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Liang J, Zeng J, Huang X, Zhu T, Gong Y, Dong C, Wang X, Zhao L, Xie L, Liang K, Tan Q, Cui Y, Kong B, Hui W. Super-assembly of integrated gold magnetic assay with loop-mediated isothermal amplification for point-of-care testing. NANO RESEARCH 2022; 16:1242-1251. [PMID: 35966151 PMCID: PMC9362447 DOI: 10.1007/s12274-022-4692-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
UNLABELLED With the increasing global threat of various diseases and infections, it is essential to develop a fast, low-cost, and easy-to-use point-of-care testing (POCT) system for inspections at all levels of medical institutions and self-examination at home. In this work, gold magnetic nanoparticles (GMNPs) are used as the key material, and a rapid visual detection method is designed through integrating loop-mediated isothermal amplification (LAMP) and lateral flow assay (LFA) biosensor for detecting a variety of analytes which includes whole blood, buccal swabs, and DNA. It is worth to note that the proposed method does not need DNA extraction. Furthermore, uracil DNA glycosylase (UDG) is employed to eliminate carrier contamination for preventing false positive results. The whole detection process can be finished within 25 min. The accuracy of detection is measured by assessing the polymorphisms of the methylenetetrahydrofolate reductase (MTHFR) C677T. The detection limit of the newly developed extraction-free detection system for MTHFR C677T is 0.16 ng/μL. A preliminary clinical study of the proposed method is carried out by analyzing 600 clinical samples (including 200 whole blood samples, 100 buccal swabs, and 300 genomic DNA samples). The results indicate that the proposed method is 100% consistent with the sequencing results which provides a new choice for POCT and shows a broad application prospect in all levels of medical clinics and at home. ELECTRONIC SUPPLEMENTARY MATERIAL Supplementary material (details for MTHFR C677T primer sequences, the cell count results of samples at different dilution ratios, genotyping results and frequency samples, a Hardy-Weinberg equilibrium test, the sensitivity of the system, detection results of multiple samples, and optimization of the system) is available in the online version of this article at 10.1007/s12274-022-4692-9.
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Affiliation(s)
- Jianping Liang
- The College of life science, Northwest University, Xi’an, 710069 China
| | - Jie Zeng
- Department of Chemistry, Shanghai Key Lab of Molecular Catalysis and Innovative Materials, Collaborative Innovation Center of Chemistry for Energy Materials, Fudan University, Shanghai, 200438 China
| | - Xiaojuan Huang
- The College of life science, Northwest University, Xi’an, 710069 China
| | - Tengteng Zhu
- The College of life science, Northwest University, Xi’an, 710069 China
| | - Yonglong Gong
- The College of life science, Northwest University, Xi’an, 710069 China
| | - Chen Dong
- The College of life science, Northwest University, Xi’an, 710069 China
| | - Xiangrong Wang
- The College of life science, Northwest University, Xi’an, 710069 China
- Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi’an, 710069 China
| | - Lingzhi Zhao
- The College of life science, Northwest University, Xi’an, 710069 China
| | - Lei Xie
- Department of Chemistry, Shanghai Key Lab of Molecular Catalysis and Innovative Materials, Collaborative Innovation Center of Chemistry for Energy Materials, Fudan University, Shanghai, 200438 China
| | - Kang Liang
- School of Chemical Engineering, Graduate School of Biomedical Engineering, and Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW 2052 Australia
| | - Qiongxiang Tan
- The College of life science, Northwest University, Xi’an, 710069 China
| | - Yali Cui
- The College of life science, Northwest University, Xi’an, 710069 China
- Shaanxi Provincial Engineering Research Center for Nano-Biomedical Detection, Xi’an, 710077 China
| | - Biao Kong
- Department of Chemistry, Shanghai Key Lab of Molecular Catalysis and Innovative Materials, Collaborative Innovation Center of Chemistry for Energy Materials, Fudan University, Shanghai, 200438 China
| | - Wenli Hui
- The College of life science, Northwest University, Xi’an, 710069 China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Northwest University, Xi’an, 710069 China
