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Huang A, Feng S, Ye Z, Zhang T, Chen S, Chen C, Chen S. Genome Assembly and Structural Variation Analysis of Luffa acutangula Provide Insights on Flowering Time and Ridge Development. PLANTS (BASEL, SWITZERLAND) 2024; 13:1828. [PMID: 38999668 PMCID: PMC11243878 DOI: 10.3390/plants13131828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 06/21/2024] [Accepted: 06/21/2024] [Indexed: 07/14/2024]
Abstract
Luffa spp. is an important worldwide cultivated vegetable and medicinal plant from the Cucurbitaceae family. In this study, we report a high-quality chromosome-level genome of the high-generation inbred line SG261 of Luffa acutangula. The genomic sequence was determined by PacBio long reads, Hi-C sequencing reads, and 10× Genomics sequencing, with an assembly size of 739.82 Mb, contig N50 of 18.38 Mb, and scaffold N50 of 56.08 Mb. The genome of L. acutangula SG261 was predicted to contain 27,312 protein-coding genes and 72.56% repetitive sequences, of which long terminal repeats (LTRs) were an important form of repetitive sequences, accounting for 67.84% of the genome. Phylogenetic analysis reveals that L. acutangula evolved later than Luffa cylindrica, and Luffa is closely related to Momodica charantia. Comparing the genome of L. acutangula SG261 and L. cylindrica with PacBio data, 67,128 high-quality structural variations (SVs) and 55,978 presence-absence variations (PAVs) were identified in SG261, resulting in 2424 and 1094 genes with variation in the CDS region, respectively, and there are 287 identical genes affected by two different structural variation analyses. In addition, we found that the transcription factor FY (FLOWERING LOCUS Y) families had a large expansion in L. acutangula SG261 (flowering in the morning) compared to L. cylindrica (flowering in the afternoon), which may result in the early flowering time in L. acutangula SG261. This study provides valuable reference for the breeding of and pan-genome research into Luffa species.
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Affiliation(s)
- Aizheng Huang
- Institute of Agricultural Science Research of Jiangmen, Jiangmen 529060, China;
| | - Shuo Feng
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (S.F.)
| | - Zhuole Ye
- Dongguan Agricultural Scientific Research Center, Dongguan 523086, China
| | - Ting Zhang
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (S.F.)
| | - Shenglong Chen
- Dongguan Agricultural Scientific Research Center, Dongguan 523086, China
| | - Changming Chen
- College of Horticulture, South China Agricultural University, Guangzhou 510642, China; (S.F.)
| | - Shijun Chen
- Institute of Agricultural Science Research of Jiangmen, Jiangmen 529060, China;
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Li YD, Liu YC, Jiang YX, Namisy A, Chung WH, Sun YH, Chen SY. Analyzing genetic diversity in luffa and developing a Fusarium wilt-susceptible linked SNP marker through a single plant genome-wide association (sp-GWAS) study. BMC PLANT BIOLOGY 2024; 24:307. [PMID: 38644483 PMCID: PMC11034075 DOI: 10.1186/s12870-024-05022-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 04/15/2024] [Indexed: 04/23/2024]
Abstract
BACKGROUND Luffa (Luffa spp.) is an economically important crop of the Cucurbitaceae family, commonly known as sponge gourd or vegetable gourd. It is an annual cross-pollinated crop primarily found in the subtropical and tropical regions of Asia, Australia, Africa, and the Americas. Luffa serves not only as a vegetable but also exhibits medicinal properties, including anti-inflammatory, antidiabetic, and anticancer effects. Moreover, the fiber derived from luffa finds extensive applications in various fields such as biotechnology and construction. However, luffa Fusarium wilt poses a severe threat to its production, and existing control methods have proven ineffective in terms of cost-effectiveness and environmental considerations. Therefore, there is an urgent need to develop luffa varieties resistant to Fusarium wilt. Single-plant GWAS (sp-GWAS) has been demonstrated as a promising tool for the rapid and efficient identification of quantitative trait loci (QTLs) associated with target traits, as well as closely linked molecular markers. RESULTS In this study, a collection of 97 individuals from 73 luffa accessions including two major luffa species underwent single-plant GWAS to investigate luffa Fusarium wilt resistance. Utilizing the double digest restriction site associated DNA (ddRAD) method, a total of 8,919 high-quality single nucleotide polymorphisms (SNPs) were identified. The analysis revealed the potential for Fusarium wilt resistance in accessions from both luffa species. There are 6 QTLs identified from 3 traits, including the area under the disease progress curve (AUDPC), a putative disease-resistant QTL, was identified on the second chromosome of luffa. Within the region of linkage disequilibrium, a candidate gene homologous to LOC111009722, which encodes peroxidase 40 and is associated with disease resistance in Cucumis melo, was identified. Furthermore, to validate the applicability of the marker associated with resistance from sp-GWAS, an additional set of 21 individual luffa plants were tested, exhibiting 93.75% accuracy in detecting susceptible of luffa species L. aegyptiaca Mill. CONCLUSION In summary, these findings give a hint of genome position that may contribute to luffa wild resistance to Fusarium and can be utilized in the future luffa wilt resistant breeding programs aimed at developing wilt-resistant varieties by using the susceptible-linked SNP marker.
