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Yan J, Cheng J, Xie D, Wang Y, Wang M, Yang S, Jiang B, Chen L, Cai J, Liu W. A nonsynonymous mutation in BhLS, encoding an acyl-CoA N-acyltransferase leads to fruit and seed size variation in wax gourd (Benincasa hispida). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:100. [PMID: 38602584 DOI: 10.1007/s00122-024-04604-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 03/18/2024] [Indexed: 04/12/2024]
Abstract
Wax gourd (Benincasa hispida (Thunb.) Cogn., 2n = 2x = 24) is an economically important vegetable crop cultivated widely in many tropical and subtropical regions, including China, India, and Japan. Both fruit and seeds are prized agronomic attributes in wax gourd breeding and production. However, the genetic mechanisms underlying these traits remain largely unexplored. In this study, we observed a strong correlation between fruit size and seed size variation in our mapping population, indicating genetic control by a single gene, BhLS, with large size being dominant over small. Through bulk segregant analysis sequencing and fine mapping with a large F2 population, we precisely located the BhLS gene within a 47.098-kb physical interval on Chromosome 10. Within this interval, only one gene, Bhi10M000649, was identified, showing homology to Arabidopsis HOOKLESS1. A nonsynonymous mutation (G to C) in the second exon of Bhi10M000649 was found to be significantly associated with both fruit and seed size variation in wax gourd. These findings collectively highlight the pleiotropic effect of the BhLS gene in regulating fruit and seed size in wax gourd. Our results offer molecular insights into the variation of fruit and seed size in wax gourd and establish a fundamental framework for breeding wax gourd cultivars with desired traits.
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Affiliation(s)
- Jinqiang Yan
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Jiaowen Cheng
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center, Guangzhou, 510642, People's Republic of China
| | - Dasen Xie
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Yi Wang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Min Wang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Songguang Yang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Biao Jiang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Lin Chen
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Jinsen Cai
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Wenrui Liu
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China.
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Borlay AJ, Mweu CM, Nyanjom SG, Omolo KM, Naitchede LHS. De novo transcriptomic analysis of Doum Palm (Hyphaene compressa) revealed an insight into its potential drought tolerance. PLoS One 2024; 19:e0292543. [PMID: 38470884 DOI: 10.1371/journal.pone.0292543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 09/24/2023] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Doum palms (Hyphaene compressa) perform a crucial starring role in the lives of Kenya's arid and semi-arid people for empowerment and sustenance. Despite the crop's potential for economic gain, there is a lack of genetic resources and detailed information about its domestication at the molecular level. Given the doum palm's vast potential as a widely distributed plant in semi-arid and arid climates and a source of many applications, coupled with the current changing climate scenario, it is essential to understand the molecular processes that provide drought resistance to this plant. RESULTS Assembly of the first transcriptome of doum palms subjected to water stress generated about 39.97 Gb of RNA-Seq data. The assembled transcriptome revealed 193,167 unigenes with an average length of 1655 bp, with 128,708 (66.63%) successfully annotated in seven public databases. Unigenes exhibited significant differentially expressed genes (DEGs) in well-watered and stressed-treated plants, with 45071 and 42457 accounting for up-regulated and down-regulated DEGs, respectively. GO term, KEGG, and KOG analysis showed that DEGs were functionally enriched cellular processes, metabolic processes, cellular and catalytic activity, metabolism, genetic information processing, signal transduction mechanisms, and posttranslational modification pathways. Transcription factors (TF), such as the MYB, WRKY, NAC family, FAR1, B3, bHLH, and bZIP, were the prominent TF families identified as doum palm DEGs encoding drought stress tolerance. CONCLUSIONS This study provides a complete understanding of DEGs involved in drought stress at the transcriptome level in doum palms. This research is, therefore, the foundation for the characterization of potential genes, leading to a clear understanding of its drought stress responses and providing resources for improved genetic modification.
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Affiliation(s)
- Allen Johnny Borlay
- Department of Biological Sciences, University of Liberia, Monrovia, Liberia
- Department of Molecular Biology and Biotechnology, Pan African University Institute for Basic Sciences, Technology and Innovation, Nairobi, Kenya
| | - Cecilia Mbithe Mweu
- Institute for Biotechnology Research, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Steven Ger Nyanjom
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Kevin Mbogo Omolo
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Labode Hospice Stevenson Naitchede
- Department of Molecular Biology and Biotechnology, Pan African University Institute for Basic Sciences, Technology and Innovation, Nairobi, Kenya
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Wang Q, Guo C, Yang S, Zhong Q, Tian J. Screening and Verification of Reference Genes for Analysis of Gene Expression in Garlic ( Allium sativum L.) under Cold and Drought Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:763. [PMID: 36840111 PMCID: PMC9963267 DOI: 10.3390/plants12040763] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
The principal objective of this study was to screen and verify reference genes appropriate for gene expression evaluation during plant growth and development under distinct growth conditions. Nine candidate reference genes were screened based on garlic transcriptome sequence data. RT-qPCR was used to detect the expression levels of the aforementioned reference genes in specific tissues under drought and cold stress. Then, geNorm, NormFinder, BestKeeper, and ReFinder were used to consider the consistency of the expression levels of candidate reference genes. Finally, the stress-responsive gene expression of ascorbate peroxidase (APX) was quantitatively evaluated to confirm the chosen reference genes. Our results indicated that there were variations in the abundance and stability of nine reference gene transcripts underneath cold and drought stress, among which ACT and UBC-E2 had the highest transcript abundance, and 18S rRNA and HIS3 had the lowest transcript abundance. UBC and UBC-E2 were the most stably expressed genes throughout all samples; UBC and UBC-E2 were the most stably expressed genes during cold stress, and ACT and UBC were the most stably expressed genes under drought stress. The most stably expressed genes in roots, pseudostems, leaves, and cloves were EF1, ACT, HIS3, UBC, and UBC-E2, respectively, while GAPDH was the most unstable gene during drought and cold stress conditions and in exclusive tissues. Taking the steady reference genes UBC-E2, UBC, and ACT as references during drought and cold stress, the reliability of the expression levels was further demonstrated by detecting the expression of AsAPX. Our work thereby offers a theoretical reference for the evaluation of gene expression in garlic in various tissues and under stress conditions.
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Affiliation(s)
- Qizhang Wang
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences of Qinghai University, Xining 810016, China
- School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Chunqian Guo
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences of Qinghai University, Xining 810016, China
| | - Shipeng Yang
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences of Qinghai University, Xining 810016, China
| | - Qiwen Zhong
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences of Qinghai University, Xining 810016, China
| | - Jie Tian
- Qinghai Key Laboratory of Vegetable Genetics and Physiology, Academy of Agriculture and Forestry Sciences of Qinghai University, Xining 810016, China
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Luo C, Yan J, He C, Liu W, Xie D, Jiang B. Genome-Wide Identification of the SAUR Gene Family in Wax Gourd ( Benincasa hispida) and Functional Characterization of BhSAUR60 during Fruit Development. Int J Mol Sci 2022; 23:ijms232214021. [PMID: 36430500 PMCID: PMC9694812 DOI: 10.3390/ijms232214021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 11/16/2022] Open
Abstract
The wax gourd (Benincasa hispida) is an important vegetable crop whose fruits contain nutrients and metabolites. Small auxin upregulated RNA (SAUR) genes constitute the largest early auxin-responsive gene family and regulate various biological processes in plants, although this gene family has not been studied in the wax gourd. Here, we performed genome-wide identification of the SAUR gene family in wax gourds and analyzed their syntenic and phylogenetic relationships, gene structures, conserved motifs, cis-acting elements, and expression patterns. A total of 68 SAUR (BhSAUR) genes were identified, which were distributed on nine chromosomes with 41 genes in two clusters. More than half of the BhSAUR genes were derived from tandem duplication events. The BhSAUR proteins were classified into seven subfamilies. BhSAUR gene promoters contained cis-acting elements involved in plant hormone and environmental signal responses. Further expression profiles showed that BhSAUR genes displayed different expression patterns. BhSAUR60 was highly expressed in fruits, and overexpression led to longer fruits in Arabidopsis. In addition, the plants with overexpression displayed longer floral organs and wavy stems. In conclusion, our results provide a systematic analysis of the wax gourd SAUR gene family and facilitate the functional study of BhSAUR60 during wax gourd fruit development.
