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Zou Y, Wang J, Peng D, Zhang X, Tembrock LR, Yang J, Zhao J, Liao H, Wu Z. Multi-integrated genomic data for Passiflora foetida provides insights into genome size evolution and floral development in Passiflora. MOLECULAR HORTICULTURE 2023; 3:27. [PMID: 38105261 PMCID: PMC10726625 DOI: 10.1186/s43897-023-00076-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/03/2023] [Indexed: 12/19/2023]
Abstract
Passiflora is a plant genus known for its extremely distinctive and colorful flowers and a wide range of genome size variation. However, how genome characteristics are related to flower traits among Passiflora species remains poorly understood. Here, we assembled a chromosome-scale genome of P. foetida, which belongs to the same subgenus as the commercial passionfruit P. edulis. The genome of P. foetida is smaller (424.16 Mb) and contains fewer copies of long terminal repeat retrotransposons (LTR-RTs). The disparity in LTR-RTs is one of the main contributors to the differences in genome sizes between these two species and possibly in floral traits. Additionally, we observed variation in insertion times and copy numbers of LTR-RTs across different transposable element (TE) lineages. Then, by integrating transcriptomic data from 33 samples (eight floral organs and flower buds at three developmental stages) with phylogenomic and metabolomic data, we conducted an in-depth analysis of the expression, phylogeny, and copy number of MIKC-type MADS-box genes and identified essential biosynthetic genes responsible for flower color and scent from glandular bracts and other floral organs. Our study pinpoints LRT-RTs as an important player in genome size variation in Passiflora species and provides insights into future genetic improvement.
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Affiliation(s)
- Yi Zou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, 650504, China
| | - Jie Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Dan Peng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- College of Agriculture, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaoni Zhang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, 80523, USA
| | - Jinliang Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, 68583, USA
| | - Jianli Zhao
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, 650504, China.
| | - Hong Liao
- Ministry of Education Key Laboratory for Transboundary Ecosecurity of Southwest China, Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Institute of Biodiversity, School of Ecology and Environmental Science, Yunnan University, Kunming, Yunnan, 650504, China.
| | - Zhiqiang Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
- Kunpeng Institute of Modern Agriculture at Foshan, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
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Abbas N, Zafar M, Ahmad M, Althobaiti AT, Ramadan MF, Makhkamov T, Gafforov Y, Khaydarov K, Kabir M, Sultana S, Majeed S, Batool T. Tendril Anatomy: A Tool for Correct Identification among Cucurbitaceous Taxa. PLANTS (BASEL, SWITZERLAND) 2022; 11:3273. [PMID: 36501313 PMCID: PMC9735582 DOI: 10.3390/plants11233273] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 06/17/2023]
Abstract
This research examined the histological micro-structure of tendril vasculature in cucurbitaceous taxa. In this research, the tendril anatomy of 17 taxa of Cucurbitaceae categorized into seven genera, including Cucumis (five species), Cucurbita and Luffa (three species each), Citrullus and Momordica (two species each) while Lagenaria and Praecitrullus (one species each), collected from different areas of the Thal desert were examined via microscopic imaging to explore its taxonomic significance. Tendril transverse sections were cut with a Shandon Microtome to prepare slides. The distinctive characteristics of taxonomic value (qualitative and quantitative) include tendril and vascular bundle shape, variation in the number of vascular bundles, tendril diameter length, layers of sclerenchyma, and shape of collenchyma and epidermal cells. Tendril shapes observed are irregular, slightly oval-shaped, slightly C shaped, angular (4-angled, 6-angled, or polygonal), and star shaped. Quantitative measurements were taken to analyze the data statistically using SPSS software. Cucurbita pepo had a maximum tendril diameter length of 656.1 µm and a minimum in Momordica balsamina of 123.05 µm. The highest number of vascular bundles (12) were noticed in Luffa acutangula var.amara. Angular type was prominent in collenchyma, and irregular shape was dominant in sclerenchyma cells. A maximum of seven to nine sclerenchyma layers were present in Lagenaria siceraria and a minimum of two or three layers in Cucumis melo subsp. agrestis, Cucumis melo var. flexuosus, and Cucumis melo var.cantalupensis. Epidermis cells also show great variations with a rectangular shape being dominant. Statistical UPGMA dendrogram clustering of tendril vasculature traits shows that histological sections studied with microscopic techniques can be used to identify species and will play a vital role in future taxonomic and phylogenic linkages.