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Affiliation(s)
- Yun-Da Li
- Department of Agronomy, National Chung-Hsing University, Taichung, Taiwan
| | - Yu-Chi Liu
- Department of Agronomy, National Chung-Hsing University, Taichung, Taiwan
| | - Yu-Xuan Jiang
- Department of Agronomy, National Chung-Hsing University, Taichung, Taiwan
| | - Ahmed Namisy
- Department of Plant Pathology, National Chung-Hsing University, Taichung, Taiwan
| | - Wen-Hsin Chung
- Department of Plant Pathology, National Chung-Hsing University, Taichung, Taiwan
| | - Ying-Hsuan Sun
- Department of Forestry, National Chung-Hsing University, Taichung, Taiwan
| | - Shu-Yun Chen
- Department of Agronomy, National Chung-Hsing University, Taichung, Taiwan.
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Qi X, Mo Q, Li J, Zi Z, Xu M, Yue S, Zhao H, Zhu H, Wang G. Establishment of virus-induced gene silencing (VIGS) system in Luffa acutangula using Phytoene desaturase (PDS) and tendril synthesis related gene (TEN). PLANT METHODS 2023; 19:94. [PMID: 37653449 PMCID: PMC10470258 DOI: 10.1186/s13007-023-01064-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 07/24/2023] [Indexed: 09/02/2023]
Abstract
BACKGROUND Virus-induced gene silencing (VIGS) is a reverse genetics technology that can efficiently and rapidly identify plant gene functions. Although a variety of VIGS vectors have been successfully used in plants, only a few reports on VIGS technology in Luffa exist. RESULTS In the present study, a new cucumber green mottle mosaic virus (CGMMV)-based VIGS vector, pV190, was applied to establish the CGMMV-VIGS to investigate the feasibility of the silencing system for Luffa. Phytoene desaturase (PDS) gene was initially selected as a VIGS marker gene to construct a recombinant vector. Plants infected with Agrobacterium harboring pV190-PDS successfully induced effective silencing in Luffa, and an effective gene silencing phenotype with obvious photobleaching was observed. To further validate the efficiency, we selected TEN for gene-silencing, which encodes a CYC/TB1-like transcription factor and is involved in tendril development. Luffa plants inoculated with the pV190-TEN exhibited shorter tendril length and nodal positions where tendrils appear are higher compared to those of non-inoculated plants. RT-qPCR showed that the expression levels of PDS and TEN were significantly reduced in the CGMMV-VIGS plants. Moreover, we evaluated the CGMMV-VIGS efficiency in three cucurbits, including cucumber, ridge gourd, and bottle gourd. CONCLUSION We successfully established a CGMMV-based VIGS system on ridge gourd and used marker genes to identify the feasibility of the silencing system in Luffa leaves and stems.
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Affiliation(s)
- Xiaoyu Qi
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Qiaoping Mo
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Jing Li
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- College of Plant Science, Tibet Agricultural and Animal Husbandry University, Tibet, 860000, Nyingchi, China
| | - Zhibo Zi
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Mengyun Xu
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Suju Yue
- College of Life Sciences, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, Guangdong, China
| | - Hongbo Zhao
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Haisheng Zhu
- Fujian Key Laboratory of Vegetable Genetics and Breeding/Crops Research Institute, Fujian Academy of Agricultural Sciences, Fujian, 350013, Fuzhou, China.
