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Zheng YY, Chen LH, Fan BL, Xu Z, Wang Q, Zhao BY, Gao M, Yuan MH, Tahir Ul Qamar M, Jiang Y, Yang L, Wang L, Li W, Cai W, Ma C, Lu L, Song JM, Chen LL. Integrative multiomics profiling of passion fruit reveals the genetic basis for fruit color and aroma. PLANT PHYSIOLOGY 2024; 194:2491-2510. [PMID: 38039148 DOI: 10.1093/plphys/kiad640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/26/2023] [Accepted: 10/29/2023] [Indexed: 12/03/2023]
Abstract
Passion fruit (Passiflora edulis) possesses a complex aroma and is widely grown in tropical and subtropical areas. Here, we conducted the de novo assembly, annotation, and comparison of PPF (P. edulis Sims) and YPF (P. edulis f. flavicarpa) reference genomes using PacBio, Illumina, and Hi-C technologies. Notably, we discovered evidence of recent whole-genome duplication events in P. edulis genomes. Comparative analysis revealed 7.6∼8.1 million single nucleotide polymorphisms, 1 million insertions/deletions, and over 142 Mb presence/absence variations among different P. edulis genomes. During the ripening of yellow passion fruit, metabolites related to flavor, aroma, and color were substantially accumulated or changed. Through joint analysis of genomic variations, differentially expressed genes, and accumulated metabolites, we explored candidate genes associated with flavor, aroma, and color distinctions. Flavonoid biosynthesis pathways, anthocyanin biosynthesis pathways, and related metabolites are pivotal factors affecting the coloration of passion fruit, and terpenoid metabolites accumulated more in PPF. Finally, by heterologous expression in yeast (Saccharomyces cerevisiae), we functionally characterized 12 terpene synthases. Our findings revealed that certain TPS homologs in both YPF and PPF varieties produce identical terpene products, while others yield distinct compounds or even lose their functionality. These discoveries revealed the genetic and metabolic basis of unique characteristics in aroma and flavor between the 2 passion fruit varieties. This study provides resources for better understanding the genome architecture and accelerating genetic improvement of passion fruits.
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Affiliation(s)
- Yu-Yu Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Lin-Hua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Bing-Liang Fan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Zhenni Xu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Qiuxia Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Bo-Yuan Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Min Gao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Min-Hui Yuan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Muhammad Tahir Ul Qamar
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Yuanyuan Jiang
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan 512005, China
| | - Liu Yang
- Guangxi Crop Genetic Improvement and Biotechnology Laboratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Lingqiang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Weihui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Wenguo Cai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Chongjian Ma
- Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan 512005, China
| | - Li Lu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
- Hubei Hongshan Laboratory, Wuhan 430071, China
| | - Jia-Ming Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
| | - Ling-Ling Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning 530004, China
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Sanyal R, Pandey S, Nandi S, Mondal R, Samanta D, Mandal S, Manokari M, Mishra T, Dhama K, Pandey DK, Shekhawat MS, Dey A. Biotechnology of Passiflora edulis: role of Agrobacterium and endophytic microbes. Appl Microbiol Biotechnol 2023; 107:5651-5668. [PMID: 37505288 DOI: 10.1007/s00253-023-12667-1] [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: 05/12/2023] [Revised: 06/22/2023] [Accepted: 06/28/2023] [Indexed: 07/29/2023]
Abstract
Two forms of the genus Passiflora, belonging to the Passifloraceae family, are commonly called yellow and purple passion. These perennial woody climbers are found in the cooler regions at higher altitudes and in lowlands of tropical areas. The presence of alkaloids, terpenes, stilbenes, flavonoids, glycosides, carotenoids, etc. in different parts of the plant provides several pharmacological properties. Because of the various uses in foods and pharmaceuticals, in vitro propagation of this genus has been performed hugely and is of great interest to researchers. From different explants via direct organogenesis under controlled aseptic conditions, callus, root, shoot, and somatic embryos are induced successfully. Different PGRs are augmented in the media for the rapid multiplication or organogenesis, especially, the high ratio of cytokinin and auxin in the basal media efficiently regenerates the shoot and root respectively. The in vitro regenerated plantlets are then acclimatized and hardened properly before transferring to the field conditions. Thus, the present first of its kind review on P. edulis exclusively encompasses the wide applications of biotechnology for this species alongside its organogenesis, embryogenesis, cytology, and endophytic microbes with special emphasis on the role of genetic transformation studies mediated by Agrobacterium sp. KEY POINTS: • Critical assessment on in vitro biotechnology in P. edulis. • Agrobacterium-mediated transformation in P. edulis. • Role of endophytic microbes in P. edulis.
