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Wen J, Wu BC, Li HM, Zhou W, Song CF. Plastome structure and phylogenetic relationships of genus Hydrocotyle (apiales): provide insights into the plastome evolution of Hydrocotyle. BMC PLANT BIOLOGY 2024; 24:778. [PMID: 39148054 PMCID: PMC11325595 DOI: 10.1186/s12870-024-05483-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 08/05/2024] [Indexed: 08/17/2024]
Abstract
BACKGROUND The genus Hydrocotyle Tourn. ex L. is a key group for further study on the evolution of Apiales, comprising around 170 species globally. Previous studies mainly focused on separate sections and provided much information about this genus, but its infrageneric relationships are still confusing. In addition, the genetic basis of its adaptive evolution remains poorly understood. To investigate the phylogeny and evolution of the genus, we selected ten representative species covering two of three diversity distribution centers and exhibiting rich morphology diversity. Comparative plastome analysis was conducted to clarify the structural character of Hydrocotyle plastomes. Positive selection analyses were implemented to assess the evolution of the genus. Phylogenetic inferences with protein-coding sequences (CDS) of Hydrocotyle and 17 related species were also performed. RESULTS Plastomes within Hydrocotyle were generally conservative in structure, gene order, and size. A total of 14 regions (rps16-trnK, trnQ-rps16, atpI-atpH, trnC-petN-psbM, ycf3-trnS, accD-psaI-ycf4, petA-psbJ, rps12-rpl20, rpl16 intron, rps3-rpl16 intron, rps9-rpl22, ndhF-rpl32, ndhA intron, and ycf1a) were recognized as hotspot regions within the genus, which suggested to be promising DNA barcodes for global phylogenetic analysis of Hydrocotyle. The ycf15 gene was suggested to be a protein-coding gene for Hydrocotyle species, and it could be used as a DNA barcode to identify Hydrocotyle. In phylogenetic analysis, three monophyletic clades (Clade I, II, III) were identified with evidence of rapid radiation speciation within Clade I. The selective pressure analysis detected that six CDS genes (ycf1b, matK, atpF, accD, rps14, and psbB) of Hydrocotyle species were under positive selection. Within the genus, the last four genes were conservative, suggesting a relation to the unique evolution of the genus in Apiales. Seven genes (atpE, matK, psbH, ycf1a, ycf1b, rpoA, and ycf2) were detected to be under some degree of positive selection in different taxa within the genus Hydrocotyle, indicating their role in the adaptive evolution of species. CONCLUSIONS Our study offers new insights into the phylogeny and adaptive evolution of Hydrocotyle. The plastome sequences could significantly enhance phylogenetic resolution and provide genomic resources and potential DNA markers useful for future studies of the genus.
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Affiliation(s)
- Jun Wen
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Bao-Cheng Wu
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Hui-Min Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Wei Zhou
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Chun-Feng Song
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China.
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Zhao S, Gao X, Yu X, Yuan T, Zhang G, Liu C, Li X, Wei P, Li X, Liu X. Comparative Analysis of Chloroplast Genome of Meconopsis (Papaveraceae) Provides Insights into Their Genomic Evolution and Adaptation to High Elevation. Int J Mol Sci 2024; 25:2193. [PMID: 38396871 PMCID: PMC10888623 DOI: 10.3390/ijms25042193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
The Meconopsis species are widely distributed in the Qinghai-Tibet Plateau, Himalayas, and Hengduan Mountains in China, and have high medicinal and ornamental value. The high diversity of plant morphology in this genus poses significant challenges for species identification, given their propensity for highland dwelling, which makes it a question worth exploring how they cope with the harsh surroundings. In this study, we recently generated chloroplast (cp) genomes of two Meconopsis species, Meconopsis paniculata (M. paniculata) and M. pinnatifolia, and compared them with those of ten Meconopsis cp genomes to comprehend cp genomic features, their phylogenetic relationships, and what part they might play in plateau adaptation. These cp genomes shared a great deal of similarities in terms of genome size, structure, gene content, GC content, and codon usage patterns. The cp genomes were between 151,864 bp and 154,997 bp in length, and contain 133 predictive genes. Through sequence divergence analysis, we identified three highly variable regions (trnD-psbD, ccsA-ndhD, and ycf1 genes), which could be used as potential markers or DNA barcodes for phylogenetic analysis. Between 22 and 38 SSRs and some long repeat sequences were identified from 12 Meconopsis species. Our phylogenetic analysis confirmed that 12 species of Meconopsis clustered into a monophyletic clade in Papaveraceae, which corroborated their intrageneric relationships. The results indicated that M. pinnatifolia and M. paniculata are sister species in the phylogenetic tree. In addition, the atpA and ycf2 genes were positively selected in high-altitude species. The functions of these two genes might be involved in adaptation to the extreme environment in the cold and low CO2 concentration conditions at the plateau.