| | - Guoping Wang
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture, College of Horticulture, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
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Bhutia ND, Sureja AK, Verma M, Gopala Krishnan S, Arya L, Bhardwaj R, Dash PK, Das Munshi A. Inheritance and molecular mapping of solitary/cluster fruit-bearing habit in Luffa. Mol Genet Genomics 2023:10.1007/s00438-023-02034-0. [PMID: 37231151 DOI: 10.1007/s00438-023-02034-0] [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: 11/07/2022] [Accepted: 05/15/2023] [Indexed: 05/27/2023]
Abstract
Fruiting behaviour and sex form are important goals for Luffa breeders and this study aimed to shed light upon inheritance patterns for both these traits. The hermaphrodite form of Luffa acutangula (known as Satputia) is an underutilized vegetable with a unique clustered fruiting habit. Its desirable traits, such as plant architecture, earliness, as well as contrasting traits like unique clustered fruiting, bisexual flower, and crossability with Luffa acutangula (monoecious ridge gourd with solitary fruits), make it a potential source for trait improvement and mapping of desirable traits in Luffa. In the present study, we have elucidated the inheritance pattern of fruiting behaviour in Luffa using F2 mapping population generated from a cross between Pusa Nutan (Luffa acutangula, monoecious, solitary fruiting) × DSat-116 (Luffa acutangula, hermaphrodite, cluster fruiting). In F2 generation, the observed distribution of plant phenotypes fitted in the expected ratio of 3:1 (solitary vs cluster) for fruit-bearing habit. This is the first report of monogenic recessive control for cluster fruit-bearing habit in Luffa. Herein, we designate for the first time the gene symbol cl for cluster fruit bearing in Luffa. Linkage analysis revealed that SRAP marker ME10 EM4-280 was linked to the fruiting trait at the distance of 4.6 cM from the Cl locus. In addition, the inheritance pattern of hermaphrodite sex form in Luffa was also studied in the F2 population of Pusa Nutan × DSat-116 that segregated into 9:3:3:1 ratio (monoecious:andromonoecious:gynoecious:hermaphrodite), suggesting a digenic recessive control of hermaphrodite sex form in Luffa, which was further confirmed by the test cross. The inheritance and identification of molecular marker for cluster fruiting trait provides a basis for breeding in Luffa species.
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Affiliation(s)
- Nangsol D Bhutia
- College of Horticulture and Forestry, Central Agricultural University, Pasighat, Arunachal Pradesh, 791102, India
| | - Amish K Sureja
- ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, 110012, India.
| | - Manjusha Verma
- ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012, India
| | - S Gopala Krishnan
- ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, 110012, India
| | - Lalit Arya
- ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012, India
| | - Rakesh Bhardwaj
- ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012, India
| | - Prasanta K Dash
- ICAR-National Institute of Plant Biotechnology, Pusa, New Delhi, 110012, India
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Kiryushkin AS, Ilina EL, Guseva ED, Pawlowski K, Demchenko KN. Lateral Root Initiation in Cucumber ( Cucumis sativus): What Does the Expression Pattern of Rapid Alkalinization Factor 34 ( RALF34) Tell Us? Int J Mol Sci 2023; 24:ijms24098440. [PMID: 37176146 PMCID: PMC10179419 DOI: 10.3390/ijms24098440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
In Arabidopsis, the small signaling peptide (peptide hormone) RALF34 is involved in the gene regulatory network of lateral root initiation. In this study, we aimed to understand the nature of the signals induced by RALF34 in the non-model plant cucumber (Cucumis sativus), where lateral root primordia are induced in the apical meristem of the parental root. The RALF family members of cucumber were identified using phylogenetic analysis. The sequence of events involved in the initiation and development of lateral root primordia in cucumber was examined in detail. To elucidate the role of the small signaling peptide CsRALF34 and its receptor CsTHESEUS1 in the initial stages of lateral root formation in the parental root meristem in cucumber, we studied the expression patterns of both genes, as well as the localization and transport of the CsRALF34 peptide. CsRALF34 is expressed in all plant organs. CsRALF34 seems to differ from AtRALF34 in that its expression is not regulated by auxin. The expression of AtRALF34, as well as CsRALF34, is regulated in part by ethylene. CsTHESEUS1 is expressed constitutively in cucumber root tissues. Our data suggest that CsRALF34 acts in a non-cell-autonomous manner and is not involved in lateral root initiation in cucumber.
