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Fan S, Georgi LL, Hebard FV, Zhebentyayeva T, Yu J, Sisco PH, Fitzsimmons SF, Staton ME, Abbott AG, Nelson CD. Mapping QTLs for blight resistance and morpho-phenological traits in inter-species hybrid families of chestnut ( Castanea spp.). FRONTIERS IN PLANT SCIENCE 2024; 15:1365951. [PMID: 38650705 PMCID: PMC11033410 DOI: 10.3389/fpls.2024.1365951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/20/2024] [Indexed: 04/25/2024]
Abstract
Chestnut blight (caused by Cryphonectria parasitica), together with Phytophthora root rot (caused by Phytophthora cinnamomi), has nearly extirpated American chestnut (Castanea dentata) from its native range. In contrast to the susceptibility of American chestnut, many Chinese chestnut (C. mollissima) genotypes are resistant to blight. In this research, we performed a series of genome-wide association studies for blight resistance originating from three unrelated Chinese chestnut trees (Mahogany, Nanking and M16) and a Quantitative Trait Locus (QTL) study on a Mahogany-derived inter-species F2 family. We evaluated trees for resistance to blight after artificial inoculation with two fungal strains and scored nine morpho-phenological traits that are the hallmarks of species differentiation between American and Chinese chestnuts. Results support a moderately complex genetic architecture for blight resistance, as 31 QTLs were found on 12 chromosomes across all studies. Additionally, although most morpho-phenological trait QTLs overlap or are adjacent to blight resistance QTLs, they tend to aggregate in a few genomic regions. Finally, comparison between QTL intervals for blight resistance and those previously published for Phytophthora root rot resistance, revealed five common disease resistance regions on chromosomes 1, 5, and 11. Our results suggest that it will be difficult, but still possible to eliminate Chinese chestnut alleles for the morpho-phenological traits while achieving relatively high blight resistance in a backcross hybrid tree. We see potential for a breeding scheme that utilizes marker-assisted selection early for relatively large effect QTLs followed by genome selection in later generations for smaller effect genomic regions.
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Affiliation(s)
- Shenghua Fan
- Forest Health Research and Education Center, Department of Horticulture, University of Kentucky, Lexington, KY, United States
| | - Laura L. Georgi
- Forest Health Research and Education Center, U.S. Department of Agriculture (USDA) Forest Service, Southern Research Station, Lexington, KY, United States
- Virginia Chapter, The American Chestnut Foundation, Meadowview, VA, United States
| | - Frederick V. Hebard
- Virginia Chapter, The American Chestnut Foundation, Meadowview, VA, United States
| | - Tetyana Zhebentyayeva
- Forest Health Research and Education Center, Department of Forestry and Natural Resources, University of Kentucky, Lexington, KY, United States
| | - Jiali Yu
- Synthetic and Systems Biology Innovation Hub, Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX, United States
| | - Paul H. Sisco
- Carolinas Chapter, The American Chestnut Foundation, Asheville, NC, United States
| | - Sara F. Fitzsimmons
- North Central Office, The American Chestnut Foundation, University Park, PA, United States
| | - Margaret E. Staton
- Department of Entomology and Plant Pathology, University of Tennessee, Knoxville, TN, United States
| | - Albert G. Abbott
- Forest Health Research and Education Center, Department of Forestry and Natural Resources, University of Kentucky, Lexington, KY, United States
| | - C. Dana Nelson
- Forest Health Research and Education Center, U.S. Department of Agriculture (USDA) Forest Service, Southern Research Station, Lexington, KY, United States
- Southern Institute of Forest Genetics, U.S. Department of Agriculture (USDA) Forest Service, Southern Research Station, Saucier, MS, United States
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Zhang Y, Zhang W, Liu Y, Zheng Y, Nie X, Wu Q, Yu W, Wang Y, Wang X, Fang K, Qin L, Xing Y. GWAS identifies two important genes involved in Chinese chestnut weight and leaf length regulation. PLANT PHYSIOLOGY 2024; 194:2387-2399. [PMID: 38114094 DOI: 10.1093/plphys/kiad674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 12/21/2023]
Abstract
There are many factors that affect the yield of Chinese chestnut (Castanea mollissima), with single nut weight (SNW) being one of the most important. Leaf length is also related to Chinese chestnut yield. However, the genetic architecture and gene function associated with Chinese chestnut nut yield have not been fully explored. In this study, we performed genotyping by sequencing 151 Chinese chestnut cultivars, followed by a genome-wide association study (GWAS) on six horticultural traits. First, we analyzed the phylogeny of the Chinese chestnut and found that the Chinese chestnut cultivars divided into two ecotypes, a northern and southern cultivar group. Differences between the cultivated populations were found in the pathways of plant growth and adaptation to the environment. In the selected regions, we also found interesting tandemly arrayed genes that may influence Chinese chestnut traits and environmental adaptability. To further investigate which horticultural traits were selected, we performed a GWAS using six horticultural traits from 151 cultivars. Forty-five loci that strongly associated with horticultural traits were identified, and six genes highly associated with these traits were screened. In addition, a candidate gene associated with SNW, APETALA2 (CmAP2), and another candidate gene associated with leaf length (LL), CRYPTOCHROME INTERACTING BASIC HELIX-LOOP-HELIX 1 (CmCIB1), were verified in Chinese chestnut and Arabidopsis (Arabidopsis thaliana). Our results showed that CmAP2 affected SNW by negatively regulating cell size. CmCIB1 regulated the elongation of new shoots and leaves by inducing cell elongation, potentially affecting photosynthesis. This study provided valuable information and insights for Chinese chestnut breeding research.
