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Narayanrao DR, Tomar RS, Sm P, Jasminkumar K, Ashish G, Chauhan NM, Singh SC, Upadhye V, Kuddus M, Kamble L, Hajare ST. De novo transcriptome sequencing of drought tolerance-associated genes in little millet (Panicum sumatrense L.). Funct Integr Genomics 2023; 23:303. [PMID: 37723408 DOI: 10.1007/s10142-023-01221-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/24/2023] [Accepted: 08/27/2023] [Indexed: 09/20/2023]
Abstract
The genome size of the little millet Panicum sumatrense is unknown, although its genome is fairly diploid (2n = 4x = 36). Despite tremendous nutritional value and adaptability to adverse climatic conditions, P. sumatrense use was limited by their low palatability, coarse grain, and lack of variety of culinary preparations. Hence, understanding how to vary their usage to offer food and nutritional security in the continuously changing modern world, the proposed study was aimed to determine potential genes and metabolites implicated in drought resistance. The drought-resistant genotype of tiny millet OLM-203/Tarini was offered in pots under both relaxed and demanding circumstances. The experimental seedlings were 32 days old and had been under water stress for 23 days. A total of 7606 genes were compared between 23 and 32 days for roots and 7264 total genes were compared between 23 and 32 days for leaves, according to a research on differential expression genes (DEGs). Twenty essential genes for drought tolerance were up-or down-regulated in the control and treated roots of the OLM-203 genotype. For instance, the genes RS193 and XB34 were up-regulated in leaves while, WLIM1 was found to be down-regulated. Gene SKI35 was up-regulated in roots, whereas MPK6 and TCMOp1 were down-regulated in root samples. The roots and leaves of the tiny millet OLM-203 genotype expressed 36 up-regulated and 21 down-regulated serine transcripts, respectively. Gene annotations for leaf samples were classified as having "molecular function" (46%), "cellular component" (19%), and "biological process" (35%), while root sample gene annotations were categorized as having "biological process" (573 contigs), "molecular function" (401 contigs), and "cellular components" (166 contigs). Noteworthy, polyamines play a crucial role in drought stress tolerance in the genotype, and it was found that top ten DEGs encoding for polyamines were common in two tissues (leaf and root). Collectively, transcriptomics profiling (RNA-seq) unveiled transcriptional stability drought stress provide a new insight in underlying modus of operandi in little millet genotype "OLM-203/Tarini" in response to heat stress.
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Affiliation(s)
| | - R S Tomar
- Department of Biotechnology, College of Agriculture, Junagadh Agricultural University, Junagadh, 362001, Gujarat, India
| | - Padhiyar Sm
- Department of Biotechnology, College of Agriculture, Junagadh Agricultural University, Junagadh, 362001, Gujarat, India
| | - Kheni Jasminkumar
- Department of Biotechnology, College of Agriculture, Junagadh Agricultural University, Junagadh, 362001, Gujarat, India
| | - Gulwe Ashish
- Department of Bioinformatics, Sub Campus Latur, Swami Ramanand Teerth Marathawada University, Nanded, India
| | - Nitin Mahendra Chauhan
- ILRI and College of Natural and Computational Sciences, Dilla University, 419, Dilla, Ethiopia
| | | | - Vijay Upadhye
- Research and Development Cell (RDC), Parul Institute of Applied Sciences (PIAS), Parul University, Vadodara, India
| | - Mohammed Kuddus
- Department of Biochemistry, College of Medicine, University of Hail, Hail, Kingdom of Saudi Arabia
| | - Laxmikant Kamble
- Deputy Director and Associate Professor (CD4D), Parul University, Vadodara, Gujarat, India
- Swami Ramanand Teerth Marathawada University, Nanded, India
| | - Sunil Tulshiram Hajare
- ILRI and College of Natural and Computational Sciences, Dilla University, 419, Dilla, Ethiopia.
