1
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Li Y, Brown SE, Li Y, Cheng Q, Wu H, Wei S, Li X, Lin C, Liu Z, Mao Z. Profiles of phenolics and their synthetic pathways in Asparagus officinalis L. FOOD CHEMISTRY. MOLECULAR SCIENCES 2024; 8:100187. [PMID: 38186632 PMCID: PMC10767369 DOI: 10.1016/j.fochms.2023.100187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/30/2023] [Accepted: 12/09/2023] [Indexed: 01/09/2024]
Abstract
The synthetic pathways of some phenolics compounds in asparagus have been reported, however, the diversified phenolics compounds including their modification and transcription regulation remains unknown. Thus, multi-omics strategies were applied to detect the phenolics profiles, contents, and screen the key genes for phenolics biosynthesis and regulation in asparagus. A total of 437 compounds, among which 204 phenolics including 105 flavonoids and 82 phenolic acids were detected with fluctuated concentrations in roots (Rs), spears (Ss) and flowering twigs (Fs) of the both green and purple cultivars. Based on the detected phenolics profiles and contents correlated to the gene expressions of screened synthetic enzymes and regulatory TFs, a full phenolics synthetic pathway of asparagus was proposed for the first time, essential for future breeding of asparagus and scaled healthy phenolics production using synthetic biological strategies.
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Affiliation(s)
- Yuping Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, Yunnan 650201, China
| | - Sylvia E. Brown
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, Yunnan 650201, China
| | - Yunbin Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, Yunnan 650201, China
| | - Qin Cheng
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, Yunnan 650201, China
| | - He Wu
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, Yunnan 650201, China
| | - Shugu Wei
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610023, China
| | - Xingyu Li
- Institute of Improvement and Utilization of Characteristic Resource Plants, YNAU, Kunming, China
- The Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming, China
| | - Chun Lin
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, Yunnan 650201, China
- Institute of Improvement and Utilization of Characteristic Resource Plants, YNAU, Kunming, China
| | - Zhengjie Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, Yunnan 650201, China
- Institute of Improvement and Utilization of Characteristic Resource Plants, YNAU, Kunming, China
| | - Zichao Mao
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, Yunnan 650201, China
- Institute of Improvement and Utilization of Characteristic Resource Plants, YNAU, Kunming, China
- The Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming, China
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2
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Li W, Dong X, Zhang X, Cao J, Liu M, Zhou X, Long H, Cao H, Lin H, Zhang L. Genome assembly and resequencing shed light on evolution, population selection, and sex identification in Vernicia montana. HORTICULTURE RESEARCH 2024; 11:uhae141. [PMID: 38988615 PMCID: PMC11233859 DOI: 10.1093/hr/uhae141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/08/2024] [Indexed: 07/12/2024]
Abstract
Vernicia montana is a dioecious plant widely cultivated for high-quality tung oil production and ornamental purposes in the Euphorbiaceae family. The lack of genomic information has severely hindered molecular breeding for genetic improvement and early sex identification in V. montana. Here, we present a chromosome-level reference genome of a male V. montana with a total size of 1.29 Gb and a contig N50 of 3.69 Mb. Genome analysis revealed that different repeat lineages drove the expansion of genome size. The model of chromosome evolution in the Euphorbiaceae family suggests that polyploidization-induced genomic structural variation reshaped the chromosome structure, giving rise to the diverse modern chromosomes. Based on whole-genome resequencing data and analyses of selective sweep and genetic diversity, several genes associated with stress resistance and flavonoid synthesis such as CYP450 genes and members of the LRR-RLK family, were identified and presumed to have been selected during the evolutionary process. Genome-wide association studies were conducted and a putative sex-linked insertion and deletion (InDel) (Chr 2: 102 799 917-102 799 933 bp) was identified and developed as a polymorphic molecular marker capable of effectively detecting the gender of V. montana. This InDel is located in the second intron of VmBASS4, suggesting a possible role of VmBASS4 in sex determination in V. montana. This study sheds light on the genome evolution and sex identification of V. montana, which will facilitate research on the development of agronomically important traits and genomics-assisted breeding.
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Affiliation(s)
- Wenying Li
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Shaoshan South Road, No.498, Tianxin District, Changsha, Hunan 410004, China
- College of Biology and Agricultural Resources, Huanggang Normal University, No.146 Xingang 2nd Road, Huangzhou District, Huanggang, Hubei 438000, China
| | - Xiang Dong
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Shaoshan South Road, No.498, Tianxin District, Changsha, Hunan 410004, China
| | - Xingtan 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, No.7 Pengfei Road, Dapeng New District, Shenzhen 518120, China
| | - Jie Cao
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Shaoshan South Road, No.498, Tianxin District, Changsha, Hunan 410004, China
| | - Meilan Liu
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Shaoshan South Road, No.498, Tianxin District, Changsha, Hunan 410004, China
| | - Xu Zhou
- College of Landscape Architecture, Central South University of Forestry and Technology, Shaoshan South Road, No.498, Tianxin District, Changsha, Hunan 410004, China
| | - Hongxu Long
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Shaoshan South Road, No.498, Tianxin District, Changsha, Hunan 410004, China
| | - Heping Cao
- U.S. Department of Agriculture, Agricultural Research Service, Southern Regional Research Center, 1100 Allen Toussaint Blvd, New Orleans, LA 70124-4305, USA
| | - Hai Lin
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Shaoshan South Road, No.498, Tianxin District, Changsha, Hunan 410004, China
| | - Lin Zhang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Shaoshan South Road, No.498, Tianxin District, Changsha, Hunan 410004, China
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3
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Eggers EJ, Su Y, van der Poel E, Flipsen M, de Vries ME, Bachem CWB, Visser RGF, Lindhout P. Identification, Elucidation and Deployment of a Cytoplasmic Male Sterility System for Hybrid Potato. BIOLOGY 2024; 13:447. [PMID: 38927327 PMCID: PMC11200408 DOI: 10.3390/biology13060447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024]
Abstract
Recent advances in diploid F1 hybrid potato breeding rely on the production of inbred lines using the S-locus inhibitor (Sli) gene. As a result of this method, female parent lines are self-fertile and require emasculation before hybrid seed production. The resulting F1 hybrids are self-fertile as well and produce many undesirable berries in the field. Utilization of cytoplasmic male sterility would eliminate the need for emasculation, resulting in more efficient hybrid seed production and male sterile F1 hybrids. We observed plants that completely lacked anthers in an F2 population derived from an interspecific cross between diploid S. tuberosum and S. microdontum. We studied the antherless trait to determine its suitability for use in hybrid potato breeding. We mapped the causal locus to the short arm of Chromosome 6, developed KASP markers for the antherless (al) locus and introduced it into lines with T and A cytoplasm. We found that antherless type male sterility is not expressed in T and A cytoplasm, proving that it is a form of CMS. We hybridized male sterile al/al plants with P cytoplasm with pollen from al/al plants with T and A cytoplasm and we show that the resulting hybrids set significantly fewer berries in the field. Here, we show that the antherless CMS system can be readily deployed in diploid F1 hybrid potato breeding to improve hybridization efficiency and reduce berry set in the field.
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Affiliation(s)
- Ernst-Jan Eggers
- Solynta, Dreijenlaan 2, 6703 HA Wageningen, The Netherlands (C.W.B.B.)
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands (R.G.F.V.)
- Graduate School Experimental Plant Sciences, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Ying Su
- Solynta, Dreijenlaan 2, 6703 HA Wageningen, The Netherlands (C.W.B.B.)
| | - Esmee van der Poel
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands (R.G.F.V.)
| | - Martijn Flipsen
- Hogeschool Arnhem Nijmegen, Laan van Scheut 2, 6525 EM Nijmegen, The Netherlands
| | | | - Christian W. B. Bachem
- Solynta, Dreijenlaan 2, 6703 HA Wageningen, The Netherlands (C.W.B.B.)
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands (R.G.F.V.)
| | - Richard G. F. Visser
- Plant Breeding, Wageningen University & Research, P.O. Box 386, 6700 AJ Wageningen, The Netherlands (R.G.F.V.)
| | - Pim Lindhout
- Solynta, Dreijenlaan 2, 6703 HA Wageningen, The Netherlands (C.W.B.B.)
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4
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Lu XM, Yu XF, Li GQ, Qu MH, Wang H, Liu C, Man YP, Jiang XH, Li MZ, Wang J, Chen QQ, Lei R, Zhao CC, Zhou YQ, Jiang ZW, Li ZZ, Zheng S, Dong C, Wang BL, Sun YX, Zhang HQ, Li JW, Mo QH, Zhang Y, Lou X, Peng HX, Yi YT, Wang HX, Zhang XJ, Wang YB, Wang D, Li L, Zhang Q, Wang WX, Liu Y, Gao L, Wu JH, Wang YC. Genome assembly of autotetraploid Actinidia arguta highlights adaptive evolution and enables dissection of important economic traits. PLANT COMMUNICATIONS 2024; 5:100856. [PMID: 38431772 PMCID: PMC11211551 DOI: 10.1016/j.xplc.2024.100856] [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: 05/28/2023] [Revised: 07/07/2023] [Accepted: 02/28/2024] [Indexed: 03/05/2024]
Abstract
Actinidia arguta, the most widely distributed Actinidia species and the second cultivated species in the genus, can be distinguished from the currently cultivated Actinidia chinensis on the basis of its small and smooth fruit, rapid softening, and excellent cold tolerance. Adaptive evolution of tetraploid Actinidia species and the genetic basis of their important agronomic traits are still unclear. Here, we generated a chromosome-scale genome assembly of an autotetraploid male A. arguta accession. The genome assembly was 2.77 Gb in length with a contig N50 of 9.97 Mb and was anchored onto 116 pseudo-chromosomes. Resequencing and clustering of 101 geographically representative accessions showed that they could be divided into two geographic groups, Southern and Northern, which first diverged 12.9 million years ago. A. arguta underwent two prominent expansions and one demographic bottleneck from the mid-Pleistocene climate transition to the late Pleistocene. Population genomics studies using paleoclimate data enabled us to discern the evolution of the species' adaptation to different historical environments. Three genes (AaCEL1, AaPME1, and AaDOF1) related to flesh softening were identified by multi-omics analysis, and their ability to accelerate flesh softening was verified through transient expression assays. A set of genes that characteristically regulate sexual dimorphism located on the sex chromosome (Chr3) or autosomal chromosomes showed biased expression during stamen or carpel development. This chromosome-level assembly of the autotetraploid A. arguta genome and the genes related to important agronomic traits will facilitate future functional genomics research and improvement of A. arguta.
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Affiliation(s)
- Xue-Mei Lu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Xiao-Fen Yu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Guo-Qiang Li
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Ming-Hao Qu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Huan Wang
- Wuhan Frasergen Bioinformatics Co., Ltd, Wuhan, Hubei, China
| | - Chuang Liu
- Institute of Soil and Fertilizer, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Yu-Ping Man
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Xiao-Han Jiang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Mu-Zi Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jian Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Qi-Qi Chen
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Rui Lei
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Cheng-Cheng Zhao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Yun-Qiu Zhou
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zheng-Wang Jiang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Zuo-Zhou Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Shang Zheng
- Wuhan Frasergen Bioinformatics Co., Ltd, Wuhan, Hubei, China
| | - Chang Dong
- College of Agricultural Sciences, Xichang University, Xichang, Sichuan, China
| | - Bai-Lin Wang
- Department of Horticulture, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Yan-Xiang Sun
- College of Life Sciences, Langfang Normal University, Langfang, Hebei, China
| | - Hui-Qin Zhang
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Jie-Wei Li
- Guangxi Institute of Botany, Chinese Academy of Sciences, Guilin, Guangxi, China
| | - Quan-Hui Mo
- Guangxi Institute of Botany, Chinese Academy of Sciences, Guilin, Guangxi, China
| | - Ying Zhang
- Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, Xi'an, Shaanxi, China
| | - Xin Lou
- Institute of Modern Agricultural Research, Dalian University, Dalian, Liaoning, China
| | - Hai-Xu Peng
- Bioinformatics Center, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - Ya-Ting Yi
- Bioinformatics Center, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China
| | - He-Xin Wang
- Institute of Modern Agricultural Research, Dalian University, Dalian, Liaoning, China
| | - Xiu-Jun Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Yi-Bo Wang
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Dan Wang
- College of Agriculture, Eastern Liaoning University, Dandong, Liaoning, China
| | - Li Li
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Qiong Zhang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Wen-Xia Wang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning, China
| | - Yongbo Liu
- State Environmental Protection Key Laboratory of Regional Eco-process and Function Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China.
| | - Lei Gao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China; Hubei Hongshan Laboratory, Wuhan, Hubei, China.
| | - Jin-Hu Wu
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand.
| | - Yan-Chang Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.
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5
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Montgomery J, Morran S, MacGregor DR, McElroy JS, Neve P, Neto C, Vila-Aiub MM, Sandoval MV, Menéndez AI, Kreiner JM, Fan L, Caicedo AL, Maughan PJ, Martins BAB, Mika J, Collavo A, Merotto A, Subramanian NK, Bagavathiannan MV, Cutti L, Islam MM, Gill BS, Cicchillo R, Gast R, Soni N, Wright TR, Zastrow-Hayes G, May G, Malone JM, Sehgal D, Kaundun SS, Dale RP, Vorster BJ, Peters B, Lerchl J, Tranel PJ, Beffa R, Fournier-Level A, Jugulam M, Fengler K, Llaca V, Patterson EL, Gaines TA. Current status of community resources and priorities for weed genomics research. Genome Biol 2024; 25:139. [PMID: 38802856 PMCID: PMC11129445 DOI: 10.1186/s13059-024-03274-y] [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: 07/11/2023] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
Weeds are attractive models for basic and applied research due to their impacts on agricultural systems and capacity to swiftly adapt in response to anthropogenic selection pressures. Currently, a lack of genomic information precludes research to elucidate the genetic basis of rapid adaptation for important traits like herbicide resistance and stress tolerance and the effect of evolutionary mechanisms on wild populations. The International Weed Genomics Consortium is a collaborative group of scientists focused on developing genomic resources to impact research into sustainable, effective weed control methods and to provide insights about stress tolerance and adaptation to assist crop breeding.
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Affiliation(s)
- Jacob Montgomery
- Department of Agricultural Biology, Colorado State University, 1177 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Sarah Morran
- Department of Agricultural Biology, Colorado State University, 1177 Campus Delivery, Fort Collins, CO, 80523, USA
| | - Dana R MacGregor
- Protecting Crops and the Environment, Rothamsted Research, Harpenden, Hertfordshire, UK
| | - J Scott McElroy
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, USA
| | - Paul Neve
- Department of Plant and Environmental Sciences, University of Copenhagen, Taastrup, Denmark
| | - Célia Neto
- Department of Plant and Environmental Sciences, University of Copenhagen, Taastrup, Denmark
| | - Martin M Vila-Aiub
- IFEVA-Conicet-Department of Ecology, University of Buenos Aires, Buenos Aires, Argentina
| | | | - Analia I Menéndez
- Department of Ecology, Faculty of Agronomy, University of Buenos Aires, Buenos Aires, Argentina
| | - Julia M Kreiner
- Department of Botany, The University of British Columbia, Vancouver, BC, Canada
| | - Longjiang Fan
- Institute of Crop Sciences, Zhejiang University, Hangzhou, China
| | - Ana L Caicedo
- Department of Biology, University of Massachusetts Amherst, Amherst, MA, USA
| | - Peter J Maughan
- Department of Plant and Wildlife Sciences, Brigham Young University, Provo, UT, USA
| | | | - Jagoda Mika
- Bayer AG, Weed Control Research, Frankfurt, Germany
| | | | - Aldo Merotto
- Department of Crop Sciences, Federal University of Rio Grande Do Sul, Porto Alegre, Rio Grande Do Sul, Brazil
| | - Nithya K Subramanian
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
| | | | - Luan Cutti
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | | | - Bikram S Gill
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Robert Cicchillo
- Crop Protection Discovery and Development, Corteva Agriscience, Indianapolis, IN, USA
| | - Roger Gast
- Crop Protection Discovery and Development, Corteva Agriscience, Indianapolis, IN, USA
| | - Neeta Soni
- Crop Protection Discovery and Development, Corteva Agriscience, Indianapolis, IN, USA
| | - Terry R Wright
- Genome Center of Excellence, Corteva Agriscience, Johnston, IA, USA
| | | | - Gregory May
- Genome Center of Excellence, Corteva Agriscience, Johnston, IA, USA
| | - Jenna M Malone
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, South Australia, Australia
| | - Deepmala Sehgal
- Jealott's Hill International Research Centre, Syngenta Ltd, Bracknell, Berkshire, UK
| | - Shiv Shankhar Kaundun
- Jealott's Hill International Research Centre, Syngenta Ltd, Bracknell, Berkshire, UK
| | - Richard P Dale
- Jealott's Hill International Research Centre, Syngenta Ltd, Bracknell, Berkshire, UK
| | - Barend Juan Vorster
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Bodo Peters
- Bayer AG, Weed Control Research, Frankfurt, Germany
| | | | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Roland Beffa
- Senior Scientist Consultant, Herbicide Resistance Action Committee / CropLife International, Liederbach, Germany
| | | | - Mithila Jugulam
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Kevin Fengler
- Genome Center of Excellence, Corteva Agriscience, Johnston, IA, USA
| | - Victor Llaca
- Genome Center of Excellence, Corteva Agriscience, Johnston, IA, USA
| | - Eric L Patterson
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Todd A Gaines
- Department of Agricultural Biology, Colorado State University, 1177 Campus Delivery, Fort Collins, CO, 80523, USA.
