1
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Dai Z, Guan J, Miao H, Beckles DM, Liu X, Gu X, Dong S, Zhang S. An intronic SNP in the Carotenoid Cleavage Dioxygenase 1 (CsCCD1) controls yellow flesh formation in cucumber fruit (Cucumis sativus L.). PLANT BIOTECHNOLOGY JOURNAL 2025; 23:2182-2193. [PMID: 40095761 PMCID: PMC12120889 DOI: 10.1111/pbi.70034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2024] [Revised: 01/09/2025] [Accepted: 02/04/2025] [Indexed: 03/19/2025]
Abstract
Vitamin A is a crucial yet scarce vitamin essential for maintaining normal metabolism and bodily functions in humans and can only be obtained from food. Carotenoids represent a diverse group of functional pigments that act as precursors for vitamins, hormones, aroma volatiles and antioxidants. As a vital vegetable in the world, elevated carotenoid levels in cucumber fruit produce yellow flesh, enhancing both visual appeal and nutritional value. However, the genetic mechanisms and regulatory networks governing yellow flesh in cucumbers remain inadequately characterized. In this study, we employed map-based cloning to identify a Carotenoid Cleavage Dioxygenase 1 (CsCCD1) as a key genetic factor influencing yellow flesh in cucumbers. A causal single nucleotide polymorphism (SNP) in the eighth intron of CsCCD1 led to aberrant splicing, resulting in a truncated transcript. The truncated protein has significantly decreased enzyme activity and increased carotenoid accumulation in the fruit. CRISPR/Cas9-generated CsCCD1 knockout mutants exhibited yellow flesh and significantly higher carotenoid content compared to wild-type cucumbers. Metabolic profiling indicated a marked accumulation of β-cryptoxanthin in the flesh of these knockout mutants. The intronic SNP was shown to perfectly segregate with yellow flesh in 159 diverse cucumber germplasms, particularly within the semi-wild ecotype Xishuangbanna, known for its substantial carotenoid accumulation. Furthermore, transient overexpression of CsCCD1 in yellow-fleshed Xishuangbanna cucumbers restored a white flesh phenotype, underscoring the critical role of CsCCD1 in determining flesh colour in both cultivated and semi-wild cucumbers. These findings lay a theoretical foundation for breeding high-nutrient yellow-fleshed cucumber varieties.
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Affiliation(s)
- Zhuonan Dai
- State Key Laboratory of Vegetable BiobreedingInstitute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijingChina
| | - Jiantao Guan
- State Key Laboratory of Vegetable BiobreedingInstitute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijingChina
| | - Han Miao
- State Key Laboratory of Vegetable BiobreedingInstitute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijingChina
| | | | - Xiaoping Liu
- State Key Laboratory of Vegetable BiobreedingInstitute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijingChina
| | - Xingfang Gu
- State Key Laboratory of Vegetable BiobreedingInstitute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijingChina
| | - Shaoyun Dong
- State Key Laboratory of Vegetable BiobreedingInstitute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijingChina
| | - Shengping Zhang
- State Key Laboratory of Vegetable BiobreedingInstitute of Vegetables and Flowers, Chinese Academy of Agricultural SciencesBeijingChina
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2
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Joshi S, Mohapatra S, Kumar D, Joshi A, Iyer M, Sowdhamini R. GenDiS3 database: census on the prevalence of protein domain superfamilies of known structure in the entire sequence database. Database (Oxford) 2025; 2025:baaf035. [PMID: 40343712 PMCID: PMC12063530 DOI: 10.1093/database/baaf035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2024] [Revised: 01/08/2025] [Accepted: 04/09/2025] [Indexed: 05/11/2025]
Abstract
Despite the vast amount of sequence data available, a significant disparity exists between the number of protein sequences identified and the relatively few structures that have been resolved. This disparity highlights the challenge in structural biology to bridge the gap between sequence information and 3D structural data, and the necessity for robust databases capable of linking distant homologs to known structures. Studies have indicated that there are a limited number of structural folds, despite the vast diversity of proteins. Hence, computational tools can enhance our ability to classify protein sequences, much before their structures are determined or their functions are characterized, thereby bridging the gap between sequence and structural data. GenDiS (Genomic Distribution of Superfamilies) is a repository with information on the genomic distribution of protein domain superfamilies, involving a one-time computational exercise to search for trusted homologs of protein domains of known structures against the vast sequence database. We have updated this database employing advanced bioinformatics tools, including DELTA-BLAST (domain enhanced lookup time accelerated BLAST) for initial detection of hits and HMMSCAN for validation, significantly improving the accuracy of domain identification. Using these tools, over 151 million sequence homologs for 2060 superfamilies [SCOPe (Structural Classification of Proteins extended)] were identified and 116 million out of them were validated as true positives. Through a case study on glycolysis-related enzymes, variations in domain architectures of these enzymes are explored, revealing evolutionary changes and functional diversity among these essential proteins. We present another case, LOG gene, where one can tune in and find significant mutations across the evolutionary lineage. The GenDiS database, GenDiS3, and the associated tools made available at https://caps.ncbs.res.in/gendis3/ offer a powerful resource for researchers in functional annotation and evolutionary studies. Database URL: https://caps.ncbs.res.in/gendis3/.
