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Toro Segovia LJ, Téllez Ramírez GA, Henao Arias DC, Rivera Duran JD, Bedoya JP, Castaño Osorio JC. Identification and characterization of novel cecropins from the Oxysternon conspicillatum neotropic dung beetle. PLoS One 2017; 12:e0187914. [PMID: 29186139 PMCID: PMC5706684 DOI: 10.1371/journal.pone.0187914] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 10/27/2017] [Indexed: 02/01/2023] Open
Abstract
Dung beetles are exposed to a complex microbiological ecosystem during their life cycle. Characterization of novel host-defense peptides (HDP) is essential to understanding the host innate immune response in insects. It constitutes a promising alternative to look for new therapeutic agents against pathogenic microbes. We identified four new HDP, Oxysterlins 1, 2, 3, and 4 from the transcriptome of the Oxysternon conspicillatum dung beetle. These HDP display a highly conserved signal peptide and a mature peptide, characterized by an overall positive charge (cationic) (pI: 10.23–11.49), a hydrophobic ratio (ΦH: 35–41), and amphipathicity. Oxysterlins 1, 2, and 3 have a linear α-helix structure, whilst Oxysterlin 4 has a mixture of both α-helix and β-sheet structures without disulfide bonds through bioinformatics prediction and circular dichroism. Oxysterlins are part of the cecropin family group in an exclusive clade related to beetle cecropins. They have predominant antimicrobial activity against Gram-negative bacteria, including multidrug resistant strains (3.12–50 μg/mL) measured by plate microdilution. Their kinetics, in a time-killing curve showed concentration-dependent bactericidal activity. Furthermore, these HDP have low toxicity against human erythrocytes (62.5–500 μg/mL) and Vero cells (250–500 μg/mL). This article describes new HDP of the cecropin family from the Oxysternon conspicillatum dung beetle, with antimicrobial activity against multidrug resistant bacteria and low toxicity.
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Affiliation(s)
- Lily Johanna Toro Segovia
- Center of Biomedical Research. Group of Molecular Immunology. Universidad del Quindío, Armenia, Quindío–Colombia
| | | | - Diana Carolina Henao Arias
- Center of Biomedical Research. Group of Molecular Immunology. Universidad del Quindío, Armenia, Quindío–Colombia
| | - Juan David Rivera Duran
- Center of Biomedical Research. Group of Molecular Immunology. Universidad del Quindío, Armenia, Quindío–Colombia
| | - Juan Pablo Bedoya
- Center of Biomedical Research. Group of Molecular Immunology. Universidad del Quindío, Armenia, Quindío–Colombia
| | - Jhon Carlos Castaño Osorio
- Center of Biomedical Research. Group of Molecular Immunology. Universidad del Quindío, Armenia, Quindío–Colombia
- * E-mail:
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Wang J, Islam F, Li L, Long M, Yang C, Jin X, Ali B, Mao B, Zhou W. Complementary RNA-Sequencing Based Transcriptomics and iTRAQ Proteomics Reveal the Mechanism of the Alleviation of Quinclorac Stress by Salicylic Acid in Oryza sativa ssp. japonica. Int J Mol Sci 2017; 18:ijms18091975. [PMID: 28906478 PMCID: PMC5618624 DOI: 10.3390/ijms18091975] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 09/08/2017] [Accepted: 09/12/2017] [Indexed: 12/16/2022] Open
Abstract
To uncover the alleviation mechanism of quinclorac stress by salicylic acid (SA), leaf samples of Oryza sativa ssp. Japonica under quinclorac stress with and without SA pre-treatment were analyzed for transcriptional and proteomic profiling to determine the differentially expressed genes (DEGs) and proteins (DEPs), respectively. Results showed that quinclorac stress altered the expression of 2207 DEGs (1427 up-regulated, 780 down-regulated) and 147 DEPs (98 down-regulated, 49 up-regulated). These genes and proteins were enriched in glutathione (GSH) metabolism, porphyrin and chlorophyll metabolism, the biosynthesis of secondary metabolites, glyoxylate and dicarboxylate metabolism, and so on. It also influenced apetala2- ethylene-responsive element binding protein (AP2-EREBP) family, myeloblastosis (MYB) family and WRKY family transcription factors. After SA pre-treatment, 697 genes and 124 proteins were differentially expressed. Pathway analysis showed similar enrichments in GSH, glyoxylate and dicarboxylate metabolism. Transcription factors were distributed in basic helix-loop-helix (bHLH), MYB, Tify and WRKY families. Quantitative real-time PCR results revealed that quinclorac stress induced the expression of glutathion reductase (GR) genes (OsGR2, OsGR3), which was further pronounced by SA pre-treatment. Quinclorac stress further mediated the accumulation of acetaldehyde in rice, while SA enhanced the expression of OsALDH2B5 and OsALDH7 to accelerate the metabolism of herbicide quinclorac for the protection of rice. Correlation analysis between transcriptome and proteomics demonstrated that, under quinclorac stress, correlated proteins/genes were mainly involved in the inhibition of intermediate steps in the biosynthesis of chlorophyll. Other interesting proteins/genes and pathways regulated by herbicide quinclorac and modulated by SA pre-treatment were also discussed, based on the transcriptome and proteomics results.
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Affiliation(s)
- Jian Wang
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China.
| | - Faisal Islam
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China.
| | - Lan Li
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China.
| | - Meijuan Long
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China.
| | - Chong Yang
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China.
| | - Xiaoli Jin
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China.
| | - Basharat Ali
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China.
- Institute of Crop Science and Resource Conservation (INRES), Abiotic Stress Tolerance in Crops, University of Bonn, 53115 Bonn, Germany.
| | - Bizeng Mao
- Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
| | - Weijun Zhou
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China.
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RNA-seq of Rice Yellow Stem Borer Scirpophaga incertulas Reveals Molecular Insights During Four Larval Developmental Stages. G3-GENES GENOMES GENETICS 2017; 7:3031-3045. [PMID: 28717048 PMCID: PMC5592929 DOI: 10.1534/g3.117.043737] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The yellow stem borer (YSB), Scirpophaga incertulas, is a prominent pest in rice cultivation causing serious yield losses. The larval stage is an important stage in YSB, responsible for maximum infestation. However, limited knowledge exists on the biology and mechanisms underlying the growth and differentiation of YSB. To understand and identify the genes involved in YSB development and infestation, so as to design pest control strategies, we performed de novo transcriptome analysis at the first, third, fifth, and seventh larval developmental stages employing Illumina Hi-seq. High-quality reads (HQR) of ∼229 Mb were assembled into 24,775 transcripts with an average size of 1485 bp. Genes associated with various metabolic processes, i.e., detoxification mechanism [CYP450, GSTs, and carboxylesterases (CarEs)], RNA interference (RNAi) machinery (Dcr-1, Dcr-2, Ago-1, Ago-2, Sid-1, Sid-2, Sid-3, and Sid-1-related gene), chemoreception (CSPs, GRs, OBPs, and ORs), and regulators [transcription factors (TFs) and hormones] were differentially regulated during the developmental stages. Identification of stage-specific transcripts made it possible to determine the essential processes of larval development. Comparative transcriptome analysis revealed that YSB has not evolved much with respect to the detoxification mechanism, but showed the presence of distinct RNAi machinery. The presence of strong specific visual recognition coupled with chemosensory mechanisms supports the monophagous nature of YSB. Designed expressed sequenced tags-simple-sequence repeats (EST-SSRs) will facilitate accurate estimation of the genetic diversity of YSB. This is the first report on characterization of the YSB transcriptome and the identification of genes involved in key processes, which will help researchers and industry to devise novel pest control strategies. This study also opens up a new avenue to develop next-generation resistant rice using RNAi or genome editing approaches.
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You Q, Yi X, Zhang K, Wang C, Ma X, Zhang X, Xu W, Li F, Su Z. Genome-wide comparative analysis of H3K4me3 profiles between diploid and allotetraploid cotton to refine genome annotation. Sci Rep 2017; 7:9098. [PMID: 28831143 PMCID: PMC5567255 DOI: 10.1038/s41598-017-09680-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 07/28/2017] [Indexed: 12/28/2022] Open
Abstract
Polyploidy is a common evolutionary occurrence in plants. Recently, published genomes of allotetraploid G. hirsutum and its donors G. arboreum and G. raimondii make cotton an accessible polyploid model. This study used chromatin immunoprecipitation with high-throughput sequencing (ChIP-Seq) to investigate the genome-wide distribution of H3K4me3 in G. arboreum and G. hirsutum, and explore the conservation and variation of genome structures between diploid and allotetraploid cotton. Our results showed that H3K4me3 modifications were associated with active transcription in both cottons. The H3K4me3 histone markers appeared mainly in genic regions and were enriched around the transcription start sites (TSSs) of genes. We integrated the ChIP-seq data of H3K4me3 with RNA-seq and ESTs data to refine the genic structure annotation. There were 6,773 and 12,773 new transcripts discovered in G. arboreum and G. hirsutum, respectively. Furthermore, co-expression networks were linked with histone modification and modularized in an attempt to explain differential H3K4me3 enrichment correlated with changes in gene transcription during cotton development and evolution. Taken together, we have combined epigenomic and transcriptomic datasets to systematically discover functional genes and compare them between G. arboreum and G. hirsutum, which may be beneficial for studying diploid and allotetraploid plants with large genomes and complicated evolution.
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Affiliation(s)
- Qi You
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xin Yi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Kang Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Chunchao Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xuelian Ma
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xueyan Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agriculture Sciences (ICR, CAAS), Anyang, Henan, 455000, China
| | - Wenying Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agriculture Sciences (ICR, CAAS), Anyang, Henan, 455000, China.
| | - Zhen Su
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
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Yang H, Zhao T, Jiang J, Chen X, Zhang H, Liu G, Zhang D, Du C, Wang S, Xu X, Li J. Transcriptome Analysis of the Sm-Mediated Hypersensitive Response to Stemphylium lycopersici in Tomato. FRONTIERS IN PLANT SCIENCE 2017; 8:1257. [PMID: 28769960 PMCID: PMC5515834 DOI: 10.3389/fpls.2017.01257] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 07/03/2017] [Indexed: 05/20/2023]
Abstract
Gray leaf spot disease caused by Stemphylium lycopersici is a major disease in cultivated tomato plants and threatens tomato-growing areas worldwide. Sm is a single dominant gene that confers resistance to tomato gray leaf spot disease agent. However, the underlying molecular mechanism remains unclear. Here, resistant (cv. Motelle, containing the Sm gene) and susceptible (cv. Moneymaker) plants were inoculated with virulent Stemphylium lycopersici isolate at a time point at which both cultivars showed a strong response to S. lycopersici infection. Transcriptome analyses were performed in both cultivars using RNA-seq. The number of differentially expressed genes (DEGs) was higher in Motelle than Moneymaker. Functional classification revealed that most DEGs were involved in plant-pathogen interactions, plant hormone signal transduction, regulation of autophagy, glycerophospholipid metabolism, and α-linolenic acid metabolism. Moreover, the genes that were significantly up-regulated in Sm tomatoes were involved in plant-pathogen interaction pathways. A total of 26 genes were selected for confirmation of differentially expressed levels by quantitative real-time PCR. This knowledge will yield new insights into the molecular mechanism of Sm responses to S. lycopersici infection.
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Affiliation(s)
- Huanhuan Yang
- College of Horticulture, Northeast Agricultural UniversityHarbin, China
| | - Tingting Zhao
- College of Horticulture, Northeast Agricultural UniversityHarbin, China
| | - Jingbin Jiang
- College of Horticulture, Northeast Agricultural UniversityHarbin, China
| | - Xiuling Chen
- College of Horticulture, Northeast Agricultural UniversityHarbin, China
| | - He Zhang
- College of Horticulture, Northeast Agricultural UniversityHarbin, China
| | - Guan Liu
- College of Horticulture, Northeast Agricultural UniversityHarbin, China
| | - Dongye Zhang
- College of Horticulture, Northeast Agricultural UniversityHarbin, China
| | - Chong Du
- College of Horticulture, Northeast Agricultural UniversityHarbin, China
| | | | - Xiangyang Xu
- College of Horticulture, Northeast Agricultural UniversityHarbin, China
| | - Jingfu Li
- College of Horticulture, Northeast Agricultural UniversityHarbin, China
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Luo K, Wu F, Zhang D, Dong R, Fan Z, Zhang R, Yan Z, Wang Y, Zhang J. Transcriptomic profiling of Melilotus albus near-isogenic lines contrasting for coumarin content. Sci Rep 2017; 7:4577. [PMID: 28676637 PMCID: PMC5496894 DOI: 10.1038/s41598-017-04111-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 05/09/2017] [Indexed: 12/30/2022] Open
Abstract
Coumarin and its derivatives are widely used as fragrances in industrial products and have medical value. The goal of the present study was to discover genes and pathways related to coumarin biosynthesis in Melilotus albus using transcriptome analysis. The genes of five M. albus near-isogenic lines (NILs) that had different coumarin content and β-glucosidase activity according to the investigation of pedigree were quantified and then analysed by RNA-Seq. Using transcriptome analysis, differentially expressed genes (DEGs) were identified in two pairwise comparisons that differed in coumarin content as well as in two pairwise comparisons that differed in β-glucosidase activity. Gene expression pattern analysis suggested similar transcriptional trends in the genotypes with the same coumarin levels. Furthermore, the Kyoto Encyclopedia of Genes and Genomes (KEGG) database of DEGs was used to identify functional pathways associated with coumarin biosynthesis. We identified 111 unigenes, with several DEGs among them possibly being related to coumarin synthesis pathways. Unigenes encoding a hexokinase, an abscisic acid receptor, a phenylalanine ammonia-lyase (PAL) and two peroxidases particularly showed correspondence with the coumarin content of different genotypes. These results will contribute to a better understanding of the coumarin biosynthesis in M. albus.