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Singh KP, Kumari P, Yadava DK. Development of de-novo transcriptome assembly and SSRs in allohexaploid Brassica with functional annotations and identification of heat-shock proteins for thermotolerance. Front Genet 2022; 13:958217. [PMID: 36186472 PMCID: PMC9524822 DOI: 10.3389/fgene.2022.958217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/23/2022] [Indexed: 11/20/2022] Open
Abstract
Crop Brassicas contain monogenomic and digenomic species, with no evidence of a trigenomic Brassica in nature. Through somatic fusion (Sinapis alba + B. juncea), a novel allohexaploid trigenomic Brassica (H1 = AABBSS; 2n = 60) was produced and used for transcriptome analysis to uncover genes for thermotolerance, annotations, and microsatellite markers for future molecular breeding. Illumina Novaseq 6000 generated a total of 76,055,546 paired-end raw reads, which were used for de-novo assembly, resulting in the development of 486,066 transcripts. A total of 133,167 coding sequences (CDSs) were predicted from transcripts with a mean length of 507.12 bp and 46.15% GC content. The BLASTX search of CDSs against public protein databases showed a maximum of 126,131 (94.72%) and a minimum of 29,810 (22.39%) positive hits. Furthermore, 953,773 gene ontology (GO) terms were found in 77,613 (58.28%) CDSs, which were divided into biological processes (49.06%), cellular components (31.67%), and molecular functions (19.27%). CDSs were assigned to 144 pathways by a pathway study using the KEGG database and 1,551 pathways by a similar analysis using the Reactome database. Further investigation led to the discovery of genes encoding over 2,000 heat shock proteins (HSPs). The discovery of a large number of HSPs in allohexaploid Brassica validated our earlier findings for heat tolerance at seed maturity. A total of 15,736 SSRs have been found in 13,595 CDSs, with an average of one SSR per 4.29 kb length and an SSR frequency of 11.82%. The first transcriptome assembly of a meiotically stable allohexaploid Brassica has been given in this article, along with functional annotations and the presence of SSRs, which could aid future genetic and genomic studies.
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Affiliation(s)
| | - Preetesh Kumari
- Genetics Division, ICAR—Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Preetesh Kumari,
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Ganie SA, Mazumder A, Kiran K, Hossain F, Sharma R, Mondal TK. Transcriptional dynamics of Zn-accumulation in developing kernels of maize reveals important Zn-uptake mechanisms. Genomics 2020; 112:3435-3447. [PMID: 32526248 DOI: 10.1016/j.ygeno.2020.06.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/19/2020] [Accepted: 06/04/2020] [Indexed: 11/16/2022]
Abstract
In the present study, transcriptomic analysis of 10-days old baby kernels of two contrasting maize genotypes, namely VQL-2 (high kernel Zn accumulator) and CM-145 (low kernel Zn accumulator), under low- and optimum- soil Zn conditions generated 1948 differentially expressed transcripts. Among these, 666 and 437 transcripts were up-regulated and down-regulated respectively in VQL-2; whereas, 437 and 408 transcripts were up-regulated and down-regulated respectively in CM-145. Remarkably, 135 transcription factors and 77 known Zn transporters expressed differentially. By comparing the transcripts differentially expressed between the optimum-Zn and low-Zn libraries of the contrasting genotypes, we identified 21,986 and 26,871 SNPs, respectively. Similarly, 6810 and 8192 InDels were found between optimum- and low-Zn growing conditions, respectively. Further, 21 differentially expressed genes were co-localized with already known QTLs associated with Zn uptake, such as qZn10, CQZnK9-1 and YNZnK6. These findings will be useful to develop high Zn-accumulator maize through marker-assisted breeding in future.
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Affiliation(s)
- Showkat Ahmad Ganie
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India
| | - Abhishek Mazumder
- ICAR-National Institute for Plant Biotechnology, IARI Pusa, LBS Building, New Delhi 110012, India
| | - Kanti Kiran
- ICAR-National Institute for Plant Biotechnology, IARI Pusa, LBS Building, New Delhi 110012, India
| | - Firoz Hossain
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Ruchika Sharma
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India
| | - Tapan Kumar Mondal
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi 110012, India; ICAR-National Institute for Plant Biotechnology, IARI Pusa, LBS Building, New Delhi 110012, India.