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Affiliation(s)
- Yu Zhang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Weiwei Zhang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Yang Liu
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Yi Zheng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
- Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Xinghua Nie
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Qinyi Wu
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Wenjie Yu
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Yafeng Wang
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Xuefeng Wang
- Longtan Forestry Station, Liyang Bureau of Natural Resources and Planning, Liyang, Jiangsu 213300, China
| | - Kefeng Fang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China
| | - Ling Qin
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
| | - Yu Xing
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China
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Jiang H, Zhou C, Ma J, Qu S, Liu F, Sun H, Zhao X, Han Y. Weighted gene co-expression network analysis identifies genes related to HG Type 0 resistance and verification of hub gene GmHg1. FRONTIERS IN PLANT SCIENCE 2023; 13:1118503. [PMID: 36777536 PMCID: PMC9911859 DOI: 10.3389/fpls.2022.1118503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
INTRODUCTION The soybean cyst nematode (SCN) is a major disease in soybean production thatseriously affects soybean yield. At present, there are no studies on weighted geneco-expression network analysis (WGCNA) related to SCN resistance. METHODS Here, transcriptome data from 36 soybean roots under SCN HG Type 0 (race 3) stresswere used in WGCNA to identify significant modules. RESULTS AND DISCUSSION A total of 10,000 differentially expressed genes and 21 modules were identified, of which the module most related to SCN was turquoise. In addition, the hub gene GmHg1 with high connectivity was selected, and its function was verified. GmHg1 encodes serine/threonine protein kinase (PK), and the expression of GmHg1 in SCN-resistant cultivars ('Dongnong L-204') and SCN-susceptible cultivars ('Heinong 37') increased significantly after HG Type 0 stress. Soybean plants transformed with GmHg1-OX had significantly increased SCN resistance. In contrast, the GmHg1-RNAi transgenic soybean plants significantly reduced SCN resistance. In transgenic materials, the expression patterns of 11 genes with the same expression trend as the GmHg1 gene in the 'turquoise module' were analyzed. Analysis showed that 11genes were co-expressed with GmHg1, which may be involved in the process of soybean resistance to SCN. Our work provides a new direction for studying the Molecular mechanism of soybean resistance to SCN.
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Affiliation(s)
- Haipeng Jiang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Changjun Zhou
- Soybean Molecular Breeding Faculty Daqing Branch, Heilongjiang Academy of Agricultrual Science, Daqing, China
| | - Jinglin Ma
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Shuo Qu
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Fang Liu
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Haowen Sun
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Xue Zhao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
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Transcriptome sequencing reveals improved ammonia nitrogen tolerance in Zebra II strain of the Manila clam Ruditapes philippinarum. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 44:101016. [PMID: 35985189 DOI: 10.1016/j.cbd.2022.101016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 07/24/2022] [Accepted: 07/24/2022] [Indexed: 01/27/2023]
Abstract
In this research, we identified genes associated with ammonia nitrogen (TAN) stress response and resistance in juveniles of the Zebra II strain and a wild population of the Manila clam Ruditapes philippinarum. Both groups were subjected to a 96 h acute toxicity test using TAN concentrations of 17.617 ± 0.634 and 16.670 ± 0.7 mg/l, respectively. We then collected samples, conducted transcriptome sequencing and screened the sequences for differentially expressed genes (DEGs) related to TAN stress response. We identified 2908 and 2861 DEGs in the Zebra II and wild clam groups, respectively, and the two groups had 626 DEGs in common. The verified DEGs had less of a detoxification effect in the wild population than that in the Zebra II group. Gene Ontology database analysis showed that Zebra II juveniles were mainly enriched in protein phosphorylation, purine nucleoside binding, and kinase activity, whereas the wild population juveniles were primarily enriched in oxidases activity, organic acid metabolic processes, and extracellular regions. Kyoto Encyclopedia of Genes and Genomes pathway analysis mainly highlighted aminoacyl tRNA biosynthesis in Zebra II juveniles and sphingolipid metabolism, FOXO signaling, biosynthesis of aminoacyl tRNA, and other pathways in the wild population. These results show that the toxic effect of TAN on the Manila clam is related to a variety of pathways, which are mainly related to immune response, inflammatory response, metabolic pathways, and nerve conduction. This study provides basic data and theoretical reference for revealing the molecular regulation mechanism of the improved TAN tolerance of Zebra II strain as compared with the wild population of Ruditapes philippinarum.