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Affiliation(s)
- Shuqi Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (S.Z.); (X.Y.); (G.Z.); (C.L.); (P.W.)
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibet Plateau of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaoman Gao
- Laboratory of Extreme Environment Biological Resources and Adaptive Evolution, School of Ecology and Environment, Tibet University, Lhasa 850000, China; (X.G.); (T.Y.); (X.L.)
| | - Xiaolei Yu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (S.Z.); (X.Y.); (G.Z.); (C.L.); (P.W.)
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibet Plateau of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Tao Yuan
- Laboratory of Extreme Environment Biological Resources and Adaptive Evolution, School of Ecology and Environment, Tibet University, Lhasa 850000, China; (X.G.); (T.Y.); (X.L.)
| | - Guiyu Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (S.Z.); (X.Y.); (G.Z.); (C.L.); (P.W.)
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibet Plateau of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Chenlai Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (S.Z.); (X.Y.); (G.Z.); (C.L.); (P.W.)
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibet Plateau of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xinzhong Li
- Laboratory of Extreme Environment Biological Resources and Adaptive Evolution, School of Ecology and Environment, Tibet University, Lhasa 850000, China; (X.G.); (T.Y.); (X.L.)
| | - Pei Wei
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (S.Z.); (X.Y.); (G.Z.); (C.L.); (P.W.)
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibet Plateau of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaoyan Li
- Biology Experimental Teaching Center, School of Life Science, Wuhan University, Wuhan 430072, China;
| | - Xing Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China; (S.Z.); (X.Y.); (G.Z.); (C.L.); (P.W.)
- Key Laboratory of Biodiversity and Environment on the Qinghai-Tibet Plateau of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Laboratory of Extreme Environment Biological Resources and Adaptive Evolution, School of Ecology and Environment, Tibet University, Lhasa 850000, China; (X.G.); (T.Y.); (X.L.)
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Zhang T, Chen X, Yan W, Li M, Huang W, Liu Q, Li Y, Guo C, Shu Y. Comparative Analysis of Chloroplast Pan-Genomes and Transcriptomics Reveals Cold Adaptation in Medicago sativa. Int J Mol Sci 2024; 25:1776. [PMID: 38339052 PMCID: PMC10855486 DOI: 10.3390/ijms25031776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/23/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Alfalfa (Medicago sativa) is a perennial forage legume that is widely distributed all over the world; therefore, it has an extremely complex genetic background. Though population structure and phylogenetic studies have been conducted on a large group of alfalfa nuclear genomes, information about the chloroplast genomes is still lacking. Chloroplast genomes are generally considered to be conservative and play an important role in population diversity analysis and species adaptation in plants. Here, 231 complete alfalfa chloroplast genomes were successfully assembled from 359 alfalfa resequencing data, on the basis of which the alfalfa chloroplast pan-genome was constructed. We investigated the genetic variations of the alfalfa chloroplast genome through comparative genomic, genetic diversity, phylogenetic, population genetic structure, and haplotype analysis. Meanwhile, the expression of alfalfa chloroplast genes under cold stress was explored through transcriptome analysis. As a result, chloroplast genomes of 231 alfalfa lack an IR region, and the size of the chloroplast genome ranges from 125,192 bp to 126,105 bp. Using population structure, haplotypes, and construction of a phylogenetic tree, it was found that alfalfa populations could be divided into four groups, and multiple highly variable regions were found in the alfalfa chloroplast genome. Transcriptome analysis showed that tRNA genes were significantly up-regulated in the cold-sensitive varieties, while rps7, rpl32, and ndhB were down-regulated, and the editing efficiency of ycf1, ycf2, and ndhF was decreased in the cold-tolerant varieties, which may be due to the fact that chloroplasts store nutrients through photosynthesis to resist cold. The huge number of genetic variants in this study provide powerful resources for molecular markers.
