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Fang J, Lin A, Yan H, Feng L, Lin S, Mason P, Zhou L, Xu X, Zhao K, Huang Y, Henry RJ. Cytoplasmic genomes of Jasminum sambac reveal divergent sub-mitogenomic conformations and a large nuclear chloroplast-derived insertion. BMC PLANT BIOLOGY 2024; 24:861. [PMID: 39272034 PMCID: PMC11401388 DOI: 10.1186/s12870-024-05557-9] [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: 06/20/2024] [Accepted: 08/30/2024] [Indexed: 09/15/2024]
Abstract
BACKGROUND Jasminum sambac, a widely recognized ornamental plant prized for its aromatic blossoms, exhibits three flora phenotypes: single-petal ("SP"), double-petal ("DP"), and multi-petal ("MP"). The lack of detailed characterization and comparison of J. sambac mitochondrial genomes (mitogenomes) hinders the exploration of the genetic and structural diversity underlying the varying floral phenotypes in jasmine accessions. RESULTS Here, we de novo assembled three mitogenomes of typical phenotypes of J. sambac, "SP", "DP", and "MP-hutou" ("HT"), with PacBio reads and the "HT" chloroplast (cp) genome with Illumina reads, and verified them with read mapping and fluorescence in situ hybridization (FISH). The three mitogenomes present divergent sub-genomic conformations, with two, two, and four autonomous circular chromosomes ranging in size from 35.7 kb to 405.3 kb. Each mitogenome contained 58 unique genes. Ribosome binding sites with conserved AAGAAx/AxAAAG motifs were detected upstream of uncanonical start codons TTG, CTG and GTG. The three mitogenomes were similar in genomic content but divergent in structure. The structural variations were mainly attributed to recombination mediated by a large (~ 5 kb) forward repeat pair and several short repeats. The three jasmine cp. genomes showed a well-conserved structure, apart from a 19.9 kb inversion in "HT". We identified a 14.3 kb "HT"-specific insertion on Chr7 of the "HT" nuclear genome, consisting of two 7 kb chloroplast-derived fragments with two intact ndhH and rps15 genes, further validated by polymerase chain reaction (PCR). The well-resolved phylogeny suggests faster mitogenome evolution in J. sambac compared to other Oleaceae species and outlines the mitogenome evolutionary trajectories within Lamiales. All evidence supports that "DP" and "HT" evolved from "SP", with "HT" being the most recent derivative of "DP". CONCLUSION The comprehensive characterization of jasmine organelle genomes has added to our knowledge of the structural diversity and evolutionary trajectories behind varying jasmine traits, paving the way for in-depth exploration of mechanisms and targeted genetic research.
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Affiliation(s)
- Jingping Fang
- College of Life Science, Fujian Normal University, Fuzhou, China.
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia.
| | - Aiting Lin
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hansong Yan
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liqing Feng
- College of Life Science, Fujian Normal University, Fuzhou, China
- Marine and Agricultural Biotechnology Laboratory, Fuzhou Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, China
| | - Shaoqing Lin
- College of Life Science, Fujian Normal University, Fuzhou, China
| | - Patrick Mason
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia
| | - Linwei Zhou
- College of Life Science, Fujian Normal University, Fuzhou, China
| | - Xiuming Xu
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kai Zhao
- College of Life Science, Fujian Normal University, Fuzhou, China
| | - Yongji Huang
- Marine and Agricultural Biotechnology Laboratory, Fuzhou Institute of Oceanography, College of Geography and Oceanography, Minjiang University, Fuzhou, China.
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, Australia.
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Hobza R, Bačovský V, Čegan R, Horáková L, Hubinský M, Janíček T, Janoušek B, Jedlička P, Kružlicová J, Kubát Z, Rodríguez Lorenzo JL, Novotná P, Hudzieczek V. Sexy ways: approaches to studying plant sex chromosomes. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:5204-5219. [PMID: 38652048 PMCID: PMC11389836 DOI: 10.1093/jxb/erae173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 04/22/2024] [Indexed: 04/25/2024]
Abstract
Sex chromosomes have evolved in many plant species with separate sexes. Current plant research is shifting from examining the structure of sex chromosomes to exploring their functional aspects. New studies are progressively unveiling the specific genetic and epigenetic mechanisms responsible for shaping distinct sexes in plants. While the fundamental methods of molecular biology and genomics are generally employed for the analysis of sex chromosomes, it is often necessary to modify classical procedures not only to simplify and expedite analyses but sometimes to make them possible at all. In this review, we demonstrate how, at the level of structural and functional genetics, cytogenetics, and bioinformatics, it is essential to adapt established procedures for sex chromosome analysis.
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Affiliation(s)
- Roman Hobza
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 00 Brno, Czech Republic
| | - Václav Bačovský
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 00 Brno, Czech Republic
| | - Radim Čegan
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 00 Brno, Czech Republic
| | - Lucie Horáková
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 00 Brno, Czech Republic
- Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Marcel Hubinský
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 00 Brno, Czech Republic
- Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Tomáš Janíček
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 00 Brno, Czech Republic
- Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Bohuslav Janoušek
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 00 Brno, Czech Republic
| | - Pavel Jedlička
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 00 Brno, Czech Republic
| | - Jana Kružlicová
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 00 Brno, Czech Republic
- Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Zdeněk Kubát
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 00 Brno, Czech Republic
| | - José Luis Rodríguez Lorenzo
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 00 Brno, Czech Republic
| | - Pavla Novotná
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 00 Brno, Czech Republic
- Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Vojtěch Hudzieczek
- Department of Plant Developmental Genetics, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 00 Brno, Czech Republic
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3
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Qiao H, Zhou X, Yi Y, Wei L, Xu X, Jin P, Su W, Weng Y, Yu D, He S, Fu M, Hou C, Pan X, Wang W, Zhang YY, Ming R, Ye C, Li QQ, Shen Y. Molecular mechanism of vivipary as revealed by the genomes of viviparous mangroves and non-viviparous relatives. Curr Biol 2024; 34:3707-3721.e7. [PMID: 39079534 DOI: 10.1016/j.cub.2024.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/31/2024] [Accepted: 07/01/2024] [Indexed: 08/22/2024]
Abstract
Vivipary is a prominent feature of mangroves, allowing seeds to complete germination while attached to the mother plant, and equips propagules to endure and flourish in challenging coastal intertidal wetlands. However, vivipary-associated genetic mechanisms remain largely elusive. Genomes of two viviparous mangrove species and a non-viviparous inland relative were sequenced and assembled at the chromosome level. Comparative genomic analyses between viviparous and non-viviparous genomes revealed that DELAY OF GERMINATION 1 (DOG1) family genes (DFGs), the proteins from which are crucial for seed dormancy, germination, and reserve accumulation, are either lost or dysfunctional in the entire lineage of true viviparous mangroves but are present and functional in their inland, non-viviparous relatives. Transcriptome dynamics at key stages of vivipary further highlighted the roles of phytohormonal homeostasis, proteins stored in mature seeds, and proanthocyanidins in vivipary under conditions lacking DFGs. Population genomic analyses elucidate dynamics of syntenic regions surrounding the missing DFGs. Our findings demonstrated the genetic foundation of constitutive vivipary in Rhizophoraceae mangroves.
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Affiliation(s)
- Hongmei Qiao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China
| | - Xiaoxuan Zhou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China
| | - Yuchong Yi
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China
| | - Liufeng Wei
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China
| | - Xiuming Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China
| | - Pengfei Jin
- Novogene Co. Ltd, Building 301, Zone A10 Jiuxianqiao North Road, Chaoyang District, Beijing 100006, China
| | - Wenyue Su
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China
| | - Yulin Weng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China
| | - Dingtian Yu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China
| | - Shanshan He
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China
| | - Meiping Fu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China
| | - Chengcheng Hou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China
| | - Xiaobao Pan
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China
| | - Wenqing Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China
| | - Yuan-Ye Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China
| | - Ray Ming
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Congting Ye
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China.
| | - Qingshun Quinn Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China; Biomedical Sciences, College of Dental Medicine, Western University of Health Sciences, Pomona, CA 91766, USA.
| | - Yingjia Shen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361102, Fujian, China.