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Affiliation(s)
- Kai Luo
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Fan Wu
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Daiyu Zhang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Rui Dong
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Zhichao Fan
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Rui Zhang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Zhuanzhuan Yan
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Yanrong Wang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
| | - Jiyu Zhang
- State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China.
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A Whole-Transcriptome Approach to Evaluating Reference Genes for Quantitative Gene Expression Studies: A Case Study in Mimulus. G3-GENES GENOMES GENETICS 2017; 7:1085-1095. [PMID: 28258113 PMCID: PMC5386857 DOI: 10.1534/g3.116.038075] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While quantitative PCR (qPCR) is widely recognized as being among the most accurate methods for quantifying gene expression, it is highly dependent on the use of reliable, stably expressed reference genes. With the increased availability of high-throughput methods for measuring gene expression, whole-transcriptome approaches may be increasingly utilized for reference gene selection and validation. In this study, RNA-seq was used to identify a set of novel qPCR reference genes and evaluate a panel of traditional “housekeeping” reference genes in two species of the evolutionary model plant genus Mimulus. More broadly, the methods proposed in this study can be used to harness the power of transcriptomes to identify appropriate reference genes for qPCR in any study organism, including emerging and nonmodel systems. We find that RNA-seq accurately estimates gene expression means in comparison to qPCR, and that expression means are robust to moderate environmental and genetic variation. However, measures of expression variability were only in agreement with qPCR for samples obtained from a shared environment. This result, along with transcriptome-wide comparisons, suggests that environmental changes have greater impacts on expression variability than on expression means. We discuss how this issue can be addressed through experimental design, and suggest that the ever-expanding pool of published transcriptomes represents a rich and low-cost resource for developing better reference genes for qPCR.
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Use of RNA-seq data to identify and validate RT-qPCR reference genes for studying the tomato-Pseudomonas pathosystem. Sci Rep 2017; 7:44905. [PMID: 28317896 PMCID: PMC5357963 DOI: 10.1038/srep44905] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 02/14/2017] [Indexed: 12/26/2022] Open
Abstract
The agronomical relevant tomato-Pseudomonas syringae pv. tomato pathosystem is widely used to explore and understand the underlying mechanisms of the plant immune response. Transcript abundance estimation, mainly through reverse transcription-quantitative PCR (RT-qPCR), is a common approach employed to investigate the possible role of a candidate gene in certain biological process under study. The accuracy of this technique relies heavily on the selection of adequate reference genes. Initially, genes derived from other techniques (such as Northern blots) were used as reference genes in RT-qPCR experiments, but recent studies in different systems suggest that many of these genes are not stably expressed. The development of high throughput transcriptomic techniques, such as RNA-seq, provides an opportunity for the identification of transcriptionally stable genes that can be adopted as novel and robust reference genes. Here we take advantage of a large set of RNA-seq data originating from tomato leaves infiltrated with different immunity inducers and bacterial strains. We assessed and validated 9 genes that are much more stable than two traditional reference genes. Specifically, ARD2 and VIN3 were the most stably expressed genes and consequently we propose they be adopted for RT-qPCR experiments involving this pathosystem.
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Chen Y, Cao Q, Tao X, Shao H, Zhang K, Zhang Y, Tan X. Analysis of de novo sequencing and transcriptome assembly and lignocellulolytic enzymes gene expression of Coriolopsis gallica HTC. Biosci Biotechnol Biochem 2017; 81:460-468. [DOI: 10.1080/09168451.2016.1182418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Abstract
White-rot basidiomycete Coriolopsis gallica HTC is one of the main biodegraders of poplar. In our previous study, we have shown the strong capacity of C. gallica HTC to degrade lignocellulose. In this study, equal amounts of total RNA fromC. Gallica HTC cultures grown in different conditions were pooled together. Illumina paired-end RNA sequencing was performed, and 13.2 million 90-bp paired-end reads were generated. We chose the Merged Assembly of Oases data-set for the following blast searches and gene ontology analyses. The reads were assembled de novo into 28,034 transcripts (≥ 100 bp) using combined assembly strategy MAO. The transcripts were annotated using Blast2GO. In all, 18,810 transcripts (≥100 bp) achieved BLASTX hits, of which, 7048 transcripts had GO term and 2074 had ECs. The expression level of 11 lignocellulolytic enzyme genes from the assembled C. gallica HTC transcriptome were detected by real-time quantitative polymerase chain reaction. The results showed that expression levels of these genes were affected by carbon source and nitrogen source at the level of transcription. The current abundant transcriptome data allowed the identification of many new transcripts in C. gallica HTC. Data provided here represent the most comprehensive and integrated genomic resources for cloning and identifying genes of interest from C. gallica HTC. Characterization of C. gallica HTC transcriptome provides an effective tool to understand mechanisms underlying cellular and molecular functions of C. gallica HTC.
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Affiliation(s)
- Yuehong Chen
- The Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, China
| | - Qinghua Cao
- The Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xiang Tao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Huanhuan Shao
- The Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, China
| | - Kun Zhang
- The Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yizheng Zhang
- The Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xuemei Tan
- The Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education, Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, China
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Lim SL, D'Agui HM, Enright NJ, He T. Characterization of Leaf Transcriptome in Banksia hookeriana. GENOMICS PROTEOMICS & BIOINFORMATICS 2017; 15:49-56. [PMID: 28161492 PMCID: PMC5339403 DOI: 10.1016/j.gpb.2016.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 11/06/2016] [Accepted: 11/24/2016] [Indexed: 12/23/2022]
Abstract
Banksia is a significant element in vegetation of southwestern Australia, a biodiversity hotspot with global significance. In particular, Banksia hookeriana represents a species with significant economic and ecological importance in the region. For better conservation and management, we reported an overview of transcriptome of B. hookeriana using RNA-seq and de novo assembly. We have generated a total of 202.7 million reads (18.91 billion of nucleotides) from four leaf samples in four plants of B. hookeriana, and assembled 59,063 unigenes (average size = 1098 bp) through de novotranscriptome assembly. Among them, 39,686 unigenes were annotated against the Swiss-Prot, Clusters of Orthologous Groups (COG), and NCBI non-redundant (NR) protein databases. We showed that there was approximately one single nucleotide polymorphism (SNP) per 5.6–7.1 kb in the transcriptome, and the ratio of transitional to transversional polymorphisms was approximately 1.82. We compared unigenes of B. hookeriana to those of Arabidopsis thaliana and Nelumbo nucifera through sequence homology, Gene Ontology (GO) annotation, and KEGG pathway analyses. The comparative analysis revealed that unigenes of B. hookeriana were closely related to those of N. nucifera. B. hookeriana, N. nucifera, and A. thaliana shared similar GO annotations but different distributions in KEGG pathways, indicating that B. hookeriana has adapted to dry-Mediterranean type shrublands via regulating expression of specific genes. In total 1927 potential simple sequence repeat (SSR) markers were discovered, which could be used in the genotype and genetic diversity studies of the Banksia genus. Our results provide valuable sequence resource for further study in Banksia.
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Affiliation(s)
- Sim Lin Lim
- Department of Environment and Agriculture, Curtin University, Perth, WA 6845, Australia
| | - Haylee M D'Agui
- Department of Environment and Agriculture, Curtin University, Perth, WA 6845, Australia
| | - Neal J Enright
- School of Veterinary and Life Sciences, Murdoch University, Perth, WA 6150, Australia
| | - Tianhua He
- Department of Environment and Agriculture, Curtin University, Perth, WA 6845, Australia.
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Xue DQ, Chen XL, Zhang H, Chai XF, Jiang JB, Xu XY, Li JF. Transcriptome Analysis of the Cf-12-Mediated Resistance Response to Cladosporium fulvum in Tomato. FRONTIERS IN PLANT SCIENCE 2017; 7:2012. [PMID: 28105042 PMCID: PMC5212946 DOI: 10.3389/fpls.2016.02012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Accepted: 12/19/2016] [Indexed: 11/25/2022]
Abstract
Cf-12 is an effective gene for resisting tomato leaf mold disease caused by Cladosporium fulvum (C. fulvum). Unlike many other Cf genes such as Cf-2, Cf-4, Cf-5, and Cf-9, no physiological races of C. fulvum that are virulent to Cf-12 carrying plant lines have been identified. In order to better understand the molecular mechanism of Cf-12 gene resistance response, RNA-Seq was used to analyze the transcriptome changes at three different stages of C. fulvum infection (0, 4, and 8 days post infection [dpi]). A total of 9100 differentially expressed genes (DEGs) between 4 and 0 dpi, 8643 DEGs between 8 and 0 dpi and 2547 DEGs between 8 and 4 dpi were identified. In addition, we found that 736 DEGs shared among the above three groups, suggesting the presence of a common core of DEGs in response to C. fulvum infection. These DEGs were significantly enriched in defense-signaling pathways such as the calcium dependent protein kinases pathway and the jasmonic acid signaling pathway. Additionally, we found that many transcription factor genes were among the DEGs, indicating that transcription factors play an important role in C. fulvum defense response. Our study provides new insight on the molecular mechanism of Cf resistance to C. fulvum, especially the unique features of Cf-12 in responding to C. fulvum infection.
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Affiliation(s)
- Dong-Qi Xue
- College of Horticulture, Northeast Agricultural UniversityHarbin, China
| | - Xiu-Ling Chen
- College of Horticulture, Northeast Agricultural UniversityHarbin, China
| | - Hong Zhang
- College of Horticulture, Northeast Agricultural UniversityHarbin, China
| | - Xin-Feng Chai
- College of Life Science, Northeast Agricultural UniversityHarbin, China
| | - Jing-Bin Jiang
- College of Horticulture, Northeast Agricultural UniversityHarbin, China
| | - Xiang-Yang Xu
- College of Horticulture, Northeast Agricultural UniversityHarbin, China
| | - Jing-Fu Li
- College of Horticulture, Northeast Agricultural UniversityHarbin, China
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Huang X, Li Y, Pan J, Li M, Lai Y, Gao J, Li X. RNA-Seq identifies redox balance related gene expression alterations under acute cadmium exposure in yeast. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:1038-1047. [PMID: 27718328 DOI: 10.1111/1758-2229.12484] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 09/29/2016] [Indexed: 06/06/2023]
Abstract
The nonessential metal cadmium can cause cell toxicity and is associated with a range of human diseases including cardiovascular diseases, neurodegenerative diseases and cancers. In this study, cadmium-induced global gene expression profile of yeast was obtained using RNA Sequencing (RNA-Seq) and further analyzed by means of informatics and experiments. A total of 912 Differentially Expressed Genes (DEGs) (FDR of q < 0.01), including 415 Cd-inducible and 497 Cd-repressed genes were identified. Based on the DEGs, 25 cadmium responsive Clusters of Orthologous Group (COG) and three types of cadmium-induced Gene Ontology (GO) including cellular components, molecular functions and biological processes were analyzed in details. Thereafter, 79 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways under cadmium exposure were assigned. Collectively, 108 redox balance related genes were extracted under cadmium exposure. Meanwhile, cadmium exposure lowered cellular Mitochondrial Membrane Potential (MMP) and increased Reactive Oxygen Species (ROS) levels significantly in the context of mitochondrial dysfunction. Furthermore, cadmium exposure increased cellular GSH levels and decreased GSSG levels and also lowered GSSG/GSH ratio of cells, which supports experimentally our claim that the redox balance is the primary mechanism for cadmium toxicity. The results present in this study may provide new strategies for cadmium detoxification and prevention or therapies of cadmium-associated diseases.