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6
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Xu Z, Chen S, Wang Y, Tian Y, Wang X, Xin T, Li Z, Hua X, Tan S, Sun W, Pu X, Yao H, Gao R, Song J. Crocus genome reveals the evolutionary origin of crocin biosynthesis. Acta Pharm Sin B 2024; 14:1878-1891. [PMID: 38572115 PMCID: PMC10985130 DOI: 10.1016/j.apsb.2023.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/22/2023] [Accepted: 11/09/2023] [Indexed: 04/05/2024] Open
Abstract
Crocus sativus (saffron) is a globally autumn-flowering plant, and its stigmas are the most expensive spice and valuable herb medicine. Crocus specialized metabolites, crocins, are biosynthesized in distant species, Gardenia (eudicot) and Crocus (monocot), and the evolution of crocin biosynthesis remains poorly understood. With the chromosome-level Crocus genome assembly, we revealed that two rounds of lineage-specific whole genome triplication occurred, contributing important roles in the production of carotenoids and apocarotenoids. According to the kingdom-wide identification, phylogenetic analysis, and functional assays of carotenoid cleavage dioxygenases (CCDs), we deduced that the duplication, site positive selection, and neofunctionalization of Crocus-specific CCD2 from CCD1 members are responsible for the crocin biosynthesis. In addition, site mutation of CsCCD2 revealed the key amino acids, including I143, L146, R161, E181, T259, and S292 related to the catalytic activity of zeaxanthin cleavage. Our study provides important insights into the origin and evolution of plant specialized metabolites, which are derived by duplication events of biosynthetic genes.
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Affiliation(s)
- Zhichao Xu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- State Key Laboratory of Basis and New Drug Development of Natural and Nuclear Drugs, Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Shanshan Chen
- College of Life Science, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, China Academy of Chinese Medical Sciences, Institute of Chinese Materia Medica, Beijing 100700, China
| | - Yalin Wang
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Ya Tian
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Xiaotong Wang
- College of Life Science, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, China Academy of Chinese Medical Sciences, Institute of Chinese Materia Medica, Beijing 100700, China
| | - Tianyi Xin
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- State Key Laboratory of Basis and New Drug Development of Natural and Nuclear Drugs, Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Zishan Li
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Xin Hua
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Shengnan Tan
- Analysis and Testing Center of Northeast Forestry University, Harbin 150040, China
| | - Wei Sun
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, China Academy of Chinese Medical Sciences, Institute of Chinese Materia Medica, Beijing 100700, China
| | - Xiangdong Pu
- School of Pharmacy, Anhui Medical University, Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei 230032, China
| | - Hui Yao
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- State Key Laboratory of Basis and New Drug Development of Natural and Nuclear Drugs, Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Ranran Gao
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, China Academy of Chinese Medical Sciences, Institute of Chinese Materia Medica, Beijing 100700, China
| | - Jingyuan Song
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- State Key Laboratory of Basis and New Drug Development of Natural and Nuclear Drugs, Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
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7
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Yang Z, Yang Q, Liu Q, Li X, Wang L, Zhang Y, Ke Z, Lu Z, Shen H, Li J, Zhou W. A chromosome-level genome assembly of Agave hybrid NO.11648 provides insights into the CAM photosynthesis. HORTICULTURE RESEARCH 2024; 11:uhad269. [PMID: 38333731 PMCID: PMC10848310 DOI: 10.1093/hr/uhad269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 12/06/2023] [Indexed: 02/10/2024]
Abstract
The subfamily Agavoideae comprises crassulacean acid metabolism (CAM), C3, and C4 plants with a young age of speciation and slower mutation accumulation, making it a model crop for studying CAM evolution. However, the genetic mechanism underlying CAM evolution remains unclear because of lacking genomic information. This study assembled the genome of Agave hybrid NO.11648, a constitutive CAM plant belonging to subfamily Agavoideae, at the chromosome level using data generated from high-throughput chromosome conformation capture, Nanopore, and Illumina techniques, resulting in 30 pseudo-chromosomes with a size of 4.87 Gb and scaffold N50 of 186.42 Mb. The genome annotation revealed 58 841 protein-coding genes and 76.91% repetitive sequences, with the dominant repetitive sequences being the I-type repeats (Copia and Gypsy accounting for 18.34% and 13.5% of the genome, respectively). Our findings also provide support for a whole genome duplication event in the lineage leading to A. hybrid, which occurred after its divergence from subfamily Asparagoideae. Moreover, we identified a gene duplication event in the phosphoenolpyruvate carboxylase kinase (PEPCK) gene family and revealed that three PEPCK genes (PEPCK3, PEPCK5, and PEPCK12) were involved in the CAM pathway. More importantly, we identified transcription factors enriched in the circadian rhythm, MAPK signaling, and plant hormone signal pathway that regulate the PEPCK3 expression by analysing the transcriptome and using yeast one-hybrid assays. Our results shed light on CAM evolution and offer an essential resource for the molecular breeding program of Agave spp.
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Affiliation(s)
- Ziping Yang
- Zhanjiang Key Laboratory of Tropical Crop Genetic Improvement, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, 524091 Zhanjiang, Guangdong, China
| | - Qian Yang
- Zhanjiang Key Laboratory of Tropical Crop Genetic Improvement, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, 524091 Zhanjiang, Guangdong, China
| | - Qi Liu
- Wuhan Onemore-tech Co., Ltd, 430076 Wuhan, Hubei, China
| | - Xiaolong Li
- Biomarker Technologies Corporation, 101300 Beijing, China
| | - Luli Wang
- Zhanjiang Key Laboratory of Tropical Crop Genetic Improvement, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, 524091 Zhanjiang, Guangdong, China
| | - Yanmei Zhang
- Zhanjiang Key Laboratory of Tropical Crop Genetic Improvement, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, 524091 Zhanjiang, Guangdong, China
| | - Zhi Ke
- Zhanjiang Key Laboratory of Tropical Crop Genetic Improvement, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, 524091 Zhanjiang, Guangdong, China
| | - Zhiwei Lu
- Zhanjiang Key Laboratory of Tropical Crop Genetic Improvement, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, 524091 Zhanjiang, Guangdong, China
| | - Huibang Shen
- Zhanjiang Key Laboratory of Tropical Crop Genetic Improvement, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, 524091 Zhanjiang, Guangdong, China
| | - Junfeng Li
- Zhanjiang Key Laboratory of Tropical Crop Genetic Improvement, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, 524091 Zhanjiang, Guangdong, China
| | - Wenzhao Zhou
- Zhanjiang Key Laboratory of Tropical Crop Genetic Improvement, South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, 524091 Zhanjiang, Guangdong, China
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8
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Bentz PC, Liu Z, Yang JB, Zhang L, Burrows S, Burrows J, Kanno A, Mao Z, Leebens-Mack J. Young evolutionary origins of dioecy in the genus Asparagus. AMERICAN JOURNAL OF BOTANY 2024; 111:e16276. [PMID: 38297448 DOI: 10.1002/ajb2.16276] [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: 05/03/2023] [Revised: 10/31/2023] [Accepted: 11/17/2023] [Indexed: 02/02/2024]
Abstract
PREMISE Dioecy (separate sexes) has independently evolved numerous times across the angiosperm phylogeny and is recently derived in many lineages. However, our understanding is limited regarding the evolutionary mechanisms that drive the origins of dioecy in plants. The recent and repeated evolution of dioecy across angiosperms offers an opportunity to make strong inferences about the ecological, developmental, and molecular factors influencing the evolution of dioecy, and thus sex chromosomes. The genus Asparagus (Asparagaceae) is an emerging model taxon for studying dioecy and sex chromosome evolution, yet estimates for the age and origin of dioecy in the genus are lacking. METHODS We use plastome sequences and fossil time calibrations in phylogenetic analyses to investigate the age and origin of dioecy in the genus Asparagus. We also review the diversity of sexual systems present across the genus to address contradicting reports in the literature. RESULTS We estimate that dioecy evolved once or twice approximately 2.78-3.78 million years ago in Asparagus, of which roughly 27% of the species are dioecious and the remaining are hermaphroditic with monoclinous flowers. CONCLUSIONS Our findings support previous work implicating a young age and the possibility of two origins of dioecy in Asparagus, which appear to be associated with rapid radiations and range expansion out of Africa. Lastly, we speculate that paleoclimatic oscillations throughout northern Africa may have helped set the stage for the origin(s) of dioecy in Asparagus approximately 2.78-3.78 million years ago.
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Affiliation(s)
- Philip C Bentz
- Department of Plant Biology, University of Georgia, Athens, GA, 30605, USA
| | - Zhengjie Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Le Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | | | | | - Akira Kanno
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Zichao Mao
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China
| | - Jim Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, 30605, USA
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9
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Sun P, Nishiyama S, Li H, Mai Y, Han W, Suo Y, Liang C, Du H, Diao S, Wang Y, Yuan J, Zhang Y, Tao R, Li F, Fu J. Genetic insights into the dissolution of dioecy in diploid persimmon Diospyros oleifera Cheng. BMC PLANT BIOLOGY 2023; 23:606. [PMID: 38030968 PMCID: PMC10688080 DOI: 10.1186/s12870-023-04610-3] [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: 08/02/2023] [Accepted: 11/15/2023] [Indexed: 12/01/2023]
Abstract
BACKGROUND Dioecy, a sexual system of single-sexual (gynoecious/androecious) individuals, is rare in flowering plants. This rarity may be a result of the frequent transition from dioecy into systems with co-sexual individuals. RESULTS In this study, co-sexual expression (monoecy and hermaphroditic development), previously thought to be polyploid-specific in Diospyros species, was identified in the diploid D. oleifeara historically. We characterized potential genetic mechanisms that underlie the dissolution of dioecy to monoecy and andro(gyno)monoecy, based on multiscale genome-wide investigations of 150 accessions of Diospyros oleifera. We found all co-sexual plants, including monoecious and andro(gyno)monoecious individuals, possessed the male determinant gene OGI, implying the presence of genetic factors controlling gynoecia development in genetically male D. oleifera. Importantly, discrepancies in the OGI/MeGI module were found in diploid monoecious D. oleifera compared with polyploid monoecious D. kaki, including no Kali insertion on the promoter of OGI, no different abundance of smRNAs targeting MeGI (a counterpart of OGI), and no different expression of MeGI between female and male floral buds. On the contrary, in both single- and co-sexual plants, female function was expressed in the presence of a genome-wide decrease in methylation levels, along with sexually distinct regulatory networks of smRNAs and their targets. Furthermore, a genome-wide association study (GWAS) identified a genomic region and a DUF247 gene cluster strongly associated with the monoecious phenotype and several regions that may contribute to andromonoecy. CONCLUSIONS Collectively, our findings demonstrate stable breakdown of the dioecious system in D. oleifera, presumably also a result of genomic features of the Y-linked region.
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Affiliation(s)
- Peng Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Soichiro Nishiyama
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwakecho, Sakyo-Ku, Kyoto, 606-8502, Japan
| | - Huawei Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Yini Mai
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Weijuan Han
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Yujing Suo
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huilong Du
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Songfeng Diao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Yiru Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Jiaying Yuan
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Yue Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China
| | - Ryutaro Tao
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwakecho, Sakyo-Ku, Kyoto, 606-8502, Japan.
| | - Fangdong Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China.
| | - Jianmin Fu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou, 450003, China.
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10
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Kanno A, Hirobe N, Zhang L. Origin of purple asparagus cultivar 'Pacific Purple' based on the sequence of sex determination gene. FRONTIERS IN PLANT SCIENCE 2023; 14:1237433. [PMID: 38034566 PMCID: PMC10687405 DOI: 10.3389/fpls.2023.1237433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023]
Abstract
Garden asparagus is one of the most important crops worldwide. Since this crop is dioecious and male plants generally have higher yields compared to female plants, several DNA markers for sex identification have been developed for acceleration of asparagus breeding. Among these markers, Asp1-T7sp and MSSTS710 were found to be effective in sex determination for many asparagus cultivars. However, we previously found that these markers were not completely suitable for sex identification in the purple asparagus cultivar 'Pacific Purple'. There are two types of male individuals in this cultivar: One type is PP-m, which is identified the sex type by Asp1-T7sp and MSSTS710 markers, while the other type is PP-m* whose sex type is not identified by these markers. Since the sex identification markers are located on the non-recombining Y region, it was expected that the sequence around this region might be different between PP-m and PP-m*. In this study, the sequence of one of the sex-determining genes, MSE1/AoMYB35/AspTDF1, was analyzed, and a comparative analysis was conducted among PP-m and PP-m* of 'Pacific Purple', A. officinalis and related species A. maritimus. The results revealed that PP-m and PP-m* has the similar sequence of MSE1/AoMYB35/AspTDF1 gene from A. officinalis and A. maritimus, respectively. 'Pacific Purple' is a cultivar developed through polycross hybrid from Italian landrace 'Violetto d'Albenga' (VA), suggesting that VA originated from an interspecific crossing between A. officinalis and A. maritimus and that the pollen parent used in 'Pacific Purple' breeding contained two types of male individuals with different MSE1/AoMYB35/AspTDF1 sequence. As a result, PP-m and PP-m* of 'Pacific Purple' harbors the similar sequences of the MSE1/AoMYB35/AspTDF1 gene from A. officinalis and A. maritimus, respectively.
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11
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Hao F, Liu X, Zhou B, Tian Z, Zhou L, Zong H, Qi J, He J, Zhang Y, Zeng P, Li Q, Wang K, Xia K, Guo X, Li L, Shao W, Zhang B, Li S, Yang H, Hui L, Chen W, Peng L, Liu F, Rong ZQ, Peng Y, Zhu W, McCallum JA, Li Z, Xu X, Yang H, Macknight RC, Wang W, Cai J. Chromosome-level genomes of three key Allium crops and their trait evolution. Nat Genet 2023; 55:1976-1986. [PMID: 37932434 DOI: 10.1038/s41588-023-01546-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 09/20/2023] [Indexed: 11/08/2023]
Abstract
Allium crop breeding remains severely hindered due to the lack of high-quality reference genomes. Here we report high-quality chromosome-level genome assemblies for three key Allium crops (Welsh onion, garlic and onion), which are 11.17 Gb, 15.52 Gb and 15.78 Gb in size with the highest recorded contig N50 of 507.27 Mb, 109.82 Mb and 81.66 Mb, respectively. Beyond revealing the genome evolutionary process of Allium species, our pathogen infection experiments and comparative metabolomic and genomic analyses showed that genes encoding enzymes involved in the metabolic pathway of Allium-specific flavor compounds may have evolved from an ancient uncharacterized plant defense system widely existing in many plant lineages but extensively boosted in alliums. Using in situ hybridization and spatial RNA sequencing, we obtained an overview of cell-type categorization and gene expression changes associated with spongy mesophyll cell expansion during onion bulb formation, thus indicating the functional roles of bulb formation genes.