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Affiliation(s)
- Sarthak Joshi
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore 560065, India
| | - Shailendu Mohapatra
- Computational Biology, Insitute of Bioinformatics and Applied Biotechnology, Bangalore 560100, India
| | - Dhwani Kumar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore 560065, India
| | - Adwait Joshi
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore 560065, India
| | - Meenakshi Iyer
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore 560065, India
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bellary Road, Bangalore 560065, India
- Computational Biology, Insitute of Bioinformatics and Applied Biotechnology, Bangalore 560100, India
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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van Beveren F, Boele Y, Puginier C, Bianconi ME, Libourel C, Bonhomme M, Keller J, Delaux P. Ectomycorrhizal symbiosis evolved independently and by convergent gene duplication in rosid lineages. THE NEW PHYTOLOGIST 2025; 246:1432-1438. [PMID: 40065498 PMCID: PMC12018775 DOI: 10.1111/nph.70054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2025] [Accepted: 02/14/2025] [Indexed: 04/25/2025]
Affiliation(s)
- Fabian van Beveren
- Laboratoire de Recherche en Sciences Végétales (LRSV)Université de Toulouse, CNRS, UPS, INPToulouseCastanet‐Tolosan31320France
| | - Yvet Boele
- Laboratory of Cell and Developmental BiologyWageningen UniversityDroevendaalsesteeg 1WageningenPBthe Netherlands
- Department of Terrestrial EcologyNetherlands Institute of Ecology (NIOO‐KNAW)Droevendaalsesteeg 10WageningenPB6708the Netherlands
| | - Camille Puginier
- Laboratoire de Recherche en Sciences Végétales (LRSV)Université de Toulouse, CNRS, UPS, INPToulouseCastanet‐Tolosan31320France
| | - Matheus E. Bianconi
- Laboratoire de Recherche en Sciences Végétales (LRSV)Université de Toulouse, CNRS, UPS, INPToulouseCastanet‐Tolosan31320France
| | - Cyril Libourel
- Laboratoire de Recherche en Sciences Végétales (LRSV)Université de Toulouse, CNRS, UPS, INPToulouseCastanet‐Tolosan31320France
| | - Maxime Bonhomme
- Laboratoire de Recherche en Sciences Végétales (LRSV)Université de Toulouse, CNRS, UPS, INPToulouseCastanet‐Tolosan31320France
| | - Jean Keller
- Laboratoire de Recherche en Sciences Végétales (LRSV)Université de Toulouse, CNRS, UPS, INPToulouseCastanet‐Tolosan31320France
| | - Pierre‐Marc Delaux
- Laboratoire de Recherche en Sciences Végétales (LRSV)Université de Toulouse, CNRS, UPS, INPToulouseCastanet‐Tolosan31320France
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4
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Benoit M, Jenike KM, Satterlee JW, Ramakrishnan S, Gentile I, Hendelman A, Passalacqua MJ, Suresh H, Shohat H, Robitaille GM, Fitzgerald B, Alonge M, Wang X, Santos R, He J, Ou S, Golan H, Green Y, Swartwood K, Karavolias NG, Sierra GP, Orejuela A, Roda F, Goodwin S, McCombie WR, Kizito EB, Gagnon E, Knapp S, Särkinen TE, Frary A, Gillis J, Van Eck J, Schatz MC, Lippman ZB. Solanum pan-genetics reveals paralogues as contingencies in crop engineering. Nature 2025; 640:135-145. [PMID: 40044854 PMCID: PMC11964936 DOI: 10.1038/s41586-025-08619-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2024] [Accepted: 01/09/2025] [Indexed: 03/30/2025]
Abstract
Pan-genomics and genome-editing technologies are revolutionizing breeding of global crops1,2. A transformative opportunity lies in exchanging genotype-to-phenotype knowledge between major crops (that is, those cultivated globally) and indigenous crops (that is, those locally cultivated within a circumscribed area)3-5 to enhance our food system. However, species-specific genetic variants and their interactions with desirable natural or engineered mutations pose barriers to achieving predictable phenotypic effects, even between related crops6,7. Here, by establishing a pan-genome of the crop-rich genus Solanum8 and integrating functional genomics and pan-genetics, we show that gene duplication and subsequent paralogue diversification are major obstacles to genotype-to-phenotype predictability. Despite broad conservation of gene macrosynteny among chromosome-scale references for 22 species, including 13 indigenous crops, thousands of gene duplications, particularly within key domestication gene families, exhibited dynamic trajectories in sequence, expression and function. By augmenting our pan-genome with African eggplant cultivars9 and applying quantitative genetics and genome editing, we dissected an intricate history of paralogue evolution affecting fruit size. The loss of a redundant paralogue of the classical fruit size regulator CLAVATA3 (CLV3)10,11 was compensated by a lineage-specific tandem duplication. Subsequent pseudogenization of the derived copy, followed by a large cultivar-specific deletion, created a single fused CLV3 allele that modulates fruit organ number alongside an enzymatic gene controlling the same trait. Our findings demonstrate that paralogue diversifications over short timescales are underexplored contingencies in trait evolvability. Exposing and navigating these contingencies is crucial for translating genotype-to-phenotype relationships across species.