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Affiliation(s)
- Alexey S Kiryushkin
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia
| | - Elena L Ilina
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia
| | - Elizaveta D Guseva
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia
| | - Katharina Pawlowski
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 10691 Stockholm, Sweden
| | - Kirill N Demchenko
- Laboratory of Cellular and Molecular Mechanisms of Plant Development, Komarov Botanical Institute, Russian Academy of Sciences, 197022 Saint Petersburg, Russia
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6
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Papa Y, Wellenreuther M, Morrison MA, Ritchie PA. Genome assembly and isoform analysis of a highly heterozygous New Zealand fisheries species, the tarakihi (Nemadactylus macropterus). G3 (BETHESDA, MD.) 2022; 13:6883520. [PMID: 36477875 PMCID: PMC9911067 DOI: 10.1093/g3journal/jkac315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 11/01/2022] [Accepted: 11/08/2022] [Indexed: 12/14/2022]
Abstract
Although being some of the most valuable and heavily exploited wild organisms, few fisheries species have been studied at the whole-genome level. This is especially the case in New Zealand, where genomics resources are urgently needed to assist fisheries management. Here, we generated 55 Gb of short Illumina reads (92× coverage) and 73 Gb of long Nanopore reads (122×) to produce the first genome assembly of the marine teleost tarakihi [Nemadactylus macropterus (Forster, 1801)], a highly valuable fisheries species in New Zealand. An additional 300 Mb of Iso-Seq reads were obtained to assist in gene annotation. The final genome assembly was 568 Mb long with an N50 of 3.37 Mb. The genome completeness was high, with 97.8% of complete Actinopterygii Benchmarking Universal Single-Copy Orthologs. Heterozygosity values estimated through k-mer counting (1.00%) and bi-allelic SNPs (0.64%) were high compared with the same values reported for other fishes. Iso-Seq analysis recovered 91,313 unique transcripts from 15,515 genes (mean ratio of 5.89 transcripts per gene), and the most common alternative splicing event was intron retention. This highly contiguous genome assembly and the isoform-resolved transcriptome will provide a useful resource to assist the study of population genomics and comparative eco-evolutionary studies in teleosts and related organisms.
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Affiliation(s)
- Yvan Papa
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
| | - Maren Wellenreuther
- Seafood Production Group, The New Zealand Institute for Plant and Food Research Limited, Nelson 7010, New Zealand,School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
| | - Mark A Morrison
- National Institute of Water and Atmospheric Research, Auckland 1010, New Zealand
| | - Peter A Ritchie
- Corresponding author: Te Toki A Rata, Gate 7, Kelburn Parade, Wellington 6012, New Zealand.
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Liu L, Gan Y, Luo J, Li J, Zheng X, Gong H, Liu X, Deng L, Zhao G, Wu H. QTL mapping reveals candidate genes for main agronomic traits in Luffa based on a high-resolution genetic map. FRONTIERS IN PLANT SCIENCE 2022; 13:1069618. [PMID: 36466279 PMCID: PMC9716215 DOI: 10.3389/fpls.2022.1069618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/02/2022] [Indexed: 06/17/2023]
Abstract
Luffa is an important medicinal and edible vegetable crop of Cucurbitaceae. Strong heterosis effects and strikingly complementary characteristics were found between the two domesticated Luffa cultivars, Luffa acutangula and Luffa cylindrica. To explore the genetic basis underlying their important agronomic traits, we constructed the first interspecific high-density genetic linkage map using a BC1 population of 110 lines derived from a cross between S1174 (Luffa acutangula) and P93075 (Luffa cylindrica). The map spanned a total of 2246.74 cM with an average distance of 0.48 cM between adjacent markers. Thereafter, a large-scale field-based quantitative trait loci (QTLs) mapping was conducted for 25 important agronomic traits and 40 significant genetic loci distributed across 11 chromosomes were detected. Notably, a vital QTL (qID2) located on chromosome 9 with a minimum distance of 23 kb was identified to be responsible for the internode diameter and explained 11% of the phenotypic variation. Lac09g006860 (LacCRWN3), encoding a nuclear lamina protein involved in the control of nuclear morphology, was the only gene harbored in qID2. Sequence alignment showed completely different promoter sequences between the two parental alleles of LacCRWN3 except for some nonsynonymous single nucleotide polymorphisms (SNPs) in exons, and the expression level in thick-stem P93075 was distinctively higher than that in thin-stem S1174. According to the natural variation analysis of a population of 183 inbred lines, two main haplotypes were found for LacCRWN3: the P93075-like and S1174-like, with the former haplotype lines exhibiting significantly thicker internode diameters than those of the latter haplotype lines. It showed that LacCRWN3, as the only CRWN3 gene in Cucurbitaceae, was the most likely candidate gene regulating the internode diameter of Luffa. Our findings will be beneficial for deciphering the molecular mechanism of key phenotypic traits and promoting maker-assisted breeding in Luffa.