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Ahrens CW, Byrne M, Rymer PD. Standing genomic variation within coding and regulatory regions contributes to the adaptive capacity to climate in a foundation tree species. Mol Ecol 2019; 28:2502-2516. [PMID: 30950536 DOI: 10.1111/mec.15092] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 03/05/2019] [Accepted: 03/25/2019] [Indexed: 12/31/2022]
Abstract
Global climate is rapidly changing, and the ability for tree species to adapt is dependent on standing genomic variation; however, the distribution and abundance of functional and adaptive variants are poorly understood in natural systems. We test key hypotheses regarding the genetics of adaptive variation in a foundation tree: genomic variation is associated with climate, and genomic variation is more likely to be associated with temperature than precipitation or aridity. To test these hypotheses, we used 9,593 independent, genomic single-nucleotide polymorphisms (SNPs) from 270 individuals sampled from Corymbia calophylla's entire distribution in south-western Western Australia, spanning orthogonal temperature and precipitation gradients. Environmental association analyses returned 537 unique SNPs putatively adaptive to climate. We identified SNPs associated with climatic variation (i.e., temperature [458], precipitation [75] and aridity [78]) across the landscape. Of these, 78 SNPs were nonsynonymous (NS), while 26 SNPs were found within gene regulatory regions. The NS and regulatory candidate SNPs associated with temperature explained more deviance (27.35%) than precipitation (5.93%) and aridity (4.77%), suggesting that temperature provides stronger adaptive signals than precipitation. Genes associated with adaptive variants include functions important in stress responses to temperature and precipitation. Patterns of allelic turnover of NS and regulatory SNPs show small patterns of change through climate space with the exception of an aldehyde dehydrogenase gene variant with 80% allelic turnover with temperature. Together, these findings provide evidence for the presence of adaptive variation to climate in a foundation species and provide critical information to guide adaptive management practices.
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Affiliation(s)
- Collin W Ahrens
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Margaret Byrne
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Perth, Western Australia, Australia
| | - Paul D Rymer
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
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Guo Y, Zhu C, Zhao S, Zhang S, Wang W, Fu H, Li X, Zhou C, Chen L, Lin Y, Lai Z. De novo transcriptome and phytochemical analyses reveal differentially expressed genes and characteristic secondary metabolites in the original oolong tea (Camellia sinensis) cultivar 'Tieguanyin' compared with cultivar 'Benshan'. BMC Genomics 2019; 20:265. [PMID: 30943892 PMCID: PMC6446291 DOI: 10.1186/s12864-019-5643-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 03/25/2019] [Indexed: 01/16/2023] Open
Abstract
Background The two original plants of the oolong tea cultivar (‘Tieguanyin’) are “Wei shuo” ‘Tieguanyin’—TGY (Wei) and “Wang shuo” ‘Tieguanyin’—TGY (Wang). Another cultivar, ‘Benshan’ (BS), is similar to TGY in its aroma, taste, and genetic make-up, but it lacks the “Yin Rhyme” flavor. We aimed to identify differences in biochemical characteristics and gene expression among these tea plants. Results The results of spectrophotometric, high performance liquid chromatography (HPLC), and gas chromatography-mass spectrometry (GC-MS) analyses revealed that TGY (Wei) and TGY (Wang) had deeper purple-colored leaves and higher contents of anthocyanin, catechins, caffeine, and limonene compared with BS. Analyses of transcriptome data revealed 12,420 differentially expressed genes (DEGs) among the cultivars. According to a Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, the flavonoid, caffeine, and limonene metabolic pathways were highly enriched. The transcript levels of the genes involved in these three metabolic pathways were not significantly different between TGY (Wei) and TGY (Wang), except for two unigenes encoding IMPDH and SAMS, which are involved in caffeine metabolism. The comparison of TGY vs. BS revealed eight up-regulated genes (PAL, C4H, CHS, F3’H, F3H, DFR, ANS, and ANR) and two down-regulated genes (FLS and CCR) in flavonoid metabolism, four up-regulated genes (AMPD, IMPDH, SAMS, and 5′-Nase) and one down-regulated XDH gene in caffeine metabolism; and two down-regulated genes (ALDH and HIBADH) in limonene degradation. In addition, the expression levels of the