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Affiliation(s)
- Xinhe Huang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Yuxing Li
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Jingmei Pan
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Ming Li
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Yongqin Lai
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Jie Gao
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Xueru Li
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
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Xie H, Hu J, Xiao C, Dai Y, Ding X, Xu Y. Exploration of ZEA cytotoxicity to mouse endometrial stromal cells and RNA-seq analysis. J Biochem Mol Toxicol 2016; 31. [DOI: 10.1002/jbt.21874] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 09/25/2016] [Accepted: 10/02/2016] [Indexed: 01/24/2023]
Affiliation(s)
- Haiqiang Xie
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing 210095 People's Republic of China
| | - Jin Hu
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing 210095 People's Republic of China
| | - Cheng Xiao
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing 210095 People's Republic of China
| | - Yujian Dai
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing 210095 People's Republic of China
| | - Xiaolin Ding
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing 210095 People's Republic of China
| | - Yinxue Xu
- College of Animal Science and Technology; Nanjing Agricultural University; Nanjing 210095 People's Republic of China
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64
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Zhang F, Hua L, Fei J, Wang F, Liao Y, Fang W, Chen F, Teng N. Chromosome doubling to overcome the chrysanthemum cross barrier based on insight from transcriptomic and proteomic analyses. BMC Genomics 2016; 17:585. [PMID: 27506621 PMCID: PMC4979184 DOI: 10.1186/s12864-016-2939-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 07/14/2016] [Indexed: 12/05/2022] Open
Abstract
Background Cross breeding is the most commonly used method in chrysanthemum (Chrysanthemum morifolium) breeding; however, cross barriers always exist in these combinations. Many studies have shown that paternal chromosome doubling can often overcome hybridization barriers during cross breeding, although the underlying mechanism has seldom been investigated. Results In this study, we performed two crosses: C. morifolium (pollen receptor) × diploid C. nankingense (pollen donor) and C. morifolium × tetraploid C. nankingense. Seeds were obtained only from the latter cross. RNA-Seq and isobaric tags for relative and absolute quantitation (iTRAQ) were used to investigate differentially expressed genes and proteins during key embryo development stages in the latter cross. A previously performed cross, C. morifolium × diploid C. nankingense, was compared to our results and revealed that transcription factors (i.e., the agamous-like MADS-box protein AGL80 and the leucine-rich repeat receptor protein kinase EXS), hormone-responsive genes (auxin-binding protein 1), genes and proteins related to metabolism (ATP-citrate synthase, citrate synthase and malate dehydrogenase) and other genes reported to contribute to embryo development (i.e., LEA, elongation factor and tubulin) had higher expression levels in the C. morifolium × tetraploid C. nankingense cross. In contrast, genes related to senescence and cell death were down-regulated in the C. morifolium × tetraploid C. nankingense cross. Conclusions The data resources helped elucidate the gene and protein expression profiles and identify functional genes during different development stages. When the chromosomes from the male parent are doubled, the genes contributing to normal embryo developmentare more abundant. However, genes with negative functions were suppressed, suggesting that chromosome doubling may epigenetically inhibit the expression of these genes and allow the embryo to develop normally. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2939-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fengjiao Zhang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.,Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology and Equipment, Nanjing, 210095, China
| | - Lichun Hua
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiangsong Fei
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fan Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuan Liao
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Weimin Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Nianjun Teng
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China. .,Jiangsu Province Engineering Lab for Modern Facility Agriculture Technology and Equipment, Nanjing, 210095, China.
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65
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Campagna D, Gasparini F, Franchi N, Vitulo N, Ballin F, Manni L, Valle G, Ballarin L. Transcriptome dynamics in the asexual cycle of the chordate Botryllus schlosseri. BMC Genomics 2016; 17:275. [PMID: 27038623 PMCID: PMC4818882 DOI: 10.1186/s12864-016-2598-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/16/2016] [Indexed: 12/15/2022] Open
Abstract
Background We performed an analysis of the transcriptome during the blastogenesis of the chordate Botryllus schlosseri, focusing in particular on genes involved in cell death by apoptosis. The tunicate B. schlosseri is an ascidian forming colonies characterized by the coexistence of three blastogenetic generations: filter-feeding adults, buds on adults, and budlets on buds. Cyclically, adult tissues undergo apoptosis and are progressively resorbed and replaced by their buds originated by asexual reproduction. This is a feature of colonial tunicates, the only known chordates that can reproduce asexually. Results Thanks to a newly developed web-based platform (http://botryllus.cribi.unipd.it), we compared the transcriptomes of the mid-cycle, the pre-take-over, and the take-over phases of the colonial blastogenetic cycle. The platform is equipped with programs for comparative analysis and allows to select the statistical stringency. We enriched the genome annotation with 11,337 new genes; 581 transcripts were resolved as complete open reading frames, translated in silico into amino acid sequences and then aligned onto the non-redundant sequence database. Significant differentially expressed genes were classified within the gene ontology categories. Among them, we recognized genes involved in apoptosis activation, de-activation, and regulation. Conclusions With the current work, we contributed to the improvement of the first released B. schlosseri genome assembly and offer an overview of the transcriptome changes during the blastogenetic cycle, showing up- and down-regulated genes. These results are important for the comprehension of the events underlying colony growth and regression, cell proliferation, colony homeostasis, and competition among different generations. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2598-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Davide Campagna
- CRIBI Biotechnology Centre, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy
| | - Fabio Gasparini
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy
| | - Nicola Franchi
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy
| | - Nicola Vitulo
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy.,Department of Biotechnology, University of Verona, Verona, Italy
| | - Francesca Ballin
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy
| | - Lucia Manni
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy.
| | - Giorgio Valle
- CRIBI Biotechnology Centre, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy.,Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy
| | - Loriano Ballarin
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy
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66
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Comprehensive profiling of EBV gene expression in nasopharyngeal carcinoma through paired-end transcriptome sequencing. Front Med 2016; 10:61-75. [DOI: 10.1007/s11684-016-0436-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Accepted: 01/15/2016] [Indexed: 12/11/2022]
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67
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Identification and analysis of mouse non-coding RNA using transcriptome data. SCIENCE CHINA-LIFE SCIENCES 2016; 59:589-603. [DOI: 10.1007/s11427-015-4929-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 10/22/2015] [Indexed: 01/08/2023]
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68
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Liu J, Li G, Chang Z, Yu T, Liu B, McMullen R, Chen P, Huang X. BinPacker: Packing-Based De Novo Transcriptome Assembly from RNA-seq Data. PLoS Comput Biol 2016; 12:e1004772. [PMID: 26894997 PMCID: PMC4760927 DOI: 10.1371/journal.pcbi.1004772] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 01/18/2016] [Indexed: 02/06/2023] Open
Abstract
High-throughput RNA-seq technology has provided an unprecedented opportunity to reveal the very complex structures of transcriptomes. However, it is an important and highly challenging task to assemble vast amounts of short RNA-seq reads into transcriptomes with alternative splicing isoforms. In this study, we present a novel de novo assembler, BinPacker, by modeling the transcriptome assembly problem as tracking a set of trajectories of items with their sizes representing coverage of their corresponding isoforms by solving a series of bin-packing problems. This approach, which subtly integrates coverage information into the procedure, has two exclusive features: 1) only splicing junctions are involved in the assembling procedure; 2) massive pell-mell reads are assembled seemingly by moving a comb along junction edges on a splicing graph. Being tested on both real and simulated RNA-seq datasets, it outperforms almost all the existing de novo assemblers on all the tested datasets, and even outperforms those ab initio assemblers on the real dog dataset. In addition, it runs substantially faster and requires less memory space than most of the assemblers. BinPacker is published under GNU GENERAL PUBLIC LICENSE and the source is available from: http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_1.0.tar.gz/download. Quick installation version is available from: http://sourceforge.net/projects/transcriptomeassembly/files/BinPacker_binary.tar.gz/download. The availability of RNA-seq technology drives the development of algorithms for transcriptome assembly from very short RNA sequences. However, the problem of how to (de novo) assemble transcriptome using RNA-seq datasets has not been modeled well; e.g. sequence coverage information has even not been accurately and effectively integrated into the appropriate assembling procedure, leading to a bottleneck that all the existing (de novo) strategies have encountered. We present a novel approach to remodel the problem as tracking a set of trajectories of items with their sizes representing the coverage of their corresponding isoforms by solving a series of bin-packing problems. This approach, which subtly integrates the coverage information into the procedure, has two exclusive features: 1) only splicing junctions are involved in the assembling procedure; 2) massive pell-mell reads are assembled seemingly by moving a comb along junction edges on a splicing graph. Being tested on both real and simulated RNA-seq datasets, it outperforms almost all existing de novo assemblers on all the tested datasets, even outperforms those ab initio assemblers on the dog dataset, in terms of commonly used comparison standards.
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Affiliation(s)
- Juntao Liu
- School of Mathematics, Shandong University, Jinan, China
| | - Guojun Li
- School of Mathematics, Shandong University, Jinan, China
- * E-mail: (GL); (XH)
| | - Zheng Chang
- School of Mathematics, Shandong University, Jinan, China
| | - Ting Yu
- School of Mathematics, Shandong University, Jinan, China
| | - Bingqiang Liu
- School of Mathematics, Shandong University, Jinan, China
| | - Rick McMullen
- High Performance Computing Center, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Pengyin Chen
- Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, Arkansas, United States of America
| | - Xiuzhen Huang
- Department of Computer Science, Arkansas State University, Jonesboro, Arkansas, United States of America
- * E-mail: (GL); (XH)
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69
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Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation. Sci Rep 2016; 6:18936. [PMID: 26729541 PMCID: PMC4733048 DOI: 10.1038/srep18936] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 12/01/2015] [Indexed: 11/12/2022] Open
Abstract
Gene expression variation largely contributes to phenotypic diversity and constructing pan-transcriptome is considered necessary for species with complex genomes. However, the regulation mechanisms and functional consequences of pan-transcriptome is unexplored systematically. By analyzing RNA-seq data from 368 maize diverse inbred lines, we identified almost one-third nuclear genes under expression presence and absence variation, which tend to play regulatory roles and are likely regulated by distant eQTLs. The ePAV was directly used as “genotype” to perform GWAS for 15 agronomic phenotypes and 526 metabolic traits to efficiently explore the associations between transcriptomic and phenomic variations. Through a modified assembly strategy, 2,355 high-confidence novel sequences with total 1.9 Mb lengths were found absent within reference genome. Ten randomly selected novel sequences were fully validated with genomic PCR, including another two NBS_LRR candidates potentially affect flavonoids and disease-resistance. A simulation analysis suggested that the pan-transcriptome of the maize whole kernel is approaching a maximum value of 63,000 genes, and through developing two test-cross populations and surveying several most important yield traits, the dispensable genes were shown to contribute to heterosis. Novel perspectives and resources to discover maize quantitative trait variations were provided to better understand the kernel regulation networks and to enhance maize breeding.
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70
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Tripathy S, Padhi SK, Sen R, Mohanty S, Samanta M, Maiti NK. Profiling of Brevibacillus borstelensis transcriptome exposed to high temperature shock. Genomics 2015; 107:33-9. [PMID: 26585522 DOI: 10.1016/j.ygeno.2015.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 11/06/2015] [Accepted: 11/13/2015] [Indexed: 10/22/2022]
Abstract
To understand the molecular mechanisms underlying the ability of the bacteria to survive at high temperature, gene expression profile of Brevibacillusborstelensis at 55°C during 5 and 10min heat shock period was carried out by high-throughput sequencing technology. A total of 2555 non-redundant transcripts were annotated. A total of 575 genes at 5min and 400 genes at 10min exhibited significant differential expression in response to temperature upshift from 50 to 55°C. Genes up-regulated under heat shock were associated with metabolism (mtnE), membrane transport, signal transduction, transcriptional regulation (ycxD, codY) and folding and sorting (hsp90). A larger number of genes encoding hypothetical proteins were identified. RT-PCR experimental results carried out on genes expressed under heat shock were found to be consistent with transcriptome data. The results enhance our understanding of adaptation strategy of thermophilic bacteria thereby providing a strong background for in depth research in thermophiles.