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Affiliation(s)
- Chen Luo
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Jinqiang Yan
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Changxia He
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Wenrui Liu
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Dasen Xie
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
| | - Biao Jiang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
- Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou 510640, China
- Correspondence: ; Tel.: +86-020-38469441
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Xu Y, Zhang H, Zhong Y, Jiang N, Zhong X, Zhang Q, Chai S, Li H, Zhang Z. Comparative genomics analysis of bHLH genes in cucurbits identifies a novel gene regulating cucurbitacin biosynthesis. HORTICULTURE RESEARCH 2022; 9:uhac038. [PMID: 35184192 PMCID: PMC9071377 DOI: 10.1093/hr/uhac038] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/22/2022] [Accepted: 01/30/2022] [Indexed: 05/08/2023]
Abstract
The basic helix-loop-helix (bHLH) family of transcription factors (TFs) participate in a variety of biological regulatory processes in plants, and have undergone significant expansion during land plant evolution by gene duplications. In cucurbit crops, several bHLH genes have been found to be responsible for the agronomic traits such as bitterness. However, the characterization of bHLH genes across the genomes of cucurbit species has not been reported, and how they have evolved and diverged remains largely unanswered. Here we identified 1160 bHLH genes in seven cucurbit crops and performed a comprehensive comparative genomics analysis. We determined orthologous and paralogous bHLH genes across cucurbit crops by syntenic analysis between or within species. Orthology and phylogenetic analysis of the tandem-duplicated bHLH genes in the Bt cluster which regulate the biosynthesis of cucurbitacins suggest that this cluster is derived from three ancestral genes after the cucurbit-common tetraploidization event. Interestingly, we identified a new conserved cluster paralogous to the Bt cluster that includes two tandem bHLH genes, and the evolutionary history and expression profiles of these two genes in the new cluster suggest the involvement of one gene (Brp) in the regulation of cucurbitacin biosynthesis in roots. Further biochemical and transgenic assays in melon hairy roots support the function of Brp. This study provides useful information for further investigating the functions of bHLH TFs and novel insights into the regulation of cucurbitacin biosynthesis in cucurbit crops and other plants.
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Affiliation(s)
- Yuanchao Xu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huimin Zhang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Yang Zhong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Naiyu Jiang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Xiaoyun Zhong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qiqi Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Sen Chai
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Hongbo Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen Key Laboratory of Agricultural Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Zhonghua Zhang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
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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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Das RR, Pradhan S, Parida A. De-novo transcriptome analysis unveils differentially expressed genes regulating drought and salt stress response in Panicum sumatrense. Sci Rep 2020; 10:21251. [PMID: 33277539 PMCID: PMC7718891 DOI: 10.1038/s41598-020-78118-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/03/2020] [Indexed: 12/15/2022] Open
Abstract
Screening the transcriptome of drought tolerant variety of little millet (Panicum sumatrense), a marginally cultivated, nutritionally rich, susbsistent crop, can identify genes responsible for its hardiness and enable identification of new sources of genetic variation which can be used for crop improvement. RNA-Seq generated ~ 230 million reads from control and treated tissues, which were assembled into 86,614 unigenes. In silico differential gene expression analysis created an overview of patterns of gene expression during exposure to drought and salt stress. Separate gene expression profiles for leaf and root tissue revealed the differences in regulatory mechanisms operating in these tissues during exposure to abiotic stress. Several transcription factors were identified and studied for differential expression. 61 differentially expressed genes were found to be common to both tissues under drought and salinity stress and were further validated using qRT-PCR. Transcriptome of P. sumatrense was also used to mine for genic SSR markers relevant to abiotic stress tolerance. This study is first report on a detailed analysis of molecular mechanisms of drought and salinity stress tolerance in a little millet variety. Resources generated in this study can be used as potential candidates for further characterization and to improve abiotic stress tolerance in food crops.
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Affiliation(s)
- Rasmita Rani Das
- Institute of Life Sciences, NALCO Square, Chandrasekharpur, Bhubaneswar, 751023, India
| | - Seema Pradhan
- Institute of Life Sciences, NALCO Square, Chandrasekharpur, Bhubaneswar, 751023, India
| | - Ajay Parida
- Institute of Life Sciences, NALCO Square, Chandrasekharpur, Bhubaneswar, 751023, India.
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Abbas HMK, Huang HX, Wang AJ, Wu TQ, Xue SD, Ahmad A, Xie DS, Li JX, Zhong YJ. Metabolic and transcriptomic analysis of two Cucurbita moschata germplasms throughout fruit development. BMC Genomics 2020; 21:365. [PMID: 32414328 PMCID: PMC7227267 DOI: 10.1186/s12864-020-6774-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 05/06/2020] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Pumpkins (Cucurbita moschata; Cucurbitaceae) are valued for their fruits and seeds and are rich in nutrients. Carotenoids and sugar contents, as main feature of pumpkin pulp, are used to determine the fruit quality. RESULTS Two pumpkin germplasms, CMO-X and CMO-E, were analyzed regarding the essential quality traits such as dry weight, soluble solids, organic acids, carotenoids and sugar contents. For the comparison of fruit development in these two germplasms, fruit transcriptome was analyzed at 5 different developmental stages from 0 d to 40 d in a time course manner. Putative pathways for carotenoids biosynthesis and sucrose metabolism were developed in C. moschata fruit and homologs were identified for each key gene involved in the pathways. Gene expression data was found consistent with the accumulation of metabolites across developmental stages and also between two germplasms. PSY, PDS, ZEP, CRTISO and SUS, SPS, HK, FK were found highly correlated with the accumulation of carotenoids and sucrose metabolites, respectively, at different growth stages of C. moschata as shown by whole transcriptomic analysis. The results of qRT-PCR analysis further confirmed the association of these genes. CONCLUSION Developmental regulation of the genes associated with the metabolite accumulation can be considered as an important factor for the determination of C. moschata fruit quality. This research will facilitate the investigation of metabolic profiles in other cultivars.
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Affiliation(s)
- Hafiz Muhammad Khalid Abbas
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - He-Xun Huang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - An-Jun Wang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Ting-Quan Wu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Shu-Dan Xue
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Aqeel Ahmad
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Da-Sen Xie
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Jun-Xing Li
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Yu-Juan Zhong
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.