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Affiliation(s)
- Matthias Benoit
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Katharine M Jenike
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - James W Satterlee
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Iacopo Gentile
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Anat Hendelman
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Michael J Passalacqua
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Hamsini Suresh
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Hagai Shohat
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Gina M Robitaille
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Blaine Fitzgerald
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Michael Alonge
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Ohalo Genetics, Aptos, CA, USA
| | - Xingang Wang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Ohalo Genetics, Aptos, CA, USA
| | - Ryan Santos
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Verve Therapeutics, Boston, MA, USA
| | - Jia He
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Shujun Ou
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
- Department of Molecular Genetics, Ohio State University, Columbus, OH, USA
| | | | - Yumi Green
- Boyce Thompson Institute, Ithaca, NY, USA
| | | | - Nicholas G Karavolias
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Gina P Sierra
- Max Planck Tandem Group, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Andres Orejuela
- Departamento de Biología, Facultad de Ciencias Exactas y Naturales, Universidad de Cartagena, Cartagena de Indias, Colombia
| | - Federico Roda
- Max Planck Tandem Group, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Elizabeth B Kizito
- Faculty of Agricultural Sciences, Uganda Christian University, Mukono, Uganda
| | - Edeline Gagnon
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
- Royal Botanic Garden Edinburgh, Edinburgh, UK
- School of Life Sciences, Technical University of Munich, Freising, Germany
| | | | | | - Amy Frary
- Department of Biological Sciences, Mount Holyoke College, South Hadley, MA, USA
| | - Jesse Gillis
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
- Physiology Department and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
| | - Joyce Van Eck
- Boyce Thompson Institute, Ithaca, NY, USA.
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.
| | - Michael C Schatz
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA.
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
| | - Zachary B Lippman
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
- School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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5
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Knapp S, Gouvêa YF, Giacomin LL. A revision of the endemic Brazilian Solanumhexandrum group (Leptostemonum, Solanum, Solanaceae). PHYTOKEYS 2025; 253:199-259. [PMID: 40115195 PMCID: PMC11923794 DOI: 10.3897/phytokeys.253.138216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2024] [Accepted: 02/09/2025] [Indexed: 03/23/2025]
Abstract
The Leptostemonum Clade, or the 'spiny solanums', represents half of the species diversity of the large cosmopolitan genus Solanum (Solanaceae). Brazil is a centre of both species and lineage diversity in 'spiny solanums' with a number of lineages occurring mostly only there. Here, we treat the Solanumhexandrum group, a monophyletic species group that is part of the larger and unresolved Erythrotrichum clade sensu lato. The six species treated here are all robust very prickly shrubs with amongst the largest and showiest flowers in Solanum and accrescent calyces in fruit that often completely cover the mature berry. All six species are endemic to the coastal Atlantic forests of south-eastern and north-eastern Brazil. We describe one new species, S.phrixothrix Gouvêa & S.Knapp, sp. nov., known only from two collections made 200 years apart. Many of the species in the group occur in very small populations around isolated gneissic/granitic inselbergs, a highly threatened habitat in the region. We provide complete nomenclatural details for all recognised species and their synonyms, complete descriptions, distributions including maps, illustrations, common names and uses and preliminary conservation assessments.