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Affiliation(s)
- Rupa Sanyal
- Department of Botany, Bhairab Ganguly College (West Bengal State University), Feeder Road, Belghoria, Kolkata, 700056, West Bengal, India
| | - Sharmila Pandey
- Department of Botany, Bhairab Ganguly College (West Bengal State University), Feeder Road, Belghoria, Kolkata, 700056, West Bengal, India
| | - Saheli Nandi
- Department of Botany, Bhairab Ganguly College (West Bengal State University), Feeder Road, Belghoria, Kolkata, 700056, West Bengal, India
| | - Rintu Mondal
- Department of Botany, Bhairab Ganguly College (West Bengal State University), Feeder Road, Belghoria, Kolkata, 700056, West Bengal, India
| | - Dipu Samanta
- Department of Botany, Dr. Kanailal Bhattacharyya College, Howrah, India
| | - Sujata Mandal
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India
| | - M Manokari
- Department of Botany, Siddha Clinical Research Unit, Central Council for Research in Siddha, Palayamkottai, 627 002, Tamil Nadu, India
| | - Tulika Mishra
- Department of Botany, DDU Gorakhpur University, Gorakhpur, India
| | - Kuldeep Dhama
- Division of Pathology, Indian Veterinary Research Institute (IVRI), Izatnagar, 243 122, Bareilly, Uttar Pradesh, India
| | - Devendra Kumar Pandey
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, 144411, Punjab, India
| | - Mahipal S Shekhawat
- Plant Biotechnology Unit, Kanchi Mamunivar Government Institute for Postgraduate Studies and Research, Lawspet, Puducherry, 605 008, India.
| | - Abhijit Dey
- Department of Life Sciences, Presidency University, Kolkata, West Bengal, India.
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Costa ZP, Varani AM, Cauz-Santos LA, Sader MA, Giopatto HA, Zirpoli B, Callot C, Cauet S, Marande W, Souza Cardoso JL, Pinheiro DG, Kitajima JP, Dornelas MC, Harand AP, Berges H, Monteiro-Vitorello CB, Carneiro Vieira ML. A genome sequence resource for the genus Passiflora, the genome of the wild diploid species Passiflora organensis. THE PLANT GENOME 2021; 14:e20117. [PMID: 34296827 DOI: 10.1002/tpg2.20117] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/09/2021] [Indexed: 06/13/2023]
Abstract
The genus Passiflora comprises a large group of plants popularly known as passionfruit, much appreciated for their exotic flowers and edible fruits. The species (∼500) are morphologically variable (e.g., growth habit, size, and color of flowers) and are adapted to distinct tropical ecosystems. In this study, we generated the genome of the wild diploid species Passiflora organensis Gardner by adopting a hybrid assembly approach. Passiflora organensis has a small genome of 259 Mbp and a heterozygosity rate of 81%, consistent with its reproductive system. Most of the genome sequences could be integrated into its chromosomes with cytogenomic markers (satellite DNA) as references. The repeated sequences accounted for 58.55% of the total DNA analyzed, and the Tekay lineage was the prevalent retrotransposon. In total, 25,327 coding genes were predicted. Passiflora organensis retains 5,609 singletons and 15,671 gene families. We focused on the genes potentially involved in the locus determining self-incompatibility and the MADS-box gene family, allowing us to infer expansions and contractions within specific subfamilies. Finally, we recovered the organellar DNA. Structural rearrangements and two mitoviruses, besides relics of other mobile elements, were found in the chloroplast and mt-DNA molecules, respectively. This study presents the first draft genome assembly of a wild Passiflora species, providing a valuable sequence resource for genomic and evolutionary studies on the genus, and support for breeding cropped passionfruit species.