transcription factor (TF) PAP1 were significantly higher in TGY than in BS. Therefore, high accumulation of flavonoids, caffeine, and limonene metabolites and the expression patterns of their related genes in TGY might be beneficial for the formation of the “Yin Rhyme” flavor. Conclusions Transcriptomic, HPLC, and GC-MS analyses of TGY (Wei), TGY (Wang), and BS indicated that the expression levels of genes related to secondary metabolism and high contents of catechins, anthocyanin, caffeine, and limonene may contribute to the formation of the “Yin Rhyme” flavor in TGY. These findings provide new insights into the relationship between the accumulation of secondary metabolites and sensory quality, and the molecular mechanisms underlying the formation of the unique flavor “Yin Rhyme” in TGY. Electronic supplementary material The online version of this article (10.1186/s12864-019-5643-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yuqiong Guo
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chen Zhu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shanshan Zhao
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Shuting Zhang
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wenjian Wang
- Anxi Tea Research Institute, Anxi, 362400, China
| | - Haifeng Fu
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaozhen Li
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chengzhe Zhou
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lan Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuling Lin
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhongxiong Lai
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Liu X, Zhang C, Zhao M, Liu K, Li H, Li N, Gao L, Yang X, Ma T, Zhu J, Hui W, Hua K, Cui Y. A direct isothermal amplification system adapted for rapid SNP genotyping of multifarious sample types. Biosens Bioelectron 2018; 115:70-76. [PMID: 29803102 PMCID: PMC7126597 DOI: 10.1016/j.bios.2018.05.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 02/06/2018] [Accepted: 05/10/2018] [Indexed: 01/10/2023]
Abstract
Genotyping of single nucleotide polymorphisms (SNPs) in point-of-care (POC) settings could be further improved through simplifying the treatment of samples. In this study, we devised an accurate, rapid and easy-to-use SNP detection system based on direct loop-mediated isothermal amplification (LAMP) without DNA extraction, known as Direct-LAMP. Samples from various sources (including whole blood, dried blood spot, buccal swab and saliva), treated with NaOH, can be used directly in amplification. The turnaround time was about 30 min from sample collection to provision of results. The accuracy was evaluated by assessing the polymorphisms of methylenetetrahydrofolate reductase (MTHFR) C677T and aldehyde dehydrogenase-2 (ALDH2) Glu504Lys, which are better known for their critical role in folate and ethanol metabolism, respectively. Completely consistent genotyping results reveal that Direct-LAMP is generally concordant with sequencing. This system can serve as a very promising platform in the fields of disease predisposition, drug metabolism and personalized medicine.
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Affiliation(s)
- Xiaonan Liu
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Chao Zhang
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Mengye Zhao
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Kewu Liu
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Hang Li
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Ningning Li
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, China
| | - Linlin Gao
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Xuemin Yang
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Ting Ma
- Shaanxi Provincial People's Hospital, Xi'an 710068, China
| | - Juanli Zhu
- Shaanxi Provincial Engineering Research Center for Nano-Biomedical Detection, Xi'an 710077, China
| | - Wenli Hui
- College of Life Sciences, Northwest University, Xi'an 710069, China; National Engineering Research Center for Miniaturized Detection System, Xi'an 710069, China
| | - Kai Hua
- College of Life Sciences, Northwest University, Xi'an 710069, China; National Engineering Research Center for Miniaturized Detection System, Xi'an 710069, China.
| | - Yali Cui
- College of Life Sciences, Northwest University, Xi'an 710069, China; Shaanxi Provincial Engineering Research Center for Nano-Biomedical Detection, Xi'an 710077, China; National Engineering Research Center for Miniaturized Detection System, Xi'an 710069, China.