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Affiliation(s)
- Fei Hao
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
- Center of Special Environmental Biomechanics & Biomedical Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Xue Liu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Botong Zhou
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Zunzhe Tian
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Lina Zhou
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Hang Zong
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Jiyan Qi
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Juan He
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Yongting Zhang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Peng Zeng
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Qiong Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Kai Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Keke Xia
- State Key Laboratory of Agricultural Genomics, BGI, Shenzhen, China
| | - Xing Guo
- State Key Laboratory of Agricultural Genomics, BGI, Shenzhen, China
- BGI Research, Wuhan, China
| | - Li Li
- State Key Laboratory of Agricultural Genomics, BGI, Shenzhen, China
| | - Wenwen Shao
- State Key Laboratory of Agricultural Genomics, BGI, Shenzhen, China
| | | | - Shengkang Li
- State Key Laboratory of Agricultural Genomics, BGI, Shenzhen, China
| | - Haifeng Yang
- Lianyungang Academy of Agricultural Sciences, Lianyungang, China
| | - Linchong Hui
- Lianyungang Academy of Agricultural Sciences, Lianyungang, China
| | - Wei Chen
- Lianyungang Academy of Agricultural Sciences, Lianyungang, China
| | - Lixin Peng
- National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, China
| | - Feipeng Liu
- Frontiers Science Center for Flexible Electronics (FSCFE), Shaanxi Institute of Flexible Electronics (SIFE) & Shaanxi Institute of Biomedical Materials and Engineering (SIBME), Northwestern Polytechnical University, Xi'an, China
| | - Zi-Qiang Rong
- Frontiers Science Center for Flexible Electronics (FSCFE), Shaanxi Institute of Flexible Electronics (SIFE) & Shaanxi Institute of Biomedical Materials and Engineering (SIBME), Northwestern Polytechnical University, Xi'an, China
| | - Yingmei Peng
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - Wenbo Zhu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China
| | - John A McCallum
- The New Zealand Institute for Plant and Food Research, Christchurch, New Zealand
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University and VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Xun Xu
- State Key Laboratory of Agricultural Genomics, BGI, Shenzhen, China.
- Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China.
| | - Hui Yang
- Center of Special Environmental Biomechanics & Biomedical Engineering, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China.
| | | | - Wen Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China.
| | - Jing Cai
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China.
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12
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Li Y, Li Z, Zhang F, Li S, Gu Y, Tian W, Tian W, Wang J, Wen J, Li J. Integrated evolutionary pattern analyses reveal multiple origins of steroidal saponins in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:823-839. [PMID: 37522396 DOI: 10.1111/tpj.16411] [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: 09/05/2022] [Revised: 07/19/2023] [Accepted: 07/22/2023] [Indexed: 08/01/2023]
Abstract
Steroidal saponins are a class of specialized metabolites essential for plant's response to biotic and abiotic stresses. They are also important raw materials for the industrial production of steroid drugs. Steroidal saponins are present in some monocots, such as Dioscorea and Paris, but their distribution, origin, and evolution in plants remain poorly understood. By reconstructing the evolutionary history of the steroidal saponin-associated module (SSAM) in plants, we reveal that the steroidal saponin pathway has its origin in Asparagus and Dioscorea. Through evaluating the distribution and evolutionary pattern of steroidal saponins in angiosperms, we further show that steroidal saponins originated multiple times in angiosperms, and exist in early diverged lineages of certain monocot lineages including Asparagales, Dioscoreales, and Liliales. In these lineages, steroidal saponins are synthesized through the high copy and/or high expression mechanisms of key genes in SSAM. Together with shifts in gene evolutionary rates and amino acid usage, these molecular mechanisms shape the current distribution and diversity of steroidal saponins in plants. Consequently, our results provide new insights into the distribution, diversity and evolutionary history of steroidal saponins in plants, and enhance our understanding of plants' resistance to abiotic and biotic stresses. Additionally, fundamental understanding of the steroidal saponin biosynthesis will facilitate their industrial production and pharmacological applications.
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Affiliation(s)
- Yi Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zihao Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Furui Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Song Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yongbing Gu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Weijun Tian
- Yunnan Baotian Agricultural Technology Co., Ltd, Kunming, 650101, China
| | - Weirong Tian
- Yunnan Baotian Agricultural Technology Co., Ltd, Kunming, 650101, China
| | - Jianbo Wang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, 20013-7012, DC, USA
| | - Jiaru Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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13
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Bruccoleri RE, Oakeley EJ, Faust AME, Altorfer M, Dessus-Babus S, Burckhardt D, Oertli M, Naumann U, Petersen F, Wong J. Genome assembly of the bearded iris, Iris pallida Lam. GIGABYTE 2023; 2023:gigabyte94. [PMID: 37829656 PMCID: PMC10565908 DOI: 10.46471/gigabyte.94] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/03/2023] [Indexed: 10/14/2023] Open
Abstract
Irises are perennial plants, representing a large genus with hundreds of species. While cultivated extensively for their ornamental value, commercial interest in irises lies in the secondary metabolites present in their rhizomes. The Dalmatian Iris (Iris pallida Lam.) is an ornamental plant that also produces secondary metabolites with potential value to the fragrance and pharmaceutical industries. In addition to providing base notes for the fragrance industry, iris tissues and extracts possess antioxidant, anti-inflammatory and immunomodulatory effects. However, study of these secondary metabolites has been hampered by a lack of genomic information, requiring difficult extraction and analysis techniques. Here, we report the genome sequence of Iris pallida Lam., generated with Pacific Bioscience long-read sequencing, resulting in a 10.04-Gbp assembly with a scaffold N50 of 14.34 Mbp and 91.8% complete BUSCOs. This reference genome will allow researchers to study the biosynthesis of these secondary metabolites in much greater detail, opening new avenues of investigation for drug discovery and fragrance formulations.
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Affiliation(s)
| | - Edward J. Oakeley
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Ann Marie E. Faust
- Novartis Institutes for BioMedical Research, 250 Massachusetts Avenue, Cambridge, MA, USA
| | - Marc Altorfer
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Sophie Dessus-Babus
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - David Burckhardt
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Mevion Oertli
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Ulrike Naumann
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Frank Petersen
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
| | - Joanne Wong
- Novartis Institutes for BioMedical Research, Novartis Campus, 4056, Basel, Switzerland
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14
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Li N, Zhou J, Zhang W, Liu W, Wang B, She H, Mirbahar AA, Li S, Zhang Y, Gao W, Qian W, Deng C. A rapid method for assembly of single chromosome and identification of sex determination region based on single-chromosome sequencing. THE NEW PHYTOLOGIST 2023; 240:892-903. [PMID: 37533136 DOI: 10.1111/nph.19176] [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: 04/18/2023] [Accepted: 07/08/2023] [Indexed: 08/04/2023]
Abstract
The sex-determining-region (SDR) may offer the best prospects for studying sex-determining gene, recombination suppression, and chromosome heteromorphism. However, current progress of SDR identification and cloning showed following shortcomings: large near-isogenic lines need to be constructed, and a relatively large population is needed; the cost of whole-genome sequencing and assembly is high. Herein, the X/Y chromosomes of Spinacia oleracea L. subsp. turkestanica were successfully microdissected and assembled using single-chromosome sequencing. The assembly length of X and Y chromosome is c. 192.1 and 195.2 Mb, respectively. Three large inversions existed between X and Y chromosome. The SDR size of X and Y chromosome is c. 13.2 and 24.1 Mb, respectively. MSY region and six male-biased genes were identified. A Y-chromosome-specific marker in SDR was constructed and used to verify the chromosome assembly quality at cytological level via fluorescence in situ hybridization. Meanwhile, it was observed that the SDR located on long arm of Y chromosome and near the centromere. Overall, a technical system was successfully established for rapid cloning the SDR and it is also applicable to rapid assembly of specific chromosome in other plants. Furthermore, this study laid a foundation for studying the molecular mechanism of sex chromosome evolution in spinach.
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Affiliation(s)
- Ning Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Jian Zhou
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Wanqing Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Wenjia Liu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Bingxin Wang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Hongbing She
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ameer Ahmed Mirbahar
- Date Palm Research Institute, Shah Abdul Latif University, Khairpur, Sindh, 66020, Pakistan
| | - Shufen Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Yulan Zhang
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Wujun Gao
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Wei Qian
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chuanliang Deng
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
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15
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Fan W, He ZS, Zhe M, Feng JQ, Zhang L, Huang Y, Liu F, Huang JL, Ya JD, Zhang SB, Yang JB, Zhu A, Li DZ. High-quality Cymbidium mannii genome and multifaceted regulation of crassulacean acid metabolism in epiphytes. PLANT COMMUNICATIONS 2023; 4:100564. [PMID: 36809882 PMCID: PMC10504564 DOI: 10.1016/j.xplc.2023.100564] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 02/10/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Epiphytes with crassulacean acid metabolism (CAM) photosynthesis are widespread among vascular plants, and repeated evolution of CAM photosynthesis is a key innovation for micro-ecosystem adaptation. However, we lack a complete understanding of the molecular regulation of CAM photosynthesis in epiphytes. Here, we report a high-quality chromosome-level genome assembly of a CAM epiphyte, Cymbidium mannii (Orchidaceae). The 2.88-Gb orchid genome with a contig N50 of 22.7 Mb and 27 192 annotated genes was organized into 20 pseudochromosomes, 82.8% of which consisted of repetitive elements. Recent expansions of long terminal repeat retrotransposon families have made a major contribution to the evolution of genome size in Cymbidium orchids. We reveal a holistic scenario of molecular regulation of metabolic physiology using high-resolution transcriptomics, proteomics, and metabolomics data collected across a CAM diel cycle. Patterns of rhythmically oscillating metabolites, especially CAM-related products, reveal circadian rhythmicity in metabolite accumulation in epiphytes. Genome-wide analysis of transcript and protein level regulation revealed phase shifts during the multifaceted regulation of circadian metabolism. Notably, we observed diurnal expression of several core CAM genes (especially βCA and PPC) that may be involved in temporal fixation of carbon sources. Our study provides a valuable resource for investigating post-transcription and translation scenarios in C. mannii, an Orchidaceae model for understanding the evolution of innovative traits in epiphytes.
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Affiliation(s)
- Weishu Fan
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Zheng-Shan He
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Mengqing Zhe
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jing-Qiu Feng
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Le Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Yiwei Huang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Fang Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | | | - Ji-Dong Ya
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Shi-Bao Zhang
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Jun-Bo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - Andan Zhu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
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16
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Llorens L, Tomàs J, Ferriol P, García MT, Gil L. Floral Aroma and Pollinator Relationships in Two Sympatric Late-Summer-Flowering Mediterranean Asparagus Species. PLANTS (BASEL, SWITZERLAND) 2023; 12:3219. [PMID: 37765383 PMCID: PMC10537274 DOI: 10.3390/plants12183219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 08/30/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023]
Abstract
This research delves into plant-pollinator relationships within the Mediterranean region, focusing on two synchronous and sympatric asparagus species: A. acutifolius and A. albus. For the first time, the floral scents of the genus Asparagus are reported. We investigate the volatile organic compounds (VOCs) present in their floral scents and their impact on pollinator attraction. Captured flower-emitted VOCs underwent solid-phase microextraction of headspace (SPME-HS) and gas chromatography and mass spectrometry (GC-MS) analysis. The investigation confirms distinctive aroma profiles for each species. A. albus predominantly emits benzene derivatives and sesquiterpenes, while A. acutifolius is characterized by carotenoid derivatives, monoterpenes, and sesquiterpenes. The only shared compounds between the two species are the sesquiterpenes (Z,E)-α-farnesene and (E,E)-α-farnesene. A positive correlation links peak floral aroma intensity (benzenoids in A. albus and ionones in A. acutifolius) with a higher pollinator visit frequency, emphasizing the critical role of intense floral scents in pollinator attraction. The study of reproductive aspects reveals almost complete gynodioecy in A. acutifolius, influencing unique dynamics for the two species. These adaptations hold significant importance within the Mediterranean ecosystem, particularly during the late dry summer period, when a limited number of plant species vie for a shared primary pollinator.
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Affiliation(s)
- Leonardo Llorens
- Interdisciplinary Ecology Group, Department of Biology, University of the Balearic Islands (UIB), Ctra. Palma-Valldemossa Km. 7.5, E-07122 Palma, Balearic Islands, Spain; (P.F.); (L.G.)
| | - Joan Tomàs
- Department of Biology (Botany), University of the Balearic Islands (UIB), Ctra. Palma-Valldemossa Km. 7.5, E-07122 Palma, Balearic Islands, Spain;
| | - Pere Ferriol
- Interdisciplinary Ecology Group, Department of Biology, University of the Balearic Islands (UIB), Ctra. Palma-Valldemossa Km. 7.5, E-07122 Palma, Balearic Islands, Spain; (P.F.); (L.G.)
| | - María Trinitat García
- Scientific and Technical Services, University of the Balearic Islands (UIB), Carretera de Valldemossa Km. 7.5, E-07122 Palma de Mallorca, Balearic Islands, Spain;
| | - Lorenzo Gil
- Interdisciplinary Ecology Group, Department of Biology, University of the Balearic Islands (UIB), Ctra. Palma-Valldemossa Km. 7.5, E-07122 Palma, Balearic Islands, Spain; (P.F.); (L.G.)
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17
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Sala T, Puglisi D, Ferrari L, Salamone F, Tassone MR, Rotino GL, Fricano A, Losa A. Genome-wide analysis of genetic diversity in a germplasm collection including wild relatives and interspecific clones of garden asparagus. FRONTIERS IN PLANT SCIENCE 2023; 14:1187663. [PMID: 37476175 PMCID: PMC10354869 DOI: 10.3389/fpls.2023.1187663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/09/2023] [Indexed: 07/22/2023]
Abstract
The Asparagus genus includes approximately 240 species, the most important of which is garden asparagus (Asparagus officinalis L.), as this is a vegetable crop cultivated worldwide for its edible spear. Along with garden asparagus, other species are also cultivated (e.g., Asparagus maritimus L.) or have been proposed as untapped sources of variability in breeding programs (e.g., Asparagus acutifolius L.). In the present work, we applied reduced-representation sequencing to examine a panel of 378 diverse asparagus genotypes, including commercial hybrids, interspecific lines, wild relatives of garden asparagus, and doubled haploids currently used in breeding programs, which enabled the identification of more than 200K single-nucleotide polymorphisms (SNPs). These SNPs were used to assess the extent of linkage disequilibrium in the diploid gene pool of asparagus and combined with preliminary phenotypic information to conduct genome-wide association studies for sex and traits tied to spear quality and production. Moreover, using the same phenotypic and genotypic information, we fitted and cross-validated genome-enabled prediction models for the same set of traits. Overall, our analyses demonstrated that, unlike the diversity detected in wild species related to garden asparagus and in interspecific crosses, cultivated and wild genotypes of A. officinalis L. show a narrow genetic basis, which is a contributing factor hampering the genetic improvement of this crop. Estimating the extent of linkage disequilibrium and providing the first example of genome-wide association study and genome-enabled prediction in this species, we concluded that the asparagus panel examined in the present study can lay the foundation for determination of the genetic bases of agronomically important traits and for the implementation of predictive breeding tools to sustain breeding.