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Lomax J, Ford R, Bar I. Multi-omic applications for understanding and enhancing tropical fruit flavour. PLANT MOLECULAR BIOLOGY 2024; 114:83. [PMID: 38972957 PMCID: PMC11228007 DOI: 10.1007/s11103-024-01480-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 06/19/2024] [Indexed: 07/09/2024]
Abstract
Consumer trends towards nutrient-rich foods are contributing to global increasing demand for tropical fruit. However, commercial cultivars in the breeding pipeline that are tailored to meet market demand are at risk of possessing reduced fruit flavour qualities. This stems from recurrent prioritised selection for superior agronomic traits and not fruit flavour, which may in turn reduce consumer satisfaction. There is realisation that fruit quality traits, inclusive of flavour, must be equally selected for; but currently, there are limited tools and resources available to select for fruit flavour traits, particularly in tropical fruit species. Although sugars, acids, and volatile organic compounds are known to define fruit flavour, the specific combinations of these, that result in defined consumer preferences, remain unknown for many tropical fruit species. To define and include fruit flavour preferences in selective breeding, it is vital to determine the metabolites that underpin them. Then, objective quantitative analysis may be implemented instead of solely relying on human sensory panels. This may lead to the development of selective genetic markers through integrated omics approaches that target biosynthetic pathways of flavour active compounds. In this review, we explore progress in the development of tools to be able to strategically define and select for consumer-preferred flavour profiles in the breeding of new cultivars of tropical fruit species.
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Affiliation(s)
- Joshua Lomax
- Centre for Planetary Health and Food Security, School of Environment and Science, Griffith University, Nathan, QLD, 4111, Australia.
| | - Rebecca Ford
- Centre for Planetary Health and Food Security, School of Environment and Science, Griffith University, Nathan, QLD, 4111, Australia
| | - Ido Bar
- Centre for Planetary Health and Food Security, School of Environment and Science, Griffith University, Nathan, QLD, 4111, Australia
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5
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Liu J, Zhou SZ, Liu YL, Zhao BY, Yu D, Zhong MC, Jiang XD, Cui WH, Zhao JX, Qiu J, Liu LM, Guo ZH, Li HT, Tan DY, Hu JY, Li DZ. Genomes of Meniocus linifolius and Tetracme quadricornis reveal the ancestral karyotype and genomic features of core Brassicaceae. PLANT COMMUNICATIONS 2024; 5:100878. [PMID: 38475995 PMCID: PMC11287156 DOI: 10.1016/j.xplc.2024.100878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 03/03/2024] [Accepted: 03/11/2024] [Indexed: 03/14/2024]
Abstract
Brassicaceae represents an important plant family from both a scientific and economic perspective. However, genomic features related to the early diversification of this family have not been fully characterized, especially upon the uplift of the Tibetan Plateau, which was followed by increasing aridity in the Asian interior, intensifying monsoons in Eastern Asia, and significantly fluctuating daily temperatures. Here, we reveal the genomic architecture that accompanied early Brassicaceae diversification by analyzing two high-quality chromosome-level genomes for Meniocus linifolius (Arabodae; clade D) and Tetracme quadricornis (Hesperodae; clade E), together with genomes representing all major Brassicaceae clades and the basal Aethionemeae. We reconstructed an ancestral core Brassicaceae karyotype (CBK) containing 9 pseudochromosomes with 65 conserved syntenic genomic blocks and identified 9702 conserved genes in Brassicaceae. We detected pervasive conflicting phylogenomic signals accompanied by widespread ancient hybridization events, which correlate well with the early divergence of core Brassicaceae. We identified a successive Brassicaceae-specific expansion of the class I TREHALOSE-6-PHOSPHATE SYNTHASE 1 (TPS1) gene family, which encodes enzymes with essential regulatory roles in flowering time and embryo development. The TPS1s were mainly randomly amplified, followed by expression divergence. Our results provide fresh insights into historical genomic features coupled with Brassicaceae evolution and offer a potential model for broad-scale studies of adaptive radiation under an ever-changing environment.
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Affiliation(s)
- Jie Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shi-Zhao Zhou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yun-Long Liu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Bin-Yan Zhao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dongmei Yu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Mi-Cai Zhong
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Xiao-Dong Jiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Wei-Hua Cui
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Jiu-Xia Zhao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Juan Qiu
- College of Life Sciences, Xinjiang Agricultural University, Ürümqi 830052, China
| | - Liang-Min Liu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen-Hua Guo
- Germplasm Bank of Wild Species & Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Hong-Tao Li
- Germplasm Bank of Wild Species & Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Dun-Yan Tan
- College of Life Sciences, Xinjiang Agricultural University, Ürümqi 830052, China
| | - Jin-Yong Hu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - De-Zhu Li
- Germplasm Bank of Wild Species & Yunnan Key Laboratory for Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
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Wang J, Kan S, Liao X, Zhou J, Tembrock LR, Daniell H, Jin S, Wu Z. Plant organellar genomes: much done, much more to do. TRENDS IN PLANT SCIENCE 2024; 29:754-769. [PMID: 38220520 DOI: 10.1016/j.tplants.2023.12.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 01/16/2024]
Abstract
Plastids and mitochondria are the only organelles that possess genomes of endosymbiotic origin. In recent decades, advances in sequencing technologies have contributed to a meteoric rise in the number of published organellar genomes, and have revealed greatly divergent evolutionary trajectories. In this review, we quantify the abundance and distribution of sequenced plant organellar genomes across the plant tree of life. We compare numerous genomic features between the two organellar genomes, with an emphasis on evolutionary trajectories, transfers, the current state of organellar genome editing by transcriptional activator-like effector nucleases (TALENs), transcription activator-like effector (TALE)-mediated deaminase, and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas), as well as genetic transformation. Finally, we propose future research to understand these different evolutionary trajectories, and genome-editing strategies to promote functional studies and eventually improve organellar genomes.
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Affiliation(s)
- 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 518120, China; College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6000-6999, Australia
| | - Shenglong Kan
- 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 518120, China; Marine College, Shandong University, Weihai, 264209, China
| | - Xuezhu Liao
- 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 518120, China
| | - Jiawei Zhou
- 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 518120, China; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Luke R Tembrock
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Henry Daniell
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104-6030, USA.
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, 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 518120, China.
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7
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Dornela AF, Soares FAF, Silva JC, Sattler MC, Clarindo WR. Carica papaya L. sex chromosome review and physical mapping of the serk 2, svp-like and mdar 4 sequences. Sci Rep 2024; 14:14830. [PMID: 38937542 PMCID: PMC11211501 DOI: 10.1038/s41598-024-65880-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/25/2024] [Indexed: 06/29/2024] Open
Abstract
Physical mapping evidences the chromosome organization and structure. Despite the data about plant cytogenomics, physical mapping has been conducted from single-copy and/or low-copy genes for few species. Carica papaya cytogenomics has been accomplished from BAC-FISH and repeatome sequences. We aimed to map the serk 2, svp-like and mdar 4 sequences in C. papaya. The sequences were amplified and the amplicons sequenced, showing similarity in relation to serk 2, svp-like and mdar 4 genes. Carica papaya diploidy was confirmed and the mitotic chromosomes characterized. The chromosome 1 exhibited the secondary constriction pericentromeric to the centromere of the long arm. So, we concluded that it is the sex chromosomes. serk 2 was mapped in the long arm interstitial portion of the sex chromosomes, and the interphase nuclei showed two fluorescence signals. Considering these results and the sequencing data from the C. papaya sex chromosomes, svp-like and mdar 4 genes were mapped in the interstitial region of the sex chromosome long arm. Both sequences showed only one fluorescence signal in the interphase nuclei. The procedure adopted here can be reproduced for other single-copy and/or low-copy genes, allowing the construction of cytogenetic maps. In addition, we revisited the cytogenomics data about C. papaya sex chromosomes, presenting a revised point of view about the structure and evolution to these chromosomes.
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Affiliation(s)
- Adeilson Frias Dornela
- Pós-Graduação em Genética e Melhoramento, Centro de Ciências Agrárias e Engenharias, Universidade Federal do Espírito Santo, Alegre, ES, 29.500-000, Brazil
| | - Fernanda Aparecida Ferrari Soares
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, Viçosa, MG, 36.570-900, Brazil
| | - Jéssica Coutinho Silva
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, Viçosa, MG, 36.570-900, Brazil
| | - Mariana Cansian Sattler
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, Viçosa, MG, 36.570-900, Brazil
| | - Wellington Ronildo Clarindo
- Laboratório de Citogenética e Citometria, Departamento de Biologia Geral, Centro de Ciências Biológicas e da Saúde, Universidade Federal de Viçosa, Viçosa, MG, 36.570-900, Brazil.