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5
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Liu X, Zhang C, Liu K, Wang H, Lu C, Li H, Hua K, Zhu J, Hui W, Cui Y, Zhang X. Multiple SNPs Detection Based on Lateral Flow Assay for Phenylketonuria Diagnostic. Anal Chem 2018; 90:3430-3436. [PMID: 29451781 DOI: 10.1021/acs.analchem.7b05113] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Single nucleotide polymorphisms (SNPs) are closely related to genetic diseases, but current SNP detection methods, such as DNA microarrays that include tedious procedures and expensive, sophisticated instruments, are unable to perform rapid SNPs detection in clinical practice, especially for those multiple SNPs related to genetic diseases. In this study, we report a sensitive, low cost, and easy-to-use point-of-care testing (POCT) system formed by combining amplification refractory mutation system (ARMS) polymerase chain reaction with gold magnetic nanoparticles (GMNPs) and lateral flow assay (LFA) noted as the ARMS-LFA system, which allow us to use a uniform condition for multiple SNPs detection simultaneously. The genotyping results can be explained by a magnetic reader automatically or through visual interpretation according to the captured GMNPs probes on the test and control lines of the LFA device. The high sensitivity (the detection limit of 0.04 pg/μL with plasmid) and specificity of this testing system were found through genotyping seven pathogenic SNPs in phenylalanine hydroxylase gene ( PAH, the etiological factor of phenylketonuria). This system can also be applied in DNA quantification with a linear range from 0.02 to 2 pg/μL of plasmid. Furthermore, this ARMS-LFA system was applied to clinical trials for screening the seven pathogenic SNPs in PAH of 23 families including 69 individuals. The concordance rate of the genotyping results detected by the ARMS-LFA system was up to 97.8% compared with the DNA sequencing results. This method is a very promising POCT in the detection of multiple SNPs caused by genetic diseases.
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Affiliation(s)
- Xiaonan Liu
- College of Life Sciences , Northwest University , Xi'an , Shaanxi 710069 , China
| | - Chao Zhang
- College of Life Sciences , Northwest University , Xi'an , Shaanxi 710069 , China
| | - Kewu Liu
- College of Life Sciences , Northwest University , Xi'an , Shaanxi 710069 , China
| | - Han Wang
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100005 , China
| | - Chaoxia Lu
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100005 , China
| | - Hang Li
- College of Life Sciences , Northwest University , Xi'an , Shaanxi 710069 , China
| | - Kai Hua
- College of Life Sciences , Northwest University , Xi'an , Shaanxi 710069 , China.,National Engineering Research Center for Miniaturized Detection System , Xi'an , Shaanxi 710069 , China
| | - Juanli Zhu
- Shaanxi Provincial Engineering Research Center for Nano-Biomedical Detection , Xi'an , Shaanxi 710077 , China
| | - Wenli Hui
- College of Life Sciences , Northwest University , Xi'an , Shaanxi 710069 , China.,National Engineering Research Center for Miniaturized Detection System , Xi'an , Shaanxi 710069 , China
| | - Yali Cui
- College of Life Sciences , Northwest University , Xi'an , Shaanxi 710069 , China.,National Engineering Research Center for Miniaturized Detection System , Xi'an , Shaanxi 710069 , China.,Shaanxi Provincial Engineering Research Center for Nano-Biomedical Detection , Xi'an , Shaanxi 710077 , China
| | - Xue Zhang
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100005 , China
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da Costa ZP, Munhoz CDF, Vieira MLC. Report on the development of putative functional SSR and SNP markers in passion fruits. BMC Res Notes 2017; 10:445. [PMID: 28874179 PMCID: PMC5585897 DOI: 10.1186/s13104-017-2771-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 08/31/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Passionflowers Passiflora edulis and Passiflora alata are diploid, outcrossing and understudied fruit bearing species. In Brazil, passion fruit cultivation began relatively recently and has earned the country an outstanding position as the world's top producer of passion fruit. The fruit's main economic value lies in the production of juice, an essential exotic ingredient in juice blends. Currently, crop improvement strategies, including those for underexploited tropical species, tend to incorporate molecular genetic approaches. In this study, we examined a set of P. edulis transcripts expressed in response to infection by Xanthomonas axonopodis, (the passion fruit's main bacterial pathogen that attacks the vines), aiming at the development of putative functional markers, i.e. SSRs (simple sequence repeats) and SNPs (single nucleotide polymorphisms). RESULTS A total of 210 microsatellites were found in 998 sequences, and trinucleotide repeats were found to be the most frequent (31.4%). Of the sequences selected for designing primers, 80.9% could be used to develop SSR markers, and 60.6% SNP markers for P. alata. SNPs were all biallelic and found within 15 gene fragments of P. alata. Overall, gene fragments generated 10,003 bp. SNP frequency was estimated as one SNP every 294 bp. Polymorphism rates revealed by SSR and SNP loci were 29.4 and 53.6%, respectively. CONCLUSIONS Passiflora edulis transcripts were useful for the development of putative functional markers for P. alata, suggesting a certain level of sequence conservation between these cultivated species. The markers developed herein could be used for genetic mapping purposes and also in diversity studies.