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Affiliation(s)
- Tea Sala
- Council for Agricultural Research and Economics – Research Centre for Genomics and Bioinformatics (CREA-GB), Montanaso Lombardo, LO, Italy
| | - Damiano Puglisi
- Council for Agricultural Research and Economics – Research Centre for Genomics and Bioinformatics (CREA-GB), Fiorenzuola d’Arda, PC, Italy
| | - Luisa Ferrari
- Council for Agricultural Research and Economics – Research Centre for Genomics and Bioinformatics (CREA-GB), Montanaso Lombardo, LO, Italy
| | - Filippo Salamone
- Council for Agricultural Research and Economics – Research Centre for Genomics and Bioinformatics (CREA-GB), Montanaso Lombardo, LO, Italy
| | - Maria Rosaria Tassone
- Council for Agricultural Research and Economics – Research Centre for Genomics and Bioinformatics (CREA-GB), Montanaso Lombardo, LO, Italy
| | - Giuseppe Leonardo Rotino
- Council for Agricultural Research and Economics – Research Centre for Genomics and Bioinformatics (CREA-GB), Montanaso Lombardo, LO, Italy
| | - Agostino Fricano
- Council for Agricultural Research and Economics – Research Centre for Genomics and Bioinformatics (CREA-GB), Fiorenzuola d’Arda, PC, Italy
| | - Alessia Losa
- Council for Agricultural Research and Economics – Research Centre for Genomics and Bioinformatics (CREA-GB), Montanaso Lombardo, LO, Italy
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18
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Zhang Z, Idrees M, Wang F, Zhang N, Chen W, Ahmad M, Sultana S, Jiao Y, Zheng X, Li M, Prodhan ZH, Arfan M. Typification and Nomenclature Notes on Twenty-Nine Names in Asparagus (Asparagaceae). PLANTS (BASEL, SWITZERLAND) 2023; 12:2537. [PMID: 37447099 DOI: 10.3390/plants12132537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/21/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023]
Abstract
Nomenclatural types for twenty-nine names belonging to the genus Asparagus are typified and discussed. The following names are lectotypified: A. altiscandens Engl. & Gilg, A. altissimus Munby, A. baumii Engl. & Gilg, A. benguellensis Baker, A. burchellii Baker, A. curillus Buch.-Ham. ex Roxb., A. deflexus Baker, A. duchesnei L.Linden, A. equisetoides Welw. ex Baker, A. fasciculatus Thunb., A. griffithii, Baker, A. homblei De Wild., A. kaessneri De Wild., A. lecardii De Wild., A. longicladus N.E.Br., A. longiflorus Franch., A. monophyllus Baker, A. palaestinus Baker, A. pastorianus Webb & Berthel., A. persicus Baker, A. poissonii H.Perrier, A. psilurus Welw. ex Baker, A. ritschardii De Wild., A. sapinii De Wild., A. scandens Thunb., A. schumanianus Schltr. ex H.Perrier, A. stellatus Baker, A. subfalcatus De Wild., and A. undulatus (L.f.) Thunb. (synonym of Dracaena undulata L.f.). A new name, Asparagus neofasciculatus, is proposed as a replacement name for A. fasciculatus Thunb., which is an illegitimate later homonym of A. fasciculatus R.Br. The original protologue of these names and the original materials are evaluated. Nomenclature remarks discussing the selection of type specimens are given for each name, and known isotypes or isolectotypes are also cited. This information could be utilized as a reference for future taxonomic and systematic studies on Asparagus around the world.
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Affiliation(s)
- Zhiyong Zhang
- College of Life Science, Neijiang Normal University, Neijiang 641000, China
| | - Muhammad Idrees
- College of Life Science, Neijiang Normal University, Neijiang 641000, China
| | - Fang Wang
- College of Life Science, Neijiang Normal University, Neijiang 641000, China
| | - Nan Zhang
- College of Life Science, Neijiang Normal University, Neijiang 641000, China
| | - Wennian Chen
- College of Life Science, Neijiang Normal University, Neijiang 641000, China
| | - Mushtaq Ahmad
- College of Life Science, Neijiang Normal University, Neijiang 641000, China
- Department of Plant Science, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
- Pakistan Academy of Science, Islamabad 45320, Pakistan
| | - Shazia Sultana
- College of Life Science, Neijiang Normal University, Neijiang 641000, China
- Department of Plant Science, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Yongqing Jiao
- State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Longzi Lake Campus, College of Agronomy, Henan Agriculture University, Zhengzhou 450046, China
| | - Xu Zheng
- State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Longzi Lake Campus, College of Agronomy, Henan Agriculture University, Zhengzhou 450046, China
| | - Meng Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Zakaria H Prodhan
- College of Life Science, Neijiang Normal University, Neijiang 641000, China
| | - Muhammad Arfan
- Department of Botany, University of Education Lahore, Vehari Campus, Vehari 61100, Pakistan
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19
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Guo X, Wang F, Fang D, Lin Q, Sahu SK, Luo L, Li J, Chen Y, Dong S, Chen S, Liu Y, Luo S, Guo Y, Liu H. The genome of Acorus deciphers insights into early monocot evolution. Nat Commun 2023; 14:3662. [PMID: 37339966 DOI: 10.1038/s41467-023-38836-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/17/2023] [Indexed: 06/22/2023] Open
Abstract
Acorales is the sister lineage to all the other extant monocot plants. Genomic resource enhancement of this genus can help to reveal early monocot genomic architecture and evolution. Here, we assemble the genome of Acorus gramineus and reveal that it has ~45% fewer genes than the majority of monocots, although they have similar genome size. Phylogenetic analyses based on both chloroplast and nuclear genes consistently support that A. gramineus is the sister to the remaining monocots. In addition, we assemble a 2.2 Mb mitochondrial genome and observe many genes exhibit higher mutation rates than that of most angiosperms, which could be the reason leading to the controversies of nuclear genes- and mitochondrial genes-based phylogenetic trees existing in the literature. Further, Acorales did not experience tau (τ) whole-genome duplication, unlike majority of monocot clades, and no large-scale gene expansion is observed. Moreover, we identify gene contractions and expansions likely linking to plant architecture, stress resistance, light harvesting, and essential oil metabolism. These findings shed light on the evolution of early monocots and genomic footprints of wetland plant adaptations.
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Affiliation(s)
- Xing Guo
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
| | - Fang Wang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Dongming Fang
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
| | - Qiongqiong Lin
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- College of Life Science, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
| | - Liuming Luo
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- College of Life Science, South China Agricultural University, Guangzhou, Guangdong, 510642, PR China
| | - Jiani Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, PR China
| | - Yewen Chen
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Shanshan Dong
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, Guangdong, 518004, PR China
| | - Sisi Chen
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, The Chinese Academy of Sciences, South China Botanical Garden, Guangzhou, Guangdong, 510650, PR China
| | - Yang Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China
- Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, Guangdong, 518004, PR China
| | - Shixiao Luo
- Key Laboratory of Plant Resource Conservation and Sustainable Utilization, The Chinese Academy of Sciences, South China Botanical Garden, Guangzhou, Guangdong, 510650, PR China
| | - Yalong Guo
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, PR China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, PR China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, PR China.
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, Heilongjiang, 150040, PR China.
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20
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Ma L, Liu KW, Li Z, Hsiao YY, Qi Y, Fu T, Tang GD, Zhang D, Sun WH, Liu DK, Li Y, Chen GZ, Liu XD, Liao XY, Jiang YT, Yu X, Hao Y, Huang J, Zhao XW, Ke S, Chen YY, Wu WL, Hsu JL, Lin YF, Huang MD, Li CY, Huang L, Wang ZW, Zhao X, Zhong WY, Peng DH, Ahmad S, Lan S, Zhang JS, Tsai WC, Van de Peer Y, Liu ZJ. Diploid and tetraploid genomes of Acorus and the evolution of monocots. Nat Commun 2023; 14:3661. [PMID: 37339946 DOI: 10.1038/s41467-023-38829-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 05/17/2023] [Indexed: 06/22/2023] Open
Abstract
Monocots are a major taxon within flowering plants, have unique morphological traits, and show an extraordinary diversity in lifestyle. To improve our understanding of monocot origin and evolution, we generate chromosome-level reference genomes of the diploid Acorus gramineus and the tetraploid Ac. calamus, the only two accepted species from the family Acoraceae, which form a sister lineage to all other monocots. Comparing the genomes of Ac. gramineus and Ac. calamus, we suggest that Ac. gramineus is not a potential diploid progenitor of Ac. calamus, and Ac. calamus is an allotetraploid with two subgenomes A, and B, presenting asymmetric evolution and B subgenome dominance. Both the diploid genome of Ac. gramineus and the subgenomes A and B of Ac. calamus show clear evidence of whole-genome duplication (WGD), but Acoraceae does not seem to share an older WGD that is shared by most other monocots. We reconstruct an ancestral monocot karyotype and gene toolkit, and discuss scenarios that explain the complex history of the Acorus genome. Our analyses show that the ancestors of monocots exhibit mosaic genomic features, likely important for that appeared in early monocot evolution, providing fundamental insights into the origin, evolution, and diversification of monocots.
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Affiliation(s)
- Liang Ma
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ke-Wei Liu
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine, Shenzhen Key Laboratory of Gene and Antibody Therapy, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan City, 701, Taiwan
| | - Yiying Qi
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China
| | - Tao Fu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Guang-Da Tang
- Henry Fok College of Biology and Agriculture, Shaoguan University, Shaoguan, 512005, China
| | - Diyang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wei-Hong Sun
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ding-Kun Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuanyuan Li
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Gui-Zhen Chen
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xue-Die Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xing-Yu Liao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yu-Ting Jiang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xia Yu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yang Hao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jie Huang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xue-Wei Zhao
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shijie Ke
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - You-Yi Chen
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Wan-Lin Wu
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan
| | - Jui-Ling Hsu
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan
| | - Yu-Fu Lin
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan
| | - Ming-Der Huang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, 80424, Taiwan
| | - Chia-Ying Li
- Department of Applied Chemistry, National Pingtung University, Pingtung City, Pingtung County, 900003, Taiwan
| | - Laiqiang Huang
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine, Shenzhen Key Laboratory of Gene and Antibody Therapy, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China
| | | | | | | | - Dong-Hui Peng
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Sagheer Ahmad
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Siren Lan
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Ji-Sen Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, 350002, Fuzhou, China.
- State Key Lab for Conservation and Utilization of Subtropical AgroBiological Resources and Guangxi Key Lab for Sugarcane Biology, Guangxi University, Nanning, 530004, China.
| | - Wen-Chieh Tsai
- Orchid Research and Development Center, National Cheng Kung University, Tainan City, 701, Taiwan.
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, 701, Taiwan.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium.
- VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium.
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
- College of Horticulture, Nanjing Agricultural University, Academy for Advanced Interdisciplinary Studies, Nanjing, 210095, China.
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine, Shenzhen Key Laboratory of Gene and Antibody Therapy, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, China.
- Institute of Vegetable and Flowers, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
- Zhejiang Institute of Subtropical Crops, Zhejiang Academy of Agricultural Sciences, Wenzhou, 325005, China.
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21
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Zhou J, He R, Liu X, Zhang B, Chen G, Wang D, Zhu Y. Manipulation of plant height in garden asparagus ( Asparagus officinalis L.) through CRISPR/Cas9-mediated aspSPL14 allele editing. HORTICULTURE RESEARCH 2023; 10:uhad096. [PMID: 37416730 PMCID: PMC10321374 DOI: 10.1093/hr/uhad096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 05/04/2023] [Indexed: 07/08/2023]
Affiliation(s)
| | | | - Xiaojing Liu
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, Nanchang Jiangxi, 330200, China
| | - Bingbing Zhang
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, Nanchang Jiangxi, 330200, China
| | - Guangyu Chen
- Institute of Vegetables and Flowers, Jiangxi Academy of Agricultural Sciences, Nanchang Jiangxi, 330200, China
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22
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Nashiki A, Matsuo H, Takano K, Fitriyah F, Isobe S, Shirasawa K, Yoshioka Y. Identification of novel sex determination loci in Japanese weedy melon. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:136. [PMID: 37231314 DOI: 10.1007/s00122-023-04381-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 05/06/2023] [Indexed: 05/27/2023]
Abstract
KEY MESSAGE Japanese weedy melon exhibits unique sex expression with interactions between previously reported sex determination genes and two novel loci. Sex expression contributes to fruit quality and yield in the Cucurbitaceae. In melon, orchestrated regulation by sex determination genes explains the mechanism of sex expression, resulting in a great variety of sexual morphologies. In this study, we examined the Japanese weedy melon UT1, which does not follow the reported model of sex expression. We conducted QTL analysis using F2 plants for flower sex on the main stem and the lateral branch and mapped "occurrence of pistil-bearing flower on the main stem" locus on Chr. 3 (Opbf3.1) and "type of pistil-bearing flower" (female or bisexual) loci on Chr. 2 (tpbf2.1) and Chr. 8 (tpbf8.1). The Opbf3.1 included the known sex determination gene CmACS11. Sequence comparison of CmACS11 between parental lines revealed three nonsynonymous SNPs. A CAPS marker developed from one of the SNPs was closely linked to the occurrence of pistil-bearing flowers on the main stem in two F2 populations with different genetic backgrounds. The UT1 allele on Opbf3.1 was dominant in F1 lines from crosses between UT1 and diverse cultivars and breeding lines. This study suggests that Opbf3.1 and tpbf8.1 may promote the development of pistil and stamen primordia by inhibiting CmWIP1 and CmACS-7 functions, respectively, making the UT1 plants hermaphrodite. The results of this study provide new insights into the molecular mechanisms of sex determination in melons and considerations for the application of femaleness in melon breeding.
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Affiliation(s)
- Akito Nashiki
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Hiroki Matsuo
- Graduate School of Life and Environmental Science, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Kota Takano
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Fauziatul Fitriyah
- Graduate School of Science and Technology, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan
| | - Yosuke Yoshioka
- Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan.
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23
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Wang X, Huang X, Chen L, Xie Z, Tan S, Qin X, Chen T, Huang Y, Xi J, Chen H, Yi K. Transcriptome Sequencing of Agave amaniensis Reveals Shoot-Related Expression Patterns of Expansin A Genes in Agave. PLANTS (BASEL, SWITZERLAND) 2023; 12:2020. [PMID: 37653937 PMCID: PMC10222593 DOI: 10.3390/plants12102020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/06/2023] [Accepted: 05/17/2023] [Indexed: 09/02/2023]
Abstract
Agave species are widely planted for fiber production. However, the molecular basis of agave fiber development has not been well understood. In this study, we performed a transcriptomic analysis in A. amaniensi, a well-known variety with high-quality fiber production. Approximately 43.87 million clean reads were obtained using Illumina sequencing. The de novo assembly produced 66,746 unigrams, 54% of which were annotated in a public database. In the Nr database, 21,490 unigenes of A. amaniensis were shown to be most closely related to Asparagus officinalis. Nine expansin A orthologs with full coding regions were obtained, which were named EXP1a, EXP1b, EXP2, EXP3, EXP4a, EXP4b, EXP11, EXP12, and EXP13. The maximum likelihood phylogenetic tree revealed the species-specific expansion of expansin genes in Arabidopsis, rice and agave. The expression analysis suggested the negative correlation between the expression of expansin genes and the leaf growth rate, except AhEXP11. Moreover, expansin genes were differentially affected by abiotic and biotic stresses. Notably, AhEXP2 expression level was highly upgraded after the infection of Phytophthora nicotiana. Nutrient deficiency also influent expansin genes expression. Together, our research will benefit future studies related to fiber development, disease resistance and nutrient usage in agave.