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8
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Huang XZ, Gong SD, Shang XH, Gao M, Zhao BY, Xiao L, Shi PL, Zeng WD, Cao S, Wu ZD, Song JM, Chen LL, Yan HB. High-integrity Pueraria montana var. lobata genome and population analysis revealed the genetic diversity of Pueraria genus. DNA Res 2024; 31:dsae017. [PMID: 38809753 PMCID: PMC11149379 DOI: 10.1093/dnares/dsae017] [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: 06/26/2023] [Revised: 04/23/2024] [Accepted: 05/24/2024] [Indexed: 05/31/2024] Open
Abstract
Pueraria montana var. lobata (P. lobata) is a traditional medicinal plant belonging to the Pueraria genus of Fabaceae family. Pueraria montana var. thomsonii (P. thomsonii) and Pueraria montana var. montana (P. montana) are its related species. However, evolutionary history of the Pueraria genus is still largely unknown. Here, a high-integrity, chromosome-level genome of P. lobata and an improved genome of P. thomsonii were reported. It found evidence for an ancient whole-genome triplication and a recent whole-genome duplication shared with Fabaceae in three Pueraria species. Population genomics of 121 Pueraria accessions demonstrated that P. lobata populations had substantially higher genetic diversity, and P. thomsonii was probably derived from P. lobata by domestication as a subspecies. Selection sweep analysis identified candidate genes in P. thomsonii populations associated with the synthesis of auxin and gibberellin, which potentially play a role in the expansion and starch accumulation of tubers in P. thomsonii. Overall, the findings provide new insights into the evolutionary and domestication history of the Pueraria genome and offer a valuable genomic resource for the genetic improvement of these species.
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Affiliation(s)
- Xuan-Zhao Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Shao-Da Gong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Xiao-hong Shang
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi 530007, China
| | - Min Gao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Bo-Yuan Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi 530004, China
| | - Liang Xiao
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi 530007, China
| | - Ping-li Shi
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi 530007, China
| | - Wen-dan Zeng
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi 530007, China
| | - Sheng Cao
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi 530007, China
| | - Zheng-dan Wu
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi 530007, China
| | - Jia-Ming Song
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi 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, Guangxi 530004, China
| | - Hua-bing Yan
- Cash Crops Research Institute, Guangxi Academy of Agricultural Sciences (GXAAS), Nanning, Guangxi 530007, China
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9
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Mabry ME, Abrahams RS, Al-Shehbaz IA, Baker WJ, Barak S, Barker MS, Barrett RL, Beric A, Bhattacharya S, Carey SB, Conant GC, Conran JG, Dassanayake M, Edger PP, Hall JC, Hao Y, Hendriks KP, Hibberd JM, King GJ, Kliebenstein DJ, Koch MA, Leitch IJ, Lens F, Lysak MA, McAlvay AC, McKibben MTW, Mercati F, Moore RC, Mummenhoff K, Murphy DJ, Nikolov LA, Pisias M, Roalson EH, Schranz ME, Thomas SK, Yu Q, Yocca A, Pires JC, Harkess AE. Complementing model species with model clades. THE PLANT CELL 2024; 36:1205-1226. [PMID: 37824826 PMCID: PMC11062466 DOI: 10.1093/plcell/koad260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/07/2023] [Accepted: 09/22/2023] [Indexed: 10/14/2023]
Abstract
Model species continue to underpin groundbreaking plant science research. At the same time, the phylogenetic resolution of the land plant tree of life continues to improve. The intersection of these 2 research paths creates a unique opportunity to further extend the usefulness of model species across larger taxonomic groups. Here we promote the utility of the Arabidopsis thaliana model species, especially the ability to connect its genetic and functional resources, to species across the entire Brassicales order. We focus on the utility of using genomics and phylogenomics to bridge the evolution and diversification of several traits across the Brassicales to the resources in Arabidopsis, thereby extending scope from a model species by establishing a "model clade." These Brassicales-wide traits are discussed in the context of both the model species Arabidopsis and the family Brassicaceae. We promote the utility of such a "model clade" and make suggestions for building global networks to support future studies in the model order Brassicales.
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Affiliation(s)
- Makenzie E Mabry
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - R Shawn Abrahams
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA
- Department of Biochemistry, Purdue University, West Lafayette, IN 47906, USA
| | | | | | - Simon Barak
- Ben-Gurion University of the Negev, French Associates Institute for Agriculture and Biotechnology of Drylands, Jacob Blaustein Institutes for Desert Research, Midreshet Ben-Gurion, 8499000, Israel
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Russell L Barrett
- National Herbarium of New South Wales, Australian Botanic Garden, Locked Bag 6002, Mount Annan, NSW 2567, Australia
| | - Aleksandra Beric
- Department of Psychiatry, Washington University in Saint Louis School of Medicine, St. Louis, MO 63110, USA
- NeuroGenomics and Informatics Center, Washington University in Saint Louis School of Medicine, St. Louis, MO 63108, USA
| | - Samik Bhattacharya
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
| | - Sarah B Carey
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Gavin C Conant
- Department of Biological Sciences, Bioinformatics Research Center, Program in Genetics, North Carolina State University, Raleigh, NC 27695, USA
| | - John G Conran
- ACEBB and SGC, School of Biological Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Maheshi Dassanayake
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI 48864, USA
| | - Jocelyn C Hall
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Yue Hao
- Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Kasper P Hendriks
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
- Functional Traits, Naturalis Biodiversity Center, PO Box 9517, Leiden 2300 RA, the Netherlands
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | | | - Marcus A Koch
- Centre for Organismal Studies (COS), Heidelberg University, 69120 Heidelberg, Germany
| | - Ilia J Leitch
- Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Frederic Lens
- Functional Traits, Naturalis Biodiversity Center, PO Box 9517, Leiden 2300 RA, the Netherlands
- Institute of Biology Leiden, Plant Sciences, Leiden University, 2333 BE Leiden, the Netherlands
| | - Martin A Lysak
- CEITEC, and NCBR, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Alex C McAlvay
- Institute of Economic Botany, New York Botanical Garden, The Bronx, NY 10458, USA
| | - Michael T W McKibben
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Francesco Mercati
- National Research Council (CNR), Institute of Biosciences and Bioresource (IBBR), Palermo 90129, Italy
| | | | - Klaus Mummenhoff
- Department of Biology, Botany, University of Osnabrück, D-49076 Osnabrück, Germany
| | - Daniel J Murphy
- Royal Botanic Gardens Victoria, Melbourne, VIC 3004, Australia
| | | | - Michael Pisias
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Eric H Roalson
- School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - M Eric Schranz
- Biosystematics Group, Wageningen University, 6708 PB Wageningen, the Netherlands
| | - Shawn K Thomas
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, USA
- Bioinformatics and Analytics Core, University of Missouri, Columbia, MO 65211, USA
| | - Qingyi Yu
- Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Hilo, HI 96720, USA
| | - Alan Yocca
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - J Chris Pires
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523-1170, USA
| | - Alex E Harkess
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
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10
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Pereira Duarte R, Cancela Ramos HC, Rodrigues Xavier L, Azevedo Vimercati Pirovani A, Souza Rodrigues A, Turquetti-Moraes DK, Rodrigues da Silva Junior I, Motta Venâncio T, Silveira V, Gonzaga Pereira M. Comparative proteomic analysis of papaya bud flowers reveals metabolic signatures and pathways driving hermaphrodite development. Sci Rep 2024; 14:8867. [PMID: 38632280 PMCID: PMC11024100 DOI: 10.1038/s41598-024-59306-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 04/09/2024] [Indexed: 04/19/2024] Open
Abstract
Papaya (Carica papaya) is a trioecious species with female, male, and hermaphrodite plants. Given the sex segregation, selecting hermaphroditic plants is vital for orchard establishment due to their greater commercial value. However, selecting hermaphrodite plants through sexing is laborious and costly. Moreover, environmental stressors can exacerbate the issue by potentially inducing abnormal flower development, thus affecting fruit quality. Despite these challenges, the molecular mechanisms governing sex development in papaya remain poorly understood. Thus, this study aimed to identify proteins associated with sex development in female and hermaphrodite flowers of papaya through comparative proteomic analysis. Proteins from flower buds at the early and late developmental stages of three papaya genotypes (UENF-CALIMAN 01, JS12, and Sunrise Solo 72/12) were studied via proteomic analysis via the combination of the shotgun method and nanoESI-HDMSE technology. In buds at an early stage of development, 496 (35.9%) proteins exhibited significantly different abundances between sexes for the SS72/12 genotype, 139 (10%) for the JS12 genotype, and 165 (11.9%) for the UC-01 genotype. At the final stage of development, there were 181 (13.5%) for SS72/12, 113 (8.4%) for JS12, and 125 (9.1%) for UC-01. The large group of differentially accumulated proteins (DAPs) between the sexes was related to metabolism, as shown by the observation of only the proteins that exhibited the same pattern of accumulation in the three genotypes. Specifically, carbohydrate metabolism proteins were up-regulated in hermaphrodite flower buds early in development, while those linked to monosaccharide and amino acid metabolism increased during late development. Enrichment of sporopollenin and phenylpropanoid biosynthesis pathways characterizes hermaphrodite samples across developmental stages, with predicted protein interactions highlighting the crucial role of phenylpropanoids in sporopollenin biosynthesis for pollen wall formation. Most of the DAPs played key roles in pectin, cellulose, and lignin synthesis and were essential for cell wall formation and male flower structure development, notably in the pollen coat. These findings suggest that hermaphrodite flowers require more energy for development, likely due to complex pollen wall formation. Overall, these insights illuminate the molecular mechanisms of papaya floral development, revealing complex regulatory networks and energetic demands in the formation of male reproductive structures.