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Affiliation(s)
- Zirlane Portugal da Costa
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Carla de Freitas Munhoz
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Maria Lucia Carneiro Vieira
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil.
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Hui W, Zhang S, Zhang C, Wan Y, Zhu J, Zhao G, Wu S, Xi D, Zhang Q, Li N, Cui Y. A novel lateral flow assay based on GoldMag nanoparticles and its clinical applications for genotyping of MTHFR C677T polymorphisms. NANOSCALE 2016; 8:3579-3587. [PMID: 26804455 DOI: 10.1039/c5nr07547e] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Current techniques for single nucleotide polymorphism (SNP) detection require tedious experimental procedures and expensive and sophisticated instruments. In this study, a visual genotyping method has been successfully established via combining ARMS-PCR with gold magnetic nanoparticle (GoldMag)-based lateral flow assay (LFA) and applied to the genotyping of methylenetetrahydrofolate reductase (MTHFR) C677T. C677T substitution of the gene MTHFR leads to an increased risk of diseases. The genotyping result is easily achievable by visual observation within 5 minutes after loading of the PCR products onto the LFA device. The system is able to accurately assess a broad detection range of initial starting genomic DNA amounts from 5 ng to 1200 ng per test sample. The limit of detection reaches 5 ng. Furthermore, our PCR-LFA system was applied to clinical trials for screening 1721 individuals for the C677T genotypes. The concordance rate of the genotyping results detected by PCR-LFA was up to 99.6% when compared with the sequencing results. Collectively, our PCR-LFA has been proven to be rapid, accurate, sensitive, and inexpensive. This new method is highly applicable for C677T SNP screening in laboratories and clinical practices. More promisingly, it could also be extended to the detection of SNPs of other genes.
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Affiliation(s)
- Wenli Hui
- College of Life Sciences, Northwest University, Xi'an, 710069, China.
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Zhang HB, Xia EH, Huang H, Jiang JJ, Liu BY, Gao LZ. De novo transcriptome assembly of the wild relative of tea tree (Camellia taliensis) and comparative analysis with tea transcriptome identified putative genes associated with tea quality and stress response. BMC Genomics 2015; 16:298. [PMID: 25881092 PMCID: PMC4404113 DOI: 10.1186/s12864-015-1494-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 03/27/2015] [Indexed: 11/24/2022] Open
Abstract
Background Camellia taliensis is one of the most important wild relatives of cultivated tea tree, C. sinensis. The species extensively occupies mountainous habitats representing a wide-range abiotic tolerance and biotic resistance and thus harbors valuable gene resources that may greatly benefit genetic improvement of cultivated tea tree. However, owning to a large genome size of ~3 Gb and structurally complex genome, there are fairly limited genetic information and particularly few genomic resources publicly available for this species. To better understand the key pathways determining tea flavor and enhance tea tree breeding programs, we performed a high-throughput transcriptome sequencing for C. taliensis. Results In this study, approximate 241.5 million high-quality paired-end reads, accounting for ~24 Gb of sequence data, were generated from tender shoots, young leaves, flower buds and flowers using Illumina HiSeq 2000 platform. De novo assembly with further processing and filtering yielded a set of 67,923 transcripts with an average length of 685 bp and an N50 of 995 bp. Based on sequence similarity searches against public databases, a total of 39,475 transcripts were annotated with gene descriptions, conserved protein domains or gene ontology (GO) terms. Candidate genes for major metabolic pathways involved in tea quality were identified and experimentally validated using RT-qPCR. Further gene expression profiles showed that they are differentially regulated at different developmental stages. To gain insights into the evolution of these genes, we aligned them to the previously cloned orthologous genes in C. sinensis, and found that considerable nucleotide variation within several genes involved in important secondary metabolic biosynthesis pathways, of which flavone synthase II gene (FNSII) is the most variable between these two species. Moreover, comparative analyses revealed that C. taliensis shows a remarkable expansion of LEA genes, compared to C. sinensis, which might contribute to the observed stronger stress resistance of C. taliensis. Conclusion We reported the first large-coverage transcriptome datasets for C. taliensis using the next-generation sequencing technology. Such comprehensive EST datasets provide an unprecedented opportunity for identifying genes involved in several major metabolic pathways and will accelerate functional genomic studies and genetic improvement efforts of tea trees in the future. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1494-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hai-Bin Zhang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650204, China. .,University of Chinese Academy of Sciences, Beijing, 100039, China.