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Fernandes P, Colavolpe MB, Serrazina S, Costa RL. European and American chestnuts: An overview of the main threats and control efforts. FRONTIERS IN PLANT SCIENCE 2022; 13:951844. [PMID: 36092400 PMCID: PMC9449730 DOI: 10.3389/fpls.2022.951844] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
Chestnuts are multipurpose trees significant for the economy and wildlife. These trees are currently found around the globe, demonstrating their genetic adaptation to different environmental conditions. Several biotic and abiotic stresses have challenged these species, contributing to the decline of European chestnut production and the functional extinction of the American chestnut. Several efforts started over the last century to understand the cellular, molecular, and genetic interactions behind all chestnut biotic and abiotic interactions. Most efforts have been toward breeding for the primary diseases, chestnut blight and ink disease caused by the pathogens, Cryphonectria parasitica and Phytophthora cinnamomi, respectively. In Europe and North America, researchers have been using the Asian chestnut species, which co-evolved with the pathogens, to introgress resistance genes into the susceptible species. Breeding woody trees has several limitations which can be mostly related to the long life cycles of these species and the big genome landscapes. Consequently, it takes decades to improve traits of interest, such as resistance to pathogens. Currently, the availability of genome sequences and next-generation sequencing techniques may provide new tools to help overcome most of the problems tree breeding is still facing. This review summarizes European and American chestnut's main biotic stresses and discusses breeding and biotechnological efforts developed over the last decades, having ink disease and chestnut blight as the main focus. Climate change is a rising concern, and in this context, the adaptation of chestnuts to adverse environmental conditions is of extreme importance for chestnut production. Therefore, we also discuss the abiotic challenges on European chestnuts, where the response to abiotic stress at the genetic and molecular level has been explored.
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Affiliation(s)
- Patrícia Fernandes
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Oeiras, Portugal
- Green-It Bioresources for Sustainability, ITQB NOVA, Oeiras, Portugal
- Department of Environmental Biology, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States
| | | | - Susana Serrazina
- BioISI – Biosystems and Integrative Sciences Institute, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| | - Rita Lourenço Costa
- Instituto Nacional de Investigação Agrária e Veterinária, I.P., Oeiras, Portugal
- Centro de Estudos Florestais, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
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Sandercock AM, Westbrook JW, Zhang Q, Johnson HA, Saielli TM, Scrivani JA, Fitzsimmons SF, Collins K, Perkins MT, Craddock JH, Schmutz J, Grimwood J, Holliday JA. Frozen in time: rangewide genomic diversity, structure, and demographic history of relict American chestnut populations. Mol Ecol 2022; 31:4640-4655. [PMID: 35880415 DOI: 10.1111/mec.16629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 11/30/2022]
Abstract
American chestnut (Castanea dentata) was once the most economically and ecologically important hardwood species in the eastern United States. In the first half of the 20th century, an exotic fungal pathogen - Cryphonectria parasitica - decimated the species, killing billions of chestnut trees. Two approaches to developing blight resistant American chestnut populations show promise, but both will require introduction of adaptive genomic diversity from wild germplasm to produce diverse, locally adapted restoration populations. Here we characterize population structure, demographic history, and genomic diversity in a range-wide sample of 384 wild American chestnuts to inform conservation and breeding with blight resistant varieties. Population structure analyses suggest that the chestnut range can be roughly divided into northeast, central, and southwest populations. Within-population genomic diversity estimates revealed a clinal pattern with the highest diversity in the southwest, which likely reflects bottleneck events associated with Quaternary glaciation. Finally, we identified genomic regions under positive selection within each population, which suggests that defense against fungal pathogens is a common target of selection across all populations. Taken together, these results show that American chestnut underwent a postglacial expansion from the southern portion of its range leading to three extant genetic populations. These populations will serve as management units for breeding adaptive genetic variation into the blight-resistant tree populations for targeted reintroduction efforts.