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Affiliation(s)
- S Tripathy
- Division of Fish Health Management, Central Institute of Freshwater Aquaculture, Kaushalyaganga, Bhubaneswar 751002, Orissa, India
| | - S K Padhi
- Division of Fish Health Management, Central Institute of Freshwater Aquaculture, Kaushalyaganga, Bhubaneswar 751002, Orissa, India
| | - R Sen
- Division of Fish Health Management, Central Institute of Freshwater Aquaculture, Kaushalyaganga, Bhubaneswar 751002, Orissa, India
| | - S Mohanty
- Division of Fish Health Management, Central Institute of Freshwater Aquaculture, Kaushalyaganga, Bhubaneswar 751002, Orissa, India
| | - M Samanta
- Division of Fish Health Management, Central Institute of Freshwater Aquaculture, Kaushalyaganga, Bhubaneswar 751002, Orissa, India
| | - N K Maiti
- Division of Fish Health Management, Central Institute of Freshwater Aquaculture, Kaushalyaganga, Bhubaneswar 751002, Orissa, India.
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Yang J, Chen X, Zhu C, Peng X, He X, Fu J, Ouyang L, Bian J, Hu L, Sun X, Xu J, He H. RNA-seq reveals differentially expressed genes of rice (Oryza sativa) spikelet in response to temperature interacting with nitrogen at meiosis stage. BMC Genomics 2015; 16:959. [PMID: 26576634 PMCID: PMC4650392 DOI: 10.1186/s12864-015-2141-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Accepted: 10/23/2015] [Indexed: 12/22/2022] Open
Abstract
Background Rice (Oryza sativa) is one of the most important cereal crops, providing food for more than half of the world’s population. However, grain yields are challenged by various abiotic stresses such as drought, fertilizer, heat, and their interaction. Rice at reproductive stage is much more sensitive to environmental temperatures, and little is known about molecular mechanisms of rice spikelet in response to high temperature interacting with nitrogen (N). Results Here we reported the transcriptional profiling analysis of rice spikelet at meiosis stage using RNA sequencing (RNA-seq) as an attempt to gain insights into molecular events associated with temperature and nitrogen. This study received four treatments: 1) NN: normal nitrogen level (165 kg ha−1) with natural temperature (30 °C); 2) HH: high nitrogen level (330 kg ha−1) with high temperature (37 °C); 3) NH: normal nitrogen level and high temperature; and 4) HN: high nitrogen level and natural temperature, respectively. The de novo assembly generated 52,553,536 clean reads aligned with 72,667 unigenes. About 10 M reads were identified from each treatment. In these differentially expressed genes (DEGs), we found 151 and 323 temperature-responsive DEGs in NN-vs-NH and HN-vs-HH, and 114 DEGs were co-expressed. Meanwhile, 203 and 144 nitrogen-responsive DEGs were focused in NN-vs-HN and NH-vs-HH, and 111 DEGs were co-expressed. The temperature-responsive genes were principally associated with calcium-dependent protein, cytochrome, flavonoid, heat shock protein, peroxidase, ubiquitin, and transcription factor while the nitrogen-responsive genes were mainly involved in glutamine synthetase, transcription factor, anthocyanin, amino acid transporter, leucine zipper protein, and hormone. It is noted that, rice spikelet fertility was significantly decreased under high temperature, but it was more reduced under higher nitrogen. Accordingly, numerous spikelet genes involved in pollen development, pollen tube growth, pollen germination, especially sporopollenin biosynthetic process, and pollen exine formation were mainly down-regulated under high temperature. Moreover, the expression levels of co-expressed DEGs including 5 sporopollenin biosynthetic process and 7 pollen exine formation genes of NN-vs-NH were lower than that of HN-vs-HH. Therefore, these spikelet genes may play important roles in response to high temperature with high nitrogen and may be good candidates for crop improvement. Conclusions This RNA-seq study will help elucidate the molecular mechanisms of rice spikelet defense response to high temperature interacting with high nitrogen level. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2141-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jun Yang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 1101 Zhimin Street, Changbei economic and technological development zone, QingShanHu District, Nanchang, Jiangxi Province, 330045, China.
| | - Xiaorong Chen
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 1101 Zhimin Street, Changbei economic and technological development zone, QingShanHu District, Nanchang, Jiangxi Province, 330045, China.
| | - Changlan Zhu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 1101 Zhimin Street, Changbei economic and technological development zone, QingShanHu District, Nanchang, Jiangxi Province, 330045, China.
| | - Xiaosong Peng
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 1101 Zhimin Street, Changbei economic and technological development zone, QingShanHu District, Nanchang, Jiangxi Province, 330045, China.
| | - Xiaopeng He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 1101 Zhimin Street, Changbei economic and technological development zone, QingShanHu District, Nanchang, Jiangxi Province, 330045, China.
| | - Junru Fu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 1101 Zhimin Street, Changbei economic and technological development zone, QingShanHu District, Nanchang, Jiangxi Province, 330045, China.
| | - Linjuan Ouyang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 1101 Zhimin Street, Changbei economic and technological development zone, QingShanHu District, Nanchang, Jiangxi Province, 330045, China.
| | - Jianmin Bian
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 1101 Zhimin Street, Changbei economic and technological development zone, QingShanHu District, Nanchang, Jiangxi Province, 330045, China.
| | - Lifang Hu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 1101 Zhimin Street, Changbei economic and technological development zone, QingShanHu District, Nanchang, Jiangxi Province, 330045, China.
| | - Xiaotang Sun
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 1101 Zhimin Street, Changbei economic and technological development zone, QingShanHu District, Nanchang, Jiangxi Province, 330045, China.
| | - Jie Xu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 1101 Zhimin Street, Changbei economic and technological development zone, QingShanHu District, Nanchang, Jiangxi Province, 330045, China.
| | - Haohua He
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, 1101 Zhimin Street, Changbei economic and technological development zone, QingShanHu District, Nanchang, Jiangxi Province, 330045, China.
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Somarowthu S. Progress and Current Challenges in Modeling Large RNAs. J Mol Biol 2015; 428:736-747. [PMID: 26585404 DOI: 10.1016/j.jmb.2015.11.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 11/03/2015] [Accepted: 11/08/2015] [Indexed: 12/21/2022]
Abstract
Recent breakthroughs in next-generation sequencing technologies have led to the discovery of several classes of non-coding RNAs (ncRNAs). It is now apparent that RNA molecules are not only just carriers of genetic information but also key players in many cellular processes. While there has been a rapid increase in the number of ncRNA sequences deposited in various databases over the past decade, the biological functions of these ncRNAs are largely not well understood. Similar to proteins, RNA molecules carry out a function by forming specific three-dimensional structures. Understanding the function of a particular RNA therefore requires a detailed knowledge of its structure. However, determining experimental structures of RNA is extremely challenging. In fact, RNA-only structures represent just 1% of the total structures deposited in the PDB. Thus, computational methods that predict three-dimensional RNA structures are in high demand. Computational models can provide valuable insights into structure-function relationships in ncRNAs and can aid in the development of functional hypotheses and experimental designs. In recent years, a set of diverse RNA structure prediction tools have become available, which differ in computational time, input data and accuracy. This review discusses the recent progress and challenges in RNA structure prediction methods.
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Affiliation(s)
- Srinivas Somarowthu
- Department of Molecular, Cellular and Developmental Biology, Yale University, 219 Prospect Street, Kline Biology Tower, New Haven, CT 06511, USA.
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Identification and analysis of house-keeping and tissue-specific genes based on RNA-seq data sets across 15 mouse tissues. Gene 2015; 576:560-70. [PMID: 26551299 DOI: 10.1016/j.gene.2015.11.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 10/27/2015] [Accepted: 11/03/2015] [Indexed: 12/31/2022]
Abstract
Recently, RNA-seq has become widely used technology for transcriptome profiling due to its single-base accuracy and high-throughput speciality. In this study, we applied a computational approach on an integrated RNA-seq dataset across 15 normal mouse tissues, and consequently assigned 8408 house-keeping (HK) genes and 2581 tissue-specific (TS) genes among UCSC RefGene annotation. Apart from some basic genomic features, we also performed expression, function and pathway analysis with clustering, DAVID and Ingenuity Pathway Analysis, indicating the physiological connections (tissues) and diverse biological roles of HK genes (fundamental processes) and TS genes (tissue-corresponding processes). Moreover, we used RT-PCR method to test 18 candidate HK genes and finally identified a novel list of highly stable internal control genes: Ywhae, Ddb 1, Eif4h, etc. In summary, this study provides a new HK gene and TS gene resource for further genetic and evolution research and helps us better understand morphogenesis and biological diversity in mouse.
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Camargo RDA, Herai RH, Santos LN, Bento FMM, Lima JE, Marques-Souza H, Figueira A. De novo transcriptome assembly and analysis to identify potential gene targets for RNAi-mediated control of the tomato leafminer (Tuta absoluta). BMC Genomics 2015; 16:635. [PMID: 26306628 PMCID: PMC4550053 DOI: 10.1186/s12864-015-1841-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 08/14/2015] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Providing double-stranded RNA (dsRNA) to insects has been proven to silence target genes, and this approach has emerged as a potential method to control agricultural pests by engineering plants to express insect dsRNAs. A critical step of this technology is the screening of effective target genes essential for insect development and/or survival. The tomato leafminer (Tuta absoluta Meyrick) is a major Solanum lycopersicum (tomato) pest that causes significant yield losses and has recently invaded Europe, from where it is spreading at an alarming rate. To explore RNA interference (RNAi) against T. absoluta, sequence information on potential target genes is necessary, but only a few sequences are available in public databases. RESULTS We sequenced six libraries from RNA samples from eggs, adults, and larvae at four stages, obtaining an overall total of around 245 million reads. The assembled T. absoluta transcriptome contained 93,477 contigs with an average size of 1,574 bp, 59.8 % of which presented positive Blast hits, with 19,995 (21.4 %) annotated by gene ontology. From the transcriptome, most of the core genes of the RNAi mechanism of Lepidoptera were identified indicating the potential suitability of T. absoluta for gene silencing. No contigs displayed significant similarity with a RNA-dependent RNA Polymerase. Genes from the juvenile hormone and ecdysteroid biosynthetic pathways were identified, representing potential target genes for systemic silencing. Comparisons of transcript profiles among stages revealed 1,577 genes differentially expressed at earlier larval stages, from which potential gene targets were identified. Five of these genes were evaluated using in vitro transcribed dsRNA absorbed by tomato leaflets, which were fed to 1(st) instar T. absoluta larvae, resulting in significant reduction of larval body weight while exhibiting significant knockdown for three of the genes. CONCLUSIONS The transcriptome we generated represents a valuable genomic resource for screening potential gene targets that affect the development or survival of T. absoluta larvae. Five novel genes that showed greater expression at the 1(st) larval stage were demonstrated to be effective potential RNAi targets by reducing larval weight and can be considered good candidates for use in RNAi-mediated crop protection.
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Affiliation(s)
- Roberto de A Camargo
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Av. Centenário, 303, CP 96, Piracicaba, SP, 13400-970, Brazil. .,Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Universidade de São Paulo, Av. Pádua Dias, 11, CP 09, Piracicaba, SP, 13418-900, Brazil.
| | - Roberto H Herai
- Department of Pediatrics, Cellular and Molecular Medicine, School of Medicine, University of California San Diego, Torrey Pines Scenic Dr, La Jolla, CA, 92093-0695, USA. .,Graduate Program in Health Science, School of Medicine, Pontifícia Universidade Católica do Paraná, R. Imaculada Conceição, 1155, Prado Velho, Curitiba, PR, 80215-901, Brazil.
| | - Luana N Santos
- Instituto de Biologia, Departamento de Histologia e Embriologia, Universidade Estadual de Campinas, R. Charles Darwin, CP 6109, Campinas, SP, 13083-863, Brazil.
| | - Flavia M M Bento
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Av. Centenário, 303, CP 96, Piracicaba, SP, 13400-970, Brazil. .,Escola Superior de Agricultura "Luiz de Queiroz" (ESALQ), Universidade de São Paulo, Av. Pádua Dias, 11, CP 09, Piracicaba, SP, 13418-900, Brazil.
| | - Joni E Lima
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Av. Centenário, 303, CP 96, Piracicaba, SP, 13400-970, Brazil.
| | - Henrique Marques-Souza
- Instituto de Biologia, Departamento de Histologia e Embriologia, Universidade Estadual de Campinas, R. Charles Darwin, CP 6109, Campinas, SP, 13083-863, Brazil.
| | - Antonio Figueira
- Centro de Energia Nuclear na Agricultura, Universidade de São Paulo, Av. Centenário, 303, CP 96, Piracicaba, SP, 13400-970, Brazil.