| | - En-Hua Xia
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650204, China. .,University of Chinese Academy of Sciences, Beijing, 100039, China.
| | - Hui Huang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650204, China.
| | - Jian-Jun Jiang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650204, China.
| | - Ben-Ying Liu
- Tea Research Institute, Yunnan Academy of Agricultural Sciences, Menghai, 666201, China.
| | - Li-Zhi Gao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, the Chinese Academy of Sciences, Kunming, 650204, China.
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Dasgupta MG, Dharanishanthi V, Agarwal I, Krutovsky KV. Development of genetic markers in Eucalyptus species by target enrichment and exome sequencing. PLoS One 2015; 10:e0116528. [PMID: 25602379 PMCID: PMC4300219 DOI: 10.1371/journal.pone.0116528] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 12/08/2014] [Indexed: 02/02/2023] Open
Abstract
The advent of next-generation sequencing has facilitated large-scale discovery, validation and assessment of genetic markers for high density genotyping. The present study was undertaken to identify markers in genes supposedly related to wood property traits in three Eucalyptus species. Ninety four genes involved in xylogenesis were selected for hybridization probe based nuclear genomic DNA target enrichment and exome sequencing. Genomic DNA was isolated from the leaf tissues and used for on-array probe hybridization followed by Illumina sequencing. The raw sequence reads were trimmed and high-quality reads were mapped to the E. grandis reference sequence and the presence of single nucleotide variants (SNVs) and insertions/ deletions (InDels) were identified across the three species. The average read coverage was 216X and a total of 2294 SNVs and 479 InDels were discovered in E. camaldulensis, 2383 SNVs and 518 InDels in E. tereticornis, and 1228 SNVs and 409 InDels in E. grandis. Additionally, SNV calling and InDel detection were conducted in pair-wise comparisons of E. tereticornis vs. E. grandis, E. camaldulensis vs. E. tereticornis and E. camaldulensis vs. E. grandis. This study presents an efficient and high throughput method on development of genetic markers for family– based QTL and association analysis in Eucalyptus.
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Affiliation(s)
- Modhumita Ghosh Dasgupta
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, P.B. No. 1061, R.S. Puram, Coimbatore–641002, India
- * E-mail:
| | - Veeramuthu Dharanishanthi
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, P.B. No. 1061, R.S. Puram, Coimbatore–641002, India
| | - Ishangi Agarwal
- Genotypic Technology Private Limited, #2/13, Balaji Complex, Poojari Layout, 80, Feet Road, R. M. V. 2nd Stage, Bangalore-560094, India
| | - Konstantin V. Krutovsky
- Department of Forest Genetics and Forest Tree Breeding, Büsgen Institute, Georg August University of Göttingen, Büsgenweg 2, D-37077 Göttingen, Germany
- Department of Ecosystem Science and Management, Texas A&M University, 2138 TAMU, College Station, TX 77843-2138, United States of America
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119333, Russia
- Genome Research and Education Center, Siberian Federal University, 50a/2 Akademgorodok, Krasnoyarsk 660036, Russia
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10
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Hayward AC, Tollenaere R, Dalton-Morgan J, Batley J. Molecular marker applications in plants. Methods Mol Biol 2015; 1245:13-27. [PMID: 25373746 DOI: 10.1007/978-1-4939-1966-6_2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Individuals within a population of a sexually reproducing species will have some degree of heritable genomic variation caused by mutations, insertion/deletions (INDELS), inversions, duplications, and translocations. Such variation can be detected and screened using molecular, or genetic, markers. By definition, molecular markers are genetic loci that can be easily tracked and quantified in a population and may be associated with a particular gene or trait of interest. This chapter will review the current major applications of molecular markers in plants.