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Affiliation(s)
- Lili Liu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yaqin Gan
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Jianning Luo
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Junxing Li
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiaoming Zheng
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Hao Gong
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Xiaoxi Liu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Liting Deng
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Gangjun Zhao
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Haibin Wu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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8
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Yu J, Wu S, Sun H, Wang X, Tang X, Guo S, Zhang Z, Huang S, Xu Y, Weng Y, Mazourek M, McGregor C, Renner SS, Branham S, Kousik C, Wechter W, Levi A, Grumet R, Zheng Y, Fei Z. CuGenDBv2: an updated database for cucurbit genomics. Nucleic Acids Res 2022; 51:D1457-D1464. [PMID: 36271794 PMCID: PMC9825510 DOI: 10.1093/nar/gkac921] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/03/2022] [Accepted: 10/06/2022] [Indexed: 01/30/2023] Open
Abstract
The Cucurbitaceae (cucurbit) family consists of about 1,000 species in 95 genera, including many economically important and popular fruit and vegetable crops. During the past several years, reference genomes have been generated for >20 cucurbit species, and variome and transcriptome profiling data have been rapidly accumulated for cucurbits. To efficiently mine, analyze and disseminate these large-scale datasets, we have developed an updated version of Cucurbit Genomics Database. The updated database, CuGenDBv2 (http://cucurbitgenomics.org/v2), currently hosts 34 reference genomes from 27 cucurbit species/subspecies belonging to 10 different genera. Protein-coding genes from these genomes have been comprehensively annotated by comparing their protein sequences to various public protein and domain databases. A novel 'Genotype' module has been implemented to facilitate mining and analysis of the functionally annotated variome data including SNPs and small indels from large-scale genome sequencing projects. An updated 'Expression' module has been developed to provide a comprehensive gene expression atlas for cucurbits. Furthermore, synteny blocks between any two and within each of the 34 genomes, representing a total of 595 pair-wise genome comparisons, have been identified and can be explored and visualized in the database.
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Affiliation(s)
- Jingyin Yu
- Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Shan Wu
- Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Honghe Sun
- Boyce Thompson Institute, Ithaca, NY 14853, USA,Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Xin Wang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuemei Tang
- Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Shaogui Guo
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Zhonghua Zhang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Sanwen Huang
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Yong Xu
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Yiqun Weng
- U.S. Department of Agriculture-Agricultural Research Service, Vegetable Crops Research Unit, Madison, WI 53706, USA,Department of Horticulture, University of Wisconsin, Madison, WI 53706, USA
| | - Michael Mazourek
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Cecilia McGregor
- Department of Horticulture, University of Georgia, Athens, GA 30602, USA
| | - Susanne S Renner
- Faculty of Biology, Systematic Botany and Mycology, University of Munich (LMU), 80638 Munich, Germany,Department of Biology, Washington University, Saint Louis, MO 63130, USA
| | - Sandra Branham
- Coastal Research and Educational Center, Clemson University, Charleston, SC 29414, USA
| | - Chandrasekar Kousik
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - W Patrick Wechter
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - Amnon Levi
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - Rebecca Grumet
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Yi Zheng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China,Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Zhangjun Fei
- To whom correspondence should be addressed. Tel: +1 607 2543234; Fax: +1 607 2541242;
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9
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Assessment of the Genetic Diversity and Population Structure of Rhizophora apiculata Blume (Rhizophoraceae) in Thailand. BIOLOGY 2022; 11:biology11101449. [PMID: 36290353 PMCID: PMC9598538 DOI: 10.3390/biology11101449] [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: 07/01/2022] [Revised: 07/23/2022] [Accepted: 07/26/2022] [Indexed: 11/09/2022]
Abstract
Rhizophora apiculata is one of the most widespread and economically important mangrove trees in the Indo-West Pacific region. Knowledge of the genetic variation of R. apiculata in Thailand is limited. Here, we generated a whole-genome sequence of R. apiculata using the 10× Genomics technology. R. apiculata genome assembly was 230.47 Mb. Based on its genome, 2640 loci of high-quality biallelic SNPs were identified from 82 R. apiculata accessions collected from 17 natural mangrove forests in Thailand to assess the genetic diversity and population structure among them. A moderate level of genetic diversity of R. apiculata was observed. The average observed heterozygosity (Ho = 0.48) was higher than the average expected heterozygosity (He = 0.36). Two subpopulations were observed and confirmed from three approaches: population structure, PCA, and phylogenetic analyses. They corresponded to the Gulf of Thailand and the Andaman Sea separated by the Malay Peninsula. AMOVA analyses indicated that genetic variation was attributable to 76.22% within populations and 23.78% among populations. A high level of genetic differentiation between the two subpopulations (FST = 0.24, p < 0.001) was observed. This study evaluated the genetic diversity and population structure of R. apiculata, providing useful information for sustainable mangrove management in Thailand.