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Affiliation(s)
- Xuxia Wang
- Urban Construction College, Wuchang Shouyi University, Wuhan 430064, China
| | - Xing Huang
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Lisha Chen
- Quality Supervision, Inspection and Testing Center of Sisal and Products, Ministry of Agriculture and Rural Affairs, Zhanjiang 524022, China
| | - Zhouli Xie
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Shibei Tan
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xu Qin
- Guangxi Subtropical Crops Research Institute, Nanning 530001, China
| | - Tao Chen
- Guangxi Subtropical Crops Research Institute, Nanning 530001, China
| | - Yanlei Huang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jingen Xi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Helong Chen
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Kexian Yi
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya 572025, China
- Key Laboratory of Integrated Pest Management on Tropical Crops, Ministry of Agriculture and Rural Affairs, Haikou 571101, China
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Haikou 571101, China
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24
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Wannitikul P, Wattana-Amorn P, Sathitnaitham S, Sakulkoo J, Suttangkakul A, Wonnapinij P, Bassel GW, Simister R, Gomez LD, Vuttipongchaikij S. Disruption of a DUF247 Containing Protein Alters Cell Wall Polysaccharides and Reduces Growth in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2023; 12:1977. [PMID: 37653894 PMCID: PMC10221614 DOI: 10.3390/plants12101977] [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: 04/13/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 09/02/2023]
Abstract
Plant cell wall biosynthesis is a complex process that requires proteins and enzymes from glycan synthesis to wall assembly. We show that disruption of At3g50120 (DUF247-1), a member of the DUF247 multigene family containing 28 genes in Arabidopsis, results in alterations to the structure and composition of cell wall polysaccharides and reduced growth and plant size. An ELISA using cell wall antibodies shows that the mutants also exhibit ~50% reductions in xyloglucan (XyG), glucuronoxylan (GX) and heteromannan (HM) epitopes in the NaOH fraction and ~50% increases in homogalacturonan (HG) epitopes in the CDTA fraction. Furthermore, the polymer sizes of XyGs and GXs are reduced with concomitant increases in short-chain polymers, while those of HGs and mHGs are slightly increased. Complementation using 35S:DUF247-1 partially recovers the XyG and HG content, but not those of GX and HM, suggesting that DUF247-1 is more closely associated with XyGs and HGs. DUF247-1 is expressed throughout Arabidopsis, particularly in vascular and developing tissues, and its disruption affects the expression of other gene members, indicating a regulatory control role within the gene family. Our results demonstrate that DUF247-1 is required for normal cell wall composition and structure and Arabidopsis growth.
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Affiliation(s)
- Pitchaporn Wannitikul
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand; (P.W.); (S.S.); (J.S.); (A.S.); (P.W.)
| | - Pakorn Wattana-Amorn
- Special Research Unit for Advanced Magnetic Resonance and Center of Excellence for Innovation in Chemistry, Department of Chemistry, Faculty of Science, Kasetsart University, Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand;
| | - Sukhita Sathitnaitham
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand; (P.W.); (S.S.); (J.S.); (A.S.); (P.W.)
| | - Jenjira Sakulkoo
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand; (P.W.); (S.S.); (J.S.); (A.S.); (P.W.)
| | - Anongpat Suttangkakul
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand; (P.W.); (S.S.); (J.S.); (A.S.); (P.W.)
- Center of Advanced studies for Tropical Natural Resources, Kasetsart University, Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand
| | - Passorn Wonnapinij
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand; (P.W.); (S.S.); (J.S.); (A.S.); (P.W.)
- Center of Advanced studies for Tropical Natural Resources, Kasetsart University, Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
| | - George W. Bassel
- School of Life Sciences, The University of Warwick, Coventry CV4 7AL, UK;
| | - Rachael Simister
- CNAP, Department of Biology, University of York, Heslington, York YO10 5DD, UK; (R.S.); (L.D.G.)
| | - Leonardo D. Gomez
- CNAP, Department of Biology, University of York, Heslington, York YO10 5DD, UK; (R.S.); (L.D.G.)
| | - Supachai Vuttipongchaikij
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand; (P.W.); (S.S.); (J.S.); (A.S.); (P.W.)
- Center of Advanced studies for Tropical Natural Resources, Kasetsart University, Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
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25
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Mao J, Wei S, Chen Y, Yang Y, Yin T. The proposed role of MSL-lncRNAs in causing sex lability of female poplars. HORTICULTURE RESEARCH 2023; 10:uhad042. [PMID: 37188057 PMCID: PMC10177001 DOI: 10.1093/hr/uhad042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/02/2023] [Indexed: 05/17/2023]
Abstract
Labile sex expression is frequently observed in dioecious plants, but the underlying genetic mechanism remains largely unknown. Sex plasticity is also observed in many Populus species. Here we carried out a systematic study on a maleness-promoting gene, MSL, detected in the Populus deltoides genome. Our results showed that both strands of MSL contained multiple cis-activating elements, which generated long non-coding RNAs (lncRNAs) promoting maleness. Although female P. deltoides did not have the male-specific MSL gene, a large number of partial sequences with high sequence similarity to this gene were detected in the female poplar genome. Based on sequence alignment, the MSL sequence could be divided into three partial sequences, and heterologous expression of these partial sequences in Arabidopsis confirmed that they could promote maleness. Since activation of the MSL sequences can only result in female sex lability, we propose that MSL-lncRNAs might play a role in causing sex lability of female poplars.
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Affiliation(s)
| | | | - Yingnan Chen
- State Key Laboratory for Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Tree Genetics and Biotechnology of Educational Department of China, Key Laboratory of Tree Genetics and Breeding of Jiangsu Province, Nanjing Forestry University, Nanjing, 210037, China
| | - Yonghua Yang
- Institute for Plant Molecular Biology, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
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26
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Lin C, Huang Q, Liu Z, Brown SE, Chen Q, Li Y, Dong Y, Wu H, Mao Z. AoSAP8-P encoding A20 and/or AN1 type zinc finger protein in asparagus officinalis L. Improving stress tolerance in transgenic Nicotiana sylvestris. Gene 2023; 862:147284. [PMID: 36781027 DOI: 10.1016/j.gene.2023.147284] [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: 09/13/2022] [Revised: 01/04/2023] [Accepted: 02/09/2023] [Indexed: 02/12/2023]
Abstract
The full length CDS of an A20 and AN1 type zinc finger gene (named AoSAP8-P), located nearby the male specific Y chromosome (MSY) region of Asparagus officinalis (garden asparagus) was amplified by RT-PCR from purple passion. This gene, predicted as the stress associated protein (SAPs) gene families, encodes 172 amino acids with multiple cis elements including light, stress response box, MYB and ERF binding sites on its promoter. To analyze its function, the gene expression of different organs in different asparagus gender were analyzed and the overexpressed transgenic Nicotiana sylvestris lines were generated. The results showed the gene was highly expressed in both flower and root of male garden asparagus; the germination rate of seeds of the T2 transgenic lines (T2-5-4 and T2-7-1) under the stress conditions of 125 mM NaCl and 150 mM mannitol were significantly higher than the wild type (WT) respectively. When the potted T2-5-4, T2-7-1 lines and WT were subjected to drought stress for 24 days and the leaf discs immerged into 20 % PEG6000 and 300 mM NaCl solution for 48 h respectively, the T2-5-4 and T2-7-1 with AoSAP8-P expression showed stronger drought, salt and osmotic stress tolerance. When compared, the effects of AoSAP8-P overexpression on productive development showed that the flowering time of transgenic lines, were ∼ 9 day earlier with larger but fewer pollens than its WT counterparts. However, there were no significant differences in anthers, stigmas and pollen viability between the transgenic lines and WT. Our results suggested that, the AoSAP8-P gene plays a role in improving the stress resistance and shortening seeds generation time for perianal survival during the growth and development of garden asparagus.
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Affiliation(s)
- Chun Lin
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, Yunnan 650201, China; Institute of Improvement and Utilization of Characteristic Resource Plants (YNAU), Kunming, China; The Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming, China
| | - Qiuqiu Huang
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, Yunnan 650201, China
| | - Zhengjie Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, Yunnan 650201, China; Institute of Improvement and Utilization of Characteristic Resource Plants (YNAU), Kunming, China; The Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming, China
| | - Sylvia E Brown
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, Yunnan 650201, China
| | - Qing Chen
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, Yunnan 650201, China
| | - Yuping Li
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, Yunnan 650201, China
| | - Yumei Dong
- Institute of Improvement and Utilization of Characteristic Resource Plants (YNAU), Kunming, China
| | - He Wu
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, Yunnan 650201, China
| | - Zichao Mao
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, Yunnan 650201, China; Institute of Improvement and Utilization of Characteristic Resource Plants (YNAU), Kunming, China; The Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming, China.
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27
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Ke SJ, Liu DK, Tu XD, He X, Zhang MM, Zhu MJ, Zhang DY, Zhang CL, Lan SR, Liu ZJ. Apostasia Mitochondrial Genome Analysis and Monocot Mitochondria Phylogenomics. Int J Mol Sci 2023; 24:ijms24097837. [PMID: 37175542 PMCID: PMC10178136 DOI: 10.3390/ijms24097837] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023] Open
Abstract
Apostasia shenzhenica belongs to the subfamily Apostasioideae and is a primitive group located at the base of the Orchidaceae phylogenetic tree. However, the A. shenzhenica mitochondrial genome (mitogenome) is still unexplored, and the phylogenetic relationships between monocots mitogenomes remain unexplored. In this study, we discussed the genetic diversity of A. shenzhenica and the phylogenetic relationships within its monocotyledon mitogenome. We sequenced and assembled the complete mitogenome of A. shenzhenica, resulting in a circular mitochondrial draft of 672,872 bp, with an average read coverage of 122× and a GC content of 44.4%. A. shenzhenica mitogenome contained 36 protein-coding genes, 16 tRNAs, two rRNAs, and two copies of nad4L. Repeat sequence analysis revealed a large number of medium and small repeats, accounting for 1.28% of the mitogenome sequence. Selection pressure analysis indicated high mitogenome conservation in related species. RNA editing identified 416 sites in the protein-coding region. Furthermore, we found 44 chloroplast genomic DNA fragments that were transferred from the chloroplast to the mitogenome of A. shenzhenica, with five plastid-derived genes remaining intact in the mitogenome. Finally, the phylogenetic analysis of the mitogenomes from A. shenzhenica and 28 other monocots showed that the evolution and classification of most monocots were well determined. These findings enrich the genetic resources of orchids and provide valuable information on the taxonomic classification and molecular evolution of monocots.
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Affiliation(s)
- Shi-Jie Ke
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ding-Kun Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiong-De Tu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xin He
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Meng-Meng Zhang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Meng-Jia Zhu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Di-Yang Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Cui-Li Zhang
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Si-Ren Lan
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhong-Jian Liu
- Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization at College of Landscape Architecture and Art, Fujian Agriculture and Forestry University, Fuzhou 350002, China
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28
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Cheng Q, Zeng L, Wen H, Brown SE, Wu H, Li X, Lin C, Liu Z, Mao Z. Steroidal saponin profiles and their key genes for synthesis and regulation in Asparagus officinalis L. by joint analysis of metabolomics and transcriptomics. BMC PLANT BIOLOGY 2023; 23:207. [PMID: 37081391 PMCID: PMC10116787 DOI: 10.1186/s12870-023-04222-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 04/10/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Asparagus officinalis L. is a worldwide cultivated vegetable enrichened in both nutrient and steroidal saponins with multiple pharmacological activities. The upstream biosynthetic pathway of steroidal saponins (USSP) for cholesterol (CHOL) synthesis has been studied, while the downstream pathway of steroidal saponins (DSSP) starting from cholesterol and its regulation in asparagus remains unknown. RESULTS Metabolomics, Illumina RNAseq, and PacBio IsoSeq strategies were applied to different organs of both cultivated green and purple asparagus to detect the steroidal metabolite profiles & contents and to screen their key genes for biosynthesis and regulation. The results showed that there is a total of 427 compounds, among which 18 steroids were detected with fluctuated concentrations in roots, spears and flowering twigs of two garden asparagus cultivars. The key genes of DSSP include; steroid-16-hydroxylase (S16H), steroid-22-hydroxylase (S22H) and steroid-22-oxidase-16-hydroxylase (S22O-16H), steroid-26-hydroxylase (S26H), steroid-3-β-glycosyltransferase (S3βGT) and furostanol glycoside 26-O-beta-glucosidases (F26GHs) which were correlated with the contents of major steroidal saponins were screened, and the transcriptional factors (TFs) co-expressing with the resulted from synthetic key genes, including zinc fingers (ZFs), MYBs and WRKYs family genes were also screened. CONCLUSIONS Based on the detected steroidal chemical structures, profiles and contents which correlated to the expressions of screened synthetic and TFs genes, the full steroidal saponin synthetic pathway (SSP) of asparagus, including its key regulation networks was proposed for the first time.
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Affiliation(s)
- Qin Cheng
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, 650201, Yunnan, China
| | - Liangqin Zeng
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, 650201, Yunnan, China
| | - Hao Wen
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, 650201, Yunnan, China
| | - Sylvia E Brown
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, 650201, Yunnan, China
| | - He Wu
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, 650201, Yunnan, China
| | - Xingyu Li
- Institute of Improvement and Utilization of Characteristic Resource Plants, YNAU, Kunming, China
- The Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming, China
| | - Chun Lin
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, 650201, Yunnan, China
- Institute of Improvement and Utilization of Characteristic Resource Plants, YNAU, Kunming, China
| | - Zhengjie Liu
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, 650201, Yunnan, China.
- Institute of Improvement and Utilization of Characteristic Resource Plants, YNAU, Kunming, China.
| | - Zichao Mao
- College of Agronomy and Biotechnology, Yunnan Agricultural University (YNAU), Kunming, 650201, Yunnan, China.
- Institute of Improvement and Utilization of Characteristic Resource Plants, YNAU, Kunming, China.
- The Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming, China.
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29
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Kenchanmane Raju SK, Ledford M, Niederhuth CE. DNA methylation signatures of duplicate gene evolution in angiosperms. PLANT PHYSIOLOGY 2023:kiad220. [PMID: 37061825 PMCID: PMC10400039 DOI: 10.1093/plphys/kiad220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/03/2023] [Accepted: 04/12/2023] [Indexed: 06/19/2023]
Abstract
Gene duplication is a source of evolutionary novelty. DNA methylation may play a role in the evolution of duplicate genes (paralogs) through its association with gene expression. While this relationship has been examined to varying extents in a few individual species, the generalizability of these results at either a broad phylogenetic scale with species of differing duplication histories or across a population remains unknown. We applied a comparative epigenomics approach to 43 angiosperm species across the phylogeny and a population of 928 Arabidopsis (Arabidopsis thaliana) accessions, examining the association of DNA methylation with paralog evolution. Genic DNA methylation was differentially associated with duplication type, the age of duplication, sequence evolution, and gene expression. Whole genome duplicates were typically enriched for CG-only gene-body methylated or unmethylated genes, while single-gene duplications were typically enriched for non-CG methylated or unmethylated genes. Non-CG methylation, in particular, was characteristic of more recent single-gene duplicates. Core angiosperm gene families differentiated into those which preferentially retain paralogs and 'duplication-resistant' families, which convergently reverted to singletons following duplication. Duplication-resistant families that still have paralogous copies were, uncharacteristically for core angiosperm genes, enriched for non-CG methylation. Non-CG methylated paralogs had higher rates of sequence evolution, higher frequency of presence-absence variation, and more limited expression. This suggests that silencing by non-CG methylation may be important to maintaining dosage following duplication and be a precursor to fractionation. Our results indicate that genic methylation marks differing evolutionary trajectories and fates between paralogous genes and have a role in maintaining dosage following duplication.