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Affiliation(s)
- Alice C Hayward
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
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11
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Liu JJ, Sniezko RA, Sturrock RN, Chen H. Western white pine SNP discovery and high-throughput genotyping for breeding and conservation applications. BMC PLANT BIOLOGY 2014; 14:380. [PMID: 25547170 PMCID: PMC4302426 DOI: 10.1186/s12870-014-0380-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 12/11/2014] [Indexed: 05/10/2023]
Abstract
BACKGROUND Western white pine (WWP, Pinus monticola Douglas ex D. Don) is of high interest in forest breeding and conservation because of its high susceptibility to the invasive disease white pine blister rust (WPBR, caused by the fungus Cronartium ribicola J. C. Fisch). However, WWP lacks genomic resource development and is evolutionarily far away from plants with available draft genome sequences. Here we report a single nucleotide polymorphism (SNP) study by bulked segregation-based RNA-Seq analysis. RESULTS A collection of resistance germplasm was used for construction of cDNA libraries and SNP genotyping. Approximately 36-89 million 2 × 100-bp reads were obtained per library and de-novo assembly generated the first shoot-tip reference transcriptome containing a total of 54,661 unique transcripts. Bioinformatic SNP detection identified >100,000 high quality SNPs in three expressed candidate gene groups: Pinus highly conserved genes (HCGs), differential expressed genes (DEGs) in plant defense response, and resistance gene analogs (RGAs). To estimate efficiency of in-silico SNP discovery, genotyping assay was developed by using Sequenom iPlex and it unveiled SNP success rates from 40.1% to 61.1%. SNP clustering analyses consistently revealed distinct populations, each composed of multiple full-sib seed families by parentage assignment in the WWP germplasm collection. Linkage disequilibrium (LD) analysis identified six genes in significant association with major gene (Cr2) resistance, including three RGAs (two NBS-LRR genes and one receptor-like protein kinase -RLK gene), two HCGs, and one DEG. At least one SNP locus provided an excellent marker for Cr2 selection across P. monticola populations. CONCLUSIONS The WWP shoot tip transcriptome and those validated SNP markers provide novel genomic resources for genetic, evolutionary and ecological studies. SNP loci of those candidate genes associated with resistant phenotypes can be used as positional and functional variation sites for further characterization of WWP major gene resistance against C. ribicola. Our results demonstrate that integration of RNA-seq-based transcriptome analysis and high-throughput genotyping is an effective approach for discovery of a large number of nucleotide variations and for identification of functional gene variants associated with adaptive traits in a non-model species.
