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Tong L, Wang J. Morphological Study on the Differentiation of Flower Buds and the Embryological Stages of Male and Female Floral Organs in Lespedeza davurica (Laxm.) Schindl. cv. JinNong ( Fabaceae). PLANTS (BASEL, SWITZERLAND) 2024; 13:1661. [PMID: 38931095 PMCID: PMC11207519 DOI: 10.3390/plants13121661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 06/09/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024]
Abstract
Lespedeza davurica (Laxm.) is a leguminous plant with significant ecological benefits, but its embryonic development mechanism remains unclear. We investigated the flower bud differentiation, megaspore and microspore formation, gametophyte development, and embryo and endosperm development in L. davurica. Our aim was to elucidate the relationship between the external morphology and internal development processes of male and female floral organs during growth, as well as the reproductive factors influencing fruiting. The results indicated that although the pistil develops later than the stamen during flower bud differentiation, both organs mature synchronously before flowering. L. davurica pollen exhibits three germination grooves, a reticulate outer wall, and papillary structures on the anther surface. In vivo pollination experiments revealed abnormal spiral growth of L. davurica pollen tubes within the style and the occurrence of callus plugs, which may reduce the seed setting rate. The anther wall development follows the dicotyledonous type, with tetrads formed through microspore meiosis exhibiting both left-right symmetry and tetrahedral arrangements. L. davurica has a single ovule, and the embryo sac develops in the monosporic polygonum type. After dormancy, the zygote undergoes multiple divisions, progressing through spherical, heart-shaped, and torpedo-shaped embryo stages, culminating in a mature embryo. A mature seed comprises cotyledons, hypocotyl, embryo, radicle, and seed coat. Phylogenetic tree analysis reveals a close genetic relationship between L. davurica and other leguminous plants from the genera Lespedeza and Medicago. This study provides valuable insights into the regulation of flowering and hybrid breeding in leguminous plants and offers a new perspective on the development of floral organs and seed setting rates.
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Affiliation(s)
- Lirong Tong
- College of Grassland Science, Shanxi Agricultural University, Taigu 030800, China;
| | - Juan Wang
- College of Grassland Science, Shanxi Agricultural University, Taigu 030800, China;
- Forage Seed Laboratory, College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
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2
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Parrish SB, Paudel D, Deng Z. Transcriptome analysis of Lantana camara flower petals reveals candidate anthocyanin biosynthesis genes mediating red flower color development. G3 (BETHESDA, MD.) 2023; 14:jkad259. [PMID: 37974306 PMCID: PMC10755171 DOI: 10.1093/g3journal/jkad259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/05/2023] [Accepted: 11/02/2023] [Indexed: 11/19/2023]
Abstract
Flower color plays a crucial role in the appeal and selection of ornamental plants, directly influencing breeding strategies and the broader horticulture industry. Lantana camara, a widely favored flowering shrub, presents a rich palette of flower colors. Yet, the intricate molecular mechanisms governing this color variation in the species have remained largely unidentified. With the aim of filling this gap, this study embarked on a comprehensive de novo transcriptome assembly and differential gene expression analysis across 3 distinct lantana accessions, each showcasing a unique flower color. By harnessing the capabilities of both PacBio and Illumina sequencing platforms, a robust transcriptome assembly, encompassing 123,492 gene clusters and boasting 94.2% BUSCO completeness, was developed. The differential expression analysis unveiled 72,862 unique gene clusters that exhibited varied expression across different flower stages. A pronounced upregulation of 8 candidate core anthocyanin biosynthesis genes in the red-flowered accession was uncovered. This was further complemented by an upregulation of candidate MYB75 (PAP1) and bHLH42 (TT8) transcription factors. A candidate carotenoid cleavage dioxygenase (CCD4a) gene cluster also manifested a marked upregulation in white flowers. The study unveils the molecular groundwork of lantana's flower color variation, offering insights for future research and potential applications in breeding ornamental plants with desired color traits.
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Affiliation(s)
- Stephen Brooks Parrish
- Department of Environmental Horticulture, Gulf Coast Research and Education Center, University of Florida, IFAS, 14625 County Road 672, Wimauma, FL 33598, USA
| | - Dev Paudel
- Department of Environmental Horticulture, Gulf Coast Research and Education Center, University of Florida, IFAS, 14625 County Road 672, Wimauma, FL 33598, USA
| | - Zhanao Deng
- Department of Environmental Horticulture, Gulf Coast Research and Education Center, University of Florida, IFAS, 14625 County Road 672, Wimauma, FL 33598, USA
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3
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White OW, Reyes-Betancort A, Carine MA, Chapman MA. Comparative transcriptomics and gene expression divergence associated with homoploid hybrid speciation in Argyranthemum. G3 (BETHESDA, MD.) 2023; 13:jkad158. [PMID: 37477910 PMCID: PMC10542503 DOI: 10.1093/g3journal/jkad158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 04/21/2023] [Accepted: 06/28/2023] [Indexed: 07/22/2023]
Abstract
Ecological isolation is increasingly thought to play an important role in speciation, especially for the origin and reproductive isolation of homoploid hybrid species. However, the extent to which divergent and/or transgressive gene expression changes are involved in speciation is not well studied. In this study, we employ comparative transcriptomics to investigate gene expression changes associated with the origin and evolution of two homoploid hybrid plant species, Argyranthemum sundingii and A. lemsii (Asteraceae). As there is no standard methodology for comparative transcriptomics, we examined five different pipelines for data assembly and analysing gene expression across the four species (two hybrid and two parental). We note biases and problems with all pipelines, and the approach used affected the biological interpretation of the data. Using the approach that we found to be optimal, we identify transcripts showing DE between the parental taxa and between the homoploid hybrid species and their parents; in several cases, putative functions of these DE transcripts have a plausible role in ecological adaptation and could be the cause or consequence of ecological speciation. Although independently derived, the homoploid hybrid species have converged on similar expression phenotypes, likely due to adaptation to similar habitats.
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Affiliation(s)
- Oliver W White
- Algae, Fungi and Plants Division, Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | | | - Mark A Carine
- Algae, Fungi and Plants Division, Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
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Chaudhary J, Gautam T, Gahlaut V, Singh K, Kumar S, Batra R, Gupta PK. Identification and characterization of RuvBL DNA helicase genes for tolerance against abiotic stresses in bread wheat (Triticum aestivum L.) and related species. Funct Integr Genomics 2023; 23:255. [PMID: 37498392 DOI: 10.1007/s10142-023-01177-y] [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: 11/02/2022] [Revised: 07/13/2023] [Accepted: 07/13/2023] [Indexed: 07/28/2023]
Abstract
Recombination UVB (sensitivity) like (RuvBL) helicase genes represent a conserved family of genes, which are known to be involved in providing tolerance against abiotic stresses like heat and drought. We identified nine wheat RuvBL genes, one each on nine different chromosomes, belonging to homoeologous groups 2, 3, and 4. The lengths of genes ranged from 1647 to 2197 bp and exhibited synteny with corresponding genes in related species including Ae. tauschii, Z. mays, O. sativa, H. vulgare, and B. distachyon. The gene sequences were associated with regulatory cis-elements and transposable elements. Two genes, namely TaRuvBL1a-4A and TaRuvBL1a-4B, also carried targets for a widely known miRNA, tae-miR164. Gene ontology revealed that these genes were closely associated with ATP-dependent formation of histone acetyltransferase complex. Analysis of the structure and function of RuvBL proteins revealed that the proteins were localized mainly in the cytoplasm. A representative gene, namely TaRuvBL1a-4A, was also shown to be involved in protein-protein interactions with ten other proteins. On the basis of phylogeny, RuvBL proteins were placed in two sub-divisions, namely RuvBL1 and RuvBL2, which were further classified into clusters and sub-clusters. In silico studies suggested that these genes were differentially expressed under heat/drought. The qRT-PCR analysis confirmed that expression of TaRuvBL genes differed among wheat cultivars, which differed in the level of thermotolerance. The present study advances our understanding of the biological role of wheat RuvBL genes and should help in planning future studies on RuvBL genes in wheat including use of RuvBL genes in breeding thermotolerant wheat cultivars.