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Yang L, Chen H, Yan W, Huang S, Cheng D, Xu H, Zhang Z. A pH- and redox-stimulated responsive hollow mesoporous silica for triggered delivery of fungicides to control downy mildew of Luffa cylindrica. PEST MANAGEMENT SCIENCE 2022; 78:3365-3375. [PMID: 35514211 DOI: 10.1002/ps.6964] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/25/2022] [Accepted: 05/06/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Downy mildew, a devastating disease of cucurbitaceous crops caused by Pseudoperonospora cubensis. Although a variety of fungicides are used to control downy mildew, choosing an effective product can be challenging. Environmental stimulus-responsive pesticide delivery systems have great potential to improve the effectiveness of disease and pest control and reduce the impact on environmentally beneficial organisms. RESULTS In this work, a disulfide bond (SS)-modified and chitosan oligosaccharide (COS)-capped hollow mesoporous silica (HMS) pesticide delivery system was synthesized using a hard template method for the control of downy mildew in cucurbit crops. The synthesized nanoparticles were loaded with dimethomorph (DMM), denoted as DMM@HMS-SS-COS, and the developmental toxicity of these nanoparticles to zebrafish embryos were evaluated. The results showed that the prepared DMM@HMS-SS-COS exhibited excellent dual response properties to pH and glutathione (GSH), with an encapsulation rate of up to 24.36%. DMM@HMS-SS-COS has good ultraviolet (UV) radiation stability and adhesion properties. Compared with dimethomorph suspension concentrate (SC), DMM@HMS-SS-COS was more effective against downy mildew for up to 21 days. Toxicity tests showed that DMM@HMS-SS-COS significantly reduced the effect of DMM on the hatching rate and survival rate of zebrafish embryos. CONCLUSIONS This work not only demonstrates that DMM@HMS-SS-COS could be used as a nanodelivery system for intelligent control of downy mildew but also emphasizes the necessity of increasing the acute toxicity of nanoformulations to non-target organisms in environmental risk assessment. © 2022 Society of Chemical Industry.
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Affiliation(s)
- Liupeng Yang
- Guangdong Biological Pesticide Engineering Technology Research Center, South China Agricultural University, Guangzhou, China
| | - Huiya Chen
- Guangdong Biological Pesticide Engineering Technology Research Center, South China Agricultural University, Guangzhou, China
| | - Wenjuan Yan
- Guangdong Biological Pesticide Engineering Technology Research Center, South China Agricultural University, Guangzhou, China
| | - Suqing Huang
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Dongmei Cheng
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - HanHong Xu
- Guangdong Biological Pesticide Engineering Technology Research Center, South China Agricultural University, Guangzhou, China
| | - Zhixiang Zhang
- Guangdong Biological Pesticide Engineering Technology Research Center, South China Agricultural University, Guangzhou, China
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11
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Pootakham W, Sonthirod C, Naktang C, Kongkachana W, U-Thoomporn S, Phetchawang P, Maknual C, Jiumjamrassil D, Pravinvongvuthi T, Tangphatsornruang S. A de novo reference assembly of the yellow mangrove Ceriops zippeliana genome. G3 (BETHESDA, MD.) 2022; 12:6519851. [PMID: 35106563 PMCID: PMC8982413 DOI: 10.1093/g3journal/jkac025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/25/2022] [Indexed: 11/13/2022]
Abstract
Mangroves are of great ecological and economical importance, providing shelters for a wide range of species and nursery habitats for commercially important marine species. Ceriops zippeliana (yellow mangrove) belongs to Rhizophoraceae family and is commonly distributed in the tropical and subtropical coastal communities. In this study, we present a high-quality assembly of the C. zippeliana genome. We constructed an initial draft assembly of 240,139,412 bases with an N50 contig length of 564,761 bases using the 10x Genomics linked-read technology. This assembly was further scaffolded with RagTag using a chromosome-scale assembly of a closely related Ceriops species as a reference. The final assembly contained 243,228,612 bases with an N50 scaffold length of 10,559,178 Mb. The size of the final assembly was close to those estimated using DNA flow cytometry (248 Mb) and the k-mer distribution analysis (246 Mb). We predicted a total of 23,474 gene models and 21,724 protein-coding genes in the C. zippeliana genome, of which 16,002 were assigned gene ontology terms. We recovered 97.1% of the highly conserved orthologs based on the Benchmarking Universal Single-Copy Orthologs analysis. The phylogenetic analysis based on single-copy orthologous genes illustrated that C. zippeliana and Ceriops tagal diverged approximately 10.2 million years ago (MYA), and their last common ancestor and Kandelia obovata diverged approximately 29.9 MYA. The high-quality assembly of C. zippeliana presented in this work provides a useful genomic resource for studying mangroves' unique adaptations to stressful intertidal habitats and for developing sustainable mangrove forest restoration and conservation programs.