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Affiliation(s)
- Sandra Knapp
- Natural History Museum, Cromwell Road, London SW7 5BD, UK Natural History Museum London United Kingdom
| | - Yuri F Gouvêa
- Departamento de Botânica, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos 6627, Belo Horizonte 31270-901, MG, Brazil Universidade Federal de Minas Gerais Belo Horizonte Brazil
| | - Leandro L Giacomin
- Departamento de Sistemática & Ecologia, Centro de Ciências Exatas e da Natureza, Universidade Federal da Paraíba, Cidade Universitária, João Pessoa, PB, 58051-0900, Brazil Universidade Federal da Paraíba João Pessoa Brazil
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6
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Zhang L, Liu Y, Huang Y, Zhang Y, Fu Y, Xiao Y, Chen S, Zhang K, Cheng F. Solanaceae pan-genomes reveal extensive fractionation and functional innovation of duplicated genes. PLANT COMMUNICATIONS 2025; 6:101231. [PMID: 39719828 PMCID: PMC11956106 DOI: 10.1016/j.xplc.2024.101231] [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: 09/13/2024] [Revised: 11/24/2024] [Accepted: 12/21/2024] [Indexed: 12/26/2024]
Abstract
The Solanaceae family contains many agriculturally important crops, including tomato, potato, pepper, and tobacco, as well as other species with potential for agricultural development, such as the orphan crops groundcherry, wolfberry, and pepino. Research progress varies greatly among these species, with model crops like tomato being far ahead. This disparity limits the broader agricultural application of other Solanaceae species. In this study, we constructed an interspecies pan-genome for the Solanaceae family and identified various gene retention patterns. Our findings reveal that the activity of specific transposable elements is closely associated with gene fractionation and transposition. The pan-genome was further resolved at the level of T subgenomes, which were generated by Solanaceae-specific paleo-hexaploidization (T event). We demonstrate substantial gene fractionation (loss) and divergence events following ancient duplications. For example, all class A and E flower model genes in Solanaceae originated from two tandemly duplicated genes, which expanded through the γ and T events before fractionating into 10 genes in tomato, each acquiring distinct functions critical for fruit development. Based on these results, we developed the Solanaceae Pan-Genome Database (SolPGD, http://www.bioinformaticslab.cn/SolPGD), which integrates datasets from both inter- and intra-species pan-genomes of Solanaceae. These findings and resources will facilitate future studies of solanaceous species, including orphan crops.
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Affiliation(s)
- Lingkui Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuanhang Liu
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yile Huang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China; College of Horticulture, Henan Agricultural University, Zhengzhou, China
| | - Yiyue Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yu Fu
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China; College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Ya Xiao
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China; Biotechnology Research Center, Xiangxi Academy of Agricultural Sciences, Hunan 416000, China
| | - Shumin Chen
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kang Zhang
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Feng Cheng
- State Key Laboratory of Vegetable Biobreeding, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
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7
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He W, Li X, Qian Q, Shang L. The developments and prospects of plant super-pangenomes: Demands, approaches, and applications. PLANT COMMUNICATIONS 2025; 6:101230. [PMID: 39722458 PMCID: PMC11897476 DOI: 10.1016/j.xplc.2024.101230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2024] [Revised: 12/04/2024] [Accepted: 12/20/2024] [Indexed: 12/28/2024]
Abstract
By integrating genomes from different accessions, pangenomes provide a more comprehensive and reference-bias-free representation of genetic information within a population compared to a single reference genome. With the rapid accumulation of genomic sequencing data and the expanding scope of plant research, plant pangenomics has gradually evolved from single-species to multi-species studies. This shift has given rise to the concept of a super-pangenome that covers all genomic sequences within a genus-level taxonomic group. By incorporating both cultivated and wild species, the super-pangenome has greatly enhanced the resolution of research in various areas such as plant genetic diversity, evolution, domestication, and molecular breeding. In this review, we present a comprehensive overview of the plant super-pangenome, emphasizing its development requirements, construction strategies, potential applications, and notable achievements. We also highlight the distinctive advantages and promising prospects of super-pangenomes while addressing current challenges and future directions.
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Affiliation(s)
- Wenchuang He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - XiaoXia Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Qian Qian
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; Yazhouwan National Laboratory, Sanya 572024, China; State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China; Academician Workstation, National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China.
| | - Lianguang Shang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; Yazhouwan National Laboratory, Sanya 572024, China; Academician Workstation, National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China.
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8
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Liu W, Xu W, Gao Y, Qi X, Liu F, Wang J, Li L, Zhou Y, Chen W, Jiang Y, Cui J, Wang Y, Wang QM. The role of the sucrose synthase gene in promoting thorn occurrence and vegetative growth in Lycium ruthenicum. PLANT MOLECULAR BIOLOGY 2025; 115:30. [PMID: 39918761 DOI: 10.1007/s11103-025-01560-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2024] [Accepted: 01/21/2025] [Indexed: 02/09/2025]
Abstract
Lycium ruthenicum is a highly valued ecological and economic shrub, but its abundant thorns disrupt production processes. Previous studies suggested that the sucrose synthase gene (LrSUS) in L. ruthenicum may influence thorn occurrence, presenting potential for breeding thornless varieties suited for cultivation. To explore this, the full-length CDS of LrSUS was cloned, and a novel stable genetic transformation system mediated by Agrobacterium tumefaciens was developed. Through this system, both LrSUS overexpression and suppression lines were generated. While suppression lines exhibited slow growth and failed to survive post-transplant, overexpression lines demonstrated accelerated growth, with significant increases in adventitious root number and length. Upon transplanting, the overexpression lines also showed enhanced thorn occurrence, alongside notable increases in thorn length, leaf size, stem diameter, photosynthetic rate, and sugar content. Subcellular localization analysis using a transient expression method based on the injection of L. ruthenicum indicated that the LrSUS gene product is localized in the chloroplasts. Key genes involved in LrSUS/ sucrose affecting thorn occurrence event were identified through high throughput transcriptome analysis and a hypothetical mechanistic model was established. This study provides valuable insights into the function of LrSUS and establishes a foundation for manipulating thorn phenotypes in L. ruthenicum and related species.