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Affiliation(s)
- Rafaela Pereira Duarte
- Laboratório de Melhoramento Genético Vegetal - LMGV, Universidade Estadual do Norte Fluminense Darcy Ribeiro-UENF, Campos dos Goytacazes, 28.013-602, Brazil.
| | - Helaine Christine Cancela Ramos
- Laboratório de Melhoramento Genético Vegetal - LMGV, Universidade Estadual do Norte Fluminense Darcy Ribeiro-UENF, Campos dos Goytacazes, 28.013-602, Brazil
| | - Lucas Rodrigues Xavier
- Laboratório de Biotecnologia - LBT, Universidade Estadual do Norte Fluminense Darcy Ribeiro-UENF, Campos dos Goytacazes, 28.013-602, Brazil
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, Universidade Estadual do Norte Fluminense Darcy Ribeiro-UENF, Campos dos Goytacazes, 28.013-602, Brazil
| | - Adriana Azevedo Vimercati Pirovani
- Laboratório de Melhoramento Genético Vegetal - LMGV, Universidade Estadual do Norte Fluminense Darcy Ribeiro-UENF, Campos dos Goytacazes, 28.013-602, Brazil
| | - Alex Souza Rodrigues
- Laboratório de Melhoramento Genético Vegetal - LMGV, Universidade Estadual do Norte Fluminense Darcy Ribeiro-UENF, Campos dos Goytacazes, 28.013-602, Brazil
| | - Dayana Kelly Turquetti-Moraes
- Laboratório de Química e Função de Proteínas e Peptídeos - LQFPP, Universidade Estadual do Norte Fluminense Darcy Ribeiro-UENF, Campos dos Goytacazes, 28.013-602, Brazil
| | - Izaias Rodrigues da Silva Junior
- Laboratório de Melhoramento Genético Vegetal - LMGV, Universidade Estadual do Norte Fluminense Darcy Ribeiro-UENF, Campos dos Goytacazes, 28.013-602, Brazil
| | - Thiago Motta Venâncio
- Laboratório de Química e Função de Proteínas e Peptídeos - LQFPP, Universidade Estadual do Norte Fluminense Darcy Ribeiro-UENF, Campos dos Goytacazes, 28.013-602, Brazil
| | - Vanildo Silveira
- Laboratório de Biotecnologia - LBT, Universidade Estadual do Norte Fluminense Darcy Ribeiro-UENF, Campos dos Goytacazes, 28.013-602, Brazil
- Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, Universidade Estadual do Norte Fluminense Darcy Ribeiro-UENF, Campos dos Goytacazes, 28.013-602, Brazil
| | - Messias Gonzaga Pereira
- Laboratório de Melhoramento Genético Vegetal - LMGV, Universidade Estadual do Norte Fluminense Darcy Ribeiro-UENF, Campos dos Goytacazes, 28.013-602, Brazil
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11
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Zhou Z, Kanchana-Udomkan C, Ford R, Bar I. Identification and Validation of Key Genes Related to Preferred Flavour Profiles in Australian Commercial Papaya ( Carica papaya L.). Int J Mol Sci 2024; 25:3046. [PMID: 38474290 DOI: 10.3390/ijms25053046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/22/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
Commercial papaya varieties grown in Australia vary greatly in taste and aroma. Previous profiling has identified undesirable 'off tastes' in existing varieties, discouraging a portion of the population from consuming papayas. Our focus on enhancing preferred flavours led to an exploration of the genetic mechanisms and biosynthesis pathways that underlie these desired taste profiles. To identify genes associated with consumer-preferred flavours, we conducted whole RNA sequencing and de novo genome assembly on papaya varieties RB1 (known for its sweet flavour and floral aroma) and 1B (less favoured due to its bitter taste and musty aroma) at both ripe and unripe stages. In total, 180,368 transcripts were generated, and 118 transcripts related to flavours were differentially expressed between the two varieties at the ripe stage. Five genes (cpBGH3B, cpPFP, cpSUS, cpGES and cpLIS) were validated through qPCR and significantly differentially expressed. These genes are suggested to play key roles in sucrose metabolism and aromatic compound production pathways, holding promise for future selective breeding strategies. Further exploration will involve assessing their potential across broader germplasm and various growth environments.
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Affiliation(s)
- Ziwei Zhou
- Centre for Planetary Health and Food Security, School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
| | - Chutchamas Kanchana-Udomkan
- Centre for Planetary Health and Food Security, School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
- Department of Horticulture, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
| | - Rebecca Ford
- Centre for Planetary Health and Food Security, School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
| | - Ido Bar
- Centre for Planetary Health and Food Security, School of Environment and Science, Griffith University, Nathan, QLD 4111, Australia
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12
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Wang Y, Jiang C, Zhang X, Yan H, Yin Z, Sun X, Gao F, Zhao Y, Liu W, Han S, Zhang J, Zhang Y, Zhang Z, Zhang H, Li J, Xie X, Zhao Q, Wang X, Ye G, Li J, Ming R, Li Z. Upland rice genomic signatures of adaptation to drought resistance and navigation to molecular design breeding. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:662-677. [PMID: 37909415 PMCID: PMC10893945 DOI: 10.1111/pbi.14215] [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: 06/06/2023] [Revised: 07/31/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023]
Abstract
Upland rice is a distinctive drought-aerobic ecotype of cultivated rice highly resistant to drought stress. However, the genetic and genomic basis for the drought-aerobic adaptation of upland rice remains largely unclear due to the lack of genomic resources. In this study, we identified 25 typical upland rice accessions and assembled a high-quality genome of one of the typical upland rice varieties, IRAT109, comprising 384 Mb with a contig N50 of 19.6 Mb. Phylogenetic analysis revealed upland and lowland rice have distinct ecotype differentiation within the japonica subgroup. Comparative genomic analyses revealed that adaptive differentiation of lowland and upland rice is likely attributable to the natural variation of many genes in promoter regions, formation of specific genes in upland rice, and expansion of gene families. We revealed differentiated gene expression patterns in the leaves and roots of the two ecotypes and found that lignin synthesis mediated by the phenylpropane pathway plays an important role in the adaptive differentiation of upland and lowland rice. We identified 28 selective sweeps that occurred during domestication and validated that the qRT9 gene in selective regions can positively regulate drought resistance in rice. Eighty key genes closely associated with drought resistance were appraised for their appreciable potential in drought resistance breeding. Our study enhances the understanding of the adaptation of upland rice and provides a genome navigation map of drought resistance breeding, which will facilitate the breeding of drought-resistant rice and the "blue revolution" in agriculture.