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Affiliation(s)
- Wirulda Pootakham
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Chutima Sonthirod
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Chaiwat Naktang
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Wasitthee Kongkachana
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Sonicha U-Thoomporn
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Phakamas Phetchawang
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Chatree Maknual
- Department of Marine and Coastal Resources, Bangkok 10210, Thailand
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12
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Pootakham W, Naktang C, Sonthirod C, Kongkachana W, Yoocha T, Jomchai N, Maknual C, Chumriang P, Pravinvongvuthi T, Tangphatsornruang S. De novo reference assembly of the upriver orange mangrove (Bruguiera sexangula) genome. Genome Biol Evol 2022; 14:6527208. [PMID: 35148390 PMCID: PMC8872974 DOI: 10.1093/gbe/evac025] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2022] [Indexed: 11/21/2022] Open
Abstract
Upriver orange mangrove (Bruguiera sexangula) is a member of the most mangrove-rich taxon (Rhizophoraceae family) and is commonly distributed in the intertidal zones in tropical and subtropical latitudes. In this study, we employed the 10× Genomics linked-read technology to obtain a preliminary de novo assembly of the B. sexangula genome, which was further scaffolded to a pseudomolecule level using the Bruguiera parviflora genome as a reference. The final assembly of the B. sexangula genome contained 260 Mb with an N50 scaffold length of 11,020,310 bases. The assembly comprised 18 pseudomolecules (corresponding to the haploid chromosome number in B. sexangula), covering 204,645,832 bases or 78.6% of the 260-Mb assembly. We predicted a total of 23,978 protein-coding sequences, 17,598 of which were associated with gene ontology terms. Our gene prediction recovered 96.6% of the highly conserved orthologs based on the Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis. The chromosome-level assembly presented in this work provides a valuable genetic resource to help strengthen our understanding of mangroves’ physiological and morphological adaptations to the intertidal zones.
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Affiliation(s)
- Wirulda Pootakham
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chaiwat Naktang
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chutima Sonthirod
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wasitthee Kongkachana
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Thippawan Yoocha
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Nukoon Jomchai
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chatree Maknual
- Department of Marine and Coastal Resources, 120 The Government Complex, Chaengwatthana Rd., Thung Song Hong, Bangkok, 10210, Thailand
| | - Pranom Chumriang
- Department of Marine and Coastal Resources, 120 The Government Complex, Chaengwatthana Rd., Thung Song Hong, Bangkok, 10210, Thailand
| | - Tamanai Pravinvongvuthi
- Department of Marine and Coastal Resources, 120 The Government Complex, Chaengwatthana Rd., Thung Song Hong, Bangkok, 10210, Thailand
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13
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Pootakham W, Sonthirod C, Naktang C, Kongkachana W, Sangsrakru D, U‐thoomporn S, Maknual C, Meepol W, Promchoo W, Maprasop P, Phormsin N, Tangphatsornruang S. A chromosome‐scale reference genome assembly of yellow mangrove (
Bruguiera parviflora
) reveals a whole genome duplication event associated with the Rhizophoraceae lineage. Mol Ecol Resour 2022; 22:1939-1953. [DOI: 10.1111/1755-0998.13587] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 01/06/2022] [Accepted: 01/12/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Wirulda Pootakham
- National Omics Center National Science and Technology Development Agency (NSTDA) Pathum Thani Thailand
| | - Chutima Sonthirod
- National Omics Center National Science and Technology Development Agency (NSTDA) Pathum Thani Thailand
| | - Chaiwat Naktang
- National Omics Center National Science and Technology Development Agency (NSTDA) Pathum Thani Thailand
| | - Wasitthee Kongkachana
- National Omics Center National Science and Technology Development Agency (NSTDA) Pathum Thani Thailand
| | - Duangjai Sangsrakru
- National Omics Center National Science and Technology Development Agency (NSTDA) Pathum Thani Thailand
| | - Sonicha U‐thoomporn
- National Omics Center National Science and Technology Development Agency (NSTDA) Pathum Thani Thailand
| | - Chatree Maknual
- Department of Marine and Coastal Resources 120 The Government Complex, Chaengwatthana Rd. Thung Song Hong, Bangkok 10210 Thailand
| | - Wijarn Meepol
- Department of Marine and Coastal Resources 120 The Government Complex, Chaengwatthana Rd. Thung Song Hong, Bangkok 10210 Thailand
| | - Waratthaya Promchoo
- Department of Marine and Coastal Resources 120 The Government Complex, Chaengwatthana Rd. Thung Song Hong, Bangkok 10210 Thailand
| | - Pasin Maprasop
- Department of Marine and Coastal Resources 120 The Government Complex, Chaengwatthana Rd. Thung Song Hong, Bangkok 10210 Thailand
| | - Nawin Phormsin
- Department of Marine and Coastal Resources 120 The Government Complex, Chaengwatthana Rd. Thung Song Hong, Bangkok 10210 Thailand
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14
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Ma L, Wang Q, Zheng Y, Guo J, Yuan S, Fu A, Bai C, Zhao X, Zheng S, Wen C, Guo S, Gao L, Grierson D, Zuo J, Xu Y. Cucurbitaceae genome evolution, gene function and molecular breeding. HORTICULTURE RESEARCH 2022; 9:uhab057. [PMID: 35043161 PMCID: PMC8969062 DOI: 10.1093/hr/uhab057] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 10/28/2021] [Indexed: 05/07/2023]