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Affiliation(s)
- Zirlane Portugal Costa
- Dep. de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Univ. de São Paulo, Piracicaba, 13418-900, Brazil
| | - Alessandro Mello Varani
- Dep. de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Univ. Estadual Paulista, Jaboticabal, 14884-900, Brazil
| | - Luiz Augusto Cauz-Santos
- Dep. de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Univ. de São Paulo, Piracicaba, 13418-900, Brazil
- Present address: Dep. of Botany and Biodiversity Research, Univ. of Vienna, Vienna, 1030, Austria
| | | | - Helena Augusto Giopatto
- Dep. de Biologia Vegetal, Instituto de Biologia, Univ. Estadual de Campinas, Campinas, 13083-862, Brazil
| | - Bruna Zirpoli
- Dep. de Botânica, Univ. Federal de Pernambuco, Recife, 50670-901, Brazil
| | - Caroline Callot
- Institut National de la Recherche Agronomique, Centre National de Ressources Génomique Végétales, Castanet-Tolosan, 31326, France
| | - Stephane Cauet
- Institut National de la Recherche Agronomique, Centre National de Ressources Génomique Végétales, Castanet-Tolosan, 31326, France
| | - Willian Marande
- Institut National de la Recherche Agronomique, Centre National de Ressources Génomique Végétales, Castanet-Tolosan, 31326, France
| | - Jessica Luana Souza Cardoso
- Dep. de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Univ. de São Paulo, Piracicaba, 13418-900, Brazil
| | - Daniel Guariz Pinheiro
- Dep. de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Univ. Estadual Paulista, Jaboticabal, 14884-900, Brazil
| | | | - Marcelo Carnier Dornelas
- Dep. de Biologia Vegetal, Instituto de Biologia, Univ. Estadual de Campinas, Campinas, 13083-862, Brazil
| | | | - Helene Berges
- Institut National de la Recherche Agronomique, Centre National de Ressources Génomique Végétales, Castanet-Tolosan, 31326, France
| | | | - Maria Lucia Carneiro Vieira
- Dep. de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Univ. de São Paulo, Piracicaba, 13418-900, Brazil
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Melo NFDE, Guerra M. The karyotype of Adenia and the origin of the base number x = 12 in Passifloroideae (Passifloraceae). AN ACAD BRAS CIENC 2021; 93:e20201852. [PMID: 34614089 DOI: 10.1590/0001-3765202120201852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 07/04/2021] [Indexed: 11/21/2022] Open
Abstract
Adenia is an Old World genus of Passifloroideae closely related to Passiflora. The two genera comprise the large majority of Passifloroideae species, although most studies are concentrated on Passiflora. Cytological analyses reveal that changes in chromosome numbers played an important role in the evolution of Passiflora, whereas in the remaining genera little is known, hindering the identification of the base number of the family. Here we analyzed the chromosome number and the 35S rDNA sites of three species of Adenia and reevaluated the base number (x) of the subfamily Passifloroideae and the family Passifloraceae, including chromosome data for Turneroideae and Malesherbioideae. The chromosome number of Adenia species seemed to be stable with 2n = 24 or 48 and one or two pairs of rDNA sites, very similar to Passiflora subgenus Astrophea, suggesting a common ancestral karyotype with x = 12. Differently, Turneroideae and Malesherbioideae present x = 7. A whole genomic duplication detected after the separation of Passifloroideae and Malesherbioideae suggests that the base number of Passifloraceae most probably was x = 7, which by dysploidy and polyploidy generated x = 12 for the subfamily Passifloroideae.