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Affiliation(s)
- Yulong Wang
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Conghui Jiang
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
- Institute of Wetland Agriculture and EcologyShandong Academy of Agricultural SciencesJinanShandongChina
| | - Xingtan Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of EducationFujian Agriculture and Forestry UniversityFuzhouFujianChina
- Agricultural Genomics Institute in ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdongChina
| | - Huimin Yan
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice BiologyHenan Agricultural UniversityZhengzhouHenanChina
| | - Zhigang Yin
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Xingming Sun
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Fenghua Gao
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Yan Zhao
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Wei Liu
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Shichen Han
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Jingjing Zhang
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Yage Zhang
- Sanya Institute of Hainan Academy of Agricultural SciencesSanyaHainanChina
| | - Zhanying Zhang
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Hongliang Zhang
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Jinjie Li
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Xianzhi Xie
- Institute of Wetland Agriculture and EcologyShandong Academy of Agricultural SciencesJinanShandongChina
| | - Quanzhi Zhao
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice BiologyHenan Agricultural UniversityZhengzhouHenanChina
| | - Xiaoning Wang
- Sanya Institute of Hainan Academy of Agricultural SciencesSanyaHainanChina
| | - Guoyou Ye
- Agricultural Genomics Institute in ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdongChina
- Institution International Rice Research InstituteLos BañosLagunaPhilippines
| | - Junzhou Li
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice BiologyHenan Agricultural UniversityZhengzhouHenanChina
| | - Ray Ming
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of EducationFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Zichao Li
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
- Sanya Institute of Hainan Academy of Agricultural SciencesSanyaHainanChina
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13
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Zou Z, Zhang L, Zhao Y. Integrative Analysis of Oleosin Genes Provides Insights into Lineage-Specific Family Evolution in Brassicales. PLANTS (BASEL, SWITZERLAND) 2024; 13:280. [PMID: 38256833 PMCID: PMC10820149 DOI: 10.3390/plants13020280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/16/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024]
Abstract
Oleosins (OLEs) are a class of small but abundant structural proteins that play essential roles in the formation and stabilization of lipid droplets (LDs) in seeds of oil crops. Despite the proposal of five oleosin clades (i.e., U, SL, SH, T, and M) in angiosperms, their evolution in eudicots has not been well-established. In this study, we employed Brassicales, an economically important order of flowering plants possessing the lineage-specific T clade, as an example to address this issue. Three to 10 members were identified from 10 species representing eight plant families, which include Caricaceae, Moringaceae, Akaniaceae, Capparaceae, and Cleomaceae. Evolutionary and reciprocal best hit-based homologous analyses assigned 98 oleosin genes into six clades (i.e., U, SL, SH, M, N, and T) and nine orthogroups (i.e., U1, U2, SL, SH1, SH2, SH3, M, N, and T). The newly identified N clade represents an ancient group that has already appeared in the basal angiosperm Amborella trichopoda, which are constitutively expressed in the tree fruit crop Carica papaya, including pulp and seeds of the fruit. Moreover, similar to Clade N, the previously defined M clade is actually not Lauraceae-specific but an ancient and widely distributed group that diverged before the radiation of angiosperm. Compared with A. trichopoda, lineage-specific expansion of the family in Brassicales was largely contributed by recent whole-genome duplications (WGDs) as well as the ancient γ event shared by all core eudicots. In contrast to the flower-preferential expression of Clade T, transcript profiling revealed an apparent seed/embryo/endosperm-predominant expression pattern of most oleosin genes in Arabidopsis thaliana and C. papaya. Moreover, the structure and expression divergence of paralogous pairs was frequently observed, and a good example is the lineage-specific gain of an intron. These findings provide insights into lineage-specific family evolution in Brassicales, which facilitates further functional studies in nonmodel plants such as C. papaya.
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Affiliation(s)
- Zhi Zou
- National Key Laboratory for Tropical Crop Breeding, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Institute of Tropical Biosciences and Biotechnology/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China;
| | - Li Zhang
- National Key Laboratory for Tropical Crop Breeding, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Institute of Tropical Biosciences and Biotechnology/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China;
- Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, College of Life Science, South-Central University for Nationalities, Wuhan 430074, China
| | - Yongguo Zhao
- National Key Laboratory for Tropical Crop Breeding, Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Institute of Tropical Biosciences and Biotechnology/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China;
- College of Biology and Food Engineering, Guangdong University of Petrochemical Technology, Maoming 525011, China
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14
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Liu D, Tian X, Shao S, Ma Y, Zhang R. Haplotype-resolved chromosomal-level genome assembly of Buzhaye (Microcos paniculata). Sci Data 2023; 10:901. [PMID: 38102170 PMCID: PMC10724166 DOI: 10.1038/s41597-023-02821-9] [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: 09/08/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023] Open
Abstract
Microcos paniculata is a shrub used traditionally as folk medicine and to make herbal teas. Previous research into this species has mainly focused on its chemical composition and medicinal value. However, the lack of a reference genome limits the study of the molecular mechanisms of active compounds in this species. Here, we assembled a haplotype-resolved chromosome-level genome of M. paniculata based on PacBio HiFi and Hi-C data. The assembly contains two haploid genomes with sizes 399.43 Mb and 393.10 Mb, with contig N50 lengths of 43.44 Mb and 30.17 Mb, respectively. About 99.93% of the assembled sequences could be anchored to 18 pseudo-chromosomes. Additionally, a total of 482 Mb repeat sequences were identified, accounting for 60.76% of the genome. A total of 49,439 protein-coding genes were identified, of which 48,979 (99%) were functionally annotated. This haplotype-resolved chromosome-level assembly and annotation of M. paniculata will serve as a valuable resource for investigating the biosynthesis and genetic basis of active compounds in this species, as well as advancing evolutionary phylogenomic studies in Malvales.
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Affiliation(s)
- Detuan Liu
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Xiaoling Tian
- Institute of International Rivers and Eco-Security, Yunnan University, Kunming, 650500, China
| | - Shicheng Shao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, China.
| | - Yongpeng Ma
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Rengang Zhang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
- University of Chinese Academy of Sciences, Beijing, 101408, China.
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15
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Zeng Q, Jia H, Ma Y, Xu L, Ming R, Yue J. Genome-Wide Identification and Expression Pattern Profiling of the Aquaporin Gene Family in Papaya ( Carica papaya L.). Int J Mol Sci 2023; 24:17276. [PMID: 38139107 PMCID: PMC10744249 DOI: 10.3390/ijms242417276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 12/02/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Aquaporins (AQPs) are mainly responsible for the transportation of water and other small molecules such as CO2 and H2O2, and they perform diverse functions in plant growth, in development, and under stress conditions. They are also active participants in cell signal transduction in plants. However, little is known about AQP diversity, biological functions, and protein characteristics in papaya. To better understand the structure and function of CpAQPs in papaya, a total of 29 CpAQPs were identified and classified into five subfamilies. Analysis of gene structure and conserved motifs revealed that CpAQPs exhibited a degree of conservation, with some differentiation among subfamilies. The predicted interaction network showed that the PIP subfamily had the strongest protein interactions within the subfamily, while the SIP subfamily showed extensive interaction with members of the PIP, TIP, NIP, and XIP subfamilies. Furthermore, the analysis of CpAQPs' promoters revealed a large number of cis-elements participating in light, hormone, and stress responses. CpAQPs exhibited different expression patterns in various tissues and under different stress conditions. Collectively, these results provided a foundation for further functional investigations of CpAQPs in ripening, as well as leaf, flower, fruit, and seed development. They also shed light on the potential roles of CpAQP genes in response to environmental factors, offering valuable insights into their biological functions in papaya.
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Affiliation(s)
- Qiuxia Zeng
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.Z.); (H.J.); (Y.M.); (L.X.)
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Haifeng Jia
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.Z.); (H.J.); (Y.M.); (L.X.)
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yaying Ma
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.Z.); (H.J.); (Y.M.); (L.X.)
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liangwei Xu
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.Z.); (H.J.); (Y.M.); (L.X.)
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ray Ming
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.Z.); (H.J.); (Y.M.); (L.X.)
| | - Jingjing Yue
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (Q.Z.); (H.J.); (Y.M.); (L.X.)
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16
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Zou Z, Zheng Y, Xie Z. Analysis of Carica papaya Informs Lineage-Specific Evolution of the Aquaporin (AQP) Family in Brassicales. PLANTS (BASEL, SWITZERLAND) 2023; 12:3847. [PMID: 38005748 PMCID: PMC10674200 DOI: 10.3390/plants12223847] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/15/2023] [Accepted: 11/01/2023] [Indexed: 11/26/2023]
Abstract
Aquaporins (AQPs), a type of intrinsic membrane proteins that transport water and small solutes across biological membranes, play crucial roles in plant growth and development. This study presents a first genome-wide identification and comparative analysis of the AQP gene family in papaya (Carica papaya L.), an economically and nutritionally important fruit tree of tropical and subtropical regions. A total of 29 CpAQP genes were identified, which represent five subfamilies, i.e., nine plasma intrinsic membrane proteins (PIPs), eight tonoplast intrinsic proteins (TIPs), seven NOD26-like intrinsic proteins (NIPs), two X intrinsic proteins (XIPs), and three small basic intrinsic proteins (SIPs). Although the family is smaller than the 35 members reported in Arabidopsis, it is highly diverse, and the presence of CpXIP genes as well as orthologs in Moringa oleifera and Bretschneidera sinensis implies that the complete loss of the XIP subfamily in Arabidopsis is lineage-specific, sometime after its split with papaya but before Brassicaceae-Cleomaceae divergence. Reciprocal best hit-based sequence comparison of 530 AQPs and synteny analyses revealed that CpAQP genes belong to 29 out of 61 identified orthogroups, and lineage-specific evolution was frequently observed in Brassicales. Significantly, the well-characterized NIP3 group was completely lost; lineage-specific loss of the NIP8 group in Brassicaceae occurred sometime before the divergence with Cleomaceae, and lineage-specific loss of NIP2 and SIP3 groups in Brassicaceae occurred sometime after the split with Cleomaceae. In contrast to a predominant role of recent whole-genome duplications (WGDs) on the family expansion in B. sinensis, Tarenaya hassleriana, and Brassicaceae plants, no recent AQP repeats were identified in papaya, and ancient WGD repeats are mainly confined to the PIP subfamily. Subfamily even group-specific evolution was uncovered via comparing exon-intron structures, conserved motifs, the aromatic/arginine selectivity filter, and gene expression profiles. Moreover, down-regulation during fruit ripening and expression divergence of duplicated CpAQP genes were frequently observed in papaya. These findings will not only improve our knowledge on lineage-specific family evolution in Brassicales, but also provide valuable information for further studies of AQP genes in papaya and species beyond.