Abstract
The Cucurbitaceae is one of the most genetically diverse plant families in the world. Many of them are important vegetables or medicinal plants and are widely distributed worldwide. The rapid development of sequencing technologies and bioinformatic algorithms has enabled the generation of genome sequences of numerous important Cucurbitaceae species. This has greatly facilitated research on gene identification, genome evolution, genetic variation and molecular breeding of cucurbit crops. So far, genome sequences of 18 different cucurbit species belonging to tribes Benincaseae, Cucurbiteae, Sicyoeae, Momordiceae and Siraitieae have been deciphered. This review summarizes the genome sequence information, evolutionary relationship, and functional genes associated with important agronomic traits (e.g., fruit quality). The progress of molecular breeding in cucurbit crops and prospects for future applications of Cucurbitaceae genome information are also discussed.
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Affiliation(s)
- Lili Ma
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- Department of Food Biotechnology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Qing Wang
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yanyan Zheng
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Jing Guo
- Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering and State Key Laboratory of Genetic Engineering, Institute of Biodiversity Sciences and Institute of Plant Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200438, China
| | - Shuzhi Yuan
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Anzhen Fu
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Chunmei Bai
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xiaoyan Zhao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Shufang Zheng
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Changlong Wen
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Shaogui Guo
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Lipu Gao
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Donald Grierson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
| | - Jinhua Zuo
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yong Xu
- Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Key Laboratory of Urban Agriculture (North) of Ministry of Agriculture, Beijing Vegetable Research Center, Institute of Agro-Products Processing and Food Nutrition, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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15
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Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers. Sci Rep 2021; 11:15311. [PMID: 34321535 PMCID: PMC8319206 DOI: 10.1038/s41598-021-94802-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 07/16/2021] [Indexed: 11/23/2022] Open
Abstract
This study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of FST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (FIS = − 0.092) and low total fixation index (FIT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.
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16
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Cheng QQ, Ouyang Y, Tang ZY, Lao CC, Zhang YY, Cheng CS, Zhou H. Review on the Development and Applications of Medicinal Plant Genomes. FRONTIERS IN PLANT SCIENCE 2021; 12:791219. [PMID: 35003182 PMCID: PMC8732986 DOI: 10.3389/fpls.2021.791219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/23/2021] [Indexed: 05/04/2023]
Abstract
With the development of sequencing technology, the research on medicinal plants is no longer limited to the aspects of chemistry, pharmacology, and pharmacodynamics, but reveals them from the genetic level. As the price of next-generation sequencing technology becomes affordable, and the long-read sequencing technology is established, the medicinal plant genomes with large sizes have been sequenced and assembled more easily. Although the review of plant genomes has been reported several times, there is no review giving a systematic and comprehensive introduction about the development and application of medicinal plant genomes that have been reported until now. Here, we provide a historical perspective on the current situation of genomes in medicinal plant biology, highlight the use of the rapidly developing sequencing technologies, and conduct a comprehensive summary on how the genomes apply to solve the practical problems in medicinal plants, like genomics-assisted herb breeding, evolution history revelation, herbal synthetic biology study, and geoherbal research, which are important for effective utilization, rational use and sustainable protection of medicinal plants.
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Affiliation(s)
- Qi-Qing Cheng
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Yue Ouyang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Zi-Yu Tang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Chi-Chou Lao
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Yan-Yu Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Chun-Song Cheng
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Hua Zhou
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
- Joint Laboratory for Translational Cancer Research of Chinese Medicine, The Ministry of Education of the People’s Republic of China, Macau University of Science and Technology, Taipa, Macao SAR, China
- *Correspondence: Hua Zhou,
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