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Affiliation(s)
- Jyoti Chaudhary
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, 250004, Meerut, India
| | - Tinku Gautam
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, 250004, Meerut, India
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Vijay Gahlaut
- Council of Scientific & Industrial Research-Institute of Himalayan Bioresource Technology, Palampur, India
- Department of Biotechnology, University Center for Research and Development, Chandigarh University, Gharuan, Mohali, Punjab, 140413, India
| | - Kalpana Singh
- Department of Bioinformatics, College of animal Biotechnology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - Sourabh Kumar
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, 250004, Meerut, India
| | - Ritu Batra
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, 250004, Meerut, India
- IIMT University, 'O' Pocket, Ganga Nagar, Meerut, India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, 250004, Meerut, India.
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Zhou T, Sun J, Zhai Y, Gao C, Ruhsam M, Wang X. Transcriptome profiles of yellowish-white and fuchsia colored flowers in the Rheum palmatum complex reveal genes related to color polymorphism. PLANT MOLECULAR BIOLOGY 2022; 110:187-197. [PMID: 35943640 DOI: 10.1007/s11103-022-01299-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 06/02/2022] [Indexed: 06/15/2023]
Abstract
Flower color variation is ubiquitous in many plant species, and several studies have been conducted to elucidate the underlying molecular mechanism. There are two flower color variants (yellowish-white and fuchsia) in the Rheum palmatum complex, however, few studies have investigated this phenomenon. Here, we used transcriptome sequencing of the two color variants to shed light on the molecular and biochemical basis for these color morphs. Comparison of the two transcriptomes identified 9641 differentially expressed unigenes (DEGs), including 6477 up-regulated and 3163 down-regulated genes. Functional analyses indicated that several DEGs were related to the anthocyanin biosynthesis pathway, and the expression profiles of these DEGs were coincident with the qRT-PCR validation results, indicating that expression levels of structural genes have a profound effect on the color variation in the R. palmatum complex. Our results suggested that the interaction of transcription factors (MYB, bHLH and WRKY) also regulated the anthocyanin biosynthesis in the R. palmatum complex. Estimation of selection pressures using the dN/dS ratio showed that 1106 pairs of orthologous genes have undergone positive selection. Of these positively selected genes, 21 were involved in the anthocyanin biosynthetic pathway, indicating that they may encode the proteins for structural alteration and affect flower color in the R. palmatum complex.
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Affiliation(s)
- Tao Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jiangyan Sun
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yunyan Zhai
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Chenxi Gao
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Markus Ruhsam
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LR, UK
| | - Xumei Wang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China.
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Chen Z, Liao M, Yang Z, Chen W, Wei S, Zou J, Peng Z. Co-expression network analysis of genes and networks associated with wheat pistillody. PeerJ 2022; 10:e13902. [PMID: 36039368 PMCID: PMC9419718 DOI: 10.7717/peerj.13902] [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: 05/07/2022] [Accepted: 07/24/2022] [Indexed: 01/19/2023] Open
Abstract
Crop male sterility has great value in theoretical research and breeding application. HTS-1, whose stamens transformed into pistils or pistil-like structures, is an important male sterility material selecting from Chinese Spring three-pistil (CSTP) wheat. However the molecular mechanism of pistillody development in HTS-1 remains a mystery. RNA-seq data of 11 wheat tissues were obtained from the National Center for Biotechnology Information (NCBI), including the stamens of CSTP and the pistils and pistillodic stamen of HTS-1. The Salmon program was utilized to quantify the gene expression levels of the 11 wheat tissues; and gene quantification results were normalized by transcripts per million (TPM). In total, 58,576 genes were used to construct block-wise network by co-expression networks analysis (WGCNA) R package. We obtained all of modules significantly associated with the 11 wheat tissues. AgriGO V2.0 was used to do Gene Ontology (GO) enrichment analysis; and genes and transcription factors (TFs) in these significant modules about wheat pistillody development were identified from GO enrichment results. Basic local alignment search tool (BLAST) was used to align HTS-1 proteins with the published pistillody-related proteins and TFs. Genes about wheat pistillody development were analyzed and validated by qRT-PCR. The MEturquoise, MEsaddlebrown, MEplum, MEcoral1, MElightsteelblue1, and MEdarkslateblue modules were significantly corelated to pistillodic stamen (correlation p < 0.05). Moreover, 206 genes related to carpel development (GO:0048440) or gynoecium development (GO:0048467) were identified only in the MEturquoise module by Gene Ontology (GO) analysis, and 42 of 206 genes were hub genes in MEturquoise module. qRT-PCR results showed that 38 of the 42 hub genes had highly expressed in pistils and pistillodic stamens than in stamens. A total of 15 pistillody development-related proteins were validated by BLAST. Transcription factors (TFs) were also analyzed in the MEturquoise module, and 618 TFs were identified. In total, 56 TFs from 11 families were considered to regulate the development of pistillodic stamen. The co-expression network showed that six of HB and three of BES1 genes were identified in 42 hub genes. This indicated that TFs played important roles in wheat pistillody development. In addition, there were 11 of ethylene-related genes connected with TFs or hub genes, suggesting the important roles of ethylene-related genes in pistillody development. These results provide important insights into the molecular interactions underlying pistillody development.
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Affiliation(s)
- Zhenyong Chen
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, Sichuan, People’s Republic of China
| | - Mingli Liao
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, Sichuan, People’s Republic of China
| | - Zaijun Yang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, Sichuan, People’s Republic of China
| | - Weiying Chen
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, Sichuan, People’s Republic of China
| | - Shuhong Wei
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, Sichuan, People’s Republic of China
| | - Jian Zou
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), College of Life Science, China West Normal University, Nanchong, Sichuan, People’s Republic of China
| | - Zhengsong Peng
- School of Agricultural Science, Xichang University, Xichang, Sichuan, People’s Republic of China
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Poulin V, Amesefe D, Gonzalez E, Alexandre H, Joly S. Testing candidate genes linked to corolla shape variation of a pollinator shift in Rhytidophyllum (Gesneriaceae). PLoS One 2022; 17:e0267540. [PMID: 35853078 PMCID: PMC9295946 DOI: 10.1371/journal.pone.0267540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/12/2022] [Indexed: 11/18/2022] Open
Abstract
Floral adaptations to specific pollinators like corolla shape variation often result in reproductive isolation and thus speciation. But despite their ecological importance, the genetic bases of corolla shape transitions are still poorly understood, especially outside model species. Hence, our goal was to identify candidate genes potentially involved in corolla shape variation between two closely related species of the Rhytidophyllum genus (Gesneriaceae family) from the Antilles with contrasting pollination strategies. Rhytidophyllum rupincola has a tubular corolla and is strictly pollinated by hummingbirds, whereas R. auriculatum has more open flowers and is pollinated by hummingbirds, bats, and insects. We surveyed the literature and used a comparative transcriptome sequence analysis of synonymous and non-synonymous nucleotide substitutions to obtain a list of genes that could explain floral variation between R. auriculatum and R. rupincola. We then tested their association with corolla shape variation using QTL mapping in a F2 hybrid population. Out of 28 genes tested, three were found to be good candidates because of a strong association with corolla shape: RADIALIS, GLOBOSA, and JAGGED. Although the role of these genes in Rhytidophyllum corolla shape variation remains to be confirmed, these findings are a first step towards identifying the genes that have been under selection by pollinators and thus involved in reproductive isolation and speciation in this genus.