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Affiliation(s)
- Naveed Abbas
- Department of Plant Systematics and Biodiversity Lab, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Muhammad Zafar
- Department of Plant Systematics and Biodiversity Lab, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Mushtaq Ahmad
- Department of Plant Systematics and Biodiversity Lab, Quaid-i-Azam University, Islamabad 45320, Pakistan
- Pakistan Academy of Sciences Islamabad, Islamabad 46000, Pakistan
| | - Ashwaq T. Althobaiti
- Department of Biology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Mohamed Fawzy Ramadan
- Department of Clinical Nutrition, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah 21961, Saudi Arabia
| | - Trobjon Makhkamov
- Department of Forestry and Landscape Design, Tashkent State Agrarian University, 2 A., Universitet Str., Kibray District, Tashkent 100700, Uzbekistan
| | - Yusufjon Gafforov
- Mycology Laboratory, Institute of Botany, Academy of Sciences of Republic of Uzbekistan, 32 Durmon Yuli, Tashkent 100125, Uzbekistan
- AKFA University, 264 Milliy Bog Street, Tashkent 111221, Uzbekistan
| | - Khislat Khaydarov
- Faculty of Biology, Samarkand State University, Universitetsty Bulvvar Street-15, Samarkand 140104, Uzbekistan
| | - Muhammad Kabir
- Department of Biological Sciences, Ex University of Sargodha Sub Campus Bhakkr, Thal University Bhakkar, Bhakkar 30000, Pakistan
| | - Shazia Sultana
- Department of Plant Systematics and Biodiversity Lab, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Salman Majeed
- Department of Plant Systematics and Biodiversity Lab, Quaid-i-Azam University, Islamabad 45320, Pakistan
- Department of Botany, University of Mianwali, Mianwali 42200, Pakistan
| | - Tajalla Batool
- Department of Plant Systematics and Biodiversity Lab, Quaid-i-Azam University, Islamabad 45320, Pakistan
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Moraes TS, Immink RGH, Martinelli AP, Angenent GC, van Esse W, Dornelas MC. Passiflora organensis FT/TFL1 gene family and their putative roles in phase transition and floral initiation. PLANT REPRODUCTION 2022; 35:105-126. [PMID: 34748087 DOI: 10.1007/s00497-021-00431-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
Comprehensive analysis of the FT/TFL1 gene family in Passiflora organensis results in understanding how these genes might be involved in the regulation of the typical plant architecture presented by Passiflora species. Passion fruit (Passiflora spp) is an economic tropical fruit crop, but there is hardly any knowledge available about the molecular control of phase transition and flower initiation in this species. The florigen agent FLOWERING LOCUS T (FT) interacts with the bZIP protein FLOWERING LOCUS D (FD) to induce flowering in the model species Arabidopsis thaliana. Current models based on research in rice suggest that this interaction is bridged by 14-3-3 proteins. We identified eight FT/TFL1 family members in Passiflora organensis and characterized them by analyzing their phylogeny, gene structure, expression patterns, protein interactions and putative biological roles by heterologous expression in Arabidopsis. PoFT was highest expressed during the adult vegetative phase and it is supposed to have an important role in flowering induction. In contrast, its paralogs PoTSFs were highest expressed in the reproductive phase. While ectopic expression of PoFT in transgenic Arabidopsis plants induced early flowering and inflorescence determinacy, the ectopic expression of PoTSFa caused a delay in flowering. PoTFL1-like genes were highest expressed during the juvenile phase and their ectopic expression caused delayed flowering in Arabidopsis. Our protein-protein interaction studies indicate that the flowering activation complexes in Passiflora might deviate from the hexameric complex found in the model system rice. Our results provide insights into the potential functions of FT/TFL1 gene family members during floral initiation and their implications in the special plant architecture of Passiflora species, contributing to more detailed studies on the regulation of passion fruit reproduction.
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Affiliation(s)
- Tatiana S Moraes
- Plant Biotechnology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil.