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Affiliation(s)
- Tianxiang Zhang
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China; (T.Z.); (M.L.); (C.G.)
| | - Xiuhua Chen
- International Agriculture Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China;
| | - Wei Yan
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (W.Y.); (Q.L.)
| | - Manman Li
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China; (T.Z.); (M.L.); (C.G.)
| | - Wangqi Huang
- National Engineering Research Center for Ornamental Horticulture, Yunnan Flower Breeding Key Laboratory, Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China;
| | - Qian Liu
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (W.Y.); (Q.L.)
| | - Yanan Li
- Institute of Tropical and Subtropical Cash Crops, Yunnan Academy of Agricultural Sciences, Baoshan 678000, China; (W.Y.); (Q.L.)
| | - Changhong Guo
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China; (T.Z.); (M.L.); (C.G.)
| | - Yongjun Shu
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, Harbin 150025, China; (T.Z.); (M.L.); (C.G.)
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Chen XH, Ding LN, Zong XY, Xu H, Wang WB, Ding R, Qu B. The complete chloroplast genome sequences of four Liparis species (Orchidaceae) and phylogenetic implications. Gene 2023; 888:147760. [PMID: 37661026 DOI: 10.1016/j.gene.2023.147760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/18/2023] [Accepted: 09/01/2023] [Indexed: 09/05/2023]
Abstract
Liparis Richard (Malaxideae, Epidendroideae) is a large and diverse genus of the family Orchidaceae, the taxonomy of which is complicated and controversial. In this study, we sequenced, assembled and analyzed four complete chloroplast genomes of Liparis species including L. kumokiri, L. makinoana, L. pauliana, and L. viridiflora, and evaluated their phylogenetic relationships with related species for the first time. These four chloroplast genomes (size range 153,095 to 158,239 bp) possess typical quadripartite structures that consist of a large single copy (LSC, 83,533-86,752 bp), a small single copy (SSC, 17,938-18,156 bp) and a pair of inverted repeats (IRs, 26,421-26,933 bp). The genomes contain 133 genes, including 87 protein coding genes, 38 tRNAs and 8 rRNA genes. The genome arrangements, gene contents, gene order, long repeats and simple sequence repeats were similar with small differences observed among these four chloroplast genomes. Five highly variable regions including ycf1, ndhA, ndhF, trnQ and trnK were identified from the comparative analysis with other nine related Liparis species, which had the potential to be used as DNA markers for species identification and phylogenetic studies of Liparis species. Phylogenetic analysis based on the complete chloroplast genome sequences strongly supported the polyphyly of Liparis and its further division into three branches. These results provided valuable information to illustrate the complicated taxonomy, phylogeny and evolution process of the Liparis genus.
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Affiliation(s)
- Xu-Hui Chen
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110161, Liaoning, PR China
| | - Li-Na Ding
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110161, Liaoning, PR China
| | - Xiao-Yan Zong
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110161, Liaoning, PR China
| | - Hua Xu
- School of Modern Industry for Selenium Science and Engineering, Wuhan Polytechnic University, Wuhan 430048, PR China
| | - Wei-Bin Wang
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110161, Liaoning, PR China
| | - Rui Ding
- College of Land and Environment, Shenyang Agricultural University, Shenyang 110161, Liaoning, PR China.
| | - Bo Qu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110161, Liaoning, PR China.