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Wu L, Taohua Z, Gui W, Xu L, Li J, Ding Y. Five pectinase gene expressions highly responding to heat stress in rice floral organs revealed by RNA-seq analysis. Biochem Biophys Res Commun 2015; 463:407-13. [DOI: 10.1016/j.bbrc.2015.05.085] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 05/27/2015] [Indexed: 11/27/2022]
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Wang P, Liu X, Guo J, Liu C, Fu N, Shen H. Identification and Expression Analysis of Candidate Genes Associated with Defense Responses to Phytophthora capsici in Pepper Line "PI 201234". Int J Mol Sci 2015; 16:11417-38. [PMID: 25993303 PMCID: PMC4463708 DOI: 10.3390/ijms160511417] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Revised: 04/27/2015] [Accepted: 04/28/2015] [Indexed: 11/16/2022] Open
Abstract
Phytophthora capsici (Leonian), classified as an oomycete, seriously threatens the production of pepper (Capsicum annuum). Current understanding of the defense responses in pepper to P. capsici is limited. In this study, RNA-sequencing analysis was utilized to identify differentially expressed genes in the resistant line "PI 201234", with 1220 differentially expressed genes detected. Of those genes, 480 were up-regulated and 740 were down-regulated, with 211 candidate genes found to be involved in defense responses based on the gene annotations. Furthermore, the expression patterns of 12 candidate genes were further validated via quantitative real-time PCR (qPCR). These genes were found to be significantly up-regulated at different time points post-inoculation (6 hpi, 24 hpi, and 5 dpi) in the resistant line "PI 201234" and susceptible line "Qiemen". Seven genes were found to be involved in cell wall modification, phytoalexin biosynthesis, symptom development, and phytohormone signaling pathways, thus possibly playing important roles in combating exogenous pathogens. The genes identified herein will provide a basis for further gene cloning and functional verification studies and will aid in an understanding of the regulatory mechanism of pepper resistance to P. capsici.
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Affiliation(s)
- Pingyong Wang
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China.
| | - Xiaodan Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China.
| | - Jinju Guo
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China.
| | - Chen Liu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China.
| | - Nan Fu
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China.
| | - Huolin Shen
- Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China.
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77
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Zhao P, Zhang L, Zhao L. Dissection of the style's response to pollination using transcriptome profiling in self-compatible (Solanum pimpinellifolium) and self-incompatible (Solanum chilense) tomato species. BMC PLANT BIOLOGY 2015; 15:119. [PMID: 25976872 PMCID: PMC4431037 DOI: 10.1186/s12870-015-0492-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 04/10/2015] [Indexed: 05/05/2023]
Abstract
BACKGROUND Tomato (Solanum lycopersicum) self-compatibility (SC) is defined as self-pollen tubes that can penetrate their own stigma, elongate in the style and fertilize their own ovules. Self-incompatibility (SI) is defined as self-pollen tubes that are prevented from developing in the style. To determine the influence of gene expression on style self-pollination, a transcriptome-wide comparative analysis of SC and SI tomato unpollinated/pollinated styles was performed using RNA-sequencing (RNA-seq) data. RESULTS Transcriptome profiles of 24-h unpollination (UP) and self-pollination (P) styles from SC and SI tomato species were generated using high-throughput next generation sequencing. From the comparison of SC self-pollinated and unpollinated styles, 1341 differentially expressed genes (DEGs) were identified, of which 753 were downregulated and 588 were upregulated. From the comparison of SI self-pollinated and unpollinated styles, 804 DEGs were identified, of which 215 were downregulated and 589 were upregulated. Nine gene ontology (GO) terms were enriched significantly in SC and 78 GO terms were enriched significantly in SI. A total of 105 enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified in SC and 80 enriched KEGG pathways were identified in SI, among which "Cysteine and methionine metabolism pathway" and "Plant hormone signal transduction pathway" were significantly enriched in SI. CONCLUSIONS This study is the first global transcriptome-wide comparative analysis of SC and SI tomato unpollinated/pollinated styles. Advanced bioinformatic analysis of DEGs uncovered the pathways of "Cysteine and methionine metabolism" and "Plant hormone signal transduction", which are likely to play important roles in the control of pollen tubes growth in SI species.
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Affiliation(s)
- Panfeng Zhao
- Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Plant Biotechnology Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Lida Zhang
- Plant Biotechnology Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Lingxia Zhao
- Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Plant Biotechnology Research Center, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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78
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Kaitetzidou E, Xiang J, Antonopoulou E, Tsigenopoulos CS, Sarropoulou E. Dynamics of gene expression patterns during early development of the European seabass (Dicentrarchus labrax). Physiol Genomics 2015; 47:158-69. [DOI: 10.1152/physiolgenomics.00001.2015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Accepted: 02/23/2015] [Indexed: 01/06/2023] Open
Abstract
Larval and embryonic stages are the most critical period in the life cycle of marine fish. Key developmental events occur early in development and are influenced by external parameters like stress, temperature, salinity, and photoperiodism. Any failure may cause malformations, developmental delays, poor growth, and massive mortalities. Advanced understanding of molecular processes underlying marine larval development may lead to superior larval rearing conditions. Today, the new sequencing and bioinformatic methods allow transcriptome screens comprising messenger (mRNA) and microRNA (miRNA) with the scope of detecting differential expression for any species of interest. In the present study, we applied Illumina technology to investigate the transcriptome of early developmental stages of the European seabass ( Dicentrarchus labrax). The European seabass, in its natural environment, is a euryhaline species and has shown high adaptation processes in early life phases. During its embryonic and larval phases the European seabass lives in a marine environment and as a juvenile it migrates to coastal zones, estuaries, and lagoons. Investigating the dynamics of gene expression in its early development may shed light on factors promoting phenotypic plasticity and may also contribute to the improvement and advancement of rearing methods of the European seabass, a species of high economic importance in European and Mediterranean aquaculture. We present the identification, characterization, and expression of mRNA and miRNA, comprising paralogous genes and differentially spliced transcripts from early developmental stages of the European seabass. We further investigated the detection of possible interactions of miRNA with mRNA.
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Affiliation(s)
- E. Kaitetzidou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Greece
- School of Biology, Faculty of Science, Aristotle University of Thessaloniki, Greece; and
| | - J. Xiang
- Genomics Resources Core Facility, Weill Cornell Medical College, New York, New York
| | - E. Antonopoulou
- School of Biology, Faculty of Science, Aristotle University of Thessaloniki, Greece; and
| | - C. S. Tsigenopoulos
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Greece
| | - E. Sarropoulou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Greece
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Zheng C, Zhao L, Wang Y, Shen J, Zhang Y, Jia S, Li Y, Ding Z. Integrated RNA-Seq and sRNA-Seq Analysis Identifies Chilling and Freezing Responsive Key Molecular Players and Pathways in Tea Plant (Camellia sinensis). PLoS One 2015; 10:e0125031. [PMID: 25901577 PMCID: PMC4406609 DOI: 10.1371/journal.pone.0125031] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 03/19/2015] [Indexed: 12/17/2022] Open
Abstract
Tea [Camellia sinensis (L) O. Kuntze, Theaceae] is one of the most popular non-alcoholic beverages worldwide. Cold stress is one of the most severe abiotic stresses that limit tea plants’ growth, survival and geographical distribution. However, the genetic regulatory network and signaling pathways involved in cold stress responses in tea plants remain unearthed. Using RNA-Seq, DGE and sRNA-Seq technologies, we performed an integrative analysis of miRNA and mRNA expression profiling and their regulatory network of tea plants under chilling (4℃) and freezing (-5℃) stress. Differentially expressed (DE) miRNA and mRNA profiles were obtained based on fold change analysis, miRNAs and target mRNAs were found to show both coherent and incoherent relationships in the regulatory network. Furthermore, we compared several key pathways (e.g., ‘Photosynthesis’), GO terms (e.g., ‘response to karrikin’) and transcriptional factors (TFs, e.g., DREB1b/CBF1) which were identified as involved in the early chilling and/or freezing response of tea plants. Intriguingly, we found that karrikins, a new group of plant growth regulators, and β-primeverosidase (BPR), a key enzyme functionally relevant with the formation of tea aroma might play an important role in both early chilling and freezing response of tea plants. Quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) analysis further confirmed the results from RNA-Seq and sRNA-Seq analysis. This is the first study to simultaneously profile the expression patterns of both miRNAs and mRNAs on a genome-wide scale to elucidate the molecular mechanisms of early responses of tea plants to cold stress. In addition to gaining a deeper insight into the cold resistant characteristics of tea plants, we provide a good case study to analyse mRNA/miRNA expression and profiling of non-model plant species using next-generation sequencing technology.
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Affiliation(s)
- Chao Zheng
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China
- Key Laboratory of Genetic Improvement and Breeding for Horticultural Plants, Qingdao, Shandong, China
| | - Lei Zhao
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China
- Key Laboratory of Genetic Improvement and Breeding for Horticultural Plants, Qingdao, Shandong, China
| | - Yu Wang
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China
- Key Laboratory of Genetic Improvement and Breeding for Horticultural Plants, Qingdao, Shandong, China
| | - Jiazhi Shen
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China
- Key Laboratory of Genetic Improvement and Breeding for Horticultural Plants, Qingdao, Shandong, China
| | - Yinfei Zhang
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China
- Key Laboratory of Genetic Improvement and Breeding for Horticultural Plants, Qingdao, Shandong, China
| | - Sisi Jia
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China
- Key Laboratory of Genetic Improvement and Breeding for Horticultural Plants, Qingdao, Shandong, China
| | - Yusheng Li
- Fruit and Tea Technology Extension Station, Jinan, Shandong, China
| | - Zhaotang Ding
- Tea Research Institute, Qingdao Agricultural University, Qingdao, Shandong, China
- Key Laboratory of Genetic Improvement and Breeding for Horticultural Plants, Qingdao, Shandong, China
- * E-mail:
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80
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RNA-Seq analysis and gene discovery of Andrias davidianus using Illumina short read sequencing. PLoS One 2015; 10:e0123730. [PMID: 25874626 PMCID: PMC4395309 DOI: 10.1371/journal.pone.0123730] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 03/05/2015] [Indexed: 11/19/2022] Open
Abstract
The Chinese giant salamander, Andrias davidianus, is an important species in the course of evolution; however, there is insufficient genomic data in public databases for understanding its immunologic mechanisms. High-throughput transcriptome sequencing is necessary to generate an enormous number of transcript sequences from A. davidianus for gene discovery. In this study, we generated more than 40 million reads from samples of spleen and skin tissue using the Illumina paired-end sequencing technology. De novo assembly yielded 87,297 transcripts with a mean length of 734 base pairs (bp). Based on the sequence similarities, searching with known proteins, 38,916 genes were identified. Gene enrichment analysis determined that 981 transcripts were assigned to the immune system. Tissue-specific expression analysis indicated that 443 of transcripts were specifically expressed in the spleen and skin. Among these transcripts, 147 transcripts were found to be involved in immune responses and inflammatory reactions, such as fucolectin, β-defensins and lymphotoxin beta. Eight tissue-specific genes were selected for validation using real time reverse transcription quantitative PCR (qRT-PCR). The results showed that these genes were significantly more expressed in spleen and skin than in other tissues, suggesting that these genes have vital roles in the immune response. This work provides a comprehensive genomic sequence resource for A. davidianus and lays the foundation for future research on the immunologic and disease resistance mechanisms of A. davidianus and other amphibians.