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Affiliation(s)
| | | | - Chad E Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA
- AgBioResearch, Michigan State University, East Lansing, MI 48824, USA
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Masuda K, Akagi T. Evolution of sex in crops: recurrent scrap and rebuild. BREEDING SCIENCE 2023; 73:95-107. [PMID: 37404348 PMCID: PMC10316312 DOI: 10.1270/jsbbs.22082] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/20/2022] [Indexed: 07/06/2023]
Abstract
Sexuality is the main strategy for maintaining genetic diversity within a species. In flowering plants (angiosperms), sexuality is derived from ancestral hermaphroditism and multiple sexualities can be expressed in an individual. The mechanisms conferring chromosomal sex determination in plants (or dioecy) have been studied for over a century by both biologists and agricultural scientists, given the importance of this field for crop cultivation and breeding. Despite extensive research, the sex determining gene(s) in plants had not been identified until recently. In this review, we dissect plant sex evolution and determining systems, with a focus on crop species. We introduced classic studies with theoretical, genetic, and cytogenic approaches, as well as more recent research using advanced molecular and genomic techniques. Plants have undergone very frequent transitions into, and out of, dioecy. Although only a few sex determinants have been identified in plants, an integrative viewpoint on their evolutionary trends suggests that recurrent neofunctionalization events are potentially common, in a "scrap and (re)build" cycle. We also discuss the potential association between crop domestication and transitions in sexual systems. We focus on the contribution of duplication events, which are particularly frequent in plant taxa, as a trigger for the creation of new sexual systems.
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Affiliation(s)
- Kanae Masuda
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
| | - Takashi Akagi
- Graduate School of Environmental and Life Science, Okayama University, Okayama 700-8530, Japan
- JST, PRESTO, Kawaguchi, Saitama 332-0012, Japan
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Sheng W, Deng J, Wang C, Kuang Q. The garden asparagus ( Asparagus officinalis L.) mitochondrial genome revealed rich sequence variation throughout whole sequencing data. FRONTIERS IN PLANT SCIENCE 2023; 14:1140043. [PMID: 37051082 PMCID: PMC10084930 DOI: 10.3389/fpls.2023.1140043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
Garden asparagus (Asparagus officinalis L.) is a horticultural crop with high nutritional and medical value, considered an ideal plant for sex determination research among many dioecious plants, whose genomic information can support genetic analysis and breeding programs. In this research, the entire mitochondrial genome of A. officinalis was sequenced, annotated and assembled using a mixed Illumina and PacBio data. The garden asparagus circular mitochondrial genome measures 492,062 bp with a GC value of 45.9%. Thirty-six protein-coding genes, 17 tRNA and 6 rRNA genes were annotated, among which 8 protein-coding genes contained 16 introns. In addition, 254 SSRs with 10 complete tandem repeats and 293 non-tandem repeats were identified. It was found that the codons of edited sites located in the amino acids showed a leucine-formation trend, and RNA editing sites mainly caused the mutual transformation of amino acids with the same properties. Furthermore, 72 sequence fragments accounting for 20,240 bp, presentating 4.11% of the whole mitochondrial genome, were observed to migrate from chloroplast to mitochondrial genome of A. officinalis. The phylogenetic analysis showed that the closest genetic relationship between A. officinalis with onion (Allium cepa) inside the Liliaceae family. Our results demonstrated that high percentage of protein-coding genes had evolutionary conservative properties, with Ka/Ks values less than 1. Therefore, this study provides a high-quality garden asparagus mitochondrial genome, useful to promote better understanding of gene exchange between organelle genomes.
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Affiliation(s)
- Wentao Sheng
- Department of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, China
| | - Jianlan Deng
- School of Foreign Language, Nanchang Normal University, Nanchang, Jiangxi, China
| | - Chao Wang
- Department of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, China
| | - Quan Kuang
- Department of Biological Technology, Nanchang Normal University, Nanchang, Jiangxi, China
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Wang F, Ren X, Jiang M, Hou K, Xin G, Yan F, Zhao P, Liu W. Male-linked gene TsRPL10a' in androdioecious tree Tapiscia sinensis: implications for sex differentiation by influencing gynoecium development. TREE PHYSIOLOGY 2023; 43:486-500. [PMID: 36401877 DOI: 10.1093/treephys/tpac131] [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: 06/26/2022] [Revised: 10/07/2022] [Accepted: 11/10/2022] [Indexed: 05/03/2023]
Abstract
The mechanism of sex differentiation in androdioecy is of great significance for illuminating the origin and evolution of dioecy. Tapiscia sinensis Oliv. is a functionally androdioecious species with both male and hermaphroditic individuals. Male flowers of T. sinensis lack the ovules of gynoecia compared with hermaphrodites. To identify sex simply and accurately, and further find the potential determinants of sex differentiation in T. sinensis, we found that TsRPL10a', a duplicate of TsRPL10a, was a male-linked gene. The promoter (5' untranslated region and the first intron) of TsRPL10a' can be used to accurately identify sex in T. sinensis. TsRPL10a is a ribosomal protein that is involved in gynoecium development, and sufficient ribosomal levels are necessary for female gametogenesis. The expression level of TsRPL10a was significantly downregulated in male flower primordia compared with hermaphrodites. The RNA fluorescence in situ hybridization (FISH) assay demonstrated that TsRPL10a was almost undetectable in male gynoecia at the gynoecial ridge stage, which was a key period of ovule formation by scanning electron microscope observation. In male flowers, although the promoter activity of TsRPL10a was significantly higher than TsRPL10a' verified by transgenic Arabidopsis thaliana, the transcriptional expression ratio of TsRPL10a was obviously lower than TsRPL10a' and reached its lowest at the gynoecial ridge stage, indicating the existence of a female suppressor. The promoter similarity of TsRPL10a and TsRPL10a' was only 45.29%; the genomic sequence similarity was 89.8%; four amino acids were altered in TsRPL10a'. The secondary structure of TsRPL10a' was different from TsRPL10a, and TsRPL10a' did not exhibit FISH and GUS expression in the gynoecium the way TsRPL10a did. From the perspective of RT-qPCR, its high expression level, followed by the low expression level of TsRPL10a in male flowers, indicates its antagonism function with TsRPL10a. The evolutionary analysis, subcellular localization and flower expression pattern suggested that TsRPL10a might be functionally conserved with AtRPL10aA, AtRPL10aB and AtRPL10aC in A. thaliana. Overall, we speculated that TsRPL10a and its duplicate TsRPL10a' might be involved in sex differentiation by influencing gynoecium development in T. sinensis.
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Affiliation(s)
- Feng Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, School of Life Science, Northwest University, Xi'an 710069, China
| | - Xiaolong Ren
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Minggao Jiang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, School of Life Science, Northwest University, Xi'an 710069, China
| | - Kunpeng Hou
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, School of Life Science, Northwest University, Xi'an 710069, China
| | - Guiliang Xin
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, School of Life Science, Northwest University, Xi'an 710069, China
| | - Feng Yan
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, School of Life Science, Northwest University, Xi'an 710069, China
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, School of Life Science, Northwest University, Xi'an 710069, China
| | - Wenzhe Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China (Northwest University), Ministry of Education, School of Life Science, Northwest University, Xi'an 710069, China
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Identifying Genes Associated with Female Flower Development of Phellodendron amurense Rupr. Using a Transcriptomics Approach. Genes (Basel) 2023; 14:genes14030661. [PMID: 36980934 PMCID: PMC10048520 DOI: 10.3390/genes14030661] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/09/2023] Open
Abstract
Phellodendron amurense Rupr., a species of Rutaceae, is a nationally protected and valuable medicinal plant. It is generally considered to be dioecious. With the discovery of monoecious P. amurense, the phenomenon that its sex development is regulated by epigenetics has been revealed, but the way epigenetics affects the sex differentiation of P. amurense is still unclear. In this study, we investigated the effect of DNA methylation on the sexual development of P. amurense. The young inflorescences of male plants were treated with the demethylation agent 5-azaC, and the induced female flowers were obtained. The induced female flowers’ morphological functions and transcriptome levels were close to those of normally developed plants. Genes associated with the development of female flowers were studied by comparing the differences in transcriptome levels between the male and female flowers. Referring to sex-related genes reported in other plants, 188 candidate genes related to the development of female flowers were obtained, including sex-regulating genes, genes related to the formation and development of sexual organs, genes related to biochemical pathways, and hormone-related genes. RPP0W, PAL3, MCM2, MCM6, SUP, PIN1, AINTEGUMENTA, AINTEGUMENTA-LIKE6, AGL11, SEUSS, SHI-RELATED SEQUENCE 5, and ESR2 were preliminarily considered the key genes for female flower development. This study has demonstrated that epigenetics was involved in the sex regulation of P. amurense, with DNA methylation as one of its regulatory modes. Moreover, some candidate genes related to the sexual differentiation of P. amurense were obtained with analysis. These results are of great significance for further exploring the mechanism of sex differentiation of P. amurense and studying of sex differentiation of plants.
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Sekimoto H, Komiya A, Tsuyuki N, Kawai J, Kanda N, Ootsuki R, Suzuki Y, Toyoda A, Fujiyama A, Kasahara M, Abe J, Tsuchikane Y, Nishiyama T. A divergent RWP-RK transcription factor determines mating type in heterothallic Closterium. THE NEW PHYTOLOGIST 2023; 237:1636-1651. [PMID: 36533897 DOI: 10.1111/nph.18662] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
The Closterium peracerosum-strigosum-littorale complex (Closterium, Zygnematophyceae) has an isogamous mating system. Members of the Zygnematophyceae are the closest relatives to extant land plants and are distantly related to chlorophytic models, for which a genetic basis of mating type (MT) determination has been reported. We thus investigated MT determination in Closterium. We sequenced genomes representing the two MTs, mt+ and mt-, in Closterium and identified CpMinus1, a gene linked to the mt- phenotype. We analyzed its function using reverse genetics methods. CpMinus1 encodes a divergent RWP-RK domain-containing-like transcription factor and is specifically expressed during gamete differentiation. Introduction of CpMinus1 into an mt+ strain was sufficient to convert it to a phenotypically mt- strain, while CpMinus1-knockout mt- strains were phenotypically mt+. We propose that CpMinus1 is the major MT determinant that acts by evoking the mt- phenotype and suppressing the mt+ phenotype in heterothallic Closterium. CpMinus1 likely evolved independently in the Zygnematophyceae lineage, which lost an egg-sperm anisogamous mating system. mt- specific regions possibly constitute an MT locus flanked by common sequences that undergo some recombination.
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Affiliation(s)
- Hiroyuki Sekimoto
- Division of Material and Biological Sciences, Graduate School of Science, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo, 112-8681, Japan
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo, 112-8681, Japan
| | - Ayumi Komiya
- Division of Material and Biological Sciences, Graduate School of Science, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo, 112-8681, Japan
| | - Natsumi Tsuyuki
- Division of Material and Biological Sciences, Graduate School of Science, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo, 112-8681, Japan
| | - Junko Kawai
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo, 112-8681, Japan
| | - Naho Kanda
- Division of Material and Biological Sciences, Graduate School of Science, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo, 112-8681, Japan
| | - Ryo Ootsuki
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo, 112-8681, Japan
| | - Yutaka Suzuki
- Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8568, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Asao Fujiyama
- Comparative Genomics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Masahiro Kasahara
- Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8568, Japan
| | - Jun Abe
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo, 112-8681, Japan
| | - Yuki Tsuchikane
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo, 112-8681, Japan
- Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Tomoaki Nishiyama
- Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kakumacho, Kanazawa, Ishikawa, 920-1192, Japan
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Mai Y, Sun P, Suo Y, Li H, Han W, Diao S, Wang L, Yuan J, Wang Y, Ye L, Zhang Y, Li F, Fu J. Regulatory mechanism of MeGI on sexuality in Diospyros oleifera. FRONTIERS IN PLANT SCIENCE 2023; 14:1046235. [PMID: 36909399 PMCID: PMC9994623 DOI: 10.3389/fpls.2023.1046235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Dioecy system is an important strategy for maintaining genetic diversity. The transcription factor MeGI, contributes to dioecy by promoting gynoecium development in Diospyros lotus and D. kaki. However, the function of MeGI in D. oleifera has not been identified. In this study, we confirmed that MeGI, cloned from D. oleifera, repressed the androecium development in Arabidopsis thaliana. Subsequently, chromatin immunoprecipitation-sequencing (ChIP-seq), DNA affinity purification-sequencing (DAP-seq), and RNA-seq were used to uncover the gene expression response to MeGI. The results showed that the genes upregulated and downregulated in response to MeGI were mainly enriched in the circadian rhythm-related and flavonoid biosynthetic pathways, respectively. Additionally, the WRKY DNA-binding protein 28 (WRKY28) gene, which was detected by ChIP-seq, DAP-seq, and RNA-seq, was emphasized. WRKY28 has been reported to inhibit salicylic acid (SA) biosynthesis and was upregulated in MeGI-overexpressing A. thaliana flowers, suggesting that MeGI represses the SA level by increasing the expression level of WRKY28. This was confirmed that SA level was lower in D. oleifera female floral buds than male. Overall, our findings indicate that the MeGI mediates its sex control function in D. oleifera mainly by regulating genes in the circadian rhythm, SA biosynthetic, and flavonoid biosynthetic pathways.
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Affiliation(s)
- Yini Mai
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Peng Sun
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Yujing Suo
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Huawei Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Weijuan Han
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Songfeng Diao
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Liyuan Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
- Chinese Academy of Sciences (CAS) Engineering Laboratory for Vegetation Ecosystem Restoration on Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Jiaying Yuan
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Yiru Wang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Lingshuai Ye
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Yue Zhang
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Fangdong Li
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
| | - Jianmin Fu
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National Forestry and Grassland Administration, Research Institute of Non-timber Forestry, Chinese Academy of Forestry, Zhengzhou, China
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Raiyemo DA, Bobadilla LK, Tranel PJ. Genomic profiling of dioecious Amaranthus species provides novel insights into species relatedness and sex genes. BMC Biol 2023; 21:37. [PMID: 36804015 PMCID: PMC9940365 DOI: 10.1186/s12915-023-01539-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 02/08/2023] [Indexed: 02/21/2023] Open
Abstract
BACKGROUND Amaranthus L. is a diverse genus consisting of domesticated, weedy, and non-invasive species distributed around the world. Nine species are dioecious, of which Amaranthus palmeri S. Watson and Amaranthus tuberculatus (Moq.) J.D. Sauer are troublesome weeds of agronomic crops in the USA and elsewhere. Shallow relationships among the dioecious Amaranthus species and the conservation of candidate genes within previously identified A. palmeri and A. tuberculatus male-specific regions of the Y (MSYs) in other dioecious species are poorly understood. In this study, seven genomes of dioecious amaranths were obtained by paired-end short-read sequencing and combined with short reads of seventeen species in the family Amaranthaceae from NCBI database. The species were phylogenomically analyzed to understand their relatedness. Genome characteristics for the dioecious species were evaluated and coverage analysis was used to investigate the conservation of sequences within the MSY regions. RESULTS We provide genome size, heterozygosity, and ploidy level inference for seven newly sequenced dioecious Amaranthus species and two additional dioecious species from the NCBI database. We report a pattern of transposable element proliferation in the species, in which seven species had more Ty3 elements than copia elements while A. palmeri and A. watsonii had more copia elements than Ty3 elements, similar to the TE pattern in some monoecious amaranths. Using a Mash-based phylogenomic analysis, we accurately recovered taxonomic relationships among the dioecious Amaranthus species that were previously identified based on comparative morphology. Coverage analysis revealed eleven candidate gene models within the A. palmeri MSY region with male-enriched coverages, as well as regions on scaffold 19 with female-enriched coverage, based on A. watsonii read alignments. A previously reported FLOWERING LOCUS T (FT) within A. tuberculatus MSY contig was also found to exhibit male-enriched coverages for three species closely related to A. tuberculatus but not for A. watsonii reads. Additional characterization of the A. palmeri MSY region revealed that 78% of the region is made of repetitive elements, typical of a sex determination region with reduced recombination. CONCLUSIONS The results of this study further increase our understanding of the relationships among the dioecious species of the Amaranthus genus as well as revealed genes with potential roles in sex function in the species.
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Affiliation(s)
- Damilola A Raiyemo
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
| | - Lucas K Bobadilla
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA
| | - Patrick J Tranel
- Department of Crop Sciences, University of Illinois, Urbana, IL, 61801, USA.