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Affiliation(s)
- Zhi Zou
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Institute of Tropical Biosciences and Biotechnology/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (Y.Z.); (Z.X.)
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17
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Hoengenaert L, Van Doorsselaere J, Vanholme R, Boerjan W. Microparticle-mediated CRISPR DNA delivery for genome editing in poplar. FRONTIERS IN PLANT SCIENCE 2023; 14:1286663. [PMID: 38023888 PMCID: PMC10679337 DOI: 10.3389/fpls.2023.1286663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023]
Abstract
The use of CRISPR/Cas9 is currently the method of choice for precise genome engineering in plants, including in the biomass crop poplar. The most commonly used method for delivering CRISPR/Cas9 and its components in poplar is via Agrobacterium-mediated transformation, that besides the desired gene-editing event also results in stable T-DNA integration. Here we explore the delivery of the gene-editing reagents via DNA-coated microparticle bombardment into the model tree Populus tremula x P. alba to evaluate its potential for developing transgene-free, gene-edited trees, as well as its potential for integrating donor DNA at specific target sites. Using an optimized transformation method, which favors the regeneration of plants that transiently express the genes on the delivered donor DNA, we regenerated gene-edited plants that are free of the Cas9 and the antibiotic resistance-encoding transgenes. In addition, we report the frequent integration of donor DNA fragments at the Cas9-induced double-strand break, opening opportunities toward targeted gene insertions.
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Affiliation(s)
- Lennart Hoengenaert
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | | | - Ruben Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
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18
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Koller F, Cieslak M. A perspective from the EU: unintended genetic changes in plants caused by NGT-their relevance for a comprehensive molecular characterisation and risk assessment. Front Bioeng Biotechnol 2023; 11:1276226. [PMID: 37965049 PMCID: PMC10641861 DOI: 10.3389/fbioe.2023.1276226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023] Open
Abstract
Several regions in the world are currently holding discussions in regard to the regulation of new genomic techniques (NGTs) and their application in agriculture. The European Commission, for instance, is proposing the introduction of specific regulation for NGT plants. Various questions need to be answered including e.g., the extent to which NGT-induced intended and unintended genetic modifications must be subjected to a mandatory risk assessment as part of an approval procedure. This review mostly focuses on findings in regard to unintended genetic changes that can be caused by the application of NGTs. More specifically, the review deals with the application of the nuclease CRISPR/Cas, which is currently the most important tool for developing NGT plants, and its potential to introduce double strand breaks (DSBs) at a targeted DNA sequence. For this purpose, we identified the differences in comparison to non-targeted mutagenesis methods used in conventional breeding. The review concludes that unintended genetic changes caused by NGT processes are relevant to risk assessment. Due to the technical characteristics of NGTs, the sites of the unintended changes, their genomic context and their frequency (in regard to specific sites) mean that the resulting gene combinations (intended or unintended) may be unlikely to occur with conventional methods. This, in turn, implies that the biological effects (phenotypes) can also be different and may cause risks to health and the environment. Therefore, we conclude that the assessment of intended as well as unintended genetic changes should be part of a mandatory comprehensive molecular characterisation and risk assessment of NGT plants that are meant for environmental releases or for market authorisation.
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Affiliation(s)
- Franziska Koller
- Fachstelle Gentechnik und Umwelt (FGU), Munich, Bavaria, Germany
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19
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Ávila-Hernández JG, Cárdenas-Aquino MDR, Camas-Reyes A, Martínez-Antonio A. Sex determination in papaya: Current status and perspectives. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 335:111814. [PMID: 37562730 DOI: 10.1016/j.plantsci.2023.111814] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 06/27/2023] [Accepted: 08/02/2023] [Indexed: 08/12/2023]
Abstract
Papaya (Carica papaya L.) is an economically significant plant that produces fruit consumed worldwide due to its organoleptic characteristics. Since their commercial production, papaya fruits have faced several problems, such as pests, which have been partly resolved using transgenic varieties. Nevertheless, a principal challenge in this cultivation is the plant's sex determination. The sex issue in papaya is complex because papaya flowers can bear three sex forms: male, female, and hermaphrodite, which affects their fruit production, shape, and yield. Fruits from hermaphrodite plants are preferred more by consumers than female ones, and male plants rarely produce fruits without commercial value. Chromosomes are responsible for sex determination in papaya, denoted as XY for male, XX for female, and XYh for hermaphrodite. However, genes related to sex have been reported but are not conclusive. Factors such as the environment, hormones, and genetic and epigenetic background can also affect sex expression. Therefore, in this review, we will discuss recent research on the sex of papaya, from reported genes to date, their biology, and sexing approaches using molecular markers and their advantages.
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Affiliation(s)
- José Guadalupe Ávila-Hernández
- Biological Engineering Laboratory, Genetic Engineering Department. Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-IPN), Irapuato Unit, 36824, Irapuato, Gto, Mexico
| | - María Del Rosario Cárdenas-Aquino
- Biological Engineering Laboratory, Genetic Engineering Department. Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-IPN), Irapuato Unit, 36824, Irapuato, Gto, Mexico
| | - Alberto Camas-Reyes
- Biological Engineering Laboratory, Genetic Engineering Department. Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-IPN), Irapuato Unit, 36824, Irapuato, Gto, Mexico
| | - Agustino Martínez-Antonio
- Biological Engineering Laboratory, Genetic Engineering Department. Center for Research and Advanced Studies of the National Polytechnic Institute (CINVESTAV-IPN), Irapuato Unit, 36824, Irapuato, Gto, Mexico..
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20
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Dai Y, Wang Y, Zeng L, Jia R, He L, Huang X, Zhao H, Liu D, Zhao H, Hu S, Gao L, Guo A, Xia W, Ji C. Genomic and Transcriptomic Insights into the Evolution and Divergence of MIKC-Type MADS-Box Genes in Carica papaya. Int J Mol Sci 2023; 24:14039. [PMID: 37762345 PMCID: PMC10531014 DOI: 10.3390/ijms241814039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 09/02/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
MIKC-type MADS-box genes, also known as type II genes, play a crucial role in regulating the formation of floral organs and reproductive development in plants. However, the genome-wide identification and characterization of type II genes as well as a transcriptomic survey of their potential roles in Carica papaya remain unresolved. Here, we identified and characterized 24 type II genes in the C. papaya genome, and investigated their evolutional scenario and potential roles with a widespread expression profile. The type II genes were divided into thirteen subclades, and gene loss events likely occurred in papaya, as evidenced by the contracted member size of most subclades. Gene duplication mainly contributed to MIKC-type gene formation in papaya, and the duplicated gene pairs displayed prevalent expression divergence, implying the evolutionary significance of gene duplication in shaping the diversity of type II genes in papaya. A large-scale transcriptome analysis of 152 samples indicated that different subclasses of these genes showed distinct expression patterns in various tissues, biotic stress response, and abiotic stress response, reflecting their divergent functions. The hub-network of male and female flowers and qRT-PCR suggested that TT16-3 and AGL8 participated in male flower development and seed germination. Overall, this study provides valuable insights into the evolution and functions of MIKC-type genes in C. papaya.
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Affiliation(s)
- Yunsu Dai
- Sanya Nanfan Research Institution of Hainan University, Sanya 572025, China; (Y.D.); (Y.W.); (D.L.)