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Affiliation(s)
- Valérie Poulin
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Canada
| | - Delase Amesefe
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Canada
| | - Emmanuel Gonzalez
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Canada
- Department of Human Genetics, Canadian Centre for Computational Genomics (C3G), McGill University, Montréal, QC, Canada
- Microbiome Research Platform, McGill Interdisciplinary Initiative in Infection and Immunity (MI4), Genome Centre, McGill University, Montréal, QC, Canada
| | - Hermine Alexandre
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Canada
| | - Simon Joly
- Département de Sciences Biologiques, Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, Canada
- Montreal Botanical Garden, Montréal, Canada
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Lin C, Xing P, Jin H, Zhou C, Li X, Song Z. Loss of anthocyanidin synthase gene is associated with white flowers of Salvia miltiorrhiza Bge. f. alba, a natural variant of S. miltiorrhiza. PLANTA 2022; 256:15. [PMID: 35725965 DOI: 10.1007/s00425-022-03921-3] [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: 03/22/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
SmANS deletion leads to white flower mutation in Salvia miltiorrhiza. SmANS deletion leads to white flower mutation in Salvia miltiorrhiza. Abstract Salvia miltiorrhiza is an essential traditional Chinese medicine (TCM) with purple flowers, and S. miltiorrhiza Bge. f. alba is a unique intraspecific variation with white flowers. The molecular mechanism of flower color formation in S. miltiorrhiza will provide vital information for the variation and evolution. Here, we performed HPLC, transcriptomic, and re-sequencing analyses of purple-flowered S. miltiorrhiza line 'Zihua105' (ZH105) and white-flowered S. miltiorrhiza Bge. f. alba line 'Baihua18' (BH18). Delphinidin was the most anthocyanidin in ZH105, which become the main different between ZH105 vs. BH18 flowers. Transcriptome analysis revealed 299 differentially expressed genes (DEGs). SmANS, the anthocyanidin synthase gene in the down-stream anthocyanin biosynthesis pathway, was significantly expressed in ZH105 corollas, suggesting it might play a key role in white petal formation. Whole-genome re-sequencing revealed that a 6.75 kb segment located on chromosome 5, which contains the complete sequence of the SmANS genes, was lost in BH18 and another S. miltiorrhiza Bge. f. alba line. In contrast, the other five purple-flowered S. miltiorrhiza lines both possessed this segment. Further molecular marker identification also confirmed that wild S. miltiorrhiza Bge. f. alba lines lost regions that contained a complete or important part of SmANS sequences. Subsequently, the research showed that the deletion mutant of SmANS genes resulted in the natural white flower color variant of S. miltiorrhiza.
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Affiliation(s)
- Caicai Lin
- Agronomy College, Shandong Agricultural University, Tai'an, 271028, Shandong, China
| | - Piyi Xing
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271028, Shandong, China
| | - Hua Jin
- Agronomy College, Shandong Agricultural University, Tai'an, 271028, Shandong, China
| | - Changhao Zhou
- Agronomy College, Shandong Agricultural University, Tai'an, 271028, Shandong, China
| | - Xingfeng Li
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271028, Shandong, China.
| | - Zhenqiao Song
- Agronomy College, Shandong Agricultural University, Tai'an, 271028, Shandong, China.
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271028, Shandong, China.
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An Integrated Analysis of Transcriptome and miRNA Sequencing Provides Insights into the Dynamic Regulations during Flower Morphogenesis in Petunia. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8040284] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Published genome sequences can facilitate multiple genome sequencing studies of flower development, which can serve as the basis for later analysis of variation in flower phenotypes. To identify potential regulators related to flower morphology, we captured dynamic expression patterns under five different developmental stages of petunia flowers, a popular bedding plant, using transcriptome and miRNA sequencing. The significant transcription factor (TF) families, including MYB, MADS, and bHLH, were elucidated. MADS-box genes exhibited co-expression patterns with BBR-BPC, GATA, and Dof genes in different modules according to a weighted gene co-expression network analysis. Through miRNA sequencing, a total of 45 conserved and 26 novel miRNAs were identified. According to GO and KEGG enrichment analysis, the carbohydrate metabolic process, photosynthesis, and phenylalanine metabolism were significant at the transcriptomic level, while the response to hormone pathways was significantly enriched by DEmiR-targeted genes. Finally, an miRNA–RNA network was constructed, which suggested the possibility of novel miRNA-mediated regulation pathways being activated during flower development. Overall, the expression data in the present study provide novel insights into the developmental gene regulatory network facilitated by TFs, miRNA, and their target genes.
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Rajabi A, Fahmideh L, Keykhasaber M, Omran VG. Genetic engineering of novel yellow color african violet (Saintpaulia ionantha) produced by accumulation of Aureusidin 6-O-glucoside. Biol Proced Online 2022; 24:3. [PMID: 35139820 PMCID: PMC8903692 DOI: 10.1186/s12575-022-00164-0] [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: 08/24/2021] [Accepted: 01/25/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Flower color is one of the main characteristics of ornamental plants. Aurones are light yellow flavonoids produced in the petals of a limited number of plant species including snapdragon (Antirrhinum majus). As a commercially-recognized species, African violet can be found in various colors except yellow. This research, aiming at changing the petals' color of African violet from white to yellow, was conducted using the simultaneous expressions of chalcone 4'-O-glucosyltransferase (4'CGT) and aureusidin synthase (AS1) genes without the need for silencing anthocyanin biosynthesis pathway genes via both transient and stable transfer methods. RESULTS The transient gene transfer among transgenic plants led to a clear change of petals' color from white to light yellow. This occurs while no change was observed in non-transgenic (Wild type) petals. In total, 15 positive transgenic plants, produced via stable gene transfer, were detected. Moreover, since their flower color was yellow, both genes were present. Meanwhile, the corresponding transformation yield was determined 20-30%. The transformation, expression and integration of genes among T0 transgenic plants were verified using the PCR, qRT-PCR and Southern blotting techniques, respectively. Furthermore, the probable color change of petals' cross-section and existence of Aureusidin 6-O-glucoside (AOG) compound were determined using a light microscope and HPLC-DAD-MSn analysis, correspondingly. CONCLUSIONS Generally, the creation of aurones biosynthesis pathway is only viable through the simultaneous expression of genes which leads to color change of African violet's petal from white to yellow. This conclusion can lead to an effective strategy to produce yellow color in ornamental plant species.
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Affiliation(s)
- Amir Rajabi
- Department of Plant Breeding and Biotechnology, University of Zabol, 98613-35856, Zabol, Iran
| | - Leila Fahmideh
- Department of Plant Breeding and Biotechnology, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran.
| | | | - Valiollah Ghasemi Omran
- Genetic and Agricultural Biotechnology Institute of Tabarestan, University of Agriculture Science and Natural Resources, Sari, Iran
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A Survey of Enhanced Cold Tolerance and Low-Temperature-Induced Anthocyanin Accumulation in a Novel Zoysia japonica Biotype. PLANTS 2022; 11:plants11030429. [PMID: 35161412 PMCID: PMC8839389 DOI: 10.3390/plants11030429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/23/2022] [Accepted: 02/01/2022] [Indexed: 11/17/2022]
Abstract
Zoysia japonica is a warm-season turfgrass that is extensively used in landscaping, sports fields, and golf courses worldwide. Uncovering the low-temperature response mechanism of Z. japonica can help to accelerate the development of new cold-tolerant cultivars, which could be used to prolong the ornamental and usage duration of turf. A novel Z. japonica biotype, YueNong-9 (YN-9), was collected from northeastern China for this study. Phenotypic measurements, cold-tolerance investigation, and whole-transcriptome surveys were performed on YN-9 and LanYin-3 (LY-3), the most popular Z. japonica cultivar in Southern China. The results indicated the following: YN-9 has longer second and third leaves than LY-3; when exposed to the natural low temperature during winter in Guangzhou, YN-9 accumulated 4.74 times more anthocyanin than LY-3; after cold acclimation and freezing treatment, 83.25 ± 9.55% of YN-9 survived while all LY-3 leaves died, and the dark green color index (DGCI) value of YN-9 was 1.78 times that of LY-3; in YN-9, there was a unique up-regulation of Phenylalanine ammonia-lyase (PAL), Homeobox-leucine Zipper IV (HD-ZIP), and ATP-Binding Cassette transporter B8 (ABCB8) expressions, as well as a unique down-regulation of zinc-regulated transporters and iron-regulated transporter-like proteins (ZIPs) expression, which may promote anthocyanin biosynthesis, transport, and accumulation. In conclusion, YN-9 exhibited enhanced cold tolerance and is thus an excellent candidate for breeding cold-tolerant Z. japonica variety, and its unique low-temperature-induced anthocyanin accumulation and gene responses provide ideas and candidate genes for the study of low-temperature tolerance mechanisms and genetic engineering breeding.