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81
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Wan Q, Dingerdissen H, Fan Y, Gulzar N, Pan Y, Wu TJ, Yan C, Zhang H, Mazumder R. BioXpress: an integrated RNA-seq-derived gene expression database for pan-cancer analysis. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav019. [PMID: 25819073 PMCID: PMC4377087 DOI: 10.1093/database/bav019] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
BioXpress is a gene expression and cancer association database in which the expression levels are mapped to genes using RNA-seq data obtained from The Cancer Genome Atlas, International Cancer Genome Consortium, Expression Atlas and publications. The BioXpress database includes expression data from 64 cancer types, 6361 patients and 17 469 genes with 9513 of the genes displaying differential expression between tumor and normal samples. In addition to data directly retrieved from RNA-seq data repositories, manual biocuration of publications supplements the available cancer association annotations in the database. All cancer types are mapped to Disease Ontology terms to facilitate a uniform pan-cancer analysis. The BioXpress database is easily searched using HUGO Gene Nomenclature Committee gene symbol, UniProtKB/RefSeq accession or, alternatively, can be queried by cancer type with specified significance filters. This interface along with availability of pre-computed downloadable files containing differentially expressed genes in multiple cancers enables straightforward retrieval and display of a broad set of cancer-related genes. Database URL:http://hive.biochemistry.gwu.edu/tools/bioxpress
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Affiliation(s)
- Quan Wan
- Department of Biochemistry and Molecular Medicine and McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC 20037, USA
| | - Hayley Dingerdissen
- Department of Biochemistry and Molecular Medicine and McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC 20037, USA
| | - Yu Fan
- Department of Biochemistry and Molecular Medicine and McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC 20037, USA
| | - Naila Gulzar
- Department of Biochemistry and Molecular Medicine and McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC 20037, USA
| | - Yang Pan
- Department of Biochemistry and Molecular Medicine and McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC 20037, USA
| | - Tsung-Jung Wu
- Department of Biochemistry and Molecular Medicine and McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC 20037, USA
| | - Cheng Yan
- Department of Biochemistry and Molecular Medicine and McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC 20037, USA
| | - Haichen Zhang
- Department of Biochemistry and Molecular Medicine and McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC 20037, USA
| | - Raja Mazumder
- Department of Biochemistry and Molecular Medicine and McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC 20037, USA Department of Biochemistry and Molecular Medicine and McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC 20037, USA
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82
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Goodswen SJ, Barratt JLN, Kennedy PJ, Ellis JT. Improving the gene structure annotation of the apicomplexan parasite Neospora caninum fulfils a vital requirement towards an in silico-derived vaccine. Int J Parasitol 2015; 45:305-18. [PMID: 25747726 DOI: 10.1016/j.ijpara.2015.01.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 01/12/2015] [Accepted: 01/12/2015] [Indexed: 12/16/2022]
Abstract
Neospora caninum is an apicomplexan parasite which can cause abortion in cattle, instigating major economic burden. Vaccination has been proposed as the most cost-effective control measure to alleviate this burden. Consequently the overriding aspiration for N. caninum research is the identification and subsequent evaluation of vaccine candidates in animal models. To save time, cost and effort, it is now feasible to use an in silico approach for vaccine candidate prediction. Precise protein sequences, derived from the correct open reading frame, are paramount and arguably the most important factor determining the success or failure of this approach. The challenge is that publicly available N. caninum sequences are mostly derived from gene predictions. Annotated inaccuracies can lead to erroneously predicted vaccine candidates by bioinformatics programs. This study evaluates the current N. caninum annotation for potential inaccuracies. Comparisons with annotation from a closely related pathogen, Toxoplasma gondii, are also made to distinguish patterns of inconsistency. More importantly, a mRNA sequencing (RNA-Seq) experiment is used to validate the annotation. Potential discrepancies originating from a questionable start codon context and exon boundaries were identified in 1943 protein coding sequences. We conclude, where experimental data were available, that the majority of N. caninum gene sequences were reliably predicted. Nevertheless, almost 28% of genes were identified as questionable. Given the limitations of RNA-Seq, the intention of this study was not to replace the existing annotation but to support or oppose particular aspects of it. Ideally, many studies aimed at improving the annotation are required to build a consensus. We believe this study, in providing a new resource on gene structure and annotation, is a worthy contributor to this endeavour.
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Affiliation(s)
- Stephen J Goodswen
- School of Medical and Molecular Sciences, University of Technology Sydney (UTS), 15 Broadway, Ultimo, NSW 2007, Australia.
| | - Joel L N Barratt
- School of Medical and Molecular Sciences, University of Technology Sydney (UTS), 15 Broadway, Ultimo, NSW 2007, Australia
| | - Paul J Kennedy
- School of Software, Faculty of Engineering and Information Technology and the Centre for Quantum Computation and Intelligent Systems at the University of Technology Sydney (UTS), 15 Broadway, Ultimo, NSW 2007, Australia
| | - John T Ellis
- School of Medical and Molecular Sciences, University of Technology Sydney (UTS), 15 Broadway, Ultimo, NSW 2007, Australia
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Cao H, Nuruzzaman M, Xiu H, Huang J, Wu K, Chen X, Li J, Wang L, Jeong JH, Park SJ, Yang F, Luo J, Luo Z. Transcriptome analysis of methyl jasmonate-elicited Panax ginseng adventitious roots to discover putative ginsenoside biosynthesis and transport genes. Int J Mol Sci 2015; 16:3035-57. [PMID: 25642758 PMCID: PMC4346879 DOI: 10.3390/ijms16023035] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 01/22/2015] [Indexed: 12/05/2022] Open
Abstract
The Panax ginseng C.A. Meyer belonging to the Araliaceae has long been used as an herbal medicine. Although public databases are presently available for this family, no methyl jasmonate (MeJA) elicited transcriptomic information was previously reported on this species, with the exception of a few expressed sequence tags (ESTs) using the traditional Sanger method. Here, approximately 53 million clean reads of adventitious root transcriptome were separately filtered via Illumina HiSeq™2000 from two samples treated with MeJA (Pg-MeJA) and equal volumes of solvent, ethanol (Pg-Con). Jointly, a total of 71,095 all-unigenes from both samples were assembled and annotated, and based on sequence similarity search with known proteins, a total of 56,668 unigenes was obtained. Out of these annotated unigenes, 54,920 were assigned to the NCBI non-redundant protein (Nr) database, 35,448 to the Swiss-prot database, 43,051 to gene ontology (GO), and 19,986 to clusters of orthologous groups (COG). Searching in the Kyoto encyclopedia of genes and genomes (KEGG) pathway database indicated that 32,200 unigenes were mapped to 128 KEGG pathways. Moreover, we obtained several genes showing a wide range of expression levels. We also identified a total of 749 ginsenoside biosynthetic enzyme genes and 12 promising pleiotropic drug resistance (PDR) genes related to ginsenoside transport.
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Affiliation(s)
- Hongzhe Cao
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Mohammed Nuruzzaman
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Hao Xiu
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Jingjia Huang
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Kunlu Wu
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Xianghui Chen
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Jijia Li
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Li Wang
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Ji-Hak Jeong
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Sun-Jin Park
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Fang Yang
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Junli Luo
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
| | - Zhiyong Luo
- Molecular Biology Research Center, State Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha 410078, China.
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84
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Wan XL, Zhou Q, Wang YY, Wang WE, Bao MZ, Zhang JW. Identification of heat-responsive genes in carnation (Dianthus caryophyllus L.) by RNA-seq. FRONTIERS IN PLANT SCIENCE 2015; 6:519. [PMID: 26236320 PMCID: PMC4500917 DOI: 10.3389/fpls.2015.00519] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 06/26/2015] [Indexed: 05/04/2023]
Abstract
Carnation (Dianthus caryophyllus L.) is an important flower crop, having substantial commercial value as a cut-flower due to the long vase-life and wide array of flower colors and forms. Standard carnation varieties perform well under cool climates but are very susceptible to high temperatures which adversely affect the yield and the quality of the cut-flowers. Despite several studies of carnation contributing to the number of expressed sequence tags (ESTs), transcriptomic information of this species remains very limited, particularly regarding abiotic stress-related genes. Here, transcriptome analysis was performed to generate expression profiles of heat stress (HS)-responsive genes in carnation. We sequenced a cDNA library constructed with mixed RNA from carnation leaves subjected to 42°C HS (0, 0.5, 1, and 2 h) and 46°C HS (0.5, 1, and 2 h), and obtained 45,604,882 high quality paired-end reads. After de novo assembly and quantitative assessment 99,255 contigs were generated with an average length of 1053 bp. We then obtained functional annotations by aligning contigs with public protein databases including NR, SwissProt, KEGG, and COG. Using the above carnation transcriptome as the reference, we compared the effects of high temperature treatments (42°C: duration 0.5, 2, or 12 h) delivered to aseptic carnation seedlings, relative to untreated controls, using the FPKM metric. Overall, 11,471 genes were identified which showed a significant response to one or more of the three HS treatment times. In addition, based on GO and metabolic pathway enrichment analyses, a series of candidate genes involved in thermo-tolerance responses were selected and characterized. This study represents the first expression profiling analysis of D. caryophyllus under heat stress treatments. Numerous genes were found to be induced in response to HS, the study of which may advance our understanding of heat response of carnation.
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Affiliation(s)
| | | | | | | | | | - Jun Wei Zhang
- *Correspondence: Jun Wei Zhang, Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, No.1, Shizishan Street, Hongshan District, Wuhan 430070, Hubei, China
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Wei F, Luo S, Zheng Q, Qiu J, Yang W, Wu M, Xiao X. Transcriptome sequencing and comparative analysis reveal long-term flowing mechanisms in Hevea brasiliensis latex. Gene 2014; 556:153-62. [PMID: 25431836 DOI: 10.1016/j.gene.2014.11.048] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 11/18/2014] [Accepted: 11/21/2014] [Indexed: 12/27/2022]
Abstract
BACKGROUND The rubber tree, Hevea brasiliensis, is a major commercial source of natural rubber. Increasing the rubber yield of rubber trees is a very serious problem since the demands for high quality rubber materials are great. Establishment of a tapping system is based on an estimate of tapping intensity from the rubber tree. Latex flowing time is one of the most critical factors that determine the rubber yield. Long-term flow is a type of phenomenon of the rubber tree latex with longer flowing time than normal latex flow, and is always caused by intensive tapping. Thus, transcriptome and expression profiling data for long-term flowing latex (LFL) are needed as an important resource to identify genes and to better understand the biological mechanisms of latex flow in rubber trees. RESULTS The transcripts were sequenced using the Illumina sequencing platform. After cleaning, quality checks and sequencing, 98,697 transcripts and 38,584 unigenes were assembled with the mean size of 1437.31bp and 923.86bp, respectively. In BLAST searches of our database against public databases, 65.17% (25,147) of the unigenes were annotated with gene descriptions, conserved protein domains, or gene ontology terms. Functional categorization further revealed 853 individual unigenes related to long-term flow. According to KEGG classification, the clusters for "cysteine and methionine metabolism", "energy", "oxidative phosphorylation", "terpenoid backbone biosynthesis", "plant hormone signal transduction" and "copper, potassium transporter" were significantly enriched metabolic pathways. CONCLUSIONS We conducted high-resolution transcriptome profiling related to LFL in H. brasiliensis. The research facilitates further studies on gene discovery and on the molecular mechanisms related to the estimation of tapping intensity and prolonging latex flowing time. We concluded that it was necessary to improve energy supplies for intensive tapping and the copper ion content of rubber tree latex could be considered as a standard to estimate tapping intensity.
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Affiliation(s)
- Fang Wei
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan 571737, China.
| | - Shiqiao Luo
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan 571737, China.
| | - Qiankun Zheng
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan 571737, China.
| | - Jian Qiu
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan 571737, China.
| | - Wenfeng Yang
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan 571737, China.
| | - Ming Wu
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan 571737, China.
| | - Xianzhou Xiao
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, Hainan 571737, China.
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Gong W, He S, Tian J, Sun J, Pan Z, Jia Y, Sun G, Du X. Comparison of the transcriptome between two cotton lines of different fiber color and quality. PLoS One 2014; 9:e112966. [PMID: 25401744 PMCID: PMC4234635 DOI: 10.1371/journal.pone.0112966] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 10/16/2014] [Indexed: 01/27/2023] Open
Abstract
To understand the mechanism of fiber development and pigmentation formation, the mRNAs of two cotton lines were sequenced: line Z128 (light brown fiber) was a selected mutant from line Z263 (dark brown fiber). The primary walls of the fiber cell in both Z263 and Z128 contain pigments; more pigments were laid in the lumen of the fiber cell in Z263 compared with that in Z128. However, Z263 contained less cellulose than Z128. A total of 71,895 unigenes were generated: 13,278 (20.26%) unigenes were defined as differentially expressed genes (DEGs) by comparing the library of Z128 with that of Z263; 5,345 (8.16%) unigenes were up-regulated and 7,933 (12.10%) unigenes were down-regulated. qRT-PCR and comparative transcriptional analysis demonstrated that the pigmentation formation in brown cotton fiber was possibly the consequence of an interaction between oxidized tannins and glycosylated anthocyanins. Furthermore, our results showed the pigmentation related genes not only regulated the fiber color but also influenced the fiber quality at the fiber elongation stage (10 DPA). The highly expressed flavonoid gene in the fiber elongation stage could be related to the fiber quality. DEGs analyses also revealed that transcript levels of some fiber development genes (Ca2+/CaM, reactive oxygen, ethylene and sucrose phosphate synthase) varied dramatically between these two cotton lines.