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Yan R, Geng Y, Jia Y, Xiang C, Zhou X, Hu G. Comparative analyses of Linderniaceae plastomes, with implications for its phylogeny and evolution. FRONTIERS IN PLANT SCIENCE 2023; 14:1265641. [PMID: 37828930 PMCID: PMC10565954 DOI: 10.3389/fpls.2023.1265641] [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: 07/23/2023] [Accepted: 09/01/2023] [Indexed: 10/14/2023]
Abstract
Introduction The recently established Linderniaceae, separated from the traditionally defined Scrophulariaceae, is a taxonomically complicated family. Although previous phylogenetic studies based on a few short DNA markers have made great contributions to the taxonomy of Linderniaceae, limited sampling and low resolution of the phylogenetic tree have failed to resolve controversies between some generic circumscriptions. The plastid genome exhibits a powerful ability to solve phylogenetic relationships ranging from shallow to deep taxonomic levels. To date, no plastid phylogenomic studies have been carried out in Linderniaceae. Methods In this study, we newly sequenced 26 plastid genomes of Linderniaceae, including eight genera and 25 species, to explore the phylogenetic relationships and genome evolution of the family through plastid phylogenomic and comparative genomic analyses. Results The plastid genome size of Linderniaceae ranged from 152,386 bp to 154,402 bp, exhibiting a typical quartile structure. All plastomes encoded 114 unique genes, comprising 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. The inverted repeat regions were more conserved compared with the single-copy regions. A total of 1803 microsatellites and 1909 long sequence repeats were identified, and five hypervariable regions (petN-psbM, rps16-trnQ, rpl32-trnL, rpl32, and ycf1) were screened out. Most protein-coding genes were relatively conserved, with only the ycf2 gene found under positive selection in a few species. Phylogenomic analyses confirmed that Linderniaceae was a distinctive lineage and revealed that the presently circumscribed Vandellia and Torenia were non-monophyletic. Discussion Comparative analyses showed the Linderniaceae plastomes were highly conservative in terms of structure, gene order, and gene content. Combining morphological and molecular evidence, we supported the newly established Yamazakia separating from Vandellia and the monotypic Picria as a separate genus. These findings provide further evidence to recognize the phylogenetic relationships among Linderniaceae and new insights into the evolution of the plastid genomes.
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Affiliation(s)
- Rongrong Yan
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, Guizhou, China
- College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Yanfei Geng
- College of Tea Science, Guizhou University, Guiyang, Guizhou, China
| | - Yuhuan Jia
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, Guizhou, China
- College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
| | - Chunlei Xiang
- Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xinxin Zhou
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong, China
| | - Guoxiong Hu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, Guizhou, China
- College of Life Sciences, Guizhou University, Guiyang, Guizhou, China
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Xia L, Wang H, Zhao X, Obel HO, Yu X, Lou Q, Chen J, Cheng C. Chloroplast Pan-Genomes and Comparative Transcriptomics Reveal Genetic Variation and Temperature Adaptation in the Cucumber. Int J Mol Sci 2023; 24:ijms24108943. [PMID: 37240287 DOI: 10.3390/ijms24108943] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/01/2023] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
Although whole genome sequencing, genetic variation mapping, and pan-genome studies have been done on a large group of cucumber nuclear genomes, organelle genome information is largely unclear. As an important component of the organelle genome, the chloroplast genome is highly conserved, which makes it a useful tool for studying plant phylogeny, crop domestication, and species adaptation. Here, we have constructed the first cucumber chloroplast pan-genome based on 121 cucumber germplasms, and investigated the genetic variations of the cucumber chloroplast genome through comparative genomic, phylogenetic, haplotype, and population genetic structure analysis. Meanwhile, we explored the changes in expression of cucumber chloroplast genes under high- and low-temperature stimulation via transcriptome analysis. As a result, a total of 50 complete chloroplast genomes were successfully assembled from 121 cucumber resequencing data, ranging in size from 156,616-157,641 bp. The 50 cucumber chloroplast genomes have typical quadripartite structures, consisting of a large single copy (LSC, 86,339-86,883 bp), a small single copy (SSC, 18,069-18,363 bp), and two inverted repeats (IRs, 25,166-25,797 bp). Comparative genomic, haplotype, and population genetic structure results showed that there is more genetic variation in Indian ecotype cucumbers compared to other cucumber cultivars, which means that many genetic resources remain to be explored in Indian ecotype cucumbers. Phylogenetic analysis showed that the 50 cucumber germplasms could be classified into 3 types: East Asian, Eurasian + Indian, and Xishuangbanna + Indian. The transcriptomic analysis showed that matK were significantly up-regulated under high- and low-temperature stresses, further demonstrating that cucumber chloroplasts respond to temperature adversity by regulating lipid metabolism and ribosome metabolism. Further, accD has higher editing efficiency under high-temperature stress, which may contribute to the heat tolerance. These studies provide useful insight into genetic variation in the chloroplast genome, and established the foundation for exploring the mechanisms of temperature-stimulated chloroplast adaptation.
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Affiliation(s)
- Lei Xia
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Han Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaokun Zhao
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Hesbon Ochieng Obel
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaqing Yu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Qunfeng Lou
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinfeng Chen
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Chunyan Cheng
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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