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12
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Banerjee SM, Stoll JA, Allen CD, Lynch JM, Harris HS, Kenyon L, Connon RE, Sterling EJ, Naro-Maciel E, McFadden K, Lamont MM, Benge J, Fernandez NB, Seminoff JA, Benson SR, Lewison RL, Eguchi T, Summers TM, Hapdei JR, Rice MR, Martin S, Jones TT, Dutton PH, Balazs GH, Komoroske LM. Species and population specific gene expression in blood transcriptomes of marine turtles. BMC Genomics 2021; 22:346. [PMID: 33985425 PMCID: PMC8117300 DOI: 10.1186/s12864-021-07656-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/23/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Transcriptomic data has demonstrated utility to advance the study of physiological diversity and organisms' responses to environmental stressors. However, a lack of genomic resources and challenges associated with collecting high-quality RNA can limit its application for many wild populations. Minimally invasive blood sampling combined with de novo transcriptomic approaches has great potential to alleviate these barriers. Here, we advance these goals for marine turtles by generating high quality de novo blood transcriptome assemblies to characterize functional diversity and compare global transcriptional profiles between tissues, species, and foraging aggregations. RESULTS We generated high quality blood transcriptome assemblies for hawksbill (Eretmochelys imbricata), loggerhead (Caretta caretta), green (Chelonia mydas), and leatherback (Dermochelys coriacea) turtles. The functional diversity in assembled blood transcriptomes was comparable to those from more traditionally sampled tissues. A total of 31.3% of orthogroups identified were present in all four species, representing a core set of conserved genes expressed in blood and shared across marine turtle species. We observed strong species-specific expression of these genes, as well as distinct transcriptomic profiles between green turtle foraging aggregations that inhabit areas of greater or lesser anthropogenic disturbance. CONCLUSIONS Obtaining global gene expression data through non-lethal, minimally invasive sampling can greatly expand the applications of RNA-sequencing in protected long-lived species such as marine turtles. The distinct differences in gene expression signatures between species and foraging aggregations provide insight into the functional genomics underlying the diversity in this ancient vertebrate lineage. The transcriptomic resources generated here can be used in further studies examining the evolutionary ecology and anthropogenic impacts on marine turtles.
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Affiliation(s)
- Shreya M Banerjee
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, USA
| | - Jamie Adkins Stoll
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, USA
| | - Camryn D Allen
- Marine Turtle Biology and Assessment Program, Protected Species Division, Pacific Islands Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Honolulu, HI, USA.,Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, USA
| | - Jennifer M Lynch
- Chemical Sciences Division, National Institute of Standards and Technology, Hawai'i Pacific University, Waimanalo, HI, USA
| | - Heather S Harris
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, USA
| | - Lauren Kenyon
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, USA
| | - Richard E Connon
- Department of Anatomy, Physiology and Cell Biology, University of California, Davis, Davis, CA, USA
| | - Eleanor J Sterling
- Center for Biodiversity and Conservation, American Museum of Natural History, New York, NY, USA
| | | | - Kathryn McFadden
- School of Agricultural, Forest, and Environmental Sciences, Clemson University, Clemson, SC, USA
| | - Margaret M Lamont
- United States Geological Survey, Wetland and Aquatic Research Center, Gainesville, FL, USA
| | - James Benge
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Nadia B Fernandez
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, USA
| | - Jeffrey A Seminoff
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, USA
| | - Scott R Benson
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Moss Landing, CA, 95039, USA.,Moss Landing Marine Laboratories, San Jose State University, Moss Landing, CA, 95039, USA
| | - Rebecca L Lewison
- Department of Biology, San Diego State University, San Diego, CA, USA
| | - Tomoharu Eguchi
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, USA
| | | | - Jessy R Hapdei
- Jessy's Tag Services, Saipan, Commonwealth of the Northern Mariana Islands, USA
| | - Marc R Rice
- Hawai'i Preparatory Academy, Kamuela, HI, USA
| | - Summer Martin
- Marine Turtle Biology and Assessment Program, Protected Species Division, Pacific Islands Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Honolulu, HI, USA
| | - T Todd Jones
- Marine Turtle Biology and Assessment Program, Protected Species Division, Pacific Islands Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Honolulu, HI, USA
| | - Peter H Dutton
- Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, USA
| | | | - Lisa M Komoroske
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, USA. .,Marine Mammal and Turtle Division, Southwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, La Jolla, CA, USA.
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13
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Sobral M, Neylan IP, Narbona E, Dirzo R. Transgenerational Plasticity in Flower Color Induced by Caterpillars. FRONTIERS IN PLANT SCIENCE 2021; 12:617815. [PMID: 33790921 PMCID: PMC8006444 DOI: 10.3389/fpls.2021.617815] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 02/19/2021] [Indexed: 05/03/2023]
Abstract
Variation in flower color due to transgenerational plasticity could stem directly from abiotic or biotic environmental conditions. Finding a link between biotic ecological interactions across generations and plasticity in flower color would indicate that transgenerational effects of ecological interactions, such as herbivory, might be involved in flower color evolution. We conducted controlled experiments across four generations of wild radish (Raphanus sativus, Brassicaceae) plants to explore whether flower color is influenced by herbivory, and to determine whether flower color is associated with transgenerational chromatin modifications. We found transgenerational effects of herbivory on flower color, partly related to chromatin modifications. Given the presence of herbivory in plant populations worldwide, our results are of broad significance and contribute to our understanding of flower color evolution.
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Affiliation(s)
- Mar Sobral
- Departamento de Biología Funcional, Universidade de Santiago de Compostela, USC, Santiago de Compostela, Spain
- Department of Biology, Stanford University, Stanford, CA, United States
| | - Isabelle P. Neylan
- Department of Biology, Stanford University, Stanford, CA, United States
- Department of Evolution and Ecology, Center for Population Biology, University of California, Davis, Davis, CA, United States
| | - Eduardo Narbona
- Departamento de Biología Molecular e Ingeniería Bioquímica, Universidad Pablo de Olavide, Seville, Spain
| | - Rodolfo Dirzo
- Department of Biology, Stanford University, Stanford, CA, United States
- Woods Institute for the Environment, Stanford University, Stanford, CA, United States
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14
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Sánchez-Cabrera M, Jiménez-López FJ, Narbona E, Arista M, Ortiz PL, Romero-Campero FJ, Ramanauskas K, Igić B, Fuller AA, Whittall JB. Changes at a Critical Branchpoint in the Anthocyanin Biosynthetic Pathway Underlie the Blue to Orange Flower Color Transition in Lysimachia arvensis. FRONTIERS IN PLANT SCIENCE 2021; 12:633979. [PMID: 33692818 PMCID: PMC7937975 DOI: 10.3389/fpls.2021.633979] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/01/2021] [Indexed: 05/27/2023]
Abstract
Anthocyanins are the primary pigments contributing to the variety of flower colors among angiosperms and are considered essential for survival and reproduction. Anthocyanins are members of the flavonoids, a broader class of secondary metabolites, of which there are numerous structural genes and regulators thereof. In western European populations of Lysimachia arvensis, there are blue- and orange-petaled individuals. The proportion of blue-flowered plants increases with temperature and daylength yet decreases with precipitation. Here, we performed a transcriptome analysis to characterize the coding sequences of a large group of flavonoid biosynthetic genes, examine their expression and compare our results to flavonoid biochemical analysis for blue and orange petals. Among a set of 140 structural and regulatory genes broadly representing the flavonoid biosynthetic pathway, we found 39 genes with significant differential expression including some that have previously been reported to be involved in similar flower color transitions. In particular, F3'5'H and DFR, two genes at a critical branchpoint in the ABP for determining flower color, showed differential expression. The expression results were complemented by careful examination of the SNPs that differentiate the two color types for these two critical genes. The decreased expression of F3'5'H in orange petals and differential expression of two distinct copies of DFR, which also exhibit amino acid changes in the color-determining substrate specificity region, strongly correlate with the blue to orange transition. Our biochemical analysis was consistent with the transcriptome data indicating that the shift from blue to orange petals is caused by a change from primarily malvidin to largely pelargonidin forms of anthocyanins. Overall, we have identified several flavonoid biosynthetic pathway loci likely involved in the shift in flower color in L. arvensis and even more loci that may represent the complex network of genetic and physiological consequences of this flower color polymorphism.