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Kumar V, Sharma AK, Rajput SK, Pal M, Dhiman N. Pharmacognostic and pharmacological evaluation of Eulaliopsis binata plant extracts by measuring in vitro/ in vivo safety profile and anti-microbial potential. Toxicol Res (Camb) 2018; 7:454-464. [PMID: 30090595 DOI: 10.1039/c8tx00017d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/09/2018] [Indexed: 11/21/2022] Open
Abstract
The present investigation emphasizes the pharmacognostic and phytochemical screening of Eulaliopsis binata and further evaluates the extracts of this plant for toxicological profile and anti-bacterial potential based on in vivo/in vitro assays. Microscopy, powder characteristics of the leaf material, and physicochemical and phytochemical screening were assessed for pharmacognostic evaluation. Dry leaves of Eulaliopsis binata were extracted using different solvents (methanol, ethyl acetate, and hexane), and the extracts obtained were further investigated for in vitro/in vivo toxicological study. Moreover, acute toxicity was assessed by evaluating the anti-oxidant defense system and anatomical damage in vital organs. In addition, anti-bacterial activity of all the extracts was assessed by the Kirby-Bauer method. Physicochemical and microscopic observations showed the unique identification mark for leaf powder and leaf transverse section. Phytochemical investigation evidenced the presence of flavonoids and phenolic contents in the methanolic extract. All extracts were found to be hemocompatible and exhibited no induction of behavioral alteration and no alteration in the anti-oxidant potential and anatomical structure of the vital organs. On the other hand, the methanolic extract showed a significant upsurge in the reduced glutathione level, whereas all extracts showed significant anti-bacterial potential in a dose-dependent manner. Eulaliopsis binata has inimitable pharmacognostical characteristics, good safety profile and significant anti-oxidant and anti-bacterial potential that show immense possibility for its further investigation for pharmacological use.
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Affiliation(s)
- Vinod Kumar
- Department of Pharmaceutical Chemistry , Amity University , Noida , Uttar Pradesh-201303 , India . ; Tel: +91 120 4392498, ext: 5557
| | - Arun K Sharma
- Department of Pharmacology , Amity University , Noida , Uttar Pradesh-201303 , India
| | - Satyendra K Rajput
- Department of Pharmacology , Amity University , Noida , Uttar Pradesh-201303 , India
| | - Mahesh Pal
- Phytochemistry Division , CSIR-National Botanical Research Institute , Lucknow , Uttar Pradesh-226001 , India
| | - Neerupma Dhiman
- Department of Pharmaceutical Chemistry , Amity University , Noida , Uttar Pradesh-201303 , India . ; Tel: +91 120 4392498, ext: 5557
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Taheri S, Lee Abdullah T, Yusop MR, Hanafi MM, Sahebi M, Azizi P, Shamshiri RR. Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants. Molecules 2018; 23:E399. [PMID: 29438290 PMCID: PMC6017569 DOI: 10.3390/molecules23020399] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 01/11/2018] [Accepted: 01/13/2018] [Indexed: 11/17/2022] Open
Abstract
Microsatellites, or simple sequence repeats (SSRs), are one of the most informative and multi-purpose genetic markers exploited in plant functional genomics. However, the discovery of SSRs and development using traditional methods are laborious, time-consuming, and costly. Recently, the availability of high-throughput sequencing technologies has enabled researchers to identify a substantial number of microsatellites at less cost and effort than traditional approaches. Illumina is a noteworthy transcriptome sequencing technology that is currently used in SSR marker development. Although 454 pyrosequencing datasets can be used for SSR development, this type of sequencing is no longer supported. This review aims to present an overview of the next generation sequencing, with a focus on the efficient use of de novo transcriptome sequencing (RNA-Seq) and related tools for mining and development of microsatellites in plants.