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Vegetable biology and breeding in the genomics era. SCIENCE CHINA. LIFE SCIENCES 2023; 66:226-250. [PMID: 36508122 DOI: 10.1007/s11427-022-2248-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/17/2022] [Indexed: 12/14/2022]
Abstract
Vegetable crops provide a rich source of essential nutrients for humanity and represent critical economic values to global rural societies. However, genetic studies of vegetable crops have lagged behind major food crops, such as rice, wheat and maize, thereby limiting the application of molecular breeding. In the past decades, genome sequencing technologies have been increasingly applied in genetic studies and breeding of vegetables. In this review, we recapitulate recent progress on reference genome construction, population genomics and the exploitation of multi-omics datasets in vegetable crops. These advances have enabled an in-depth understanding of their domestication and evolution, and facilitated the genetic dissection of numerous agronomic traits, which jointly expedites the exploitation of state-of-the-art biotechnologies in vegetable breeding. We further provide perspectives of further directions for vegetable genomics and indicate how the ever-increasing omics data could accelerate genetic, biological studies and breeding in vegetable crops.
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38
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Meng Q, Kim SJ, Costa MA, Moinuddin SGA, Celoy RM, Smith CA, Cort JR, Davin LB, Lewis NG. Dirigent protein subfamily function and structure in terrestrial plant phenol metabolism. Methods Enzymol 2023; 683:101-150. [PMID: 37087184 DOI: 10.1016/bs.mie.2023.02.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023]
Abstract
Aquatic plant transition to land, and subsequent terrestrial plant species diversification, was accompanied by the emergence and massive elaboration of plant phenol chemo-diversity. Concomitantly, dirigent protein (DP) and dirigent-like protein subfamilies, derived from large multigene families, emerged and became extensively diversified. DP biochemical functions as gateway entry points into new and diverse plant phenol skeletal types then markedly expanded. DPs have at least eight non-uniformly distributed subfamilies, with different DP subfamily members of known biochemical/physiological function now implicated as gateway entries to lignan, lignin, aromatic diterpenoid, pterocarpan and isoflavene pathways. While some other DP subfamily members have jacalin domains, both these and indeed the majority of DPs throughout the plant kingdom await discovery of their biochemical roles. Methods and approaches were developed to discover DP biochemical function as gateway entry points to distinct plant phenol skeletal types in land plants. Various DP 3D X-ray structural determinations enabled structure-based comparative sequence analysis and modeling to understand similarities and differences among the different DP subfamilies. We consider that the core DP β-barrel fold and associated characteristics are likely common to all DPs, with several residues conserved and nearly invariant. There is also considerable variation in residue composition and topography of the putative substrate binding pockets, as well as substantial differences in several loops, such as the β1-β2 loop. All DPs likely bind and stabilize quinone methide intermediates, while guiding distinctive regio- and/or stereo-chemical entry into Nature's chemo-diverse land plant phenol metabolic classes.
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Affiliation(s)
- Qingyan Meng
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Sung-Jin Kim
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Michael A Costa
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Syed G A Moinuddin
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Rhodesia M Celoy
- School of Plant Sciences, University of Arizona, Tucson, AZ, United States
| | - Clyde A Smith
- Stanford Synchrotron Radiation Lightsource, Menlo Park, CA, United States
| | - John R Cort
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Laurence B Davin
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Norman G Lewis
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States.
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Xu Y, Zhang K, Zhang Z, Liu Y, Lv F, Sun P, Gao S, Wang Q, Yu C, Jiang J, Li C, Song M, Gao Z, Sui C, Li H, Jin Y, Guo X, Wei J. A chromosome-level genome assembly for Dracaena cochinchinensis reveals the molecular basis of its longevity and formation of dragon's blood. PLANT COMMUNICATIONS 2022; 3:100456. [PMID: 36196059 PMCID: PMC9700203 DOI: 10.1016/j.xplc.2022.100456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 08/15/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Dracaena, a remarkably long-lived and slowly maturing species of plant, is world famous for its ability to produce dragon's blood, a precious traditional medicine used by different cultures since ancient times. However, there is no detailed and high-quality genome available for this species at present; thus, the molecular mechanisms that underlie its important traits are largely unknown. These factors seriously limit the protection and regeneration of this rare and endangered plant resource. Here, we sequenced and assembled the genome of Dracaena cochinchinensis at the chromosome level. The D. cochinchinensis genome covers 1.21 Gb with a scaffold N50 of 50.06 Mb and encodes 31 619 predicted protein-coding genes. Analysis showed that D. cochinchinensis has undergone two whole-genome duplications and two bursts of long terminal repeat insertions. The expansion of two gene classes, cis-zeatin O-glucosyltransferase and small auxin upregulated RNA, were found to account for its longevity and slow growth. Two transcription factors (bHLH and MYB) were found to be core regulators of the flavonoid biosynthesis pathway, and reactive oxygen species were identified as the specific signaling molecules responsible for the injury-induced formation of dragon's blood. Our study provides high-quality genomic information relating to D. cochinchinensis and significant insight into the molecular mechanisms responsible for its longevity and formation of dragon's blood. These findings will facilitate resource protection and sustainable utilization of Dracaena.
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Affiliation(s)
- Yanhong Xu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Kaijian Zhang
- Novogene Bioinformatics Institute, Beijing 100083, China
| | - Zhonglian Zhang
- Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Jinghong 666100, China
| | - Yang Liu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Feifei Lv
- Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou 570311, China
| | - Peiwen Sun
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Shixi Gao
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Qiuling Wang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Cuicui Yu
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Jiemei Jiang
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Chuangjun Li
- Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Meifang Song
- Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Jinghong 666100, China
| | - Zhihui Gao
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Chun Sui
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Haitao Li
- Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Jinghong 666100, China
| | - Yue Jin
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Xinwei Guo
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China
| | - Jianhe Wei
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou 570311, China.
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Liao N, Hu Z, Miao J, Hu X, Lyu X, Fang H, Zhou YM, Mahmoud A, Deng G, Meng YQ, Zhang K, Ma YY, Xia Y, Zhao M, Yang H, Zhao Y, Kang L, Wang Y, Yang JH, Zhou YH, Zhang MF, Yu JQ. Chromosome-level genome assembly of bunching onion illuminates genome evolution and flavor formation in Allium crops. Nat Commun 2022; 13:6690. [PMID: 36335132 PMCID: PMC9637129 DOI: 10.1038/s41467-022-34491-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
The Allium genus is cultivated globally as vegetables, condiments, or medicinal plants and is characterized by large genomes and strong pungency. However, the genome evolution and genomic basis underlying their unique flavor formation remain poorly understood. Herein, we report an 11.27-Gb chromosome-scale genome assembly for bunching onion (A. fistulosum). The uneven bursts of long-terminal repeats contribute to diversity in genome constituents, and dispersed duplication events largely account for gene expansion in Allium genomes. The extensive duplication and differentiation of alliinase and lachrymatory factor synthase manifest as important evolutionary events during flavor formation in Allium crops. Furthermore, differential selective preference for flavor-related genes likely lead to the variations in isoalliin content in bunching onions. Moreover, we reveal that China is the origin and domestication center for bunching onions. Our findings provide insights into Allium genome evolution, flavor formation and domestication history and enable future genome-assisted breeding of important traits in these crops.
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Affiliation(s)
- Nanqiao Liao
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China
| | - Zhongyuan Hu
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China
| | - Jinshan Miao
- grid.460150.60000 0004 1759 7077Horticultural Institute of Science and Technology, Weifang University of Science and Technology, 262700 Weifang, Shandong P. R. China
| | - Xiaodi Hu
- grid.410753.4Novogene Bioinformatics Institute, 100083 Beijing, P. R. China
| | - Xiaolong Lyu
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China ,grid.418524.e0000 0004 0369 6250Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture and Rural Affairs, 310058 Hangzhou, Zhejiang P. R. China ,grid.13402.340000 0004 1759 700XHainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, 572025 Sanya, Hainan P. R. China
| | - Haitian Fang
- grid.260987.20000 0001 2181 583XNingxia Key Laboratory for Food Microbial-applications Technology and Safety Control, School of Food & Wine, Ningxia University, 750021 Yinchuan, Ningxia P. R. China
| | - Yi-Mei Zhou
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China
| | - Ahmed Mahmoud
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China
| | - Guancong Deng
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China
| | - Yi-Qing Meng
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China
| | - Kejia Zhang
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China
| | - Yu-Yuan Ma
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China
| | - Yuelin Xia
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China
| | - Meng Zhao
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China
| | - Haiyang Yang
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China
| | - Yong Zhao
- grid.410753.4Novogene Bioinformatics Institute, 100083 Beijing, P. R. China
| | - Ling Kang
- grid.410753.4Novogene Bioinformatics Institute, 100083 Beijing, P. R. China
| | - Yiming Wang
- grid.410753.4Novogene Bioinformatics Institute, 100083 Beijing, P. R. China
| | - Jing-Hua Yang
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China ,grid.418524.e0000 0004 0369 6250Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture and Rural Affairs, 310058 Hangzhou, Zhejiang P. R. China ,grid.13402.340000 0004 1759 700XHainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, 572025 Sanya, Hainan P. R. China
| | - Yan-Hong Zhou
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China ,grid.418524.e0000 0004 0369 6250Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture and Rural Affairs, 310058 Hangzhou, Zhejiang P. R. China
| | - Ming-Fang Zhang
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China ,grid.418524.e0000 0004 0369 6250Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture and Rural Affairs, 310058 Hangzhou, Zhejiang P. R. China ,grid.13402.340000 0004 1759 700XHainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, 572025 Sanya, Hainan P. R. China
| | - Jing-Quan Yu
- grid.13402.340000 0004 1759 700XInstitute of Vegetable Science, Zhejiang University, 310058 Hangzhou, Zhejiang P. R. China ,grid.418524.e0000 0004 0369 6250Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture and Rural Affairs, 310058 Hangzhou, Zhejiang P. R. China
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Liu H, Xiao S, Sui S, Huang R, Wang X, Wu H, Liu X. A tandem CCCH type zinc finger protein gene CpC3H3 from Chimonanthus praecox promotes flowering and enhances drought tolerance in Arabidopsis. BMC PLANT BIOLOGY 2022; 22:506. [PMID: 36309643 PMCID: PMC9617390 DOI: 10.1186/s12870-022-03877-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND CCCH-type zinc finger proteins play important roles in plant development and biotic/abiotic stress responses. Wintersweet (Chimonanthus praecox) is a popular ornamental plant with strong resistance to various stresses, which is a good material for exploring gene resource for stress response. In this study, we isolated a CCCH type zinc finger protein gene CpC3H3 (MZ964860) from flower of wintersweet and performed functional analysis with a purpose of identifying gene resource for floral transition and stress tolerance. RESULTS CpC3H3 was predicted a CCCH type zinc finger protein gene encoding a protein containing 446 amino acids with five conserved C-X8-C-X5-C-X3-H motifs. CpC3H3 was localized in the cell membrane but with a nuclear export signal at the N-terminal. Transcripts of CpC3H3 were significantly accumulated in flower buds at floral meristem formation stage, and were induced by polyethylene glycol. Overexpression of CpC3H3 promoted flowering, and enhanced drought tolerance in transgenic A. thaliana. CpC3H3 overexpression affects the expression level of genes involved in flower inducement and stress responses. Further comparative studies on physiological indices showed the contents of proline and soluble sugar, activity of peroxidase and the rates of electrolyte leakage were significantly increased and the content of malondialdehyde and osmotic potential was significantly reduced in transgenic A. thaliana under PEG stress. CONCLUSION Overall, CpC3H3 plays a role in flowering inducement and drought tolerance in transgenic A. thaliana. The CpC3H3 gene has the potential to be used to promote flowering and enhance drought tolerance in plants.
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Affiliation(s)
- Huamin Liu
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, 402160, China
| | - Shiqi Xiao
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Horticulture Science for Southern Mountainous Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Shunzhao Sui
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Horticulture Science for Southern Mountainous Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Renwei Huang
- College of Chemistry and Life Sciences, Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu Normal University, Chengdu, 611130, China
| | - Xia Wang
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Horticulture Science for Southern Mountainous Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Huafeng Wu
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Horticulture Science for Southern Mountainous Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Xia Liu
- College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, Chongqing, 402160, China.
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Kazama Y, Kitoh M, Kobayashi T, Ishii K, Krasovec M, Yasui Y, Abe T, Kawano S, Filatov DA. A CLAVATA3-like Gene Acts as a Gynoecium Suppression Function in White Campion. Mol Biol Evol 2022; 39:msac195. [PMID: 36166820 PMCID: PMC9550985 DOI: 10.1093/molbev/msac195] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
How do separate sexes originate and evolve? Plants provide many opportunities to address this question as they have diverse mating systems and separate sexes (dioecy) that evolved many times independently. The classic "two-factor" model for evolution of separate sexes proposes that males and females can evolve from hermaphrodites via the spread of male and female sterility mutations that turn hermaphrodites into females and males, respectively. This widely accepted model was inspired by early genetic work in dioecious white campion (Silene latifolia) that revealed the presence of two sex-determining factors on the Y-chromosome, though the actual genes remained unknown. Here, we report identification and functional analysis of the putative sex-determining gene in S. latifolia, corresponding to the gynoecium suppression factor (GSF). We demonstrate that GSF likely corresponds to a Y-linked CLV3-like gene that is specifically expressed in early male flower buds and encodes the protein that suppresses gynoecium development in S. latifolia. Interestingly, GSFY has a dysfunctional X-linked homolog (GSFX) and their synonymous divergence (dS = 17.9%) is consistent with the age of sex chromosomes in this species. We propose that female development in S. latifolia is controlled via the WUSCHEL-CLAVATA feedback loop, with the X-linked WUSCHEL-like and Y-linked CLV3-like genes, respectively. Evolution of dioecy in the S. latifolia ancestor likely involved inclusion of ancestral GSFY into the nonrecombining region on the nascent Y-chromosome and GSFX loss of function, which resulted in disbalance of the WUSCHEL-CLAVATA feedback loop between the sexes and ensured gynoecium suppression in males.
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Affiliation(s)
- Yusuke Kazama
- Graduate School of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Kenjojima, Matsuoka, Eiheiji-cho, Japan
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Moe Kitoh
- Graduate School of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Kenjojima, Matsuoka, Eiheiji-cho, Japan
| | - Taiki Kobayashi
- Graduate School of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Kenjojima, Matsuoka, Eiheiji-cho, Japan
| | - Kotaro Ishii
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- National Institutes for Quantum and Radiological Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
| | - Marc Krasovec
- Department of Plant Sciences, 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
| | - Yasuo Yasui
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Tomoko Abe
- RIKEN Nishina Center, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Shigeyuki Kawano
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, FSB-601, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
- Future Center Initiative, The University of Tokyo, 178-4-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan
| | - Dmitry A Filatov
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
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You C, Wen R, Zhang Z, Cheng G, Zhang Y, Li N, Deng C, Li S, Gao W. Development and applications of a collection of single copy gene-based cytogenetic DNA markers in garden asparagus. FRONTIERS IN PLANT SCIENCE 2022; 13:1010664. [PMID: 36247554 PMCID: PMC9559582 DOI: 10.3389/fpls.2022.1010664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
Garden asparagus (Asparagus officinalis, 2n = 2x = 20 chromosomes) is an important dioecious vegetable crop and a model species for studying sex chromosome formation and evolution. However, few molecular cytogenetic studies on garden asparagus have been reported because of its small metaphase chromosomes, the scarcity of distinguished cytogenetic markers, and the high content of repetitive sequences. In this study, a set of single copy genes free of repetitive sequences with sizes ranging from 4.3 kb to 8.2 kb were screened and used as probes for fluorescence in situ hybridization (FISH) to identify individual chromosomes of garden asparagus. The chromosome-specific signal distribution patterns of these probes enabled the distinguishment of each pair of chromosomes. The sequence assembly and cytogenetic map were successfully integrated, and the results confirmed that the chromosome 1 representing the sex chromosome in the genome assembly is chromosome 5 in the karyotype analysis. The cytogenetic identification of the male-specific region of the Y chromosome (MSY) was implemented using a mixed probe derived from a number of MSY-specific single copy sequences. In addition, the chromosome orthologous relationship between garden asparagus (A1-A10, karyotypic analysis) and its hermaphrodite close relative, A. setaceus (B1-B10, karyotypic analysis), was analyzed using this collection of chromosome-specific cytological markers. The results showed that B3 is the ortholog of sex chromosome A5 and thus may represent the ancestral autosome of the current sex chromosome in garden asparagus. Chromosomes B5, B4, B1, B8, B7, and B9 are the orthologs of A2, A3, A4, A7, A8, and A10, respectively. The chromosome identification, cytogenetic recognition of MSY, and the orthologous relationship analysis between garden asparagus and A. setaceus are valuable for the further investigation of the sex chromosome emergence and evolutionary mechanism of garden asparagus and genome structure evolution in the Asparagus genus.