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Affiliation(s)
- Mercedes Sánchez-Cabrera
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, Spain
| | | | - Eduardo Narbona
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Seville, Spain
| | - Montserrat Arista
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, Spain
| | - Pedro L. Ortiz
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, Spain
| | - Francisco J. Romero-Campero
- Institute for Plant Biochemistry and Photosynthesis, University of Seville – Centro Superior de Investigación Científica, Seville, Spain
- Department of Computer Science and Artificial Intelligence, University of Seville, Seville, Spain
| | - Karolis Ramanauskas
- Department of Biological Science, University of Illinois at Chicago, Chicago, IL, United States
| | - Boris Igić
- Department of Biological Science, University of Illinois at Chicago, Chicago, IL, United States
| | - Amelia A. Fuller
- Department of Chemistry and Biochemistry, Santa Clara University, Santa Clara, CA, United States
| | - Justen B. Whittall
- Department of Biology, College of Arts and Sciences, Santa Clara University, Santa Clara, CA, United States
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15
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Liu H, Luo C, Chen D, Wang Y, Guo S, Chen X, Bai J, Li M, Huang X, Cheng X, Huang C. Whole-transcriptome analysis of differentially expressed genes in the mutant and normal capitula of Chrysanthemum morifolium. BMC Genom Data 2021; 22:2. [PMID: 33568073 PMCID: PMC7853313 DOI: 10.1186/s12863-021-00959-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 01/05/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chrysanthemum morifolium is one of the most economically important and popular floricultural crops in the family Asteraceae. Chrysanthemum flowers vary considerably in terms of colors and shapes. However, the molecular mechanism controlling the development of chrysanthemum floral colors and shapes remains an enigma. We analyzed a cut-flower chrysanthemum variety that produces normal capitula composed of ray florets with normally developed pistils and purple corollas and mutant capitula comprising ray florets with green corollas and vegetative buds instead of pistils. RESULTS We conducted a whole-transcriptome analysis of the differentially expressed genes (DEGs) in the mutant and normal capitula using third-generation and second-generation sequencing techniques. We identified the DEGs between the mutant and normal capitula to reveal important regulators underlying the differential development. Many transcription factors and genes related to the photoperiod and GA pathways, floral organ identity, and the anthocyanin biosynthesis pathway were differentially expressed between the normal and mutant capitula. A qualitative analysis of the pigments in the florets of normal and mutant capitula indicated anthocyanins were synthesized and accumulated in the florets of normal capitula, but not in the florets of mutant capitula. These results provide clues regarding the molecular basis of the replacement of Chrysanthemum morifolium ray florets with normally developed pistils and purple corollas with mutant ray florets with green corollas and vegetative buds. Additionally, the study findings will help to elucidate the molecular mechanisms underlying floral organ development and contribute to the development of techniques for studying the regulation of flower shape and color, which may enhance chrysanthemum breeding. CONCLUSIONS The whole-transcriptome analysis of DEGs in mutant and normal C. morifolium capitula described herein indicates the anthocyanin deficiency of the mutant capitula may be related to the mutation that replaces ray floret pistils with vegetative buds. Moreover, pistils may be required for the anthocyanin biosynthesis in the corollas of chrysanthemum ray florets.
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Affiliation(s)
- Hua Liu
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Chang Luo
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Dongliang Chen
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Yaqin Wang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Shuang Guo
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Xiaoxi Chen
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Jingyi Bai
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Mingyuan Li
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Xinlei Huang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Xi Cheng
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Conglin Huang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China.
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16
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Liu H, Luo C, Chen D, Wang Y, Guo S, Chen X, Bai J, Li M, Huang X, Cheng X, Huang C. Whole-transcriptome analysis of differentially expressed genes in the mutant and normal capitula of Chrysanthemum morifolium. BMC Genom Data 2021; 22:2. [PMID: 33568073 DOI: 10.21203/rs.3.rs-27505/v2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 01/05/2021] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND Chrysanthemum morifolium is one of the most economically important and popular floricultural crops in the family Asteraceae. Chrysanthemum flowers vary considerably in terms of colors and shapes. However, the molecular mechanism controlling the development of chrysanthemum floral colors and shapes remains an enigma. We analyzed a cut-flower chrysanthemum variety that produces normal capitula composed of ray florets with normally developed pistils and purple corollas and mutant capitula comprising ray florets with green corollas and vegetative buds instead of pistils. RESULTS We conducted a whole-transcriptome analysis of the differentially expressed genes (DEGs) in the mutant and normal capitula using third-generation and second-generation sequencing techniques. We identified the DEGs between the mutant and normal capitula to reveal important regulators underlying the differential development. Many transcription factors and genes related to the photoperiod and GA pathways, floral organ identity, and the anthocyanin biosynthesis pathway were differentially expressed between the normal and mutant capitula. A qualitative analysis of the pigments in the florets of normal and mutant capitula indicated anthocyanins were synthesized and accumulated in the florets of normal capitula, but not in the florets of mutant capitula. These results provide clues regarding the molecular basis of the replacement of Chrysanthemum morifolium ray florets with normally developed pistils and purple corollas with mutant ray florets with green corollas and vegetative buds. Additionally, the study findings will help to elucidate the molecular mechanisms underlying floral organ development and contribute to the development of techniques for studying the regulation of flower shape and color, which may enhance chrysanthemum breeding. CONCLUSIONS The whole-transcriptome analysis of DEGs in mutant and normal C. morifolium capitula described herein indicates the anthocyanin deficiency of the mutant capitula may be related to the mutation that replaces ray floret pistils with vegetative buds. Moreover, pistils may be required for the anthocyanin biosynthesis in the corollas of chrysanthemum ray florets.
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Affiliation(s)
- Hua Liu
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Chang Luo
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Dongliang Chen
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Yaqin Wang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Shuang Guo
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Xiaoxi Chen
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Jingyi Bai
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Mingyuan Li
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Xinlei Huang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Xi Cheng
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China
| | - Conglin Huang
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center of Functional Floriculture, Beijing, Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing, 100097, China.
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17
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Landis JB, Kurti A, Lawhorn AJ, Litt A, McCarthy EW. Differential Gene Expression with an Emphasis on Floral Organ Size Differences in Natural and Synthetic Polyploids of Nicotiana tabacum (Solanaceae). Genes (Basel) 2020; 11:E1097. [PMID: 32961813 PMCID: PMC7563459 DOI: 10.3390/genes11091097] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 11/16/2022] Open
Abstract
Floral organ size, especially the size of the corolla, plays an important role in plant reproduction by facilitating pollination efficiency. Previous studies have outlined a hypothesized organ size pathway. However, the expression and function of many of the genes in the pathway have only been investigated in model diploid species; therefore, it is unknown how these genes interact in polyploid species. Although correlations between ploidy and cell size have been shown in many systems, it is unclear whether there is a difference in cell size between naturally occurring and synthetic polyploids. To address these questions comparing floral organ size and cell size across ploidy, we use natural and synthetic polyploids of Nicotiana tabacum (Solanaceae) as well as their known diploid progenitors. We employ a comparative transcriptomics approach to perform analyses of differential gene expression, focusing on candidate genes that may be involved in floral organ size, both across developmental stages and across accessions. We see differential expression of several known floral organ candidate genes including ARF2, BIG BROTHER, and GASA/GAST1. Results from linear models show that ploidy, cell width, and cell number positively influence corolla tube circumference; however, the effect of cell width varies by ploidy, and diploids have a significantly steeper slope than both natural and synthetic polyploids. These results demonstrate that polyploids have wider cells and that polyploidy significantly increases corolla tube circumference.
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Affiliation(s)
- Jacob B. Landis
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA; (A.K.); (A.J.L.); (A.L.)