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Affiliation(s)
- Natoniel Franklin DE Melo
- Embrapa Semiárido, Laboratório de Biotecnologia, BR-428, km 152, Caixa Postal 23, 56302-970 Petrolina, PE, Brazil
| | - Marcelo Guerra
- Universidade Federal de Pernambuco, CB, Departamento de Botânica, Rua Prof. Nelson Chaves, s/n, Cidade Universitária, 50670-420 Recife, PE, Brazil
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Sader M, Vaio M, Cauz-Santos LA, Dornelas MC, Vieira MLC, Melo N, Pedrosa-Harand A. Large vs small genomes in Passiflora: the influence of the mobilome and the satellitome. PLANTA 2021; 253:86. [PMID: 33792791 DOI: 10.1007/s00425-021-03598-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 03/18/2021] [Indexed: 05/22/2023]
Abstract
While two lineages of retrotransposons were more abundant in larger Passiflora genomes, the satellitome was more diverse and abundant in the smallest genome analysed. Repetitive sequences are ubiquitous and fast-evolving elements responsible for size variation and large-scale organization of plant genomes. Within Passiflora genus, a tenfold variation in genome size, not attributed to polyploidy, is known. Here, we applied a combined in silico and cytological approach to study the organization and diversification of repetitive elements in three species of this genus representing its known range in genome size variation. Sequences were classified in terms of type and repetitiveness and the most abundant were mapped to chromosomes. We identified long terminal repeat (LTR) retrotransposons as the most abundant elements in the three genomes, showing a considerable variation among species. Satellite DNAs (satDNAs) were less representative, but highly diverse between subgenera. Our results clearly confirm that the largest genome species (Passiflora quadrangularis) presents a higher accumulation of repetitive DNA sequences, specially Angela and Tekay elements, making up most of its genome. Passiflora cincinnata, with intermediate genome and from the same subgenus, showed similarity with P. quadrangularis regarding the families of repetitive DNA sequences, but in different proportions. On the other hand, Passiflora organensis, the smallest genome, from a different subgenus, presented greater diversity and the highest proportion of satDNA. Altogether, our data indicates that while large genomes evolved by an accumulation of retrotransposons, the smallest genome known for the genus has evolved by diversification of different repeat types, particularly satDNAs.
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Affiliation(s)
- Mariela Sader
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Pernambuco, Brazil.
| | - Magdalena Vaio
- Laboratory of Plant Genome Evolution and Domestication, Department of Plant Biology, Faculty of Agronomy, University of the Republic, Montevideo, Uruguay
| | - Luiz Augusto Cauz-Santos
- Genetics Department, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | | | - Maria Lucia Carneiro Vieira
- Genetics Department, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Natoniel Melo
- Laboratory of Biotechnology, Embrapa Semiarid, Petrolina, Pernambuco, Brazil
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Recife, Pernambuco, Brazil
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Merlo MA, Portela-Bens S, Rodríguez ME, García-Angulo A, Cross I, Arias-Pérez A, García E, Rebordinos L. A Comprehensive Integrated Genetic Map of the Complete Karyotype of Solea senegalensis (Kaup 1858). Genes (Basel) 2020; 12:genes12010049. [PMID: 33396249 PMCID: PMC7824234 DOI: 10.3390/genes12010049] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/24/2020] [Accepted: 12/28/2020] [Indexed: 12/23/2022] Open
Abstract
Solea senegalensis aquaculture production has experienced a great increase in the last decade and, consequently, the genome knowledge of the species is gaining attention. In this sense, obtaining a high-density genome mapping of the species could offer clues to the aquaculture improvement in those aspects not resolved so far. In the present article, a review and new processed data have allowed to obtain a high-density BAC-based cytogenetic map of S. senegalensis beside the analysis of the sequences of such BAC clones to achieve integrative data. A total of 93 BAC clones were used to localize the chromosome complement of the species and 588 genes were annotated, thus almost reaching the 2.5% of the S. senegalensis genome sequences. As a result, important data about its genome organization and evolution were obtained, such as the lesser gene density of the large metacentric pair compared with the other metacentric chromosomes, which supports the theory of a sex proto-chromosome pair. In addition, chromosomes with a high number of linked genes that are conserved, even in distant species, were detected. This kind of result widens the knowledge of this species’ chromosome dynamics and evolution.
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da Costa ZP, Cauz-Santos LA, Ragagnin GT, Van Sluys MA, Dornelas MC, Berges H, de Mello Varani A, Vieira MLC. Transposable element discovery and characterization of LTR-retrotransposon evolutionary lineages in the tropical fruit species Passiflora edulis. Mol Biol Rep 2019; 46:6117-6133. [DOI: 10.1007/s11033-019-05047-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 08/28/2019] [Indexed: 12/23/2022]
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