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
| | - Yu Wang
- Sanya Nanfan Research Institution of Hainan University, Sanya 572025, China; (Y.D.); (Y.W.); (D.L.)
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- National Key Laboratory for Tropical Crop Breeding, Sanya 572025, China
| | - Liwang Zeng
- Key Laboratory of Applied Research on Tropical Crop Information Technology of Hainan Province, Institute of Scientific and Technical Information, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Ruizong Jia
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- National Key Laboratory for Tropical Crop Breeding, Sanya 572025, China
| | - Linwen He
- College of Marine Science, Hainan University, Haikou 570228, China;
| | - Xueying Huang
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- College of Marine Science, Hainan University, Haikou 570228, China;
| | - Hui Zhao
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- National Key Laboratory for Tropical Crop Breeding, Sanya 572025, China
| | - Difa Liu
- Sanya Nanfan Research Institution of Hainan University, Sanya 572025, China; (Y.D.); (Y.W.); (D.L.)
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Haixu Zhao
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
| | - Shuai Hu
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- National Key Laboratory for Tropical Crop Breeding, Sanya 572025, China
| | - Ling Gao
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Anping Guo
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- National Key Laboratory for Tropical Crop Breeding, Sanya 572025, China
| | - Wei Xia
- Sanya Nanfan Research Institution of Hainan University, Sanya 572025, China; (Y.D.); (Y.W.); (D.L.)
| | - Changmian Ji
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions, Sanya Research Institute & Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China; (R.J.); (X.H.); (H.Z.); (H.Z.); (S.H.); (L.G.); (A.G.)
- National Key Laboratory for Tropical Crop Breeding, Sanya 572025, China
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21
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Chen Y, Guo Y, Xie X, Wang Z, Miao L, Yang Z, Jiao Y, Xie C, Liu J, Hu Z, Xin M, Yao Y, Ni Z, Sun Q, Peng H, Guo W. Pangenome-based trajectories of intracellular gene transfers in Poaceae unveil high cumulation in Triticeae. PLANT PHYSIOLOGY 2023; 193:578-594. [PMID: 37249052 PMCID: PMC10469385 DOI: 10.1093/plphys/kiad319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 05/04/2023] [Indexed: 05/31/2023]
Abstract
Intracellular gene transfers (IGTs) between the nucleus and organelles, including plastids and mitochondria, constantly reshape the nuclear genome during evolution. Despite the substantial contribution of IGTs to genome variation, the dynamic trajectories of IGTs at the pangenomic level remain elusive. Here, we developed an approach, IGTminer, that maps the evolutionary trajectories of IGTs using collinearity and gene reannotation across multiple genome assemblies. We applied IGTminer to create a nuclear organellar gene (NOG) map across 67 genomes covering 15 Poaceae species, including important crops. The resulting NOGs were verified by experiments and sequencing data sets. Our analysis revealed that most NOGs were recently transferred and lineage specific and that Triticeae species tended to have more NOGs than other Poaceae species. Wheat (Triticum aestivum) had a higher retention rate of NOGs than maize (Zea mays) and rice (Oryza sativa), and the retained NOGs were likely involved in photosynthesis and translation pathways. Large numbers of NOG clusters were aggregated in hexaploid wheat during 2 rounds of polyploidization, contributing to the genetic diversity among modern wheat accessions. We implemented an interactive web server to facilitate the exploration of NOGs in Poaceae. In summary, this study provides resources and insights into the roles of IGTs in shaping interspecies and intraspecies genome variation and driving plant genome evolution.
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Affiliation(s)
- Yongming Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yiwen Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Xiaoming Xie
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zihao Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Lingfeng Miao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhengzhao Yang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chaojie Xie
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Jie Liu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhaorong Hu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Mingming Xin
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yingyin Yao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
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22
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Arroyo-Álvarez E, Chan-León A, Girón-Ramírez A, Fuentes G, Estrella-Maldonado H, Santamaría JM. Genome-Wide Analysis of WRKY and NAC Transcription Factors in Carica papaya L. and Their Possible Role in the Loss of Drought Tolerance by Recent Cultivars through the Domestication of Their Wild Ancestors. PLANTS (BASEL, SWITZERLAND) 2023; 12:2775. [PMID: 37570929 PMCID: PMC10421361 DOI: 10.3390/plants12152775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/18/2023] [Accepted: 02/07/2023] [Indexed: 08/13/2023]
Abstract
A genome-wide analysis for two families of key transcription factors (TF; WRKY and NAC) involved in drought response revealed 46 WRKY and 66 NAC members of the Carica papaya genome. A phylogenetic analysis grouped the CpWRKY proteins into three groups (I, II a, b, c, d, e and III), while the CpNAC proteins were clustered into 15 groups. The conserved domains, chromosomal localization and promoter cis-acting elements were also analyzed. In addition, from a previous transcriptome study of two contrasting genotypes in response to 14 days of water deficit stress (WDS), we found that 29 of the 46 CpWRKYs genes and 25 of the 66 CpNACs genes were differentially expressed in response to the WDS. In the present paper, the native wild genotype (WG) (collected in its center of origin) consistently showed a higher expression (transcripts per million; TPM and fold change; FC) than the commercial genotype (CG) in almost all the members of the CpWRKY and CpNAC gene families. To corroborate this, we selected CpWRKY50 and CpNAC83.1 for further evaluation by RT-qPCR. Consistently, the WG showed higher relative expression levels (REL) after 14 days of WDS than the CG, in both the leaves and roots. The results suggest that the CpWRKY and CpNAC TF families are important for drought tolerance in this species. The results may also suggest that, during the domestication process, the ability of the native (wild) C. papaya genotypes to respond to drought (including the overexpression of the CpWRKY and CpNAC genes) was somehow reduced in the current commercial genotypes.
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Affiliation(s)
- Erick Arroyo-Álvarez
- Centro de Investigación Científica de Yucatán A.C., Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida 97205, Yucatán, Mexico
| | - Arianna Chan-León
- Centro de Investigación Científica de Yucatán A.C., Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida 97205, Yucatán, Mexico
| | - Amaranta Girón-Ramírez
- Centro de Investigación Científica de Yucatán A.C., Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida 97205, Yucatán, Mexico
| | - Gabriela Fuentes
- Independent Researcher, Calle 6ª, 279 a, Jardines de Vista Alegre, Mérida 97138, Yucatán, Mexico
| | - Humberto Estrella-Maldonado
- Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Campo Experimental Ixtacuaco, Km 4.5 Carretera Martínez de la Torre-Tlapacoyan, Tlapacoyan 93600, Veracruz, Mexico
| | - Jorge M. Santamaría
- Centro de Investigación Científica de Yucatán A.C., Calle 43 No. 130, Colonia Chuburná de Hidalgo, Mérida 97205, Yucatán, Mexico
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23
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Kocsisova Z, Coneva V. Strategies for delivery of CRISPR/Cas-mediated genome editing to obtain edited plants directly without transgene integration. Front Genome Ed 2023; 5:1209586. [PMID: 37545761 PMCID: PMC10398581 DOI: 10.3389/fgeed.2023.1209586] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/28/2023] [Indexed: 08/08/2023] Open
Abstract
Increased understanding of plant genetics and the development of powerful and easier-to-use gene editing tools over the past century have revolutionized humankind's ability to deliver precise genotypes in crops. Plant transformation techniques are well developed for making transgenic varieties in certain crops and model organisms, yet reagent delivery and plant regeneration remain key bottlenecks to applying the technology of gene editing to most crops. Typical plant transformation protocols to produce transgenic, genetically modified (GM) varieties rely on transgenes, chemical selection, and tissue culture. Typical protocols to make gene edited (GE) varieties also use transgenes, even though these may be undesirable in the final crop product. In some crops, the transgenes are routinely segregated away during meiosis by performing crosses, and thus only a minor concern. In other crops, particularly those propagated vegetatively, complex hybrids, or crops with long generation times, such crosses are impractical or impossible. This review highlights diverse strategies to deliver CRISPR/Cas gene editing reagents to regenerable plant cells and to recover edited plants without unwanted integration of transgenes. Some examples include delivering DNA-free gene editing reagents such as ribonucleoproteins or mRNA, relying on reagent expression from non-integrated DNA, using novel delivery mechanisms such as viruses or nanoparticles, using unconventional selection methods to avoid integration of transgenes, and/or avoiding tissue culture altogether. These methods are advancing rapidly and already enabling crop scientists to make use of the precision of CRISPR gene editing tools.