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Affiliation(s)
| | | | | | | | | | | | | | - Shufen Li
- *Correspondence: Wujun Gao, ; Shufen Li,
| | - Wujun Gao
- *Correspondence: Wujun Gao, ; Shufen Li,
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Wang D, Li Y, Li M, Yang W, Ma X, Zhang L, Wang Y, Feng Y, Zhang Y, Zhou R, Sanderson BJ, Keefover-Ring K, Yin T, Smart LB, DiFazio SP, Liu J, Olson M, Ma T. Repeated turnovers keep sex chromosomes young in willows. Genome Biol 2022; 23:200. [PMID: 36151581 PMCID: PMC9502649 DOI: 10.1186/s13059-022-02769-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 09/08/2022] [Indexed: 01/10/2023] Open
Abstract
Background Salicaceae species have diverse sex determination systems and frequent sex chromosome turnovers. However, compared with poplars, the diversity of sex determination in willows is poorly understood, and little is known about the evolutionary forces driving their turnover. Here, we characterized the sex determination in two Salix species, S. chaenomeloides and S. arbutifolia, which have an XY system on chromosome 7 and 15, respectively. Results Based on the assemblies of their sex determination regions, we found that the sex determination mechanism of willows may have underlying similarities with poplars, both involving intact and/or partial homologs of a type A cytokinin response regulator (RR) gene. Comparative analyses suggested that at least two sex turnover events have occurred in Salix, one preserving the ancestral pattern of male heterogamety, and the other changing heterogametic sex from XY to ZW, which could be partly explained by the “deleterious mutation load” and “sexually antagonistic selection” theoretical models. We hypothesize that these repeated turnovers keep sex chromosomes of willow species in a perpetually young state, leading to limited degeneration. Conclusions Our findings further improve the evolutionary trajectory of sex chromosomes in Salicaceae species, explore the evolutionary forces driving the repeated turnovers of their sex chromosomes, and provide a valuable reference for the study of sex chromosomes in other species. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02769-w.
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Affiliation(s)
- Deyan Wang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Yiling Li
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Mengmeng Li
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Wenlu Yang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Xinzhi Ma
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Lei Zhang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Yubo Wang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Yanlin Feng
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Yuanyuan Zhang
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China
| | - Ran Zhou
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Brian J Sanderson
- Department of Biology, West Virginia University, Morgantown, WV, USA.,Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA
| | - Ken Keefover-Ring
- Departments of Botany and Geography, University of Wisconsin-Madison, Madison, WI, USA
| | - Tongming Yin
- The Key Laboratory of Tree Genetics and Biotechnology of Jiangsu Province and Education Department of China, Nanjing Forestry University, Nanjing, China
| | - Lawrence B Smart
- Horticulture Section, School of Integrative Plant Science, Cornell University, Cornell AgriTech, Geneva, NY, USA
| | - Stephen P DiFazio
- Department of Biology, West Virginia University, Morgantown, WV, USA
| | - Jianquan Liu
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China.
| | - Matthew Olson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA.
| | - Tao Ma
- Key Laboratory for Bio-Resource and Eco-Environment of Ministry of Education & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Science, Sichuan University, Chengdu, China.
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Yu T, Ma X, Liu Z, Feng X, Wang Z, Ren J, Cao R, Zhang Y, Nie F, Song X. TVIR: a comprehensive vegetable information resource database for comparative and functional genomic studies. HORTICULTURE RESEARCH 2022; 9:uhac213. [PMID: 36483087 PMCID: PMC9719039 DOI: 10.1093/hr/uhac213] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 09/14/2022] [Indexed: 06/17/2023]
Abstract
Vegetables are an indispensable part of the daily diet of humans. Therefore, it is vital to systematically study the genomic data of vegetables and build a platform for data sharing and analysis. In this study, a comprehensive platform for vegetables with a user-friendly Web interface-The Vegetable Information Resource (TVIR, http://tvir.bio2db.com)-was built based on the genomes of 59 vegetables. TVIR database contains numerous important functional genes, including 5215 auxin genes, 2437 anthocyanin genes, 15 002 flowering genes, 79 830 resistance genes, and 2639 glucosinolate genes of 59 vegetables. In addition, 2597 N6-methyladenosine (m6A) genes were identified, including 513 writers, 1058 erasers, and 1026 readers. A total of 2 101 501 specific clustered regularly interspaced short palindromic repeat (CRISPR) guide sequences and 17 377 miRNAs were detected and deposited in TVIR database. Information on gene synteny, duplication, and orthologs is also provided for 59 vegetable species. TVIR database contains 2 346 850 gene annotations by the Swiss-Prot, TrEMBL, Gene Ontology (GO), Pfam, and Non-redundant (Nr) databases. Synteny, Primer Design, Blast, and JBrowse tools are provided to facilitate users in conducting comparative genomic analyses. This is the first large-scale collection of vegetable genomic data and bioinformatic analysis. All genome and gene sequences, annotations, and bioinformatic results can be easily downloaded from TVIR. Furthermore, transcriptome data of 98 vegetables have been collected and collated, and can be searched by species, tissues, or different growth stages. TVIR is expected to become a key hub for vegetable research globally. The database will be updated with newly assembled vegetable genomes and comparative genomic studies in the future.
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Affiliation(s)
| | | | | | | | - Zhiyuan Wang
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Jun Ren
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Rui Cao
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Yingchao Zhang
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Fulei Nie
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei 063210, China
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46
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Heyduk K, McAssey EV, Leebens‐Mack J. Differential timing of gene expression and recruitment in independent origins of CAM in the Agavoideae (Asparagaceae). THE NEW PHYTOLOGIST 2022; 235:2111-2126. [PMID: 35596719 PMCID: PMC9796715 DOI: 10.1111/nph.18267] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Crassulacean acid metabolism (CAM) photosynthesis has evolved repeatedly across the plant tree of life, however our understanding of the genetic convergence across independent origins remains hampered by the lack of comparative studies. Here, we explore gene expression profiles in eight species from the Agavoideae (Asparagaceae) encompassing three independent origins of CAM. Using comparative physiology and transcriptomics, we examined the variable modes of CAM in this subfamily and the changes in gene expression across time of day and between well watered and drought-stressed treatments. We further assessed gene expression and the molecular evolution of genes encoding phosphoenolpyruvate carboxylase (PPC), an enzyme required for primary carbon fixation in CAM. Most time-of-day expression profiles are largely conserved across all eight species and suggest that large perturbations to the central clock are not required for CAM evolution. By contrast, transcriptional response to drought is highly lineage specific. Yucca and Beschorneria have CAM-like expression of PPC2, a copy of PPC that has never been shown to be recruited for CAM in angiosperms. Together the physiological and transcriptomic comparison of closely related C3 and CAM species reveals similar gene expression profiles, with the notable exception of differential recruitment of carboxylase enzymes for CAM function.
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Affiliation(s)
- Karolina Heyduk
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHI96822USA
- Department of Plant BiologyUniversity of GeorgiaAthensGA30602USA
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenCT06520USA
| | - Edward V. McAssey
- School of Life SciencesUniversity of Hawaiʻi at MānoaHonoluluHI96822USA
| | - Jim Leebens‐Mack
- Department of Plant BiologyUniversity of GeorgiaAthensGA30602USA
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Zhang X, Pan L, Guo W, Li Y, Wang W. A convergent mechanism of sex determination in dioecious plants: Distinct sex-determining genes display converged regulation on floral B-class genes. FRONTIERS IN PLANT SCIENCE 2022; 13:953445. [PMID: 36092432 PMCID: PMC9459113 DOI: 10.3389/fpls.2022.953445] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/27/2022] [Indexed: 06/12/2023]
Abstract
Sex determination in dioecious plants has been broadly and progressively studied with the blooming of genome sequencing and editing techniques. This provides us with a great opportunity to explore the evolution and genetic mechanisms underlining the sex-determining system in dioecious plants. In this study, comprehensively reviewing advances in sex-chromosomes, sex-determining genes, and floral MADS-box genes in dioecious plants, we proposed a convergent model that governs plant dioecy across divergent species using a cascade regulation pathway connecting sex-determining genes and MADS-box genes e.g., B-class genes. We believe that this convergent mechanism of sex determination in dioecious plants will shed light on our understanding of gene regulation and evolution of plant dioecy. Perspectives concerning the evolutionary pathway of plant dioecy are also suggested.
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Affiliation(s)
- Xianzhi Zhang
- Department of Horticulture, College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Linsi Pan
- Department of Horticulture, College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Wei Guo
- Department of Horticulture, College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yongquan Li
- Department of Horticulture, College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Wencai Wang
- Department of Molecular of Biology, Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, China
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Xia Z, Dai X, Fan W, Liu C, Zhang M, Bian P, Zhou Y, Li L, Zhu B, Liu S, Li Z, Wang X, Yu M, Xiang Z, Jiang Y, Zhao A. Chromosome-level Genomes Reveal the Genetic Basis of Descending Dysploidy and Sex Determination in Morus Plants. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:1119-1137. [PMID: 36055564 DOI: 10.1016/j.gpb.2022.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 07/02/2022] [Accepted: 08/23/2022] [Indexed: 12/13/2022]
Abstract
Multiple plant lineages have independently evolved sex chromosomes and variable karyotypes to maintain their sessile lifestyles through constant biological innovation. Morus notabilis, a dioecious mulberry species, has the fewest chromosomes among Morus spp., but the genetic basis of sex determination and karyotype evolution in this species has not been identified. In this study, three high-quality genome assemblies were generated for Morus spp. [including dioecious M. notabilis (male and female) and Morus yunnanensis (female)] with genome sizes of 301-329 Mb and were grouped into six pseudochromosomes. Using a combination of genomic approaches, we found that the putative ancestral karyotype of Morus species was close to 14 protochromosomes, and that several chromosome fusion events resulted in descending dysploidy (2n = 2x = 12). We also characterized a ∼ 6.2-Mb sex-determining region on chromosome 3. Four potential male-specific genes, a partially duplicatedDNA helicase gene (named MSDH) and three Ty3_Gypsy long terminal repeat retrotransposons (named MSTG1/2/3), were identified in the Y-linked area and considered to be strong candidate genes for sex determination or differentiation. Population genomic analysis showed that Guangdong accessions in China were genetically similar to Japanese accessions of mulberry. In addition, genomic areas containing selective sweeps that distinguish domesticated mulberry from wild populations in terms of flowering and disease resistance were identified. Our findings provide an important genetic resource for sex identification research and molecular breeding in mulberry.
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Affiliation(s)
- Zhongqiang Xia
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400716, China
| | - Xuelei Dai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Wei Fan
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400716, China
| | - Changying Liu
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu 610106, China
| | - Meirong Zhang
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400716, China
| | - Peipei Bian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yuping Zhou
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400716, China
| | - Liang Li
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400716, China
| | - Baozhong Zhu
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400716, China
| | - Shuman Liu
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400716, China
| | - Zhengang Li
- The Sericultural and Apicultural Research Institute, Yunnan Academy of Agricultural Sciences, Mengzi 661100, China
| | - Xiling Wang
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400716, China
| | - Maode Yu
- College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing 400716, China
| | - Zhonghuai Xiang
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400716, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
| | - Aichun Zhao
- State Key Laboratory of Silkworm Genome Biology, Institute of Sericulture and Systems Biology, Southwest University, Chongqing 400716, China.
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She H, Xu Z, Zhang H, Wu J, Wang X, Liu Z, Qian W. Remarkable Divergence of the Sex-Linked Region between Two Wild Spinach Progenitors, Spinacia turkestanica and Spinacia tetrandra. BIOLOGY 2022; 11:1138. [PMID: 36009765 PMCID: PMC9404990 DOI: 10.3390/biology11081138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
The sex-linked region (SLR) plays an important role in determining the sex of a plant. The SLR of the Y chromosome, composed of a 14.1-Mb inversion and a 10-Mb Y-duplication region (YDR), was deciphered in Spinacia oleracea previously. However, our understanding of the SLR in its wild relatives, S. turkestanica and S. tetrandra, remains limited. In this study, we used 63 resequencing data from the three Spinacia species to infer the evolution of the SLR among the Spinacia species. In the SLR, all the cultivated spinach and S. turkestanica accessions were clustered into two distinct categories with both sexes, while the S. tetrandra accessions of both sexes were grouped. This suggests that S. oleracea shared a similar SLR with S. turkestanica, but not with S. tetrandra, which was further confirmed based on the population structure and principal component analysis. Furthermore, we identified 3910 fully sex-linked SNPs in S. oleracea and 92.82% of them were available in S. turkestanica, while none of the SNPs were adopted in S. tetrandra. Genome coverage in males and females supported the hypothesis that the YDR increasingly expanded during its evolution. Otherwise, we identified 13 sex-linked transposable element insertion polymorphisms within the inversion in both S. oleracea and S. turkestanica, demonstrating that the transposable element insertions might have occurred before the recombination suppression event of the inversion. The SLR was conserved compared with the pseudoautosomal region given that the genetic hitchhiking process occurred in the SLR during its evolution. Our findings will significantly advance our understanding of the characteristics and evolution of the SLR in Spinacia species.
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Affiliation(s)
| | | | | | | | | | - Zhiyuan Liu
- Correspondence: (Z.L.); (W.Q.); Tel.: +86-010-62194559 (W.Q.)
| | - Wei Qian
- Correspondence: (Z.L.); (W.Q.); Tel.: +86-010-62194559 (W.Q.)
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50
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Filatov DA. Recent expansion of the non-recombining sex-linked region on Silene latifolia sex chromosomes. J Evol Biol 2022; 35:1696-1708. [PMID: 35834179 PMCID: PMC10083954 DOI: 10.1111/jeb.14063] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 06/19/2022] [Accepted: 06/21/2022] [Indexed: 11/27/2022]
Abstract
Evolution of a non-recombining sex-specific region on the Y (or W) chromosome (NRY) is a key step in sex chromosome evolution, but how recombination suppression evolves is not well understood. Studies in many different organisms indicated that NRY evolution often involves several expansion steps. Why such NRY expansions occur remains unclear, although it is though that they are likely driven by sexually antagonistic selection. This paper describes a recent NRY expansion due to shift of the pseudoautosomal boundary on the sex chromosomes of a dioecious plant Silene latifolia. The shift resulted in inclusion of at least 16 pseudoautosomal genes into the NRY. This region is pseudoautosomal in closely related Silene dioica and Silene diclinis, indicating that the NRY expansion occurred in S. latifolia after it speciated from the other species ~120 thousand years ago. As S. latifolia and S. dioica actively hybridise across Europe, interspecific gene flow could blur the PAR boundary in these species. The pseudoautosomal genes have significantly elevated genetic diversity (π ~ 3% at synonymous sites), which is consistent with balancing selection maintaining diversity in this region. The recent shift of the PAR boundary in S. latifolia offers an opportunity to study the process of on-going NRY expansion.
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