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Zhao X, Wang M, Chai J, Li Q, Zhou Y, Li Y, Cai X. De novo assembly and characterization of the transcriptome and development of microsatellite markers in a Chinese endemic Euphorbia kansui. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1788992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Xueyan Zhao
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi’an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi’an, PR China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, PR China
| | - Meng Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, PR China
| | - Jia Chai
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital and School of Basic Medicine, Fourth Military Medical University (Air Force Medical University), Xi’an, PR China
| | - Qian Li
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi’an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi’an, PR China
| | - Yafu Zhou
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi’an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi’an, PR China
| | - Yan Li
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi’an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi’an, PR China
| | - Xia Cai
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, PR China
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10
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Xie D, Xu Y, Wang J, Liu W, Zhou Q, Luo S, Huang W, He X, Li Q, Peng Q, Yang X, Yuan J, Yu J, Wang X, Lucas WJ, Huang S, Jiang B, Zhang Z. The wax gourd genomes offer insights into the genetic diversity and ancestral cucurbit karyotype. Nat Commun 2019; 10:5158. [PMID: 31727887 PMCID: PMC6856369 DOI: 10.1038/s41467-019-13185-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 10/25/2019] [Indexed: 12/12/2022] Open
Abstract
The botanical family Cucurbitaceae includes a variety of fruit crops with global or local economic importance. How their genomes evolve and the genetic basis of diversity remain largely unexplored. In this study, we sequence the genome of the wax gourd (Benincasa hispida), which bears giant fruit up to 80 cm in length and weighing over 20 kg. Comparative analyses of six cucurbit genomes reveal that the wax gourd genome represents the most ancestral karyotype, with the predicted ancestral genome having 15 proto-chromosomes. We also resequence 146 lines of diverse germplasm and build a variation map consisting of 16 million variations. Combining population genetics and linkage mapping, we identify a number of regions/genes potentially selected during domestication and improvement, some of which likely contribute to the large fruit size in wax gourds. Our analyses of these data help to understand genome evolution and function in cucurbits. Cucurbits fruits have diverse shapes and sizes, but their genomes evolution and genetic basis of diversity are unclear. Here, the authors show that the wax gourd genome has the most ancestral karyotype among cucurbits and identify candidate genes which contribute to large fruit size by comparative and population genomics analyses.
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Affiliation(s)
- Dasen Xie
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Yuanchao Xu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.,Agricultural Genomic Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Jinpeng Wang
- School of Life Sciences, North China University of Science and Technology, Caofeidian Dist., Tangshan, Hebei, 063200, China
| | - Wenrui Liu
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Qian Zhou
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.,Agricultural Genomic Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Shaobo Luo
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Wu Huang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaoming He
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Qing Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qingwu Peng
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
| | - Xueyong Yang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiaqing Yuan
- School of Life Sciences, North China University of Science and Technology, Caofeidian Dist., Tangshan, Hebei, 063200, China
| | - Jigao Yu
- School of Life Sciences, North China University of Science and Technology, Caofeidian Dist., Tangshan, Hebei, 063200, China
| | - Xiyin Wang
- School of Life Sciences, North China University of Science and Technology, Caofeidian Dist., Tangshan, Hebei, 063200, China
| | - William J Lucas
- Agricultural Genomic Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.,Department of Plant Biology, University of California, Davis, CA, USA
| | - Sanwen Huang
- Agricultural Genomic Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Biao Jiang
- Guangdong Key Laboratory for New Technology Research of Vegetables, Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China.
| | - Zhonghua Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. .,College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, China.
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11
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Comparative transcriptome and metabolite profiling of four tissues from Alisma orientale (Sam.) Juzep reveals its inflorescence developmental and medicinal characteristics. Sci Rep 2019; 9:12310. [PMID: 31444376 PMCID: PMC6707231 DOI: 10.1038/s41598-019-48806-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 08/13/2019] [Indexed: 12/11/2022] Open
Abstract
Alisma orientale (Sam.) Juzep (A. orientale) is an important medicinal plant in traditional Chinese medicine. In this study, de novo RNA-seq of A. orientale was performed based on the cDNA libraries from four different tissues, roots, leaves, scapes and inflorescences. A total of 41,685 unigenes were assembled, 25,024 unigene functional annotations were obtained by searching against the five public sequence databases, and 3,411 simple sequence repeats in A. orientale were reported for the first time. 15,402 differentially expressed genes were analysed. The morphological characteristics showed that compared to the other tissues, the leaves had more chlorophyll, the scapes had more vascular bundles, and the inflorescences contained more starch granules and protein. In addition, the metabolic profiles of eight kinds of alisols metabolite profiling, which were measured by ultra-Performance liquid chromatography-triple quadrupole-mass spectrometry showed that alisol B 23-acetate and alisol B were the major components of the four tissues at amounts of 0.068~0.350 mg/g and 0.046~0.587 mg/g, respectively. In addition, qRT-PCR validated that farnesyl pyrophosphate synthase and 3-hydroxy-3-methylglutaryl-CoA reductase should be considered the critical candidate genes involved in alisol biosynthesis. These transcriptome and metabolic profiles of A. orientale may help clarify the molecular mechanisms underlying the medicinal characteristics of A. orientale.
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12
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Transcriptome analysis and codominant markers development in caper, a drought tolerant orphan crop with medicinal value. Sci Rep 2019; 9:10411. [PMID: 31320697 PMCID: PMC6639398 DOI: 10.1038/s41598-019-46613-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 06/27/2019] [Indexed: 01/08/2023] Open
Abstract
Caper (Capparis spinosa L.) is a xerophytic shrub cultivated for its flower buds and fruits, used as food and for their medicinal properties. Breeding programs and even proper taxonomic classification of the genus Capparis has been hampered so far by the lack of reliable genetic information and molecular markers. Here, we present the first genomic resource for C. spinosa, generated by transcriptomic approach and de novo assembly. The sequencing effort produced nearly 80 million clean reads assembled into 124,723 unitranscripts. Careful annotation and comparison with public databases revealed homologs to genes with a key role in important metabolic pathways linked to abiotic stress tolerance and bio-compounds production, such purine, thiamine and phenylpropanoid biosynthesis, α-linolenic acid and lipid metabolism. Additionally, a panel of genes involved in stomatal development/distribution and encoding for Stress Associated Proteins (SAPs) was also identified. We also used the transcriptomic data to uncover novel molecular markers for caper. Out of 50 SSRs tested, 14 proved polymorphic and represent the first set of SSR markers for the genus Capparis. This transcriptome will be an important contribution to future studies and breeding programs for this orphan crop, aiding to the development of improved varieties to sustain agriculture in arid conditions.
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13
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Liu B, Liu Y, Wang L, Hou C, An M. RNA-seq-based analysis of the hypertrophic scarring with and without pressure therapy in a Bama minipig model. Sci Rep 2018; 8:11831. [PMID: 30087370 PMCID: PMC6081447 DOI: 10.1038/s41598-018-29840-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 07/19/2018] [Indexed: 11/09/2022] Open
Abstract
Pressure therapy has been proved to be an effective treatment for hypertrophic scars in a clinical setting. However, evidence-based data are controversial and the precise mechanism of action of this technique remains unknown. The aim of this study was to investigate the potential molecular mechanisms of pressure therapy for hypertrophic scars. We established a Bama minipig (Sus scrofa) model of hypertrophic scarring in which the scars were treated with pressure to explore the mechanism of action of the treatment. There were 568 differentially expressed genes (289 upregulated, 279 downregulated) after pressure therapy at 90 days post-injury, whereas only 365 genes were differentially expressed (250 upregulated, 115 downregulated) at 120 days post-injury. These genes were associated with metabolic pathways, ECM-receptor interaction, the PI3K-Akt and MAPK signaling pathways, focal adhesion and cytokine-cytokine receptor interaction. In addition, the qRT-PCR results indicated that the trend of gene expression following pressure therapy was mostly consistent across the two methods. In conclusion, our systematic analysis of the transcriptome has provided a better understanding of the molecular mechanisms involved in pressure therapy and offers an important basis for further studies of the complex signaling pathways regulated by the treatment.