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Affiliation(s)
- Wenfang Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shoupu He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jiahuan Tian
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Junling Sun
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zhaoe Pan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yinhua Jia
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Gaofei Sun
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Department of Computer Science and Information Engineering, Anyang Institute of Technology, Anyang, China
| | - Xiongming Du
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- * E-mail:
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Jazayeri SM, Melgarejo-Muñoz LM, Romero HM. RNA-SEQ: A GLANCE AT TECHNOLOGIES AND METHODOLOGIES. ACTA BIOLÓGICA COLOMBIANA 2014. [DOI: 10.15446/abc.v20n2.43639] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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88
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Belizário JE. The humankind genome: from genetic diversity to the origin of human diseases. Genome 2014; 56:705-16. [PMID: 24433206 DOI: 10.1139/gen-2013-0125] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Genome-wide association studies have failed to establish common variant risk for the majority of common human diseases. The underlying reasons for this failure are explained by recent studies of resequencing and comparison of over 1200 human genomes and 10 000 exomes, together with the delineation of DNA methylation patterns (epigenome) and full characterization of coding and noncoding RNAs (transcriptome) being transcribed. These studies have provided the most comprehensive catalogues of functional elements and genetic variants that are now available for global integrative analysis and experimental validation in prospective cohort studies. With these datasets, researchers will have unparalleled opportunities for the alignment, mining, and testing of hypotheses for the roles of specific genetic variants, including copy number variations, single nucleotide polymorphisms, and indels as the cause of specific phenotypes and diseases. Through the use of next-generation sequencing technologies for genotyping and standardized ontological annotation to systematically analyze the effects of genomic variation on humans and model organism phenotypes, we will be able to find candidate genes and new clues for disease's etiology and treatment. This article describes essential concepts in genetics and genomic technologies as well as the emerging computational framework to comprehensively search websites and platforms available for the analysis and interpretation of genomic data.
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Affiliation(s)
- Jose E Belizário
- Departamento de Farmacologia, Instituto de Ciências Biomédicas da Universidade de São Paulo, Avenida Lineu Prestes, 1524 CEP 05508-900, São Paulo, SP, Brazil
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Li S, Tighe SW, Nicolet CM, Grove D, Levy S, Farmerie W, Viale A, Wright C, Schweitzer PA, Gao Y, Kim D, Boland J, Hicks B, Kim R, Chhangawala S, Jafari N, Raghavachari N, Gandara J, Garcia-Reyero N, Hendrickson C, Roberson D, Rosenfeld J, Smith T, Underwood JG, Wang M, Zumbo P, Baldwin DA, Grills GS, Mason CE. Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study. Nat Biotechnol 2014; 32:915-925. [PMID: 25150835 PMCID: PMC4167418 DOI: 10.1038/nbt.2972] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 07/01/2014] [Indexed: 01/17/2023]
Abstract
High-throughput RNA sequencing (RNA-seq) greatly expands the potential for genomics discoveries, but the wide variety of platforms, protocols and performance capabilitites has created the need for comprehensive reference data. Here we describe the Association of Biomolecular Resource Facilities next-generation sequencing (ABRF-NGS) study on RNA-seq. We carried out replicate experiments across 15 laboratory sites using reference RNA standards to test four protocols (poly-A-selected, ribo-depleted, size-selected and degraded) on five sequencing platforms (Illumina HiSeq, Life Technologies PGM and Proton, Pacific Biosciences RS and Roche 454). The results show high intraplatform (Spearman rank R > 0.86) and inter-platform (R > 0.83) concordance for expression measures across the deep-count platforms, but highly variable efficiency and cost for splice junction and variant detection between all platforms. For intact RNA, gene expression profiles from rRNA-depletion and poly-A enrichment are similar. In addition, rRNA depletion enables effective analysis of degraded RNA samples. This study provides a broad foundation for cross-platform standardization, evaluation and improvement of RNA-seq.
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Affiliation(s)
- Sheng Li
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, USA
| | - Scott W. Tighe
- Vermont Cancer Center, University of Vermont, Burlington, Vermont, USA
| | - Charles M. Nicolet
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Deborah Grove
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
| | - William Farmerie
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA
| | - Agnes Viale
- Memorial Sloan-Kettering Cancer Institute, New York, New York, USA
| | - Chris Wright
- Roy J. Carver Biotechnology Center, University of Illinois, Urbana, Illinois, USA
| | - Peter A. Schweitzer
- Biotechnology Resource Center, Institute of Biotechnology, Cornell University, Ithaca, New York, USA
| | - Yuan Gao
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Dewey Kim
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Joe Boland
- NIH/NCI/SAIC-Frederick, Gaithersburg, Maryland, USA
| | | | - Ryan Kim
- Genome Center, University of California, Davis, Davis, California, USA
| | - Sagar Chhangawala
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, USA
| | - Nadereh Jafari
- Center for Genetic Medicine, Northwestern University, Chicago, Illinois, USA
| | | | - Jorge Gandara
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, USA
| | - Natàlia Garcia-Reyero
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Starkville, Mississippi, USA
| | | | | | - Jeffrey Rosenfeld
- Division of High Performance and Research Computing, University of Medicine and Dentistry of New Jersey, Newark, New Jersey, USA
| | - Todd Smith
- PerkinElmer Inc., Seattle, Washington, USA
| | - Jason G. Underwood
- University of Washington, Department of Genome Sciences. Seattle, Washington, USA
| | - May Wang
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, USA
| | - Paul Zumbo
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, USA
| | | | - George S. Grills
- Biotechnology Resource Center, Institute of Biotechnology, Cornell University, Ithaca, New York, USA
| | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medical College, New York, New York, USA
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Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing. G3-GENES GENOMES GENETICS 2014; 4:2065-78. [PMID: 25122667 PMCID: PMC4232532 DOI: 10.1534/g3.114.012526] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The mapping and functional analysis of quantitative traits in Brassica rapa can be greatly improved with the availability of physically positioned, gene-based genetic markers and accurate genome annotation. In this study, deep transcriptome RNA sequencing (RNA-Seq) of Brassica rapa was undertaken with two objectives: SNP detection and improved transcriptome annotation. We performed SNP detection on two varieties that are parents of a mapping population to aid in development of a marker system for this population and subsequent development of high-resolution genetic map. An improved Brassica rapa transcriptome was constructed to detect novel transcripts and to improve the current genome annotation. This is useful for accurate mRNA abundance and detection of expression QTL (eQTLs) in mapping populations. Deep RNA-Seq of two Brassica rapa genotypes—R500 (var. trilocularis, Yellow Sarson) and IMB211 (a rapid cycling variety)—using eight different tissues (root, internode, leaf, petiole, apical meristem, floral meristem, silique, and seedling) grown across three different environments (growth chamber, greenhouse and field) and under two different treatments (simulated sun and simulated shade) generated 2.3 billion high-quality Illumina reads. A total of 330,995 SNPs were identified in transcribed regions between the two genotypes with an average frequency of one SNP in every 200 bases. The deep RNA-Seq reassembled Brassica rapa transcriptome identified 44,239 protein-coding genes. Compared with current gene models of B. rapa, we detected 3537 novel transcripts, 23,754 gene models had structural modifications, and 3655 annotated proteins changed. Gaps in the current genome assembly of B. rapa are highlighted by our identification of 780 unmapped transcripts. All the SNPs, annotations, and predicted transcripts can be viewed at http://phytonetworks.ucdavis.edu/.
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91
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Chen J, Hou K, Qin P, Liu H, Yi B, Yang W, Wu W. RNA-Seq for gene identification and transcript profiling of three Stevia rebaudiana genotypes. BMC Genomics 2014; 15:571. [PMID: 25001368 PMCID: PMC4108789 DOI: 10.1186/1471-2164-15-571] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 06/18/2014] [Indexed: 01/15/2023] Open
Abstract
Background Stevia (Stevia rebaudiana) is an important medicinal plant that yields diterpenoid steviol glycosides (SGs). SGs are currently used in the preparation of medicines, food products and neutraceuticals because of its sweetening property (zero calories and about 300 times sweeter than sugar). Recently, some progress has been made in understanding the biosynthesis of SGs in Stevia, but little is known about the molecular mechanisms underlying this process. Additionally, the genomics of Stevia, a non-model species, remains uncharacterized. The recent advent of RNA-Seq, a next generation sequencing technology, provides an opportunity to expand the identification of Stevia genes through in-depth transcript profiling. Results We present a comprehensive landscape of the transcriptome profiles of three genotypes of Stevia with divergent SG compositions characterized using RNA-seq. 191,590,282 high-quality reads were generated and then assembled into 171,837 transcripts with an average sequence length of 969 base pairs. A total of 80,160 unigenes were annotated, and 14,211 of the unique sequences were assigned to specific metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes. Gene sequences of all enzymes known to be involved in SG synthesis were examined. A total of 143 UDP-glucosyltransferase (UGT) unigenes were identified, some of which might be involved in SG biosynthesis. The expression patterns of eight of these genes were further confirmed by RT-QPCR. Conclusion RNA-seq analysis identified candidate genes encoding enzymes responsible for the biosynthesis of SGs in Stevia, a non-model plant without a reference genome. The transcriptome data from this study yielded new insights into the process of SG accumulation in Stevia. Our results demonstrate that RNA-Seq can be successfully used for gene identification and transcript profiling in a non-model species. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-571) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | - Wei Wu
- Agronomy College of Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China.
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92
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Maji RK, Sarkar A, Khatua S, Dasgupta S, Ghosh Z. PVT: an efficient computational procedure to speed up next-generation sequence analysis. BMC Bioinformatics 2014; 15:167. [PMID: 24894600 PMCID: PMC4063226 DOI: 10.1186/1471-2105-15-167] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 05/07/2014] [Indexed: 12/05/2022] Open
Abstract
Background High-throughput Next-Generation Sequencing (NGS) techniques are advancing genomics and molecular biology research. This technology generates substantially large data which puts up a major challenge to the scientists for an efficient, cost and time effective solution to analyse such data. Further, for the different types of NGS data, there are certain common challenging steps involved in analysing those data. Spliced alignment is one such fundamental step in NGS data analysis which is extremely computational intensive as well as time consuming. There exists serious problem even with the most widely used spliced alignment tools. TopHat is one such widely used spliced alignment tools which although supports multithreading, does not efficiently utilize computational resources in terms of CPU utilization and memory. Here we have introduced PVT (Pipelined Version of TopHat) where we take up a modular approach by breaking TopHat’s serial execution into a pipeline of multiple stages, thereby increasing the degree of parallelization and computational resource utilization. Thus we address the discrepancies in TopHat so as to analyze large NGS data efficiently. Results We analysed the SRA dataset (SRX026839 and SRX026838) consisting of single end reads and SRA data SRR1027730 consisting of paired-end reads. We used TopHat v2.0.8 to analyse these datasets and noted the CPU usage, memory footprint and execution time during spliced alignment. With this basic information, we designed PVT, a pipelined version of TopHat that removes the redundant computational steps during ‘spliced alignment’ and breaks the job into a pipeline of multiple stages (each comprising of different step(s)) to improve its resource utilization, thus reducing the execution time. Conclusions PVT provides an improvement over TopHat for spliced alignment of NGS data analysis. PVT thus resulted in the reduction of the execution time to ~23% for the single end read dataset. Further, PVT designed for paired end reads showed an improved performance of ~41% over TopHat (for the chosen data) with respect to execution time. Moreover we propose PVT-Cloud which implements PVT pipeline in cloud computing system.
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Affiliation(s)
| | | | | | | | - Zhumur Ghosh
- Bioinformatics Centre, Bose Institute, Kolkata 700054, India.
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93
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Kumar S, Shah N, Garg V, Bhatia S. Large scale in-silico identification and characterization of simple sequence repeats (SSRs) from de novo assembled transcriptome of Catharanthus roseus (L.) G. Don. PLANT CELL REPORTS 2014; 33:905-918. [PMID: 24482265 DOI: 10.1007/s00299-014-1569-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 12/17/2013] [Accepted: 01/09/2014] [Indexed: 06/03/2023]
Abstract
Transcriptomic data of C. roseus offering ample sequence resources for providing better insights into gene diversity: large resource of genic SSR markers to accelerate genomic studies and breeding in Catharanthus . Next-generation sequencing is an efficient system for generating high-throughput complete transcripts/genes and developing molecular markers. We present here the transcriptome sequencing of a 26-day-old Catharanthus roseus seedling tissue using Illumina GAIIX platform that resulted in a total of 3.37 Gb of nucleotide sequence data comprising 29,964,104 reads which were de novo assembled into 26,581 unigenes. Based on similarity searches 58 % of the unigenes were annotated of which 13,580 unique transcripts were assigned 5016 gene ontology terms. Further, 7,687 of the unigenes were found to have Cluster of Orthologous Group classifications, and 4,006 were assigned to 289 Kyoto Encyclopedia of Genes and Genome pathways. Also, 5,221 (19.64 %) of transcripts were distributed to 81 known transcription factor (TF) families. In-silico analysis of the transcriptome resulted in identification of 11,004 SSRs in 26.62 % transcripts from which 2,520 SSR markers were designed which exhibited a non-random pattern of distribution. The most abundant was the trinucleotide repeats (AAG/CTT) followed by the dinucleotide repeats (AG/CT). Location specific analysis of SSRs revealed that SSRs were preferentially associated with the 5'-UTRs with a predicted role in regulation of gene expression. A PCR validation of a set of 48 primers revealed 97.9 % successful amplification, and 76.6 % of them showed polymorphism across different Catharanthus species as well as accessions of C. roseus. In summary, this study will provide an insight into understanding the seedling development and resources for novel gene discovery and SSR development for utilization in marker-assisted selective breeding in C. roseus.