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24
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Yue J, Krasovec M, Kazama Y, Zhang X, Xie W, Zhang S, Xu X, Kan B, Ming R, Filatov DA. The origin and evolution of sex chromosomes, revealed by sequencing of the Silene latifolia female genome. Curr Biol 2023:S0960-9822(23)00678-4. [PMID: 37290443 DOI: 10.1016/j.cub.2023.05.046] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 04/07/2023] [Accepted: 05/19/2023] [Indexed: 06/10/2023]
Abstract
White campion (Silene latifolia, Caryophyllaceae) was the first vascular plant where sex chromosomes were discovered. This species is a classic model for studies on plant sex chromosomes due to presence of large, clearly distinguishable X and Y chromosomes that originated de novo about 11 million years ago (mya), but lack of genomic resources for this relatively large genome (∼2.8 Gb) remains a significant hurdle. Here we report S. latifolia female genome assembly integrated with sex-specific genetic maps of this species, focusing on sex chromosomes and their evolution. The analysis reveals a highly heterogeneous recombination landscape with strong reduction in recombination rate in the central parts of all chromosomes. Recombination on the X chromosome in female meiosis primarily occurs at the very ends, and over 85% of the X chromosome length is located in a massive (∼330 Mb) gene-poor, rarely recombining pericentromeric region (Xpr). The results indicate that the non-recombining region on the Y chromosome (NRY) initially evolved in a relatively small (∼15 Mb), actively recombining region at the end of the q-arm, possibly as a result of inversion on the nascent X chromosome. The NRY expanded about 6 mya via linkage between the Xpr and the sex-determining region, which may have been caused by expanding pericentromeric recombination suppression on the X chromosome. These findings shed light on the origin of sex chromosomes in S. latifolia and yield genomic resources to assist ongoing and future investigations into sex chromosome evolution.
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Affiliation(s)
- Jingjing Yue
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Marc Krasovec
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK; Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Yusuke Kazama
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Kenjojima, Matsuoka, Eiheiji-cho, Fukui 910-1195, Japan
| | - Xingtan Zhang
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518100, China
| | - Wangyang Xie
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shencheng Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518100, China
| | - Xiuming Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361100, China
| | - Baolin Kan
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ray Ming
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Dmitry A Filatov
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK.
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25
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Liu Q, Zhao C, Sun K, Deng Y, Li Z. Engineered biocontainable RNA virus vectors for non-transgenic genome editing across crop species and genotypes. MOLECULAR PLANT 2023; 16:616-631. [PMID: 36751129 DOI: 10.1016/j.molp.2023.02.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/13/2023] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
CRISPR/Cas genome-editing tools provide unprecedented opportunities for basic plant biology research and crop breeding. However, the lack of robust delivery methods has limited the widespread adoption of these revolutionary technologies in plant science. Here, we report an efficient, non-transgenic CRISPR/Cas delivery platform based on the engineered tomato spotted wilt virus (TSWV), an RNA virus with a host range of over 1000 plant species. We eliminated viral elements essential for insect transmission to liberate genome space for accommodating large genetic cargoes without sacrificing the ability to infect plant hosts. The resulting non-insect-transmissible viral vectors enabled effective and stable in planta delivery of Cas12a and Cas9 nucleases as well as adenine and cytosine base editors. In systemically infected plant tissues, the deconstructed TSWV-derived vectors induced efficient somatic gene mutations and base conversions in multiple crop species with little genotype dependency. Plants with heritable, bi-allelic mutations could be readily regenerated by culturing the virus-infected tissues in vitro without antibiotic selection. Moreover, we showed that antiviral treatment with ribavirin during tissue culture cleared the viral vectors in 100% of regenerated plants and further augmented the recovery of heritable mutations. Because many plants are recalcitrant to stable transformation, the viral delivery system developed in this work provides a promising tool to overcome gene delivery bottlenecks for genome editing in various crop species and elite varieties.
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Affiliation(s)
- Qian Liu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Chenglu Zhao
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Kai Sun
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yinlu Deng
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhenghe Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China; Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou, China.
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26
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Yang M, Zhou C, Yang H, Kuang R, Liu K, Huang B, Wei Y. Comparative transcriptomics and genomic analyses reveal differential gene expression related to Colletotrichum brevisporum resistance in papaya ( Carica papaya L.). FRONTIERS IN PLANT SCIENCE 2022; 13:1038598. [PMID: 36618670 PMCID: PMC9816866 DOI: 10.3389/fpls.2022.1038598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Colletotrichum brevisporum is an important causal pathogen of anthracnose that seriously affects the fruit quality and yield of papaya (Carica papaya L.). Although many genes and biological processes involved in anthracnose resistance have been reported in other species, the molecular mechanisms involved in the response or resistance to anthracnose in post-harvest papaya fruits remain unclear. In this study, we compared transcriptome changes in the post-harvest fruits of the anthracnose-susceptible papaya cultivar Y61 and the anthracnose-resistant cultivar G20 following C. brevisporum inoculation. More differentially expressed genes (DEGs) and differentially expressed long non-coding RNAs (DElnRNAs) were identified in G20 than in Y61, especially at 24 h post-inoculation (hpi), suggesting a prompt activation of defense responses in G20 in the first 24 h after C. brevisporum inoculation. These DEGs were mainly enriched in plant-pathogen interaction, phenylpropanoid biosynthesis/metabolism, and peroxisome and flavonoid biosynthesis pathways in both cultivars. However, in the first 24 hpi, the number of DEGs related to anthracnose resistance was greater in G20 than in Y61, and changes in their expression levels were faster in G20 than in Y61. We also identified a candidate anthracnose-resistant gene cluster, which consisted of 12 genes, 11 in G20 and Y61, in response to C. brevisporum inoculation. Moreover, 529 resistance gene analogs were identified in papaya genome, most of which responded to C. brevisporum inoculation and were genetically different between papaya cultivars and wild-type populations. The total expression dose of the resistance gene analogs may help papaya resist C. brevisporum infection. This study revealed the mechanisms underlying different anthracnose resistance between the anthracnose-resistant and anthracnose-susceptible cultivars based on gene expression, and identified some potential anthracnose resistance-related candidate genes/major regulatory factors. Our findings provided potential targets for developing novel genetic strategies to overcome anthracnose in papaya.
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Affiliation(s)
- Min Yang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Chenping Zhou
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Hu Yang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Ruibin Kuang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Kaidong Liu
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, China
| | - Bingxiong Huang
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yuerong Wei
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization (Ministry of Agriculture and Rural Affairs), Guangdong Province Key Laboratory of Tropical and Subtropical Fruit Tree Research, Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China
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Genomic Analysis of LEA Genes in Carica papaya and Insight into Lineage-Specific Family Evolution in Brassicales. Life (Basel) 2022; 12:life12091453. [PMID: 36143489 PMCID: PMC9502557 DOI: 10.3390/life12091453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/08/2022] [Accepted: 09/15/2022] [Indexed: 11/21/2022] Open
Abstract
Late embryogenesis abundant (LEA) proteins comprise a diverse superfamily involved in plant development and stress responses. This study presents a first genome-wide analysis of LEA genes in papaya (Carica papaya L., Caricaceae), an economically important tree fruit crop widely cultivated in the tropics and subtropics. A total of 28 members were identified from the papaya genome, which belong to eight families with defined Pfam domains, i.e., LEA_1 (3), LEA_2 (4), LEA_3 (5), LEA_4 (5), LEA_5 (2), LEA_6 (2), DHN (4), and SMP (3). The family numbers are comparable to those present in Ricinus communis (Euphorbiaceae, 28) and Moringa oleifera (Moringaceae, 29), but relatively less than that found in Moringa oleifera (Cleomaceae, 39) and Arabidopsis thaliana (Brassicaceae, 51), implying lineage-specific evolution in Brassicales. Indeed, best-reciprocal-hit-based sequence comparison and synteny analysis revealed the presence of 29 orthogroups, and significant gene expansion in Tarenaya and Arabidopsis was mainly contributed by whole-genome duplications that occurred sometime after their split with the papaya. Though a role of transposed duplication was also observed, tandem duplication was shown to be a key contributor in gene expansion of most species examined. Further comparative analyses of exon-intron structures and protein motifs supported fast evolution of this special superfamily, especially in Arabidopsis. Transcriptional profiling revealed diverse expression patterns of CpLEA genes over various tissues and different stages of developmental fruit. Moreover, the transcript level of most genes appeared to be significantly regulated by drought, cold, and salt stresses, corresponding to the presence of cis-acting elements associated with stress response in their promoter regions. These findings not only improve our knowledge on lineage-specific family evolution in Brassicales, but also provide valuable information for further functional analysis of LEA genes in papaya.
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