- School of Integrative Plant Science, Section of Plant Biology and the L.H. Bailey Hortorium, Cornell University, Ithaca, NY 14853, USA
| | - Amelda Kurti
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA; (A.K.); (A.J.L.); (A.L.)
| | - Amber J. Lawhorn
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA; (A.K.); (A.J.L.); (A.L.)
| | - Amy Litt
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA; (A.K.); (A.J.L.); (A.L.)
| | - Elizabeth W. McCarthy
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA; (A.K.); (A.J.L.); (A.L.)
- Department of Biology, SUNY Cortland, Cortland, NY 13045, USA
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18
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Chen LY, Morales-Briones DF, Passow CN, Yang Y. Performance of gene expression analyses using de novo assembled transcripts in polyploid species. Bioinformatics 2020; 35:4314-4320. [PMID: 31400193 DOI: 10.1093/bioinformatics/btz620] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 07/12/2019] [Accepted: 08/09/2019] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Quality of gene expression analyses using de novo assembled transcripts in species that experienced recent polyploidization remains unexplored. RESULTS Differential gene expression (DGE) analyses using putative genes inferred by Trinity, Corset and Grouper performed slightly differently across five plant species that experienced various polyploidy histories. In species that lack recent polyploidy events that occurred in the past several millions of years, DGE analyses using de novo assembled transcriptomes identified 54-82% of the differentially expressed genes recovered by mapping reads to the reference genes. However, in species that experienced more recent polyploidy events, the percentage decreased to 21-65%. Gene co-expression network analyses using de novo assemblies versus mapping to the reference genes recovered the same module that significantly correlated with treatment in one species that lacks recent polyploidization. AVAILABILITY AND IMPLEMENTATION Commands and scripts used in this study are available at https://bitbucket.org/lychen83/chen_et_al_2018_benchmark_dge/; Analysis files are available at Dryad doi: 10.5061/dryad.4p6n481. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ling-Yun Chen
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, Saint Paul, MN, USA
| | - Diego F Morales-Briones
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, Saint Paul, MN, USA
| | - Courtney N Passow
- Department of Ecology Evolution and Behavior, University of Minnesota, Twin Cities, Saint Paul, MN, USA.,University of Minnesota Genomics Center, University of Minnesota, Twin Cities, Saint Paul, MN, USA
| | - Ya Yang
- Department of Plant and Microbial Biology, University of Minnesota, Twin Cities, Saint Paul, MN, USA
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19
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Roberts WR, Roalson EH. Co-expression clustering across flower development identifies modules for diverse floral forms in Achimenes (Gesneriaceae). PeerJ 2020; 8:e8778. [PMID: 32201652 PMCID: PMC7071821 DOI: 10.7717/peerj.8778] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/21/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Genetic pathways involved with flower color and shape are thought to play an important role in the development of flowers associated with different pollination syndromes, such as those associated with bee, butterfly, or hummingbird pollination. Because pollination syndromes are complex traits that are orchestrated by multiple genes and pathways, the gene regulatory networks have not been explored. Gene co-expression networks provide a systems level approach to identify important contributors to floral diversification. METHODS RNA-sequencing was used to assay gene expression across two stages of flower development (an early bud and an intermediate stage) in 10 species of Achimenes (Gesneriaceae). Two stage-specific co-expression networks were created from 9,503 orthologs and analyzed to identify module hubs and the network periphery. Module association with bee, butterfly, and hummingbird pollination syndromes was tested using phylogenetic mixed models. The relationship between network connectivity and evolutionary rates (d N/d S) was tested using linear models. RESULTS Networks contained 65 and 62 modules that were largely preserved between developmental stages and contained few stage-specific modules. Over a third of the modules in both networks were associated with flower color, shape, and pollination syndrome. Within these modules, several hub nodes were identified that related to the production of anthocyanin and carotenoid pigments and the development of flower shape. Evolutionary rates were decreased in highly connected genes and elevated in peripheral genes. DISCUSSION This study aids in the understanding of the genetic architecture and network properties underlying the development of floral form and provides valuable candidate modules and genes for future studies.
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Affiliation(s)
- Wade R. Roberts
- School of Biological Sciences, Washington State University, Pullman, WA, USA
- Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Eric H. Roalson
- School of Biological Sciences, Washington State University, Pullman, WA, USA
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20
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Chang H, Sun F. Temporal Distinction between Male and Female Floral Organ Development in Nicotiana tabacum cv. Xanthi (Solanaceae). PLANTS (BASEL, SWITZERLAND) 2020; 9:E127. [PMID: 31963844 PMCID: PMC7020162 DOI: 10.3390/plants9010127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 01/16/2020] [Accepted: 01/17/2020] [Indexed: 01/13/2023]
Abstract
Early floral developmental investigations provide crucial evidence for phylogenetic and molecular studies of plants. The developmental and evolutionary mechanisms underlying the variations in floral organs are critical for a thorough understanding of the diversification of flowers. Ontogenetic comparisons between anthers and pistil within single flowers were characterized over time in Nicotiana tabacum cv. Xanthi. The ages of 42 tobacco flower or flower primordia were estimated using corolla growth analysis. Results showed that the protodermal layer in carpel primordia contributes to carpel development by both anticlinal and periclinal divisions. Periclinal divisions in the hypodermal layer of the placenta were observed around 4.8 ± 1.3 days after the formation of early carpel primordia (ECP) and ovule initiation occurred 10.0 ± 0.5 days after ECP. Meiosis in anthers and ovules began about 8.9 ± 1.1 days and 14.4 ± 1.3 days after ECP, respectively. Results showed an evident temporal distinction between megasporogenesis and microsporogenesis. Flower ages spanned a 17-day interval, starting with flower primordia containing the ECP and anther primordia to the tetrad stage of meiosis in megasporocytes and the bicellular stage in pollen grains. These results establish a solid foundation for future studies in order to identify the developmental and molecular mechanisms responsible for the mating system in tobacco.
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Affiliation(s)
- Hongli Chang
- Shaanxi Key Laboratory for Animal Conservation, School of Life Sciences, Northwest University, Xi’an 710069, China;
| | - Fengjie Sun
- School of Science and Technology, Georgia Gwinnett College, Lawrenceville, GA 30043, USA
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Ogutcen E, Durand K, Wolowski M, Clavijo L, Graham C, Glauser G, Perret M. Chemical Basis of Floral Color Signals in Gesneriaceae: The Effect of Alternative Anthocyanin Pathways. FRONTIERS IN PLANT SCIENCE 2020; 11:604389. [PMID: 33381138 PMCID: PMC7767864 DOI: 10.3389/fpls.2020.604389] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 11/23/2020] [Indexed: 05/14/2023]
Abstract
Changes in floral pigmentation can have dramatic effects on angiosperm evolution by making flowers either attractive or inconspicuous to different pollinator groups. Flower color largely depends on the type and abundance of pigments produced in the petals, but it is still unclear whether similar color signals rely on same biosynthetic pathways and to which extent the activation of certain pathways influences the course of floral color evolution. To address these questions, we investigated the physical and chemical aspects of floral color in the Neotropical Gesnerioideae (ca. 1,200 spp.), in which two types of anthocyanins, hydroxyanthocyanins, and deoxyanthocyanins, have been recorded as floral pigments. Using spectrophotometry, we measured flower reflectance for over 150 species representing different clades and pollination syndromes. We analyzed these reflectance data to estimate how the Gesnerioideae flowers are perceived by bees and hummingbirds using the visual system models of these pollinators. Floral anthocyanins were further identified using high performance liquid chromatography coupled to mass spectrometry. We found that orange/red floral colors in Gesnerioideae are produced either by deoxyanthocyanins (e.g., apigenidin, luteolinidin) or hydroxyanthocyanins (e.g., pelargonidin). The presence of deoxyanthocyanins in several lineages suggests that the activation of the deoxyanthocyanin pathway has evolved multiple times in the Gesnerioideae. The hydroxyanthocyanin-producing flowers span a wide range of colors, which enables them to be discriminated by hummingbirds or bees. By contrast, color diversity among the deoxyanthocyanin-producing species is lower and mainly represented at longer wavelengths, which is in line with the hue discrimination optima for hummingbirds. These results indicate that Gesnerioideae have evolved two different biochemical mechanisms to generate orange/red flowers, which is associated with hummingbird pollination. Our findings also suggest that the activation of the deoxyanthocyanin pathway has restricted flower color diversification to orange/red hues, supporting the potential constraining role of this alternative biosynthetic pathway on the evolutionary outcome of phenotypical and ecological diversification.
