasm EnhancementCollaborative Innovation Center for Modern Crop Production co‐sponsored by Province and Ministry (CIC‐MCP)Nanjing Agricultural UniversityNanjingChina
| | - Xin Li
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
- University of Chinese Academy of SciencesBeijingChina
| | - Dongying Gao
- Small Grains and Potato Germplasm Research UnitUSDA ARSAberdeenIDUSA
| | - Mingfeng Tang
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
| | - Chengbing Liu
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU)/Biotechnology Research CenterChina Three Gorges UniversityYichangChina
| | - Dan Wu
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
| | - Liangli Bai
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
- College of Life SciencesHunan Normal UniversityChangshaChina
| | - Zhankun He
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
- College of AgronomyHunan Agriculture UniversityChangshaChina
| | - Xiaodong Wang
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
- University of Chinese Academy of SciencesBeijingChina
| | - Lei Yang
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
- Longping BranchGraduate School of Hunan UniversityChangshaChina
| | - Yuxing Zhu
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
| | - Dechun Zhang
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement (CTGU)/Biotechnology Research CenterChina Three Gorges UniversityYichangChina
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm EnhancementCollaborative Innovation Center for Modern Crop Production co‐sponsored by Province and Ministry (CIC‐MCP)Nanjing Agricultural UniversityNanjingChina
| | - Caiyan Chen
- Key Laboratory of Agro‐Ecological Processes in Subtropical RegionInstitute of Subtropical AgricultureChinese Academy of SciencesChangshaChina
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Teng J, Wang J, Zhang L, Wei C, Shen S, Xiao Q, Yue Y, Hao Y, Ge W, Wang J. Paleopolyploidies and Genomic Fractionation in Major Eudicot Clades. FRONTIERS IN PLANT SCIENCE 2022; 13:883140. [PMID: 35712579 PMCID: PMC9194900 DOI: 10.3389/fpls.2022.883140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Eudicots account for ~75% of living angiosperms, containing important food and energy crops. Recently, high-quality genome sequences of several eudicots including Aquilegia coerulea and Nelumbo nucifera have become available, providing an opportunity to investigate the early evolutionary characteristics of eudicots. We performed genomic hierarchical and event-related alignments to infer homology within and between representative species of eudicots. The results provide strong evidence for multiple independent polyploidization events during the early diversification of eudicots, three of which are likely to be allopolyploids: The core eudicot-common hexaploidy (ECH), Nelumbo-specific tetraploidy (NST), and Ranunculales-common tetraploidy (RCT). Using different genomes as references, we constructed genomic alignment to list the orthologous and paralogous genes produced by polyploidization and speciation. This could provide a fundamental framework for studying other eudicot genomes and gene(s) evolution. Further, we revealed significantly divergent evolutionary rates among these species. By performing evolutionary rate correction, we dated RCT to be ~118-134 million years ago (Mya), after Ranunculales diverged with core eudicots at ~123-139 Mya. Moreover, we characterized genomic fractionation resulting from gene loss and retention after polyploidizations. Notably, we revealed a high degree of divergence between subgenomes. In particular, synonymous nucleotide substitutions at synonymous sites (Ks) and phylogenomic analyses implied that A. coerulea might provide the subgenome(s) for the gamma-hexaploid hybridization.
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Affiliation(s)
- Jia Teng
- Department of Bioinformatics, School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Jianyu Wang
- Department of Bioinformatics, School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Lan Zhang
- Department of Bioinformatics, School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Chendan Wei
- Department of Bioinformatics, School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Shaoqi Shen
- Department of Bioinformatics, School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Qimeng Xiao
- Department of Bioinformatics, School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Yuanshuai Yue
- Department of Bioinformatics, School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Yanan Hao
- Department of Bioinformatics, School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Weina Ge
- Department of Bioinformatics, School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Jinpeng Wang
- Department of Bioinformatics, School of Life Sciences and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing, China
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Sokoloff DD, El ES, Pechenyuk EV, Carrive L, Nadot S, Rudall PJ, Remizowa MV. Refined Interpretation of the Pistillate Flower in Ceratophyllum Sheds Fresh Light on Gynoecium Evolution in Angiosperms. Front Cell Dev Biol 2022; 10:868352. [PMID: 35573671 PMCID: PMC9098228 DOI: 10.3389/fcell.2022.868352] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
Molecular phylogenetic analyses have revealed a superclade of mesangiosperms with five extant lineages: monocots, eudicots, magnoliids, Ceratophyllum and Chloranthaceae. Both Ceratophyllum and Chloranthaceae are ancient lineages with a long fossil record; their precise placement within mesangiosperms is uncertain. Morphological studies have suggested that they form a clade together with some Cretaceous fossils, including Canrightia, Montsechia and Pseudoasterophyllites. Apart from Canrightia, members of this clade share unilocular gynoecia commonly interpreted as monomerous with ascidiate carpels. Alternatively, the gynoecium of Ceratophyllum has also been interpreted as syncarpous with a single fertile carpel (pseudomonomerous). We investigate patterns of morphological, anatomical and developmental variation in gynoecia of three Ceratophyllum species to explore the controversial interpretation of its gynoecium as either monomerous or pseudomonomerous. We use an angiosperm-wide morphological data set and contrasting tree topologies to estimate the ancestral gynoecium type in both Ceratophyllum and mesangiosperms. Gynoecia of all three Ceratophyllum species possess a small (sometimes vestigial) glandular appendage on the abaxial side and an occasionally bifurcating apex. The ovary is usually unilocular with two procambium strands, but sometimes bilocular and/or with three strands in C. demersum. None of the possible phylogenetic placements strongly suggest apocarpy in the stem lineage of Ceratophyllum. Rescoring Ceratophyllum as having two united carpels affects broader-scale reconstructions of the ancestral gynoecium in mesangiosperms. Our interpretation of the glandular appendage as a tepal or staminode homologue makes the Ceratophyllum ovary inferior, thus resembling (semi)inferior ovaries of most Chloranthaceae and potentially related fossils Canrightia and Zlatkocarpus. The entire structure of the flower of Ceratophyllum suggests strong reduction following a long and complex evolutionary history. The widely accepted notion that apocarpy is ancestral in mesangiosperms (and angiosperms) lacks robust support, regardless of which modes of carpel fusion are considered. Our study highlights the crucial importance of incorporating fossils into large-scale analyses to understand character evolution.