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Affiliation(s)
- Baimei Liu
- Institute of Applied Mechanics and Biomedical Engineering, Taiyuan University of Technology, Taiyuan, 030024, China.,Shanxi Key Laboratory of Material Strength & Structural Impact, College of Mechanics, Taiyuan University of Technology, Taiyuan, 030024, China.,National Demonstration Center for Experimental Mechanics Education (Taiyuan University of Technology), Taiyuan, 030024, China
| | - Yang Liu
- Institute of Applied Mechanics and Biomedical Engineering, Taiyuan University of Technology, Taiyuan, 030024, China.,Shanxi Key Laboratory of Material Strength & Structural Impact, College of Mechanics, Taiyuan University of Technology, Taiyuan, 030024, China.,National Demonstration Center for Experimental Mechanics Education (Taiyuan University of Technology), Taiyuan, 030024, China
| | - Li Wang
- Institute of Applied Mechanics and Biomedical Engineering, Taiyuan University of Technology, Taiyuan, 030024, China.,Shanxi Key Laboratory of Material Strength & Structural Impact, College of Mechanics, Taiyuan University of Technology, Taiyuan, 030024, China.,National Demonstration Center for Experimental Mechanics Education (Taiyuan University of Technology), Taiyuan, 030024, China
| | - Chunsheng Hou
- Department of Burns and Plastic Surgery, Taigang General Hospital, Taiyuan, 030009, China
| | - Meiwen An
- Institute of Applied Mechanics and Biomedical Engineering, Taiyuan University of Technology, Taiyuan, 030024, China. .,Shanxi Key Laboratory of Material Strength & Structural Impact, College of Mechanics, Taiyuan University of Technology, Taiyuan, 030024, China. .,National Demonstration Center for Experimental Mechanics Education (Taiyuan University of Technology), Taiyuan, 030024, China.
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14
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Guo WL, Chen BH, Chen XJ, Guo YY, Yang HL, Li XZ, Wang GY. Transcriptome profiling of pumpkin (Cucurbita moschata Duch.) leaves infected with powdery mildew. PLoS One 2018; 13:e0190175. [PMID: 29320569 PMCID: PMC5761878 DOI: 10.1371/journal.pone.0190175] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 12/08/2017] [Indexed: 01/08/2023] Open
Abstract
Cucurbit powdery mildew (PM) is one of the most severe fungal diseases, but the molecular mechanisms underlying PM resistance remain largely unknown, especially in pumpkin (Cucurbita moschata Duch.). The goal of this study was to identify gene expression differences in PM-treated plants (harvested at 24 h and 48 h after inoculation) and untreated (control) plants of inbred line “112–2” using RNA sequencing (RNA-Seq). The inbred line “112–2” has been purified over 8 consecutive generations of self-pollination and shows high resistance to PM. More than 7600 transcripts were examined in pumpkin leaves, and 3129 and 3080 differentially expressed genes (DEGs) were identified in inbred line “112–2” at 24 and 48 hours post inoculation (hpi), respectively. Based on the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway database and GO (Gene Ontology) database, a complex regulatory network for PM resistance that may involve hormone signal transduction pathways, transcription factors and defense responses was revealed at the transcription level. In addition, the expression profiles of 16 selected genes were analyzed using quantitative RT-PCR. Among these genes, the transcript levels of 6 DEGs, including bHLH87 (Basic Helix-loop-helix transcription factor), ERF014 (Ethylene response factor), WRKY21 (WRKY domain), HSF (heat stress transcription factor A), MLO3 (Mildew Locus O), and SGT1 (Suppressor of G-Two Allele of Skp1), in PM-resistant “112–2” were found to be significantly up- or down-regulated both before 9 hpi and at 24 hpi or 48 hpi; this behavior differed from that observed in the PM-susceptible material (cultivar “Jiujiangjiaoding”). The transcriptome data provide novel insights into the response of Cucurbita moschata to PM stress and are expected to be highly useful for dissecting PM defense mechanisms in this major vegetable and for improving pumpkin breeding with enhanced resistance to PM.
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Affiliation(s)
- Wei-Li Guo
- School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, Xin Xiang, China
| | - Bi-Hua Chen
- School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, Xin Xiang, China
| | - Xue-Jin Chen
- School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, Xin Xiang, China
| | - Yan-Yan Guo
- School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, Xin Xiang, China
| | - He-Lian Yang
- School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, Xin Xiang, China
| | - Xin-Zheng Li
- School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, Xin Xiang, China
- * E-mail:
| | - Guang-Yin Wang
- School of Horticulture Landscape Architecture, Henan Institute of Science and Technology, Xin Xiang, China
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15
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Ruangnam S, Wanchana S, Phoka N, Saeansuk C, Mahatheeranont S, de Hoop SJ, Toojinda T, Vanavichit A, Arikit S. A deletion of the gene encoding amino aldehyde dehydrogenase enhances the "pandan-like" aroma of winter melon (Benincasa hispida) and is a functional marker for the development of the aroma. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:2557-2565. [PMID: 28887587 DOI: 10.1007/s00122-017-2976-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Accepted: 08/30/2017] [Indexed: 05/16/2023]
Abstract
The gene conferring a "pandan-like" aroma of winter melon was identified. The sequence variation (804-bp deletion) found in the gene was used as the target for functional marker development. Winter melon (Benincasa hispida), a member of the Cucurbitaceae family, is a commonly consumed vegetable in Asian countries that is popular for its nutritional and medicinal value. A "pandan-like" aroma, which is economically important in crops including rice and soybean, is rarely found in most commercial varieties of winter melon, but is present in some landraces. This aroma is a value-added potential trait in breeding winter melon with a higher economic value. In this study, we confirmed that the aroma of winter melon is due to the potent volatile compound 2-acetyl-1-pyrroline (2AP) as previously identified in other plants. Based on an analysis of public transcriptome data, BhAMADH encoding an aminoaldehyde dehydrogenase (AMADH) was identified as a candidate gene conferring aroma of winter melon. A sequence comparison of BhAMADH between the aromatic and non-aromatic accessions revealed an 804-bp deletion encompassing exons 11-13 in the aromatic accession. The deletion caused several premature stop codons and could result in a truncated protein with a length of only 208 amino acids compared with 503 amino acids in the normal protein. A functional marker was successfully developed based on the 804-bp deletion and validated in 237 F2 progenies. A perfect association of the marker genotypes and aroma phenotypes indicates that BhAMADH is the major gene conferring the aroma. The recently developed functional marker could be efficiently used in breeding programs for the aroma trait in winter melon.