| | - Richard G H Immink
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University & Research, Wageningen, The Netherlands
- Bioscience, Wageningen University & Research, Wageningen, The Netherlands
| | - Adriana P Martinelli
- Plant Biotechnology Laboratory, Center for Nuclear Energy in Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Gerco C Angenent
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University & Research, Wageningen, The Netherlands
- Bioscience, Wageningen University & Research, Wageningen, The Netherlands
| | - Wilma van Esse
- Cluster of Plant Developmental Biology, Laboratory of Molecular Biology, Wageningen University & Research, Wageningen, The Netherlands
| | - Marcelo C Dornelas
- Department of Plant Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil
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Functional Conservation and Divergence of Five AP1/FUL-like Genes in Marigold ( Tagetes erecta L.). Genes (Basel) 2021; 12:genes12122011. [PMID: 34946960 PMCID: PMC8700864 DOI: 10.3390/genes12122011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/10/2021] [Accepted: 12/13/2021] [Indexed: 11/17/2022] Open
Abstract
Members of AP1/FUL subfamily genes play an essential role in the regulation of floral meristem transition, floral organ identity, and fruit ripping. At present, there have been insufficient studies to explain the function of the AP1/FUL-like subfamily genes in Asteraceae. Here, we cloned two euAP1 clade genes TeAP1-1 and TeAP1-2, and three euFUL clade genes TeFUL1, TeFUL2, and TeFUL3 from marigold (Tagetes erecta L.). Expression profile analysis demonstrated that TeAP1-1 and TeAP1-2 were mainly expressed in receptacles, sepals, petals, and ovules. TeFUL1 and TeFUL3 were expressed in flower buds, stems, and leaves, as well as reproductive tissues, while TeFUL2 was mainly expressed in flower buds and vegetative tissues. Overexpression of TeAP1-2 or TeFUL2 in Arabidopsis resulted in early flowering, implying that these two genes might regulate the floral transition. Yeast two-hybrid analysis indicated that TeAP1/FUL proteins only interacted with TeSEP proteins to form heterodimers and that TeFUL2 could also form a homodimer. In general, TeAP1-1 and TeAP1-2 might play a conserved role in regulating sepal and petal identity, similar to the functions of MADS-box class A genes, while TeFUL genes might display divergent functions. This study provides a theoretical basis for the study of AP1/FUL-like genes in Asteraceae species.
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Sousa-Baena MS, Hernandes-Lopes J, Van Sluys MA. Reaching the top through a tortuous path: helical growth in climbing plants. CURRENT OPINION IN PLANT BIOLOGY 2021; 59:101982. [PMID: 33395610 DOI: 10.1016/j.pbi.2020.101982] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 11/19/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Climbing plants have voluble organs, for example, tendrils and modified stems, which twine up neighboring plants to reach the canopy. These organs perform exaggerated circumnutation, during which they grow towards the shaded areas of the forest (skototropism) to find a host. In response to mechanical stimulus, they grow towards the support (thigmotropism), tailoring their development to firmly attach to it (thigmomorphogenesis). The underlying molecular pathways of these crucial mechanisms are virtually unknown. Here, we review current progress on molecular regulation of the development and growth of climber's voluble organs. Recent advances in the subject point epigenetics and sensory biology as the emerging frontiers in the study of climbing plant's growth and functioning. We briefly review new developments on the molecular basis of plants' mechanosensory system, discussing the findings in the context of the climbing habit.
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Affiliation(s)
- Mariane S Sousa-Baena
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo (USP), Rua do Matão 277, 05508-090 São Paulo, SP, Brazil.
| | - José Hernandes-Lopes
- Genomics for Climate Change Research Center, Universidade Estadual de Campinas (UNICAMP), 13083-875, Campinas, SP, Brazil; Embrapa Informática Agropecuária, 13083-886, Campinas, SP, Brazil
| | - Marie-Anne Van Sluys
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo (USP), Rua do Matão 277, 05508-090 São Paulo, SP, Brazil
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Cheng X, Wang H, Wei H, Gu L, Hao P, Sun H, Wu A, Cheng S, Yu S. The MADS transcription factor GhAP1.7 coordinates the flowering regulatory pathway in upland cotton (Gossypium hirsutum L.). Gene 2020; 769:145235. [PMID: 33148424 DOI: 10.1016/j.gene.2020.145235] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 09/26/2020] [Accepted: 10/09/2020] [Indexed: 11/26/2022]
Abstract
MADS-box gene family plays an important role in the molecular regulatory network of flower development. APETALA1 (AP1), a MADS-box gene, plays an important role in the development of flower organs. Although many studies about MADS-box family genes have been reported, the function of AP1 is still not clear in cotton. In this study, GhAP1.7 (Gh_D03G0922), a candidate gene for cotton flower time and plant height obtained from our previous studies, was cloned from CCRI50 cotton variety and functionally characterized. Subcellular localization demonstrated that GhAP1.7 was located in nucleus. Infection test of Arabidopsis revealed that GhAP1.7 could cause precocious flowering and virus-induced gene silence (VIGS) assay demonstrated that GhAP1.7 could lead to delayed flowering of cotton plants. Yeast one-hybrid assays and transient dual-luciferase assays suggested that floral meristem identity control gene LEAFY (LFY) can bind the promoter of GhAP1.7 and negatively regulate it. Our research indicated that GhAP1.7 might work as a positive regulator in plant flowering. Moreover, GhAP1.7 may negatively regulated by GhLFY in the regulatory pathways. This work laid the foundation for subsequent functional studies of GhAP1.7.
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Affiliation(s)
- Xiaoqian Cheng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China; College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Lijiao Gu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Pengbo Hao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Huiru Sun
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Aimin Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Shuaishuai Cheng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang 455000, China.
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