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Affiliation(s)
- Sima Taheri
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Thohirah Lee Abdullah
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mohd Rafii Yusop
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mohamed Musa Hanafi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
- Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mahbod Sahebi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Parisa Azizi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Redmond Ramin Shamshiri
- Smart Farming Technology Research Center, Department of Biological and Agricultural Engineering, Faculty of Engineering, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
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Enriching Genomic Resources and Transcriptional Profile Analysis of Miscanthus sinensis under Drought Stress Based on RNA Sequencing. Int J Genomics 2017; 2017:9184731. [PMID: 29318138 PMCID: PMC5727683 DOI: 10.1155/2017/9184731] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 10/18/2017] [Indexed: 11/23/2022] Open
Abstract
Miscanthus × giganteus is wildly cultivated as a potential biofuel feedstock around the world; however, the narrow genetic basis and sterile characteristics have become a limitation for its utilization. As a progenitor of M. × giganteus, M. sinensis is widely distributed around East Asia providing well abiotic stress tolerance. To enrich the M. sinensis genomic databases and resources, we sequenced and annotated the transcriptome of M. sinensis by using an Illumina HiSeq 2000 platform. Approximately 316 million high-quality trimmed reads were generated from 349 million raw reads, and a total of 114,747 unigenes were obtained after de novo assembly. Furthermore, 95,897 (83.57%) unigenes were annotated to at least one database including NR, Swiss-Prot, KEGG, COG, GO, and NT, supporting that the sequences obtained were annotated properly. Differentially expressed gene analysis indicates that drought stress 15 days could be a critical period for M. sinensis response to drought stress. The high-throughput transcriptome sequencing of M. sinensis under drought stress has greatly enriched the current genomic available resources. The comparison of DEGs under different periods of drought stress identified a wealth of candidate genes involved in drought tolerance regulatory networks, which will facilitate further genetic improvement and molecular studies of the M. sinensis.
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Yang X, Hu H, Yu D, Sun Z, He X, Zhang J, Chen Q, Tian R, Fan J. Candidate Resistant Genes of Sand Pear (Pyrus pyrifolia Nakai) to Alternaria alternata Revealed by Transcriptome Sequencing. PLoS One 2015; 10:e0135046. [PMID: 26292286 PMCID: PMC4546377 DOI: 10.1371/journal.pone.0135046] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 07/17/2015] [Indexed: 11/18/2022] Open
Abstract
Pear black spot (PBS) disease, which is caused by Alternaria alternata (Aa), is one of the most serious diseases affecting sand pear (Pyrus pyrifolia Nakai) cultivation worldwide. To investigate the defense mechanisms of sand pear in response to Aa, the transcriptome of a sand pear germplasm with differential resistance to Aa was analyzed using Illumina paired-end sequencing. Four libraries derived from PBS-resistant and PBS-susceptible sand pear leaves were characterized through inoculation or mock-inoculation. In total, 20.5 Gbp of sequence data and 101,632,565 reads were generated, representing 44717 genes. Approximately 66% of the genes or sequenced reads could be aligned to the pear reference genome. A large number (5213) of differentially expressed genes related to PBS resistance were obtained; 34 microsatellites were detected in these genes, and 28 genes were found to be closely related to PBS resistance. Using a transcriptome analysis in response to PBS inoculation and comparison analysis to the PHI database, 4 genes (Pbr039001, Pbr001627, Pbr025080 and Pbr023112) were considered to be promising candidates for sand pear resistance to PBS. This study provides insight into changes in the transcriptome of sand pear in response to PBS infection, and the findings have improved our understanding of the resistance mechanism of sand pear to PBS and will facilitate future gene discovery and functional genome studies of sand pear.