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Affiliation(s)
- Jun-Jun Liu
- />Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada
| | - Richard A Sniezko
- />USDA Forest Service, Dorena Genetic Resource Center, 34963 Shoreview Road, Cottage Grove, OR 97424 USA
| | - Rona N Sturrock
- />Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada
| | - Hao Chen
- />Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, 506 West Burnside Road, Victoria, BC V8Z 1M5 Canada
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12
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Zhao X, Yu H, Kong L, Liu S, Li Q. Comparative transcriptome analysis of two oysters, Crassostrea gigas and Crassostrea hongkongensis provides insights into adaptation to hypo-osmotic conditions. PLoS One 2014; 9:e111915. [PMID: 25369077 PMCID: PMC4219811 DOI: 10.1371/journal.pone.0111915] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 10/01/2014] [Indexed: 12/29/2022] Open
Abstract
Environmental salinity creates a key barrier to limit the distribution of most aquatic organisms. Adaptation to osmotic fluctuation is believed to be a factor facilitating species diversification. Adaptive evolution often involves beneficial mutations at more than one locus. Bivalves hold great interest, with numerous species living in waters, as osmoconformers, who maintain the osmotic pressure balance mostly by free amino acids. In this study, 107,076,589 reads from two groups of Crassostrea hongkongensis were produced and the assembled into 130,629 contigs. Transcripts putatively involved in stress-response, innate immunity and cell processes were identified according to Gene ontology and KEGG pathway analyses. Comparing with the transcriptome of C. gigas to characterize the diversity of transcripts between species with osmotic divergence, we identified 182,806 high-quality single nucleotide polymorphisms (SNPs) for C. hongkongensis, and 196,779 SNPs for C. gigas. Comparison of 11,602 pairs of putative orthologs allowed for identification of 14 protein-coding genes that experienced strong positive selection (Ka/Ks>1). In addition, 45 genes that may show signs of moderate positive selection (1 ≥ Ka/Ks>0.5) were also identified. Based on Ks ratios and divergence time between the two species published previously, we estimated a neutral transcriptome-wide substitution mutation rate of 1.39 × 10(-9) per site per year. Several genes were differentially expressed across the control and treated groups of each species. This is the first time to sequence the transcriptome of C. hongkongensis and provide the most comprehensive transcriptomic resource available for it. The increasing amount of transcriptome data on Crassostrea provides an excellent resource for phylogenetic analysis. A large number of SNPs identified in this work are expected to provide valuable resources for future marker and genotyping assay development. The analysis of natural selection provides an innovative view on the adaptation within species and sets the basis for future genetic and evolutionary studies.
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Affiliation(s)
- Xuelin Zhao
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Hong Yu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Lingfeng Kong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Shikai Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Qi Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
- * E-mail:
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Neale DB, Langley CH, Salzberg SL, Wegrzyn JL. Open access to tree genomes: the path to a better forest. Genome Biol 2013; 14:120. [PMID: 23796049 PMCID: PMC3706761 DOI: 10.1186/gb-2013-14-6-120] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
An open-access culture and a well-developed comparative-genomics infrastructure must be developed in forest trees to derive the full potential of genome sequencing in this diverse group of plants that are the dominant species in much of the earth's terrestrial ecosystems.
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DeWoody JA, Abts KC, Fahey AL, Ji Y, Kimble SJA, Marra NJ, Wijayawardena BK, Willoughby JR. Of contigs and quagmires: next‐generation sequencing pitfalls associated with transcriptomic studies. Mol Ecol Resour 2013; 13:551-8. [PMID: 23615313 DOI: 10.1111/1755-0998.12107] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 03/13/2013] [Accepted: 03/14/2013] [Indexed: 12/15/2022]
Affiliation(s)
- J. Andrew DeWoody
- Department of Biological Sciences Purdue University West Lafayette IN 47907 USA
- Department of Forestry & Natural Resources Purdue University West Lafayette IN 47907 USA
| | - Kendra C. Abts
- Department of Forestry & Natural Resources Purdue University West Lafayette IN 47907 USA
| | - Anna L. Fahey
- Department of Forestry & Natural Resources Purdue University West Lafayette IN 47907 USA
| | - Yanzhu Ji
- Department of Forestry & Natural Resources Purdue University West Lafayette IN 47907 USA
| | - Steven J. A. Kimble
- Department of Forestry & Natural Resources Purdue University West Lafayette IN 47907 USA
| | - Nicholas J. Marra
- Department of Forestry & Natural Resources Purdue University West Lafayette IN 47907 USA
| | | | - Janna R. Willoughby
- Department of Forestry & Natural Resources Purdue University West Lafayette IN 47907 USA
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Edwards D, Henry RJ, Edwards KJ. Preface: advances in DNA sequencing accelerating plant biotechnology. PLANT BIOTECHNOLOGY JOURNAL 2012; 10:621-2. [PMID: 22765873 DOI: 10.1111/j.1467-7652.2012.00724.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
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