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Affiliation(s)
- Wenhui Liu
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, China
| | - Weiman Xu
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yue Gao
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, China
| | - Xinyu Qi
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, China
| | - Fuqiang Liu
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, China
| | - Jiawen Wang
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, China
| | - Lujia Li
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yuliang Zhou
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, China
| | - Wenxin Chen
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yingyue Jiang
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, China
| | - Jianguo Cui
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yucheng Wang
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, China
| | - Qin-Mei Wang
- Key Laboratory of Forest Tree Genetics, Breeding and Cultivation of Liaoning Province, College of Forestry, Shenyang Agricultural University, Shenyang, 110866, China.
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Wright ES. Tandem Repeats Provide Evidence for Convergent Evolution to Similar Protein Structures. Genome Biol Evol 2025; 17:evaf013. [PMID: 39852593 PMCID: PMC11812678 DOI: 10.1093/gbe/evaf013] [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: 12/16/2024] [Accepted: 01/17/2025] [Indexed: 01/26/2025] Open
Abstract
Homology is a key concept underpinning the comparison of sequences across organisms. Sequence-level homology is based on a statistical framework optimized over decades of work. Recently, computational protein structure prediction has enabled large-scale homology inference beyond the limits of accurate sequence alignment. In this regime, it is possible to observe nearly identical protein structures lacking detectable sequence similarity. In the absence of a robust statistical framework for structure comparison, it is largely assumed similar structures are homologous. However, it is conceivable that matching structures could arise through convergent evolution, resulting in analogous proteins without shared ancestry. Large databases of predicted structures offer a means of determining whether analogs are present among structure matches. Here, I find that a small subset (∼2.6%) of Foldseek clusters lack sequence-level support for homology, including ∼1% of strong structure matches with template modeling score ≥ 0.5. This result by itself does not imply these structure pairs are nonhomologous, since their sequences could have diverged beyond the limits of recognition. Yet, strong matches without sequence-level support for homology are enriched in structures with predicted repeats that could induce spurious matches. Some of these structural repeats are underpinned by sequence-level tandem repeats in both matching structures. I show that many of these tandem repeat units have genealogies inconsistent with their corresponding structures sharing a common ancestor, implying these highly similar structure pairs are analogous rather than homologous. This result suggests caution is warranted when inferring homology from structural resemblance alone in the absence of sequence-level support for homology.
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Affiliation(s)
- Erik S Wright
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA 15219, USA
- Center for Evolutionary Biology and Medicine, Pittsburgh, PA 15219, USA
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10
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Whiteman NK. Insect herbivory: An inordinate fondness for plant cell wall degrading enzymes. Curr Biol 2025; 35:R107-R109. [PMID: 39904308 DOI: 10.1016/j.cub.2024.12.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2025]
Abstract
Tens of thousands of species of leaf beetles rely on plant cell wall degrading enzymes in order to make the most of nutritionally depauperate plant tissues. Many of the genes encoding these enzymes were acquired from microbial donors, either through horizontal gene transfer or by hosting microbial endosymbionts. A new study explores how these insects have leveraged this metabolic potential to diversify and expand into new niches.
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Affiliation(s)
- Noah K Whiteman
- Department of Integrative Biology, Department of Molecular and Cell Biology, University of California, Berkeley, CA 94618, USA.