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Affiliation(s)
- Dmitry D Sokoloff
- Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | - Elena S El
- Biological Faculty, Lomonosov Moscow State University, Moscow, Russia
| | | | - Laetitia Carrive
- Université Paris-Saclay, CNRS, AgroParisTech, Écologie, Systématique et Évolution, Orsay, France
| | - Sophie Nadot
- Université Paris-Saclay, CNRS, AgroParisTech, Écologie, Systématique et Évolution, Orsay, France
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48
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Zhou W, Zhang X, Wang A, Yang L, Gan Q, Yi L, Summons RE, Volkman JK, Lu Y. Widespread Sterol Methyltransferase Participates in the Biosynthesis of Both C4α- and C4β-Methyl Sterols. J Am Chem Soc 2022; 144:9023-9032. [PMID: 35561259 PMCID: PMC9136925 DOI: 10.1021/jacs.2c01401] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The 4-methyl steranes
serve as molecular fossils and are used for
studying both eukaryotic evolution and geological history. The occurrence
of 4α-methyl steranes in sediments has long been considered
evidence of products of partial demethylation mediated by sterol methyl
oxidases (SMOs), while 4β-methyl steranes are attributed entirely
to diagenetic generation from 4α-methyl steroids since possible
biological sources of their precursor 4β-methyl sterols are
unknown. Here, we report a previously unknown C4-methyl sterol biosynthetic
pathway involving a sterol methyltransferase rather than the SMOs.
We show that both C4α- and C4β-methyl sterols are end
products of the sterol biosynthetic pathway in an endosymbiont of
reef corals, Breviolum minutum, while
this mechanism exists not only in dinoflagellates but also in eukaryotes
from alveolates, haptophytes, and aschelminthes. Our discovery provides
a previously untapped route for the generation of C4-methyl steranes
and overturns the paradigm that all 4β-methyl steranes are diagenetically
generated from the 4α isomers. This may facilitate the interpretation
of molecular fossils and understanding of the evolution of eukaryotic
life in general.
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Affiliation(s)
- Wenxu Zhou
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Oceanology, Hainan University, Haikou 570228, China
| | - Xu Zhang
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Oceanology, Hainan University, Haikou 570228, China
| | - Aoqi Wang
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Oceanology, Hainan University, Haikou 570228, China
| | - Lin Yang
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Oceanology, Hainan University, Haikou 570228, China
| | - Qinhua Gan
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Oceanology, Hainan University, Haikou 570228, China
| | - Liang Yi
- State Key Laboratory of Marine Geology, Tongji University, Shanghai 200092, China
| | - Roger E Summons
- Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - John K Volkman
- CSIRO Oceans and Atmosphere, GPO Box 1538, Hobart, Tasmania 7001, Australia
| | - Yandu Lu
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Oceanology, Hainan University, Haikou 570228, China
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Jiang R, Chen X, Liao X, Peng D, Han X, Zhu C, Wang P, Hufnagel DE, Wang L, Li K, Li C. A Chromosome-Level Genome of the Camphor Tree and the Underlying Genetic and Climatic Factors for Its Top-Geoherbalism. FRONTIERS IN PLANT SCIENCE 2022; 13:827890. [PMID: 35592577 PMCID: PMC9112071 DOI: 10.3389/fpls.2022.827890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 02/24/2022] [Indexed: 06/15/2023]
Abstract
Camphor tree [Cinnamomum camphora (L.) J. Presl], a species in the magnoliid family Lauraceae, is known for its rich volatile oils and is used as a medical cardiotonic and as a scent in many perfumed hygiene products. Here, we present a high-quality chromosome-scale genome of C. camphora with a scaffold N50 of 64.34 Mb and an assembled genome size of 755.41 Mb. Phylogenetic inference revealed that the magnoliids are a sister group to the clade of eudicots and monocots. Comparative genomic analyses identified two rounds of ancient whole-genome duplication (WGD). Tandem duplicated genes exhibited a higher evolutionary rate, a more recent evolutionary history and a more clustered distribution on chromosomes, contributing to the production of secondary metabolites, especially monoterpenes and sesquiterpenes, which are the principal essential oil components. Three-dimensional analyses of the volatile metabolites, gene expression and climate data of samples with the same genotype grown in different locations showed that low temperature and low precipitation during the cold season modulate the expression of genes in the terpenoid biosynthesis pathways, especially TPS genes, which facilitates the accumulation of volatile compounds. Our study lays a theoretical foundation for policy-making regarding the agroforestry applications of camphor tree.