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Affiliation(s)
- Saowalak Ruangnam
- Faculty of Agriculture at Kamphaeng Saen, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand
- Hortigenetics Research (S.E. Asia) Limited, Suphanburi, 72190, Thailand
| | - Samart Wanchana
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, 12120, Thailand
| | - Nongnat Phoka
- King Mongkut's University of Technology Thonburi, Ratchaburi Campus, Ratchaburi, 70150, Thailand
| | - Chatree Saeansuk
- Rice Science Center, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand
- Interdisciplinary Graduate Program in Genetic Engineering, Kasetsart University, Bangkok, Thailand
| | - Sugunya Mahatheeranont
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Simon Jan de Hoop
- Hortigenetics Research (S.E. Asia) Limited, Suphanburi, 72190, Thailand
| | - Theerayut Toojinda
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, 12120, Thailand
| | - Apichart Vanavichit
- Rice Science Center, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 7314, Thailand
| | - Siwaret Arikit
- Rice Science Center, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand.
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom, 7314, Thailand.
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16
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De novo transcriptome sequencing and assembly from apomictic and sexual Eragrostis curvula genotypes. PLoS One 2017; 12:e0185595. [PMID: 29091722 PMCID: PMC5665505 DOI: 10.1371/journal.pone.0185595] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 09/15/2017] [Indexed: 11/19/2022] Open
Abstract
A long-standing goal in plant breeding has been the ability to confer apomixis to agriculturally relevant species, which would require a deeper comprehension of the molecular basis of apomictic regulatory mechanisms. Eragrostis curvula (Schrad.) Nees is a perennial grass that includes both sexual and apomictic cytotypes. The availability of a reference transcriptome for this species would constitute a very important tool toward the identification of genes controlling key steps of the apomictic pathway. Here, we used Roche/454 sequencing technologies to generate reads from inflorescences of E. curvula apomictic and sexual genotypes that were de novo assembled into a reference transcriptome. Near 90% of the 49568 assembled isotigs showed sequence similarity to sequences deposited in the public databases. A gene ontology analysis categorized 27448 isotigs into at least one of the three main GO categories. We identified 11475 SSRs, and several of them were assayed in E curvula germoplasm using SSR-based primers, providing a valuable set of molecular markers that could allow direct allele selection. The differential contribution to each library of the spliced forms of several transcripts revealed the existence of several isotigs produced via alternative splicing of single genes. The reference transcriptome presented and validated in this work will be useful for the identification of a wide range of gene(s) related to agronomic traits of E. curvula, including those controlling key steps of the apomictic pathway in this species, allowing the extrapolation of the findings to other plant species.
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17
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Zhang L, Yang X, Qi X, Guo C, Jing Z. Characterizing the transcriptome and microsatellite markers for almond ( Amygdalus communis L.) using the Illumina sequencing platform. Hereditas 2017; 155:14. [PMID: 29075165 PMCID: PMC5649074 DOI: 10.1186/s41065-017-0049-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 10/09/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The almond tree (Prunus amygdalus Batsch) is an important nut tree grown in subtropical regions that produces nutrient-rich nuts. However, a paucity of genomic information and DNA markers has restricted the development of modern breeding technologies for almond trees. RESULTS In this study, almonds were sequenced with Illumina paired-end sequencing technology to obtain transcriptome data and develop simple sequence repeats (SSR) markers. We generated approximately 64 million clean reads from the various tissues of mixed almonds, and a total of 42,135 unigenes with an average length of 988 bp were obtained in the present study. A total of 27,586 unigenes (57.7% of all unigenes generated) were annotated using several databases. A total of 112,812 unigenes were annotated with the Gene Ontology (GO) database and assigned to 82 functional sub-groups, and 29,075 unigenes were assigned to the KOG database and classified into 25 function classifications. There were 9470 unigenes assigned to 129 Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathways from five categories in the KEGG pathway database. We further identified 8641 SSR markers from 48,012 unigenes. A total of 100 SSR markers were randomly selected to validate quality, and 82 markers could amplify the specific products of A. communis L., whereas 70 markers were successfully transferable to five species (A. ledebouriana, A. mongolica, A. pedunculata, A. tangutica, and A. triloba). CONCLUSIONS Our study was the first to produce public transcriptome data from almonds. The development of SSR markers will promote genetics research and breeding programmes for almonds.
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Affiliation(s)
- Linsen Zhang
- College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi People's Republic of China
| | - Xiaoni Yang
- College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi People's Republic of China
| | - Xiangning Qi
- College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi People's Republic of China
| | - Chunhui Guo
- College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi People's Republic of China
| | - Zhaobin Jing
- College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi People's Republic of China
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18
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Han C, Li Q, Li X, Zhang Z, Huang J. De novo assembly, characterization and annotation for the transcriptome of Sphaeroma terebrans and microsatellite marker discovery. Genes Genomics 2017; 40:167-176. [PMID: 29892920 DOI: 10.1007/s13258-017-0618-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 10/05/2017] [Indexed: 12/12/2022]
Abstract
Sphaeroma terebrans, an economically and ecologically important marine wood-boring isopod, is mainly distributed in tropical and subtropical mangroves. Nevertheless, available genomic and transcriptomic information for this isopod is extremely deficient. Here, we first performed the assembly of S. terebrans transcriptome by Illumina sequencing. A total of 51,092 high-quality unigenes with an average length of 641 bp were obtained and 19,915 unigenes were successfully annotated in four public databases. Only 9932 out of 19915 unigenes were commonly annotated by all four databases. In addition, 9609 unigenes were categorized into 54 function categories of Gene Ontology (GO), and 14,512 unigenes were successfully grouped into 25 functional categories of the EuKaryotic Orthologous Groups (KOG) database. Moreover, 11,507 unigenes were assigned to 228 pathways of the Kyoto Encyclopedia of Genes and Genomes (KEGG). Out of 51,092 unigenes, a total of 4257 different microsatellites with motifs range from di- to hexa-nucleotide were identified from 3324 unigene sequences. Among 64 primer pairs selected for validation, 35 were successful in PCR amplification and 13 exhibited obvious repeat polymorphisms in the wild population of S. terebrans in Dongzhaigang (Hainan Island). The transcriptome dataset and the identified microsatellite markers (SSRs) will provide abundant information for researches on the discovery of new genes, metabolic mechanism and genetic diversity of S. terebrans.
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Affiliation(s)
- Chong Han
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Qiang Li
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Xiufeng Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Zhipeng Zhang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Jianrong Huang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, Sun Yat-Sen University, Guangzhou, 510275, China.