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11
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Omondi E, Barchi L, Gaccione L, Portis E, Toppino L, Tassone MR, Alonso D, Prohens J, Rotino GL, Schafleitner R, van Zonneveld M, Giuliano G. Association analyses reveal both anthropic and environmental selective events during eggplant domestication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2025; 121:e17229. [PMID: 39918113 PMCID: PMC11803709 DOI: 10.1111/tpj.17229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Revised: 11/25/2024] [Accepted: 12/16/2024] [Indexed: 02/11/2025]
Abstract
Eggplant (Solanum melongena) is one of the four most important Solanaceous crops, widely cultivated and consumed in Asia, the Mediterranean basin, and Southeast Europe. We studied the genome-wide association of historical genebank phenotypic data on a genotyped worldwide collection of 3449 eggplant accessions. Overall, 334 significant associations for key agronomic traits were detected. Significant correlations were obtained between different types of phenotypic data, some of which were not obvious, such as between fruit size/yield and fruit color components, suggesting simultaneous anthropic selection for genetically unrelated traits. Anthropic selection of traits like leaf prickles, fruit color, and yield, acted on distinct genomic regions in the two domestication centers (India and Southeast Asia), further confirming the multiple domestication of eggplant. To discriminate anthropic from environmental selection in domestication centers, we conducted a genotype-environment association (GEA) on a subset of georeferenced accessions from the Indian subcontinent. The population structure in this area revealed four genetic clusters, corresponding to a latitudinal gradient, and environmental factors explained 31% of the population structure when the effect of spatial distances was removed. GEA and outlier association identified 305 candidate regions under environmental selection, containing genes for abiotic stress responses, plant development, and flowering transition. Finally, in the Indian domestication center anthropic and environmental selection acted largely independently, and on different genomic regions. These data allow a better understanding of the different effects of environmental and anthropic selection during domestication of a crop, and the different world regions where some traits were initially selected by humans.
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Affiliation(s)
| | - Lorenzo Barchi
- DISAFA – Plant GeneticsUniversity of TurinGrugliascoTO10095Italy
| | - Luciana Gaccione
- DISAFA – Plant GeneticsUniversity of TurinGrugliascoTO10095Italy
| | - Ezio Portis
- DISAFA – Plant GeneticsUniversity of TurinGrugliascoTO10095Italy
| | - Laura Toppino
- CREA Research Centre for Genomics and BioinformaticsVia Paullese 28Montanaso LombardoLO26836Italy
| | - Maria Rosaria Tassone
- CREA Research Centre for Genomics and BioinformaticsVia Paullese 28Montanaso LombardoLO26836Italy
| | - David Alonso
- Universitat Politècnica de ValènciaCamino de Vera 1446022ValenciaSpain
| | - Jaime Prohens
- Universitat Politècnica de ValènciaCamino de Vera 1446022ValenciaSpain
| | - Giuseppe Leonardo Rotino
- CREA Research Centre for Genomics and BioinformaticsVia Paullese 28Montanaso LombardoLO26836Italy
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12
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Figueiredo YG, Gasparini K, Bulut M, Fernie AR, Zsögön A. The genetic basis of prickle loss in the Solanaceae. TRENDS IN PLANT SCIENCE 2025; 30:119-121. [PMID: 39389892 DOI: 10.1016/j.tplants.2024.09.016] [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: 08/02/2024] [Revised: 09/24/2024] [Accepted: 09/24/2024] [Indexed: 10/12/2024]
Abstract
In a recent study, Satterlee et al. found that the repeated emergence of prickleless varieties in Solanaceae species is a convergent trait caused by loss of function in the cytokinin-activating enzyme LONELY GUY (LOG). New prickleless forms can be created in wild and domesticated forms using gene editing.
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Affiliation(s)
- Yuri G Figueiredo
- National Institute of Science and Technology on Plant Physiology Under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil
| | - Karla Gasparini
- National Institute of Science and Technology on Plant Physiology Under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil
| | - Mustafa Bulut
- Max-Planck-Institute for Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Alisdair R Fernie
- Max-Planck-Institute for Molecular Plant Physiology, 14476 Potsdam, Germany
| | - Agustin Zsögön
- National Institute of Science and Technology on Plant Physiology Under Stress Conditions, Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900, Viçosa, MG, Brazil.
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13
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Feng H, Fan W, Liu M, Huang J, Li B, Sang Q, Song B. Cross-species single-nucleus analysis reveals the potential role of whole-genome duplication in the evolution of maize flower development. BMC Genomics 2025; 26:3. [PMID: 39754060 PMCID: PMC11699695 DOI: 10.1186/s12864-024-11186-1] [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: 09/21/2024] [Accepted: 12/26/2024] [Indexed: 01/06/2025] Open
Abstract
BACKGROUND The evolution and development of flowers are biologically essential and of broad interest. Maize and sorghum have similar morphologies and phylogeny while harboring different inflorescence architecture. The difference in flower architecture between these two species is likely due to spatiotemporal gene expression regulation, and they are a good model for researching the evolution of flower development. RESULTS In this study, we generated single nucleus and spatial RNA-seq data for maize ear, tassel, and sorghum inflorescence. By combining single nucleus and spatial transcriptome, we can track the spatial expression of single nucleus cluster marker genes and map single nucleus clusters to spatial positions. This ability provides great power to annotate the single nucleus clusters. Combining the cell cluster resolved transcriptome comparison with genome alignment, our analysis suggested that maize ear and tassel inflorescence diversity is associated with the maize-specific whole genome duplication. Taking sorghum as the outgroup, it is likely that the loss of gene expression profiling contributes to the inflorescence diversity between tassel and ear, resulting in the unisexual flower architecture of maize. The sequence of highly expressed genes in the tassel is more conserved than the highly expressed genes in the ear. CONCLUSION This study provides a high-resolution atlas of gene activity during inflorescence development and helps to unravel the potential evolution associated with the differentiation of the ear and tassel in maize.