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Affiliation(s)
- Ezgi Ogutcen
- Conservatoire et Jardin botaniques de la Ville de Genève, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Karine Durand
- Conservatoire et Jardin botaniques de la Ville de Genève, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
| | - Marina Wolowski
- Institute of Natural Sciences, Federal University of Alfenas, Alfenas, Brazil
| | - Laura Clavijo
- Instituto de Ciencias Naturales, National University of Colombia, UNAL, Bogotá, Colombia
| | - Catherine Graham
- Swiss Federal Research Institute (WSL), Birmensdorf, Switzerland
| | - Gaétan Glauser
- Neuchatel Platform of Analytical Chemistry, University of Neuchatel, Neuchâtel, Switzerland
| | - Mathieu Perret
- Conservatoire et Jardin botaniques de la Ville de Genève, Department of Botany and Plant Biology, University of Geneva, Geneva, Switzerland
- *Correspondence: Mathieu Perret,
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Lallemand F, Martin-Magniette ML, Gilard F, Gakière B, Launay-Avon A, Delannoy É, Selosse MA. In situ transcriptomic and metabolomic study of the loss of photosynthesis in the leaves of mixotrophic plants exploiting fungi. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:826-841. [PMID: 30735596 DOI: 10.1111/tpj.14276] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 01/31/2019] [Accepted: 02/01/2019] [Indexed: 05/15/2023]
Abstract
Mycoheterotrophic plants have lost photosynthesis and obtain carbon through mycorrhizal fungi colonizing their roots. They are likely to have evolved from mixotrophic ancestors, which rely on both photosynthesis and fungal carbon for their development. Whereas our understanding of the ecological and genomic changes associated with the evolutionary shift to mycoheterotrophy is deepening, little information is known about the specific metabolic and physiological features driving this evolution. We investigated this issue in naturally occurring achlorophyllous variants of temperate mixotrophic orchids. We carried out an integrated transcriptomic and metabolomic analysis of the response to achlorophylly in the leaves of three mixotrophic species sampled in natura. Achlorophyllous leaves showed major impairment of their photosynthetic and mineral nutrition functions, strong accumulation of free amino acids, overexpression of enzymes and transporters related to sugars, amino acids and fatty acid catabolism, as well as induction of some autophagy-related and biotic stress genes. Such changes were reminiscent of these reported for variegated leaves and appeared to be symptomatic of a carbon starvation response. Rather than decisive metabolic innovations, we suggest that the evolution towards mycoheterotrophy in orchids is more likely to be reliant on the versatility of plant metabolism and an ability to exploit fungal organic resources, especially amino acids, to replace missing photosynthates.
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Affiliation(s)
- Félix Lallemand
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, CP 39, 57 rue Cuvier, 75005, Paris, France
| | - Marie-Laure Martin-Magniette
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, 91405, Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris-Diderot, Sorbonne Paris-Cité, 91405, Orsay, France
- UMR MIA-Paris, AgroParisTech, INRA, Université Paris-Saclay, Paris, France
| | - Françoise Gilard
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, 91405, Orsay, France
- Plateforme Métabolisme Métabolome, Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Univ. Paris-Sud, Univ. Evry, Univ. Paris-Diderot, Univ. Paris-Saclay, Bâtiment 630 Rue Noetzlin, 91192, Gif-sur-Yvette Cedex, France
| | - Bertrand Gakière
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, 91405, Orsay, France
- Plateforme Métabolisme Métabolome, Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Univ. Paris-Sud, Univ. Evry, Univ. Paris-Diderot, Univ. Paris-Saclay, Bâtiment 630 Rue Noetzlin, 91192, Gif-sur-Yvette Cedex, France
| | - Alexandra Launay-Avon
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, 91405, Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris-Diderot, Sorbonne Paris-Cité, 91405, Orsay, France
| | - Étienne Delannoy
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Sud, Université Evry, Université Paris-Saclay, 91405, Orsay, France
- Institute of Plant Sciences Paris-Saclay IPS2, Paris-Diderot, Sorbonne Paris-Cité, 91405, Orsay, France
| | - Marc-André Selosse
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, CP 39, 57 rue Cuvier, 75005, Paris, France
- Faculty of Biology, University of Gdańsk, ul. Wita Stwosza 59, 80-308, Gdańsk, Poland
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Ng WL, Wu W, Zou P, Zhou R. Comparative transcriptomics sheds light on differential adaptation and species diversification between two Melastoma species and their F 1 hybrid. AOB PLANTS 2019; 11:plz019. [PMID: 31037213 PMCID: PMC6481908 DOI: 10.1093/aobpla/plz019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 03/27/2019] [Indexed: 06/09/2023]
Abstract
Variation in gene expression has been shown to promote adaptive divergence, and can lead to speciation. The plant genus Melastoma, thought to have diversified through adaptive radiation, provides an excellent model for the study of gene expressional changes during adaptive differentiation and following interspecific hybridization. In this study, we performed RNA-seq on M. candidum, M. sanguineum and their F1 hybrid, to investigate the role of gene expression in species diversification within the genus. Reference transcriptomes were assembled using combined data from both parental species, resulting in 50 519 and 48 120 transcripts for the leaf and flower petal, after removing redundancy. Differential expression analysis uncovered 3793 and 2116 differentially expressed (DE) transcripts, most of which are between M. candidum and M. sanguineum. Differential expression was observed for genes related to light responses, as well as genes that regulate the development of leaf trichomes, a trait that among others is thought to protect plants against sunlight, suggesting the differential adaptation of the species to sunlight intensity. The analysis of positively selected genes between the two species also revealed possible differential adaptation to other abiotic stresses such as drought and temperature. In the hybrid, almost all possible modes of expression were observed at the DE transcripts, although at most transcripts, the expression levels were similar to that of either parent instead of being intermediate. A small number of transgressively expressed transcripts that matched genes known to promote plant growth and adaptation to stresses in new environments were also found, possibly explaining the vigour observed in the hybrid. The findings in this study provided insights into the role of gene expression in the diversification of Melastoma, which we believe is an important example for more cross-taxa comparisons in the future.
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Affiliation(s)
- Wei Lun Ng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, Selangor, Malaysia
| | - Wei Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Peishan Zou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
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Damerval C, Citerne H, Conde e Silva N, Deveaux Y, Delannoy E, Joets J, Simonnet F, Staedler Y, Schönenberger J, Yansouni J, Le Guilloux M, Sauquet H, Nadot S. Unraveling the Developmental and Genetic Mechanisms Underpinning Floral Architecture in Proteaceae. FRONTIERS IN PLANT SCIENCE 2019; 10:18. [PMID: 30740117 PMCID: PMC6357683 DOI: 10.3389/fpls.2019.00018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 01/08/2019] [Indexed: 05/30/2023]
Abstract
Proteaceae are a basal eudicot family with a highly conserved floral groundplan but which displays considerable variation in other aspects of floral and inflorescence morphology. Their morphological diversity and phylogenetic position make them good candidates for understanding the evolution of floral architecture, in particular the question of the homology of the undifferentiated perianth with the differentiated perianth of core eudicots, and the mechanisms underlying the repeated evolution of zygomorphy. In this paper, we combine a morphological approach to explore floral ontogenesis and a transcriptomic approach to access the genes involved in floral organ identity and development, focusing on Grevillea juniperina, a species from subfamily Grevilleoideae. We present developmental data for Grevillea juniperina and three additional species that differ in their floral symmetry using stereomicroscopy, SEM and High Resolution X-Ray Computed Tomography. We find that the adnation of stamens to tepals takes place at early developmental stages, and that the establishment of bilateral symmetry coincides with the asymmetrical growth of the single carpel. To set a framework for understanding the genetic basis of floral development in Proteaceae, we generated and annotated de novo a reference leaf/flower transcriptome from Grevillea juniperina. We found Grevillea homologs of all lineages of MADS-box genes involved in floral organ identity. Using Arabidopsis thaliana gene expression data as a reference, we found homologs of other genes involved in floral development in the transcriptome of G. juniperina. We also found at least 21 class I and class II TCP genes, a gene family involved in the regulation of growth processes, including floral symmetry. The expression patterns of a set of floral genes obtained from the transcriptome were characterized during floral development to assess their organ specificity and asymmetry of expression.