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19
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Comparative Transcriptome Analysis Reveals Adaptive Evolution of Notopterygium incisum and Notopterygium franchetii, Two High-Alpine Herbal Species Endemic to China. Molecules 2017; 22:molecules22071158. [PMID: 28696392 PMCID: PMC6152189 DOI: 10.3390/molecules22071158] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 07/07/2017] [Accepted: 07/07/2017] [Indexed: 02/04/2023] Open
Abstract
The extreme conditions (e.g., cold, low oxygen, and strong ultraviolet radiation) of the high mountains provide an ideal natural laboratory for studies on speciation and the adaptive evolution of organisms. Up to now, few genome/transcriptome-based studies have been carried out on how plants adapt to conditions at extremely high altitudes. Notopterygium incisum and Notopterygiumfranchetii (Notopterygium, Apiaceae) are two endangered high-alpine herbal plants endemic to China. To explore the molecular genetic mechanisms of adaptation to high altitudes, we performed high-throughput RNA sequencing (RNA-seq) to characterize the transcriptomes of the two species. In total, more than 130 million sequence reads, 81,446 and 63,153 unigenes with total lengths of 86,924,837 and 62,615,693 bp, were generated for the two herbal species, respectively. OrthoMCL analysis identified 6375 single-copy orthologous genes between N. incisum and N. franchetii. In total, 381 positively-selected candidate genes were identified for both plants by using estimations of the non-synonymous to synonymous substitution rate. At least 18 of these genes potentially participate in RNA splicing, DNA repair, glutathione metabolism and the plant–pathogen interaction pathway, which were further enriched in various functional gene categories possibly responsible for environment adaptation in high mountains. Meanwhile, we detected various transcription factors that regulated the material and energy metabolism in N. incisum and N. franchetii, which probably play vital roles in the tolerance to stress in surroundings. In addition, 60 primer pairs based on orthologous microsatellite-containing sequences between the both Notopterygium species were determined. Finally, 17 polymorphic microsatellite markers (SSR) were successfully characterized for the two endangered species. Based on these candidate orthologous and SSR markers, we detected that the adaptive evolution and species divergence of N. incisum and N. franchetii were significantly associated with the extremely heterogeneous environments and climatic oscillations in high-altitude areas. This work provides important insights into the molecular mechanisms of adaptation to high-altitudes in alpine herbal plants.
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Cloning and characterization of WRKY gene homologs in Chieh-qua (Benincasa hispida Cogn. var. Chieh-qua How) and their expression in response to fusaric acid treatment. 3 Biotech 2017; 7:86. [PMID: 28501986 DOI: 10.1007/s13205-017-0711-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 03/30/2017] [Indexed: 10/19/2022] Open
Abstract
The WRKY transcription factors play an important role in plant resistance for biotic and abiotic stresses. In the present study, we cloned 10 WRKY gene homologs (CqWRKY) in Chieh-qua (Benincasa hispida Cogn. var. Chieh-qua) using the rapid-amplification of cDNA ends (RACE) or homology-based cloning methods. We characterized the structure of these CqWRKY genes. Phylogenetic analysis of these sequences with cucumber homologs suggested possible structural conservation of these genes among cucurbit crops. We examined the expression levels of these genes in response to fusaric acid (FA) treatment between resistant and susceptible Chieh-qua lines with quantitative real-time PCR. All genes could be upregulated upon FA treatment, but four CqWRKY genes exhibited differential expression between resistant and susceptible lines before and after FA application. CqWRKY31 seemed to be a positive regulator while CqWRKY1, CqWRKY23 and CqWRKY53 were negative regulators of fusaric resistance. This is the first report of characterization of WRKY family genes in Chieh-qua. The results may also be useful in breeding Chieh-qua for Fusarium wilt resistance.
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Liu XY, Li J, Liu MM, Yao Q, Chen JZ. Transcriptome Profiling to Understand the Effect of Citrus Rootstocks on the Growth of 'Shatangju' Mandarin. PLoS One 2017; 12:e0169897. [PMID: 28081213 PMCID: PMC5231354 DOI: 10.1371/journal.pone.0169897] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Accepted: 12/24/2016] [Indexed: 01/01/2023] Open
Abstract
To obtain insight into potential mechanisms underlying the influence of rootstock on scion growth, we performed a comparative analysis of 'Shatangju' mandarin grafted onto 5 rootstocks: Fragrant orange (Citrus junons Sieb. ex. Tanaka), Red tangerine (Citrus reticulata Blanco), 'Shatangju' mandarin (Citrus reticulata Blanco), Rough lemon (Citrus jambhiri Lush) and Canton lemon (Citrus limonia Osbeck). The tree size of 'Shatangju' mandarin grafted onto Canton lemon and Rough lemon were the largest, followed by self-rooted rootstock trees, and the lowest tree sizes correspond to ones grafted on Red tangerine and Fragrant orange rootstocks. The levels of indoleacetic acid (IAA) and gibberellin (GA) were significantly and positively related to growth vigor. The differences of gene expression in leaves of trees grafted onto Red tangerine, Canton lemon and 'Shatangju' mandarin were analyzed by RNA-Seq. Results showed that more differentially expressed genes involved in oxidoreductase function, hormonal signal transduction and the glycolytic pathway were enriched in 'Red tangerine vs Canton lemon'. qRT-PCR analysis showed that expression levels of ARF1, ARF8, GH3 and IAA4 were negatively correlated with the growth vigor and IAA content. The metabolism of GA was influenced by the differential expression of KO1 and GA2OX1 in grafted trees. In addition, most of antioxidant enzyme genes were up-regulated in leaves of trees grafted onto Red tangerine, resulting in a higher peroxidase activity. We concluded that different rootstocks significantly affected the expression of genes involved in auxin signal transduction pathway and GA biosynthesis pathway in the grafted plants, and then regulated the hormone levels and their signal pathways.
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Affiliation(s)
- Xiang-Yu Liu
- College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, China
- Qingdao Agricultural University, Qingdao, Shandong, China
| | - Juan Li
- Department of Horticulture, Zhongkai University of Agriculture and Engineering, Guangzhou, Guangdong, China
| | - Meng-Meng Liu
- College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Qing Yao
- College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, China
| | - Jie-Zhong Chen
- College of Horticulture, South China Agricultural University, Guangzhou, Guangdong, China
- * E-mail:
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Song X, Liu G, Huang Z, Duan W, Tan H, Li Y, Hou X. Temperature expression patterns of genes and their coexpression with LncRNAs revealed by RNA-Seq in non-heading Chinese cabbage. BMC Genomics 2016; 17:297. [PMID: 27103267 PMCID: PMC4840866 DOI: 10.1186/s12864-016-2625-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 04/16/2016] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Non-heading Chinese cabbage (NHCC, Brassica rapa ssp. chinensis) is an important leaf vegetable grown worldwide. However, little is known about the molecular mechanisms underlying tolerance for extreme temperature in NHCC. The limited availability of NHCC genomic information has greatly hindered functional analysis and molecular breeding. RESULTS Here, we conduct comprehensive analyses of cold and heat treatments in NHCC using RNA-seq. Approximately 790 million paired-end reads representing 136,189 unigenes with N50 length of 1705 bp were obtained. Totally, 14,329 differentially expressed genes (DEGs) were detected. Among which, 10 DEGs were detected in all treatments, including 7 up-regulated and 3 down-regulated. The enrichment analyses showed 25 and 33 genes were enriched under cold and heat treatments, respectively. Additionally, 10,001 LncRNAs were identified, and 9,687 belonged to novel LncRNAs. The expression of miRNAs were more than that of pri-miRNAs and LncRNAs. Furthermore, we constructed a coexpression network for LncRNAs and miRNAs. It showed 67 and 192 genes were regulated by LncRNAs under cold and heat treatments, respectively. We constructed the flowchart for identifying LncRNAs of NHCC using transcriptome. Except conducting the de novo transcriptome analyses, we also compared these unigenes with the Chinese cabbage proteins. We identified several most important genes, and discussed their regulatory networks and crosstalk in cold and heat stresses. CONCLUSIONS We presented the first comprehensive characterization for NHCC crops and constructed the flowchart for identifying LncRNAs using transcriptome. Therefore, this study represents a fully characterized NHCC transcriptome, and provides a valuable resource for genetic and genomic studies under abiotic stress.