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Affiliation(s)
- Rihong Jiang
- Guangxi Key Laboratory for Cultivation and Utilization of Special Non-Timber Forest Crops, Guangxi Engineering and Technology Research Center for Woody Spices, Guangxi Forestry Research Institute, Nanning, China
- College of Environmental Sciences and Engineering, Central South University of Forestry and Technology, Changsha, China
| | - Xinlian Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Xuezhu Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Dan Peng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiaoxu Han
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Changsan Zhu
- Guangxi Key Laboratory for Cultivation and Utilization of Special Non-Timber Forest Crops, Guangxi Engineering and Technology Research Center for Woody Spices, Guangxi Forestry Research Institute, Nanning, China
| | - Ping Wang
- College of Environmental Sciences and Engineering, Central South University of Forestry and Technology, Changsha, China
| | - David E. Hufnagel
- Virus and Prion Research Unit, National Animal Disease Center, The Agricultural Research Service (ARS) of the United States Department of Agriculture (USDA), Ames, IA, United States
| | - Li Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
| | - Kaixiang Li
- Guangxi Key Laboratory for Cultivation and Utilization of Special Non-Timber Forest Crops, Guangxi Engineering and Technology Research Center for Woody Spices, Guangxi Forestry Research Institute, Nanning, China
| | - Cheng Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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50
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Huang W, Zhang L, Columbus JT, Hu Y, Zhao Y, Tang L, Guo Z, Chen W, McKain M, Bartlett M, Huang CH, Li DZ, Ge S, Ma H. A well-supported nuclear phylogeny of Poaceae and implications for the evolution of C 4 photosynthesis. MOLECULAR PLANT 2022; 15:755-777. [PMID: 35093593 DOI: 10.1016/j.molp.2022.01.015] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 06/09/2021] [Accepted: 01/24/2022] [Indexed: 05/11/2023]
Abstract
Poaceae (the grasses) includes rice, maize, wheat, and other crops, and is the most economically important angiosperm family. Poaceae is also one of the largest plant families, consisting of over 11 000 species with a global distribution that contributes to diverse ecosystems. Poaceae species are classified into 12 subfamilies, with generally strong phylogenetic support for their monophyly. However, many relationships within subfamilies, among tribes and/or subtribes, remain uncertain. To better resolve the Poaceae phylogeny, we generated 342 transcriptomic and seven genomic datasets; these were combined with other genomic and transcriptomic datasets to provide sequences for 357 Poaceae species in 231 genera, representing 45 tribes and all 12 subfamilies. Over 1200 low-copy nuclear genes were retrieved from these datasets, with several subsets obtained using additional criteria, and used for coalescent analyses to reconstruct a Poaceae phylogeny. Our results strongly support the monophyly of 11 subfamilies; however, the subfamily Puelioideae was separated into two non-sister clades, one for each of the two previously defined tribes, supporting a hypothesis that places each tribe in a separate subfamily. Molecular clock analyses estimated the crown age of Poaceae to be ∼101 million years old. Ancestral character reconstruction of C3/C4 photosynthesis supports the hypothesis of multiple independent origins of C4 photosynthesis. These origins are further supported by phylogenetic analysis of the ppc gene family that encodes the phosphoenolpyruvate carboxylase, which suggests that members of three paralogous subclades (ppc-aL1a, ppc-aL1b, and ppc-B2) were recruited as functional C4ppc genes. This study provides valuable resources and a robust phylogenetic framework for evolutionary analyses of the grass family.
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Affiliation(s)
- Weichen Huang
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Lin Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - J Travis Columbus
- Rancho Santa Ana Botanic Garden and Claremont Graduate University, 1500 North College Avenue, Claremont, CA 91711, USA
| | - Yi Hu
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA
| | - Yiyong Zhao
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA; Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Lin Tang
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA; College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zhenhua Guo
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201 China
| | - Wenli Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Michael McKain
- Department of Biological Sciences, University of Alabama, 411 Mary Harmon Bryant Hall, Tuscaloosa, AL 35487, USA
| | - Madelaine Bartlett
- Biology Department, University of Massachusetts Amherst, 611 North Pleasant Street, 221 Morrill 3, Amherst, MA 01003 USA
| | - Chien-Hsun Huang
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA; Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - De-Zhu Li
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201 China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Hong Ma
- Department of Biology, 510 Mueller Laboratory, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA 16802, USA.
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