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Affiliation(s)
- Santosh Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box 10531, New Delhi, 110067, India
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Azim MK, Khan IA, Zhang Y. Characterization of mango (Mangifera indica L.) transcriptome and chloroplast genome. PLANT MOLECULAR BIOLOGY 2014; 85:193-208. [PMID: 24515595 DOI: 10.1007/s11103-014-0179-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Accepted: 02/04/2014] [Indexed: 05/07/2023]
Abstract
We characterized mango leaf transcriptome and chloroplast genome using next generation DNA sequencing. The RNA-seq output of mango transcriptome generated >12 million reads (total nucleotides sequenced >1 Gb). De novo transcriptome assembly generated 30,509 unigenes with lengths in the range of 300 to ≥3,000 nt and 67× depth of coverage. Blast searching against nonredundant nucleotide databases and several Viridiplantae genomic datasets annotated 24,593 mango unigenes (80% of total) and identified Citrus sinensis as closest neighbor of mango with 9,141 (37%) matched sequences. The annotation with gene ontology and Clusters of Orthologous Group terms categorized unigene sequences into 57 and 25 classes, respectively. More than 13,500 unigenes were assigned to 293 KEGG pathways. Besides major plant biology related pathways, KEGG based gene annotation pointed out active presence of an array of biochemical pathways involved in (a) biosynthesis of bioactive flavonoids, flavones and flavonols, (b) biosynthesis of terpenoids and lignins and (c) plant hormone signal transduction. The mango transcriptome sequences revealed 235 proteases belonging to five catalytic classes of proteolytic enzymes. The draft genome of mango chloroplast (cp) was obtained by a combination of Sanger and next generation sequencing. The draft mango cp genome size is 151,173 bp with a pair of inverted repeats of 27,093 bp separated by small and large single copy regions, respectively. Out of 139 genes in mango cp genome, 91 found to be protein coding. Sequence analysis revealed cp genome of C. sinensis as closest neighbor of mango. We found 51 short repeats in mango cp genome supposed to be associated with extensive rearrangements. This is the first report of transcriptome and chloroplast genome analysis of any Anacardiaceae family member.
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Affiliation(s)
- M Kamran Azim
- Jamil-ur-Rehman Center for Genome Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan,
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95
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Podnar J, Deiderick H, Huerta G, Hunicke-Smith S. Next-Generation Sequencing RNA-Seq Library Construction. CURRENT PROTOCOLS IN MOLECULAR BIOLOGY 2014; 106:4.21.1-4.21.19. [PMID: 24733242 DOI: 10.1002/0471142727.mb0421s106] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
This unit presents protocols for construction of next-generation sequencing (NGS) directional RNA sequencing libraries for the Illumina HiSeq and MiSeq from a wide variety of input RNA sources. The protocols are based on the New England Biolabs (NEB) small RNA library preparation set for Illumina, although similar kits exist from different vendors. The protocol preserves the orientation of the original RNA in the final sequencing library, enabling strand-specific analysis of the resulting data. These libraries have been used for differential gene expression analysis and small RNA discovery and are currently being tested for de novo transcriptome assembly. The protocol is robust and applicable to a broad range of RNA input types and RNA quality, making it ideal for high-throughput laboratories.
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Affiliation(s)
- Jessica Podnar
- Genomic Sequencing and Analysis Facility, University of Texas at Austin, Austin, Texas
| | - Heather Deiderick
- Genomic Sequencing and Analysis Facility, University of Texas at Austin, Austin, Texas
| | - Gabriella Huerta
- Genomic Sequencing and Analysis Facility, University of Texas at Austin, Austin, Texas
| | - Scott Hunicke-Smith
- Genomic Sequencing and Analysis Facility, University of Texas at Austin, Austin, Texas
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Li B, Bi CL, Lang N, Li YZ, Xu C, Zhang YQ, Zhai AX, Cheng ZF. RNA-seq methods for identifying differentially expressed gene in human pancreatic islet cells treated with pro-inflammatory cytokines. Mol Biol Rep 2014; 41:1917-25. [PMID: 24619356 DOI: 10.1007/s11033-013-3016-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 12/30/2013] [Indexed: 01/22/2023]
Abstract
Type 1 diabetes is a chronic autoimmune disease in which pancreatic beta cells are killed by the infiltrating immune cells as well as the cytokines released by these cells. Many studies indicate that inflammatory mediators have an essential role in this disease. In the present study, we profiled the transcriptome in human islets of langerhans under control conditions or following exposure to the pro-inflammatory cytokines based on the RNA sequencing dataset downloaded from SRA database. After filtered the low-quality ones, the RNA readers was aligned to human genome hg19 by TopHat and then assembled by Cufflinks. The expression value of each transcript was calculated and consequently differentially expressed genes were screened out. Finally, a total of 63 differentially expressed genes were identified including 60 up-regulated and three down-regulated genes. GBP5 and CXCL9 stood out as the top two most up-regulated genes in cytokines treated samples with the log2 fold change of 12.208 and 10.901, respectively. Meanwhile, PTF1A and REG3G were identified as the top two most down-regulated genes with the log2 fold change of -3.759 and -3.606, respectively. Of note, we also found 262 lncRNAs (long non-coding RNA), 177 of which were inferred as novel lncRNAs. Further in-depth follow-up analysis of the transcriptional regulation reported in this study may shed light on the specific function of these lncRNA.
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Affiliation(s)
- Bo Li
- Department of Endocrinology, Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, China
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97
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Chow KS, Ghazali AK, Hoh CC, Mohd-Zainuddin Z. RNA sequencing read depth requirement for optimal transcriptome coverage in Hevea brasiliensis. BMC Res Notes 2014; 7:69. [PMID: 24484543 PMCID: PMC3926681 DOI: 10.1186/1756-0500-7-69] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 01/17/2014] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND One of the concerns of assembling de novo transcriptomes is determining the amount of read sequences required to ensure a comprehensive coverage of genes expressed in a particular sample. In this report, we describe the use of Illumina paired-end RNA-Seq (PE RNA-Seq) reads from Hevea brasiliensis (rubber tree) bark to devise a transcript mapping approach for the estimation of the read amount needed for deep transcriptome coverage. FINDINGS We optimized the assembly of a Hevea bark transcriptome based on 16 Gb Illumina PE RNA-Seq reads using the Oases assembler across a range of k-mer sizes. We then assessed assembly quality based on transcript N50 length and transcript mapping statistics in relation to (a) known Hevea cDNAs with complete open reading frames, (b) a set of core eukaryotic genes and (c) Hevea genome scaffolds. This was followed by a systematic transcript mapping process where sub-assemblies from a series of incremental amounts of bark transcripts were aligned to transcripts from the entire bark transcriptome assembly. The exercise served to relate read amounts to the degree of transcript mapping level, the latter being an indicator of the coverage of gene transcripts expressed in the sample. As read amounts or datasize increased toward 16 Gb, the number of transcripts mapped to the entire bark assembly approached saturation. A colour matrix was subsequently generated to illustrate sequencing depth requirement in relation to the degree of coverage of total sample transcripts. CONCLUSIONS We devised a procedure, the "transcript mapping saturation test", to estimate the amount of RNA-Seq reads needed for deep coverage of transcriptomes. For Hevea de novo assembly, we propose generating between 5-8 Gb reads, whereby around 90% transcript coverage could be achieved with optimized k-mers and transcript N50 length. The principle behind this methodology may also be applied to other non-model plants, or with reads from other second generation sequencing platforms.
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MESH Headings
- Databases, Genetic
- Gene Expression Profiling/methods
- Gene Expression Regulation, Plant
- Gene Library
- Genes, Plant
- Hevea/chemistry
- Hevea/genetics
- High-Throughput Nucleotide Sequencing
- Open Reading Frames
- Plant Bark/metabolism
- Plant Leaves/metabolism
- Plant Proteins/genetics
- RNA, Messenger/biosynthesis
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/isolation & purification
- RNA, Plant/biosynthesis
- RNA, Plant/chemistry
- RNA, Plant/genetics
- RNA, Plant/isolation & purification
- Reproducibility of Results
- Transcriptome
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Affiliation(s)
- Keng-See Chow
- Biotechnology Unit, Malaysian Rubber Board, Rubber Research Institute of Malaysia, Experiment Station, Kuala Lumpur 47000, Sungai Buloh, Selangor, Malaysia
| | - Ahmad-Kamal Ghazali
- Codon Genomics SB, No. 26, Jalan Dutamas 7, Taman Dutamas, Balakong 43200, Seri Kembangan Balakong, Selangor, Malaysia
| | - Chee-Choong Hoh
- Codon Genomics SB, No. 26, Jalan Dutamas 7, Taman Dutamas, Balakong 43200, Seri Kembangan Balakong, Selangor, Malaysia
| | - Zainorlina Mohd-Zainuddin
- Biotechnology Unit, Malaysian Rubber Board, Rubber Research Institute of Malaysia, Experiment Station, Kuala Lumpur 47000, Sungai Buloh, Selangor, Malaysia
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98
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Justo GZ, Suarez ER, Melo C, Lima MA, Nader HB, Pinhal MAS. From Combinatorial Display Techniques to Microarray Technology: New Approaches to the Development and Toxicological Profiling of Targeted Nanomedicines. Nanotoxicology 2014. [DOI: 10.1007/978-1-4614-8993-1_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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99
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Application of “Omics” Technologies to In Vitro Toxicology. METHODS IN PHARMACOLOGY AND TOXICOLOGY 2014. [DOI: 10.1007/978-1-4939-0521-8_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
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100
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Pombo MA, Zheng Y, Fernandez-Pozo N, Dunham DM, Fei Z, Martin GB. Transcriptomic analysis reveals tomato genes whose expression is induced specifically during effector-triggered immunity and identifies the Epk1 protein kinase which is required for the host response to three bacterial effector proteins. Genome Biol 2014; 15:492. [PMID: 25323444 PMCID: PMC4223163 DOI: 10.1186/s13059-014-0492-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 10/09/2014] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Plants have two related immune systems to defend themselves against pathogen attack. Initially,pattern-triggered immunity is activated upon recognition of microbe-associated molecular patterns by pattern recognition receptors. Pathogenic bacteria deliver effector proteins into the plant cell that interfere with this immune response and promote disease. However, some plants express resistance proteins that detect the presence of specific effectors leading to a robust defense response referred to as effector-triggered immunity. The interaction of tomato with Pseudomonas syringae pv. tomato is an established model system for understanding the molecular basis of these plant immune responses. RESULTS We apply high-throughput RNA sequencing to this pathosystem to identify genes whose expression changes specifically during pattern-triggered or effector-triggered immunity. We then develop reporter genes for each of these responses that will enable characterization of the host response to the large collection of P. s. pv. tomato strains that express different combinations of effectors. Virus-induced gene silencing of 30 of the effector-triggered immunity-specific genes identifies Epk1 which encodes a predicted protein kinase from a family previously unknown to be involved in immunity. Knocked-down expression of Epk1 compromises effector-triggered immunity triggered by three bacterial effectors but not by effectors from non-bacterial pathogens. Epistasis experiments indicate that Epk1 acts upstream of effector-triggered immunity-associated MAP kinase signaling. CONCLUSIONS Using RNA-seq technology we identify genes involved in specific immune responses. A functional genomics screen led to the discovery of Epk1, a novel predicted protein kinase required for plant defense activation upon recognition of three different bacterial effectors.
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Affiliation(s)
- Marina A Pombo
- />Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY 14853-1801 USA
| | - Yi Zheng
- />Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY 14853-1801 USA
| | - Noe Fernandez-Pozo
- />Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY 14853-1801 USA
| | - Diane M Dunham
- />Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY 14853-1801 USA
| | - Zhangjun Fei
- />Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY 14853-1801 USA
| | - Gregory B Martin
- />Boyce Thompson Institute for Plant Research, 533 Tower Road, Ithaca, NY 14853-1801 USA
- />Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853-1801 USA
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