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Affiliation(s)
- Huawei Feng
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Wenjuan Fan
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Min Liu
- Baimaike Intelligent Manufacturing, Qingdao, Shandong, 266500, China
| | - Jiaqian Huang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
- Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Bosheng Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China
| | - Qing Sang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China.
| | - Baoxing Song
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong, 261325, China.
- Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region, Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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14
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Han Y. Decoding the genetic basis of secretory tissues in plants. HORTICULTURE RESEARCH 2025; 12:uhae263. [PMID: 39802735 PMCID: PMC11718388 DOI: 10.1093/hr/uhae263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2024] [Accepted: 09/08/2024] [Indexed: 01/16/2025]
Abstract
Although plant secretory tissues play important roles in host defense against herbivores and pathogens and the attraction of insect pollinators, their genetic control remains elusive. Here, it is focused that current progress has been made in the genetic regulatory mechanisms underpinning secretory tissue development in land plants. C1HDZ transcription factors (TFs) are found to play crucial roles in the regulation of internal secretory tissues in liverworts and Citrus as well as external secretory tissues in peach. C1HDZ TFs regulate secretory tissue development via synergistic interaction with AP2/ERF and MYC TFs. Thus, a set of genes are speculated to be recruited convergently for the formation of secretory tissues in land plants.
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Affiliation(s)
- Yuepeng Han
- State Key Laboratory of Plant Diversity and Specialty Crops, Wuhan Botanical Garden of Chinese Academy of Sciences, Wuhan 430074, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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15
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Zhang Z, Yang T, Liu Y, Wu S, Sun H, Wu J, Li Y, Zheng Y, Ren H, Yang Y, Shi S, Wang W, Pan Q, Lian L, Duan S, Zhu Y, Cai Y, Zhou H, Zhang H, Tang K, Cui J, Gao D, Chen L, Jiang Y, Sun X, Zhou X, Fei Z, Ma N, Gao J. Haplotype-resolved genome assembly and resequencing provide insights into the origin and breeding of modern rose. NATURE PLANTS 2024; 10:1659-1671. [PMID: 39394508 DOI: 10.1038/s41477-024-01820-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 09/13/2024] [Indexed: 10/13/2024]
Abstract
Modern rose (Rosa hybrida) is a recently formed interspecific hybrid and has become one of the most important and widely cultivated ornamentals. Here we report the haplotype-resolved chromosome-scale genome assembly of the tetraploid R. hybrida 'Samantha' ('JACmantha') and a genome variation map of 233 Rosa accessions involving various wild species, and old and modern cultivars. Homologous chromosomes of 'Samantha' exhibit frequent homoeologous exchanges. Population genomic and genomic composition analyses reveal the contributions of wild Rosa species to modern roses and highlight that R. odorata and its derived cultivars are important contributors to modern roses, much like R. chinensis 'Old Blush'. Furthermore, selective sweeps during modern rose breeding associated with major agronomic traits, including continuous and recurrent flowering, double flower, flower senescence and disease resistance, are identified. This study provides insights into the genetic basis of modern rose origin and breeding history, and offers unprecedented genomic resources for rose improvement.
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Affiliation(s)
- Zhao Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China
| | - Tuo Yang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China
| | - Yang Liu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China
| | - Shan Wu
- Boyce Thompson Institute, Ithaca, NY, USA
| | - Honghe Sun
- Boyce Thompson Institute, Ithaca, NY, USA
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
| | - Jie Wu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China
| | - Yonghong Li
- School of Food and Drug, Shenzhen Polytechnic University, Shenzhen, Guangdong, China
| | - Yi Zheng
- Bioinformatics Center, Beijing University of Agriculture, Beijing, China
- College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Haoran Ren
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China
| | - Yuyong Yang
- Kunming Yang Chinese Rose Gardening Co. Ltd., Kunming, Yunnan, China
| | - Shaochuan Shi
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China
| | - Wenyan Wang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China
| | - Qi Pan
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China
| | - Lijuan Lian
- People's Government of Weishanzhuang Town, Daxing, Beijing, China
| | | | - Yingxiong Zhu
- Yunnan Xinhaihui Flower Industry Co. Ltd., Tonghai, Yunnan, China
| | - Youming Cai
- Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Hougao Zhou
- College Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China
| | - Hao Zhang
- National Engineering Research Center for Ornamental Horticulture, Flower Research Institute of Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Kaixue Tang
- National Engineering Research Center for Ornamental Horticulture, Flower Research Institute of Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | | | - Dan Gao
- Smartgenomics Technology Institute, Tianjin, China
| | - Liyang Chen
- Smartgenomics Technology Institute, Tianjin, China
| | - Yunhe Jiang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China
| | - Xiaoming Sun
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China
| | - Xiaofeng Zhou
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China
| | - Zhangjun Fei
- Boyce Thompson Institute, Ithaca, NY, USA.