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Affiliation(s)
- Xiaoping Yang
- School of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, P. R. China
- Research Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, Hubei, 430064, P. R. China
| | - Hongju Hu
- Research Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, Hubei, 430064, P. R. China
| | - Dazhao Yu
- School of Life Sciences, Wuhan University, Wuhan, Hubei, 430072, P. R. China
- Hubei Laboratory of Crop Diseases, Insect Pests and Weeds Control, Wuhan, Hubei, 430064, P. R. China
- * E-mail: (DZY); (ZHS)
| | - Zhonghai Sun
- Research Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, Hubei, 430064, P. R. China
- * E-mail: (DZY); (ZHS)
| | - Xiujuan He
- Research Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, Hubei, 430064, P. R. China
| | - Jingguo Zhang
- Research Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, Hubei, 430064, P. R. China
| | - Qiliang Chen
- Research Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, Hubei, 430064, P. R. China
| | - Rui Tian
- Research Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, Hubei, 430064, P. R. China
| | - Jing Fan
- Research Institute of Fruit and Tea, Hubei Academy of Agricultural Science, Wuhan, Hubei, 430064, P. R. China
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Huang LK, Yan HD, Zhao XX, Zhang XQ, Wang J, Frazier T, Yin G, Huang X, Yan DF, Zang WJ, Ma X, Peng Y, Yan YH, Liu W. Identifying differentially expressed genes under heat stress and developing molecular markers in orchardgrass (Dactylis glomerataL.) through transcriptome analysis. Mol Ecol Resour 2015; 15:1497-509. [DOI: 10.1111/1755-0998.12418] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 04/08/2015] [Accepted: 04/15/2015] [Indexed: 11/29/2022]
Affiliation(s)
- L. K. Huang
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - H. D. Yan
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - X. X. Zhao
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - X. Q. Zhang
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - J. Wang
- Agronomy Department; University of Florida; Gainesville FL 32611 USA
| | - T. Frazier
- Department of Horticulture; Virginia Tech; Blacksburg VA 24061 USA
| | - G. Yin
- Department of Crop, Soil, and Environmental Sciences; University of Arkansas; Fayetteville AR 72704 USA
| | - X. Huang
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - D. F. Yan
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - W. J. Zang
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - X. Ma
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - Y. Peng
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - Y. H. Yan
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
| | - W. Liu
- Department of Grassland Science, Animal Science and Technology College; Sichuan Agricultural University; Ya'an Sichuan 625014 China
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Yang M, Xu L, Liu Y, Yang P. RNA-Seq Uncovers SNPs and Alternative Splicing Events in Asian Lotus (Nelumbo nucifera). PLoS One 2015; 10:e0125702. [PMID: 25928215 PMCID: PMC4416007 DOI: 10.1371/journal.pone.0125702] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/21/2015] [Indexed: 01/11/2023] Open
Abstract
RNA-Seq is an efficient way to comprehensively identify single nucleotide polymorphisms (SNPs) and alternative splicing (AS) events from the expressed genes. In this study, we conducted transcriptome sequencing of four Asian lotus (Nelumbo nucifera) cultivars using Illumina HiSeq2000 platform to identify SNPs and AS events in lotus. A total of 505 million pair-end RNA-Seq reads were generated from four cultivars, of which 86% were mapped to the lotus reference genome. Using the four sets of data together, a total of 357,689 putative SNPs were identified with an average density of one SNP per 2.2 kb. These SNPs were located in 1,253 scaffolds and 15,016 expressed genes. A/G and C/T were the two major types of SNPs in the Asian lotus transcriptome. In parallel, a total of 177,540 AS events were detected in the four cultivars and were distributed in 64% of the expressed genes of lotus. The predominant type of AS events was alternative 5’ first exon, which accounted for 41.2% of all the observed AS events, and exon skipping only accounted for 4.3% of all AS. Gene Ontology analysis was conducted to analyze the function of the genes containing SNPs and AS events. Validation of selected SNPs and AS events revealed that 74% of SNPs and 80% of AS events were reliable, which indicates that RNA-Seq is an efficient approach to uncover gene-associated SNPs and AS events. A large number of SNPs and AS events identified in our study will facilitate further genetic and functional genomics research in lotus.