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Affiliation(s)
- Xiaoming Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- Center of Genomics and Computational Biology, College of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, 063000, China
| | - Gaofeng Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhinan Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weike Duan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huawei Tan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ying Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.
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Huang J, Gao Y, Jia H, Zhang Z. Characterization of the teosinte transcriptome reveals adaptive sequence divergence during maize domestication. Mol Ecol Resour 2016; 16:1465-1477. [DOI: 10.1111/1755-0998.12526] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 02/26/2016] [Accepted: 02/26/2016] [Indexed: 11/30/2022]
Affiliation(s)
- Jun Huang
- National Key Laboratory of Crop Genetic Improvement; Huazhong Agricultural University; Wuhan 430070 China
| | - Youjun Gao
- National Key Laboratory of Crop Genetic Improvement; Huazhong Agricultural University; Wuhan 430070 China
| | - Haitao Jia
- National Key Laboratory of Crop Genetic Improvement; Huazhong Agricultural University; Wuhan 430070 China
| | - Zuxin Zhang
- National Key Laboratory of Crop Genetic Improvement; Huazhong Agricultural University; Wuhan 430070 China
- College of Life Science; Huanggang Normal University; Huanggang 438000 China
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Development and cross-species transferability of EST-SSR markers in Siberian wildrye (Elymus sibiricus L.) using Illumina sequencing. Sci Rep 2016; 6:20549. [PMID: 26853106 PMCID: PMC4744933 DOI: 10.1038/srep20549] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 01/06/2016] [Indexed: 11/09/2022] Open
Abstract
Siberian wildrye (Elymus sibiricus L.) is a perennial, self-fertilizing grass that plays an important role in animal husbandry and environmental sustenance. However, the transcriptomic and genomic information on this species is very limited, which hinders genetic and breeding studies. In the present study, 76,686,804 clean reads were generated from 11 different tissue samples of E. sibiricus by Illumina paired-end sequencing, and the reads were deposited into the NCBI SRA database (SRX574376). A total of 8,769 EST-SSRs were identified from 94,458 unigene sequences, which were obtained by de novo assembly. Moreover, 1,078 primer pairs were successfully designed, and 500 pairs were randomly selected to assess polymorphisms in 15 E. sibiricus accessions. A total of 112 primer pairs were polymorphic, and the polymorphism information content (PIC) values ranged from 0.39 to 0.81, indicating a high level of informativeness. Furthermore, these 112 polymorphic primer pairs were used to evaluate the transferability to 13 other related species, and 55 EST-SSR markers were found to be polymorphic among these 13 Elymus species. This study collected the global sequence data for E. sibiricus, and the newly developed markers will prove valuable in facilitating genetic diversity in E. sibiricus and related Elymus species.
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Deng T, Pang C, Lu X, Zhu P, Duan A, Tan Z, Huang J, Li H, Chen M, Liang X. De Novo Transcriptome Assembly of the Chinese Swamp Buffalo by RNA Sequencing and SSR Marker Discovery. PLoS One 2016; 11:e0147132. [PMID: 26766209 PMCID: PMC4713091 DOI: 10.1371/journal.pone.0147132] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/29/2015] [Indexed: 01/11/2023] Open
Abstract
The Chinese swamp buffalo (Bubalis bubalis) is vital to the lives of small farmers and has tremendous economic importance. However, a lack of genomic information has hampered research on augmenting marker assisted breeding programs in this species. Thus, a high-throughput transcriptomic sequencing of B. bubalis was conducted to generate transcriptomic sequence dataset for gene discovery and molecular marker development. Illumina paired-end sequencing generated a total of 54,109,173 raw reads. After trimming, de novo assembly was performed, which yielded 86,017 unigenes, with an average length of 972.41 bp, an N50 of 1,505 bp, and an average GC content of 49.92%. A total of 62,337 unigenes were successfully annotated. Among the annotated unigenes, 27,025 (43.35%) and 23,232 (37.27%) unigenes showed significant similarity to known proteins in NCBI non-redundant protein and Swiss-Prot databases (E-value < 1.0E-5), respectively. Of these annotated unigenes, 14,439 and 15,813 unigenes were assigned to the Gene Ontology (GO) categories and EuKaryotic Ortholog Group (KOG) cluster, respectively. In addition, a total of 14,167 unigenes were assigned to 331 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Furthermore, 17,401 simple sequence repeats (SSRs) were identified as potential molecular markers. One hundred and fifteen primer pairs were randomly selected for amplification to detect polymorphisms. The results revealed that 110 primer pairs (95.65%) yielded PCR amplicons and 69 primer pairs (60.00%) presented polymorphisms in 35 individual buffaloes. A phylogenetic analysis showed that the five swamp buffalo populations were clustered together, whereas two river buffalo breeds clustered separately. In the present study, the Illumina RNA-seq technology was utilized to perform transcriptome analysis and SSR marker discovery in the swamp buffalo without using a reference genome. Our findings will enrich the current SSR markers resources and help spearhead molecular genetic research studies on the swamp buffalo.
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Affiliation(s)
- Tingxian Deng
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Chunying Pang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Xingrong Lu
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Peng Zhu
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Anqin Duan
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Zhengzhun Tan
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Jian Huang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Hui Li
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Mingtan Chen
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
| | - Xianwei Liang
- Key Laboratory of Buffalo Genetics, Breeding and Reproduction technology, Ministry of Agriculture, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, Guangxi, P. R. China
- * E-mail:
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Jiang B, Liu W, Xie D, Peng Q, He X, Lin Y, Liang Z. High-density genetic map construction and gene mapping of pericarp color in wax gourd using specific-locus amplified fragment (SLAF) sequencing. BMC Genomics 2015; 16:1035. [PMID: 26647294 PMCID: PMC4673774 DOI: 10.1186/s12864-015-2220-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 11/16/2015] [Indexed: 11/10/2022] Open
Abstract
Background High-density map is a valuable tool for genetic and genomic analysis. Although wax gourd is a widely distributed vegetable of Cucurbitaceae and has important medicinal and health value, no genetic map has been constructed because of the lack of efficient markers. Specific-locus amplified fragment sequencing (SLAF-seq) is a newly developed high-throughput strategy for large-scale single nucleotide polymorphism (SNP) discovery and genotyping. Results In our present study, we constructed a high-density genetic map by using SLAF-seq and identified a locus controlling pericarp color in wax gourd. An F2 population of 140 individuals and their two parents were subjected to SLAF-seq. A total of 143.38 M pair-end reads were generated. The average sequencing depth was 26.51 in the maternal line (B214), 27.01 in the parental line (B227), and 5.11 in each F2 individual. When filtering low-depth SLAF tags, a total of 142,653 high-quality SLAFs were detected, and 22,151 of them were polymorphic, with a polymorphism rate of 15.42 %. And finally, 4,607 of the polymorphic markers were selected for genetic map construction, and 12 linkage groups (LGs) were generated. The map spanned 2,172.86 cM with an average distance between adjacent markers for 0.49 cM. The inheritance of pericarp color was also studied, which showed that the pericarp color was controlled by one single gene. And based on the newly constructed high-density map, a single locus locating on chromosome 5 was identified for controlling the pericarp color of wax gourd. Conclusions This is the first report of high-density genetic map construction and gene mapping in wax gourd, which will be served as an invaluable tool for gene mapping, marker assisted breeding, map-based gene cloning, comparative mapping and draft genome assembling of wax gourd. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2220-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Biao Jiang
- Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China.,Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou, 510640, China
| | - Wenrui Liu
- Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China.,Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou, 510640, China
| | - Dasen Xie
- Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China. .,Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou, 510640, China.