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Affiliation(s)
- Catherine Damerval
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Hélène Citerne
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Natalia Conde e Silva
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Yves Deveaux
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Etienne Delannoy
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Universités Paris Diderot, Paris-Sud, Evry, Paris-Saclay, Gif-sur-Yvette, France
| | - Johann Joets
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Franck Simonnet
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
- Ecologie Systématique Evolution, AgroParisTech, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Yannick Staedler
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Jürg Schönenberger
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Jennifer Yansouni
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Universités Paris Diderot, Paris-Sud, Evry, Paris-Saclay, Gif-sur-Yvette, France
| | - Martine Le Guilloux
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Hervé Sauquet
- Ecologie Systématique Evolution, AgroParisTech, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Orsay, France
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, NSW, Australia
| | - Sophie Nadot
- Ecologie Systématique Evolution, AgroParisTech, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Orsay, France
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25
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Bayat S, Schranz ME, Roalson EH, Hall JC. Lessons from Cleomaceae, the Sister of Crucifers. TRENDS IN PLANT SCIENCE 2018; 23:808-821. [PMID: 30006074 DOI: 10.1016/j.tplants.2018.06.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 06/06/2018] [Accepted: 06/17/2018] [Indexed: 05/21/2023]
Abstract
Cleomaceae is a diverse group well-suited to addressing fundamental genomic and evolutionary questions as the sister group to Brassicaceae, facilitating transfer of knowledge from the model Arabidopsis thaliana. Phylogenetic and taxonomic revisions provide a framework for examining the evolution of substantive morphological and physiology diversity in Cleomaceae, but not necessarily in Brassicaceae. The investigation of both nested and contrasting whole-genome duplications (WGDs) between Cleomaceae and Brassicaceae allows comparisons of independently duplicated genes and investigation of whether they may be drivers of the observed innovations. Further, a wealth of outstanding genetic research has provided insight into how the important alternative carbon fixation pathway, C4 photosynthesis, has evolved via differential expression of a suite of genes, of which the underlying mechanisms are being elucidated.
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Affiliation(s)
- Soheila Bayat
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada; RG Plant Cytogenomics, Central European Institute of Technology, 625 00 Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, 6708 PB Wageningen, The Netherlands
| | - Eric H Roalson
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Jocelyn C Hall
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada.
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Vinson CC, Mota APZ, Oliveira TN, Guimaraes LA, Leal-Bertioli SCM, Williams TCR, Nepomuceno AL, Saraiva MAP, Araujo ACG, Guimaraes PM, Brasileiro ACM. Early responses to dehydration in contrasting wild Arachis species. PLoS One 2018; 13:e0198191. [PMID: 29847587 PMCID: PMC5976199 DOI: 10.1371/journal.pone.0198191] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 05/14/2018] [Indexed: 12/04/2022] Open
Abstract
Wild peanut relatives (Arachis spp.) are genetically diverse and were selected throughout evolution to a range of environments constituting, therefore, an important source of allelic diversity for abiotic stress tolerance. In particular, A. duranensis and A. stenosperma, the parents of the reference Arachis A-genome genetic map, show contrasting transpiration behavior under limited water conditions. This study aimed to build a comprehensive gene expression profile of these two wild species under dehydration stress caused by the withdrawal of hydroponic nutrient solution. For this purpose, roots of both genotypes were collected at seven time-points during the early stages of dehydration and used to construct cDNA paired-end libraries. Physiological analyses indicated initial differences in gas exchange parameters between the drought-tolerant genotype of A. duranensis and the drought-sensitive genotype of A. stenosperma. High-quality Illumina reads were mapped against the A. duranensis reference genome and resulted in the identification of 1,235 and 799 Differentially Expressed Genes (DEGs) that responded to the stress treatment in roots of A. duranensis and A. stenosperma, respectively. Further analysis, including functional annotation and identification of biological pathways represented by these DEGs confirmed the distinct gene expression behavior of the two contrasting Arachis species genotypes under dehydration stress. Some species-exclusive and common DEGs were then selected for qRT-PCR analysis, which corroborated the in silico expression profiling. These included genes coding for regulators and effectors involved in drought tolerance responses, such as activation of osmosensing molecular cascades, control of hormone and osmolyte content, and protection of macromolecules. This dataset of transcripts induced during the dehydration process in two wild Arachis genotypes constitute new tools for the understanding of the distinct gene regulation processes in these closely related species but with contrasting drought responsiveness. In addition, our findings provide insights into the nature of drought tolerance in wild germoplasm, which might be explored as novel sources of diversity and useful wild alleles to develop climate-resilient crop varieties.
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Affiliation(s)
- Christina Cleo Vinson
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP, Final W5 Norte, Brasília, DF–Brazil
- Universidade de Brasília, Campus Darcy Ribeiro, Brasília, DF–Brazil
| | - Ana Paula Zotta Mota
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP, Final W5 Norte, Brasília, DF–Brazil
- Universidade Federal do Rio Grande do Sul, Campus do Vale, Porto Alegre, RS—Brazil
| | - Thais Nicolini Oliveira
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP, Final W5 Norte, Brasília, DF–Brazil
- Universidade Federal do Rio Grande do Sul, Campus do Vale, Porto Alegre, RS—Brazil
| | - Larissa Arrais Guimaraes
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP, Final W5 Norte, Brasília, DF–Brazil
| | | | | | | | | | - Ana Claudia Guerra Araujo
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP, Final W5 Norte, Brasília, DF–Brazil
| | | | - Ana C. M. Brasileiro
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, CP, Final W5 Norte, Brasília, DF–Brazil
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Roberts WR, Roalson EH. Phylogenomic analyses reveal extensive gene flow within the magic flowers (Achimenes). AMERICAN JOURNAL OF BOTANY 2018; 105:726-740. [PMID: 29702729 DOI: 10.1002/ajb2.1058] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 02/02/2018] [Indexed: 06/08/2023]
Abstract
PREMISE OF THE STUDY The Neotropical Gesneriaceae is a lineage known for its colorful and diverse flowers, as well as an extensive history of intra- and intergeneric hybridization, particularly among Achimenes (the magic flowers) and other members of subtribe Gloxiniinae. Despite numerous studies seeking to elucidate the evolutionary relationships of these lineages, relatively few have sought to infer specific patterns of gene flow despite evidence of widespread hybridization. METHODS To explore the utility of phylogenomic data for reassessing phylogenetic relationships and inferring patterns of gene flow among species of Achimenes, we sequenced 12 transcriptomes. We used a variety of methods to infer the species tree, examine gene tree discordance, and infer patterns of gene flow. KEY RESULTS Phylogenomic analyses resolve clade relationships at the crown of the lineage with strong support. In contrast to previous analyses, we recovered strong support for several new relationships despite a significant amount of gene tree discordance. We present evidence for at least two introgression events between two species pairs that share pollinators, and suggest that the species status of Achimenes admirabilis be reexamined. CONCLUSIONS Our study demonstrates the utility of transcriptome data for phylogenomic analyses, and inferring patterns of gene flow despite gene tree discordance. Moreover, these data provide another example of prevalent interspecific gene flow among Neotropical plants that share pollinators.
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Affiliation(s)
- Wade R Roberts
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, Washington, 99164-1030, USA
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164-4236, USA
| | - Eric H Roalson
- Molecular Plant Sciences Graduate Program, Washington State University, Pullman, Washington, 99164-1030, USA
- School of Biological Sciences, Washington State University, Pullman, Washington, 99164-4236, USA
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