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Affiliation(s)
- Mei Yang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Liming Xu
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Yanling Liu
- Key Laboratory of Aquatic Plant and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Pingfang Yang
- Key Laboratory of Plant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China
- * E-mail:
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Chakraborty A, Sarkar D, Satya P, Karmakar PG, Singh NK. Pathways associated with lignin biosynthesis in lignomaniac jute fibres. Mol Genet Genomics 2015; 290:1523-42. [PMID: 25724692 DOI: 10.1007/s00438-015-1013-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 02/15/2015] [Indexed: 01/09/2023]
Abstract
We generated the bast transcriptomes of a deficient lignified phloem fibre mutant and its wild-type jute (Corchorus capsularis) using Illumina paired-end sequencing. A total of 34,163 wild-type and 29,463 mutant unigenes, with average lengths of 1442 and 1136 bp, respectively, were assembled de novo, ~77-79 % of which were functionally annotated. These annotated unigenes were assigned to COG (~37-40 %) and GO (~22-28 %) classifications and mapped to 189 KEGG pathways (~19-21 %). We discovered 38 and 43 isoforms of 16 and 10 genes of the upstream shikimate-aromatic amino acid and downstream monolignol biosynthetic pathways, respectively, rendered their sequence similarities, confirmed the identities of 22 of these candidate gene families by phylogenetic analyses and reconstructed the pathway leading to lignin biosynthesis in jute fibres. We also identified major genes and bast-related transcription factors involved in secondary cell wall (SCW) formation. The quantitative RT-PCRs revealed that phenylalanine ammonia-lyase 1 (CcPAL1) was co-down-regulated with several genes of the upstream shikimate pathway in mutant bast tissues at an early growth stage, although its expression relapsed to the normal level at the later growth stage. However, cinnamyl alcohol dehydrogenase 7 (CcCAD7) was strongly down-regulated in mutant bast tissues irrespective of growth stages. CcCAD7 disruption at an early growth stage was accompanied by co-up-regulation of SCW-specific genes cellulose synthase A7 (CcCesA7) and fasciclin-like arabinogalactan 6 (CcFLA6), which was predicted to be involved in coordinating the S-layers' deposition in the xylan-type jute fibres. Our results identified CAD as a promising target for developing low-lignin jute fibres using genomics-assisted molecular approaches.
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Affiliation(s)
- Avrajit Chakraborty
- Biotechnology Unit, Division of Crop Improvement, ICAR-Central Research Institute for Jute and Allied Fibres (CRIJAF), Barrackpore, Kolkata, 700 120, West Bengal, India
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High-throughput sequencing and De Novo assembly of the Isatis indigotica transcriptome. PLoS One 2014; 9:e102963. [PMID: 25259890 PMCID: PMC4178013 DOI: 10.1371/journal.pone.0102963] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Accepted: 06/25/2014] [Indexed: 12/03/2022] Open
Abstract
Background Isatis indigotica, the source of the traditional Chinese medicine Radix isatidis (Ban-Lan-Gen), is an extremely important economical crop in China. To facilitate biological, biochemical and molecular research on the medicinal chemicals in I. indigotica, here we report the first I. indigotica transcriptome generated by RNA sequencing (RNA-seq). Results RNA-seq library was created using RNA extracted from a mixed sample including leaf and root. A total of 33,238 unigenes were assembled from more than 28 million of high quality short reads. The quality of the assembly was experimentally examined by cDNA sequencing of seven randomly selected unigenes. Based on blast search 28,184 unigenes had a hit in at least one of the protein and nucleotide databases used in this study, and 8 unigenes were found to be associated with biosynthesis of indole and its derivatives. According to Gene Ontology classification, 22,365 unigenes were categorized into 48 functional groups. Furthermore, Clusters of Orthologous Group and Swiss-Port annotation were assigned for 7,707 and 18,679 unigenes, respectively. Analysis of repeat motifs identified 6,400 simple sequence repeat markers in 4,509 unigenes. Conclusion Our data provide a comprehensive sequence resource for molecular study of I. indigotica. Our results will facilitate studies on the functions of genes involved in the indole alkaloid biosynthesis pathway and on metabolism of nitrogen and indole alkaloids in I. indigotica and its related species.