- USDA-ARS Robert W Holley Center for Agriculture and Health, Ithaca, NY, USA.
| | - Nan Ma
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China.
| | - Junping Gao
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, China.
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16
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Zhao C, Yin H, Li Y, Zhou J, Bi S, Yan W, Li Y. Evolutionary Analysis and Catalytic Function of LOG Proteins in Plants. Genes (Basel) 2024; 15:1420. [PMID: 39596620 PMCID: PMC11593424 DOI: 10.3390/genes15111420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2024] [Revised: 10/21/2024] [Accepted: 10/30/2024] [Indexed: 11/29/2024] Open
Abstract
BACKGROUND The plant hormone cytokinin is a conserved regulator of plant development. LONELY GUY (LOG) proteins are pivotal in cytokinin biosynthesis. However, their origin, evolutionary history, and enzymatic characteristics remain largely uncharacterized. METHODS To elucidate LOG family evolution history and protein motif composition, we conducted phylogenetic and motif analyses encompassing representative species across the whole green plant lineage. Catalytic activity and structure analysis were conducted to thoroughly characterize the LOG proteins. RESULTS Our phylogeny showed that LOG proteins could be divided into five groups and revealed three major duplication events giving rise to four distinct groups of vascular LOG proteins. LOG proteins share a conserved structure characterized by a canonical motif arrangement comprising motifs 1, 2, 3, 4, 5, 6, and 7. Two significant changes in LOG motif composition occurred during the transition to land plants: the emergence of motif 3 in charophyte LOG sequences and the subsequent acquisition of motif 8 at the C-terminus of LOG proteins. Enzymatic assays demonstrated that LOG proteins can be classified into two groups based on their enzyme activity. One group act as cytokinin riboside 5'-monophosphate phosphoribohydrolase and primarily convert iPRMP to iP, while the other group act as 5'-ribonucleotide phosphohydrolase, and preferentially produce iPR from the same substrates. TaLOG5-4A1, TaLOG5-4A2, TaLOG5-5B2, and TaLOG5-D1 shared conserved residues in the critical motif and were predicted to have similar protein structures, but displayed distinct enzymatic activities. CONCLUSIONS Our findings provide a comprehensive overview of LOG protein phylogeny and lay a foundation for further investigations into their functional diversification.
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Affiliation(s)
| | | | | | | | | | | | - Yunzhen Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
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17
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Isko EC, Harpole CE, Zheng XM, Zhan H, Davis MB, Zador AM, Banerjee A. Selective expansion of motor cortical projections in the evolution of vocal novelty. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.13.612752. [PMID: 39484467 PMCID: PMC11526862 DOI: 10.1101/2024.09.13.612752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/03/2024]
Abstract
Deciphering how cortical architecture evolves to drive behavioral innovations is a long-standing challenge in neuroscience and evolutionary biology. Here, we leverage a striking behavioral novelty in the Alston's singing mouse (Scotinomys teguina), compared to the laboratory mouse (Mus musculus), to quantitatively test models of motor cortical evolution. We used bulk tracing, serial two-photon tomography, and high-throughput DNA sequencing of over 76,000 barcoded neurons to discover a specific and substantial expansion (200%) of orofacial motor cortical (OMC) projections to the auditory cortical region (AudR) and the midbrain periaqueductal gray (PAG), both implicated in vocal behaviors. Moreover, analysis of individual OMC neurons' projection motifs revealed preferential expansion of exclusive projections to AudR. Our results imply that selective expansion of ancestral motor cortical projections can underlie behavioral divergence over short evolutionary timescales, suggesting potential mechanisms for the evolution of enhanced cortical control over vocalizations-a crucial preadaptation for human language.
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Affiliation(s)
- Emily C Isko
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
- Cold Spring Harbor Laboratory School for Biological Sciences, Cold Spring Harbor, NY
| | | | - Xiaoyue Mike Zheng
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
- Cold Spring Harbor Laboratory School for Biological Sciences, Cold Spring Harbor, NY
| | - Huiqing Zhan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
| | | | - Anthony M Zador
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
- Cold Spring Harbor Laboratory School for Biological Sciences, Cold Spring Harbor, NY
| | - Arkarup Banerjee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
- Cold Spring Harbor Laboratory School for Biological Sciences, Cold Spring Harbor, NY
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18
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Ertl H. Convergent evolution of prickles across crops. Nat Rev Genet 2024; 25:676. [PMID: 39174811 DOI: 10.1038/s41576-024-00771-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2024]
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