| | - Qingwu Peng
- Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China
| | - Xiaoming He
- Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China.,Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou, 510640, China
| | - Yu'e Lin
- Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China
| | - Zhaojun Liang
- Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China
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De novo assembly and characterization of the leaf, bud, and fruit transcriptome from the vulnerable tree Juglans mandshurica for the development of 20 new microsatellite markers using Illumina sequencing. Mol Genet Genomics 2015; 291:849-62. [DOI: 10.1007/s00438-015-1147-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/13/2015] [Indexed: 01/08/2023]
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Chen SF, Li MW, Jing HJ, Zhou RC, Yang GL, Wu W, Fan Q, Liao WB. De Novo Transcriptome Assembly in Firmiana danxiaensis, a Tree Species Endemic to the Danxia Landform. PLoS One 2015; 10:e0139373. [PMID: 26427005 PMCID: PMC4591120 DOI: 10.1371/journal.pone.0139373] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 09/11/2015] [Indexed: 11/19/2022] Open
Abstract
Many Firmiana species are locally endemic, providing an interesting system for studying adaptation and speciation. Among these species, F. danxiaensis is a tree species endemic to Mount Danxia in Guangdong, China, which is an area known for presenting the Danxia landform. How F. danxiaensis could have adapted to the stressful environment of rocky cliffs covered with barren soils in the Danxia landform is still unknown. In this study, we performed de novo assembly of the transcriptome of F. danxiaensis, obtaining 47,221 unigenes with an N50 value of 987 bp. Homology analysis showed that 32,318 of the unigenes presented hits in the NCBI non-redundant database, and 31,857 exhibited significant matches with the protein database of Theobroma cacao. Gene Ontology (GO) annotation showed that hundreds of unigenes participated in responses to various stresses or nutritional starvation, which may help us to understand the adaptation of F. danxiaensis to Danxia landform. Additionally, we found 263 genes related to responses to Cd, partially explaining the high accumulation of Cd observed in Firmiana species. The EuKaryotic Orthologous Groups (KOG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations revealed many genes playing roles in the biosynthesis of secondary metabolites and environmental adaptation, which may also contribute to the survivor and success of Firmiana species in extreme environments. Based on the obtained transcriptome, we further identified a Firmiana-specific whole-genome duplication event that occurred approximately 20 Mya, which may have provided raw materials for the diversification of Firmiana species.
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Affiliation(s)
- Su-Fang Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ming-Wan Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Hui-Juan Jing
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ren-Chao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Gui-Li Yang
- National Engineering Resarch Center of Plant Space Breeding, South China Agricultural University, Guangzhou 510642, China
| | - Wei Wu
- South China Botanical Garden, Chinese Academy of Science, Guangzhou 510650, China
| | - Qiang Fan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- * E-mail: (QF); (WL)
| | - Wen-Bo Liao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- * E-mail: (QF); (WL)
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De novo transcriptome assembly, gene annotation, marker development, and miRNA potential target genes validation under abiotic stresses in Oenanthe javanica. Mol Genet Genomics 2014; 290:671-83. [PMID: 25416420 DOI: 10.1007/s00438-014-0953-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 11/10/2014] [Indexed: 10/24/2022]
Abstract
Oenanthe javanica is an aquatic perennial herb with known medicinal properties and an edible vegetable with high vitamin and mineral content. The understanding of the biology of O. javanica is limited by the absence of information on its genome, transcriptome, and small RNA. In this study, transcriptome sequencing and small RNA sequencing were performed to annotate function genes, develop SSR markers and analyze potential target genes of miRNAs in O. javanica. All reads with total nucleotides number of 1,440,321,408 bp were assembled into 58,072 transcripts and 40,208 unigenes. A total of 1,233 SSRs were identified from O. javanica. Generated unigenes were aligned against seven databases and annotated with functions. A total of 29 potential targets were predicted. Expression of 10 miRNAs and their corresponding target genes under abiotic stresses (heat, cold, salinity, and drought) was validated. All ten miRNAs were confirmed to response to abiotic stresses. A pair of miRNA and its target gene was found. This study can serve as a valuable resource for future studies on O. javanica, which may focus on novel gene discovery, SSR development, gene mapping, and miRNA-affected processes and pathways. This can promote the development of the useful medicinal properties of O. javanica in medical science.
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Chen X, Zhang J, Liu Q, Guo W, Zhao T, Ma Q, Wang G. Transcriptome sequencing and identification of cold tolerance genes in hardy Corylus species (C. heterophylla Fisch) floral buds. PLoS One 2014; 9:e108604. [PMID: 25268521 PMCID: PMC4182504 DOI: 10.1371/journal.pone.0108604] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 09/01/2014] [Indexed: 11/22/2022] Open
Abstract
Background The genus Corylus is an important woody species in Northeast China. Its products, hazelnuts, constitute one of the most important raw materials for the pastry and chocolate industry. However, limited genetic research has focused on Corylus because of the lack of genomic resources. The advent of high-throughput sequencing technologies provides a turning point for Corylus research. In the present study, we performed de novo transcriptome sequencing for the first time to produce a comprehensive database for the Corylus heterophylla Fisch floral buds. Results The C. heterophylla Fisch floral buds transcriptome was sequenced using the Illumina paired-end sequencing technology. We produced 28,930,890 raw reads and assembled them into 82,684 contigs. A total of 40,941 unigenes were identified, among which 30,549 were annotated in the NCBI Non-redundant (Nr) protein database and 18,581 were annotated in the Swiss-Prot database. Of these annotated unigenes, 25,311 and 10,514 unigenes were assigned to gene ontology (GO) categories and clusters of orthologous groups (COG), respectively. We could map 17,207 unigenes onto 128 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG) database. Additionally, based on the transcriptome, we constructed a candidate cold tolerance gene set of C. heterophylla Fisch floral buds. The expression patterns of selected genes during four stages of cold acclimation suggested that these genes might be involved in different cold responsive stages in C. heterophylla Fisch floral buds. Conclusion The transcriptome of C. heterophylla Fisch floral buds was deep sequenced, de novo assembled, and annotated, providing abundant data to better understand the C. heterophylla Fisch floral buds transcriptome. Candidate genes potentially involved in cold tolerance were identified, providing a material basis for future molecular mechanism analysis of C. heterophylla Fisch floral buds tolerant to cold stress.
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Affiliation(s)
- Xin Chen
- Shandong Institute of Pomology, Shandong Provincial Key Laboratory of Fruit Tree Biotechnology Breeding, Tai'an, Shandong, China
| | - Jin Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Qingzhong Liu
- Shandong Institute of Pomology, Shandong Provincial Key Laboratory of Fruit Tree Biotechnology Breeding, Tai'an, Shandong, China
| | - Wei Guo
- School of Forest Resources and Conservation, University of Florida, Gainesville, Florida, United States of America
| | - Tiantian Zhao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Qinghua Ma
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Guixi Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- * E-mail:
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