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De novo sequencing and transcriptome analysis of Ustilaginoidea virens by using Illumina paired-end sequencing and development of simple sequence repeat markers. Gene 2014; 547:202-10. [DOI: 10.1016/j.gene.2014.06.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/03/2014] [Accepted: 06/05/2014] [Indexed: 02/06/2023]
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Characterization of the global transcriptome for cotton (Gossypium hirsutum L.) anther and development of SSR marker. Gene 2014; 551:206-13. [PMID: 25178523 DOI: 10.1016/j.gene.2014.08.058] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Revised: 08/26/2014] [Accepted: 08/29/2014] [Indexed: 11/20/2022]
Abstract
Cotton is an important fiber plant, and it's attractive to elucidate the molecular mechanism of anther development due to the close relationship between the anther fertility and boll-setting, and also fiber yield. In the present paper, 47.2 million paired-end reads with average length of 82.87 bp from the anthers of TM-1 (Gossypium hirsutum L.), a genetic standard line, were generated through transcriptome sequencing, and 210,965 unigenes of more than 100 bp were obtained. BLAST, KEGG, COG, and GO analyses showed that the genes were enriched in the processes of transcription, translation, and post-translation as well as hormone signal transduction, the transcription factor families, and cell wall-related genes mainly participating in cell expansion and carbohydrate metabolism. Further analysis identified 11,153 potential SSRs. A suit of 5122 primer pair sequences were designed, and 82 of 300 randomly selected primer pairs produced reproducible amplicons that were polymorphic among 22 cotton accessions from G. hirsutum, Gossypium barbadense and Gossypium arboreum. The UPGMA clustering analysis further confirmed high quality and effectiveness of these novel SSR markers. The present study provided insights into the transcriptome profile of the cotton and established a public information platform for functional genomics and molecular breeding.
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Transcriptome and gene expression analysis during flower blooming in Rosa chinensis ‘Pallida’. Gene 2014; 540:96-103. [DOI: 10.1016/j.gene.2014.02.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 01/29/2014] [Accepted: 02/08/2014] [Indexed: 11/22/2022]
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Wei DD, Chen EH, Ding TB, Chen SC, Dou W, Wang JJ. De novo assembly, gene annotation, and marker discovery in stored-product pest Liposcelis entomophila (Enderlein) using transcriptome sequences. PLoS One 2013; 8:e80046. [PMID: 24244605 PMCID: PMC3828239 DOI: 10.1371/journal.pone.0080046] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 09/27/2013] [Indexed: 12/18/2022] Open
Abstract
Background As a major stored-product pest insect, Liposcelis entomophila has developed high levels of resistance to various insecticides in grain storage systems. However, the molecular mechanisms underlying resistance and environmental stress have not been characterized. To date, there is a lack of genomic information for this species. Therefore, studies aimed at profiling the L. entomophila transcriptome would provide a better understanding of the biological functions at the molecular levels. Methodology/Principal Findings We applied Illumina sequencing technology to sequence the transcriptome of L. entomophila. A total of 54,406,328 clean reads were obtained and that de novo assembled into 54,220 unigenes, with an average length of 571 bp. Through a similarity search, 33,404 (61.61%) unigenes were matched to known proteins in the NCBI non-redundant (Nr) protein database. These unigenes were further functionally annotated with gene ontology (GO), cluster of orthologous groups of proteins (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. A large number of genes potentially involved in insecticide resistance were manually curated, including 68 putative cytochrome P450 genes, 37 putative glutathione S-transferase (GST) genes, 19 putative carboxyl/cholinesterase (CCE) genes, and other 126 transcripts to contain target site sequences or encoding detoxification genes representing eight types of resistance enzymes. Furthermore, to gain insight into the molecular basis of the L. entomophila toward thermal stresses, 25 heat shock protein (Hsp) genes were identified. In addition, 1,100 SSRs and 57,757 SNPs were detected and 231 pairs of SSR primes were designed for investigating the genetic diversity in future. Conclusions/Significance We developed a comprehensive transcriptomic database for L. entomophila. These sequences and putative molecular markers would further promote our understanding of the molecular mechanisms underlying insecticide resistance or environmental stress, and will facilitate studies on population genetics for psocids, as well as providing useful information for functional genomic research in the future.
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Affiliation(s)
- Dan-Dan Wei
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, P. R. China
| | - Er-Hu Chen
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, P. R. China
| | - Tian-Bo Ding
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, P. R. China
| | - Shi-Chun Chen
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, P. R. China
| | - Wei Dou
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, P. R. China
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, P. R. China
- * E-mail:
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