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Affiliation(s)
| | | | - Qian Zhang
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, VA, USA
| | - Hayley A Johnson
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, VA, USA
| | | | | | | | | | - M Taylor Perkins
- Department of Biology, Geology, and Environmental Science, The University of Tennessee at Chattanooga, Chattanooga, TN, USA
| | - J Hill Craddock
- Department of Biology, Geology, and Environmental Science, The University of Tennessee at Chattanooga, Chattanooga, TN, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jason A Holliday
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, VA, USA
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Li X, Li M, Liu X, Jiang Y, Zhao D, Gao J, Wang Z, Jiang Y, Chen C. RNA-Seq Provides Insights into the Mechanisms Underlying Ilyonectria robusta Responding to Secondary Metabolites of Bacillus methylotrophicus NJ13. J Fungi (Basel) 2022; 8:jof8080779. [PMID: 35893148 PMCID: PMC9332032 DOI: 10.3390/jof8080779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 07/21/2022] [Accepted: 07/21/2022] [Indexed: 11/26/2022] Open
Abstract
(1) Background: Ilyonectria robusta can cause ginseng to suffer from rusty root rot. Secondary metabolites (SMs) produced by Bacillus methylotrophicus NJ13 can inhibit the mycelial growth of I. robusta. However, the molecular mechanism of the inhibition and response remains unclear. (2) Methods: Through an in vitro trial, the effect of B. methylotrophicus NJ13’s SMs on the hyphae and conidia of I. robusta was determined. The change in the physiological function of I. robusta was evaluated in response to NJ13’s SMs by measuring the electrical conductivity, malondialdehyde (MDA) content, and glucose content. The molecular interaction mechanism of I. robusta’s response to NJ13’s SMs was analyzed by using transcriptome sequencing. (3) Results: NJ13’s SMs exhibited antifungal activity against I. robusta: namely, the hyphae swelled and branched abnormally, and their inclusions leaked out due to changes in the cell membrane permeability and the peroxidation level; the EC50 value was 1.21% (v/v). In transcripts at 4 dpi and 7 dpi, the number of differentially expressed genes (DEGs) (|log2(fold change)| > 1, p adj ≤ 0.05) was 1960 and 354, respectively. NJ13’s SMs affected the glucose metabolism pathway, and the sugar-transporter-related genes were downregulated, which are utilized by I. robusta for energy production. The cell wall structure of I. robusta was disrupted, and chitin-synthase-related genes were downregulated. (4) Conclusions: A new dataset of functional responses of the ginseng pathogenic fungus I. robusta was obtained. The results will benefit the development of targeted biological fungicides for I. robusta and the study of the molecular mechanisms of interaction between biocontrol bacteria and phytopathogenic fungi.
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Affiliation(s)
- Xiang Li
- College of Life Science, Jilin Agricultural University, Changchun 130118, China;
| | - Mengtao Li
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China; (M.L.); (X.L.); (Y.J.); (J.G.)
| | - Xiangkai Liu
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China; (M.L.); (X.L.); (Y.J.); (J.G.)
| | - Yilin Jiang
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China; (M.L.); (X.L.); (Y.J.); (J.G.)
| | - Dongfang Zhao
- Jilin Provincial Agro-Tech Extension Center, Changchun 130031, China;
| | - Jie Gao
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China; (M.L.); (X.L.); (Y.J.); (J.G.)
| | - Zhenhui Wang
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China;
| | - Yun Jiang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China;
- Correspondence: (Y.J.); (C.C.)
| | - Changqing Chen
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China; (M.L.); (X.L.); (Y.J.); (J.G.)
- Correspondence: (Y.J.); (C.C.)
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Shirasawa K, Nishio S, Terakami S, Botta R, Marinoni DT, Isobe S. Chromosome-level genome assembly of Japanese chestnut (Castanea crenata Sieb. et Zucc.) reveals conserved chromosomal segments in woody rosids. DNA Res 2021; 28:6356520. [PMID: 34424280 PMCID: PMC8435554 DOI: 10.1093/dnares/dsab016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 08/20/2021] [Indexed: 11/14/2022] Open
Abstract
Japanese chestnut (Castanea crenata Sieb. et Zucc.), unlike other Castanea species, is resistant to most diseases and wasps. However, genomic data of Japanese chestnut that could be used to determine its biotic stress resistance mechanisms have not been reported to date. In this study, we employed long-read sequencing and genetic mapping to generate genome sequences of Japanese chestnut at the chromosome level. Long reads (47.7 Gb; 71.6× genome coverage) were assembled into 781 contigs, with a total length of 721.2 Mb and a contig N50 length of 1.6 Mb. Genome sequences were anchored to the chestnut genetic map, comprising 14,973 single nucleotide polymorphisms (SNPs) and covering 1,807.8 cM map distance, to establish a chromosome-level genome assembly (683.8 Mb), with 69,980 potential protein-encoding genes and 425.5 Mb repetitive sequences. Furthermore, comparative genome structure analysis revealed that Japanese chestnut shares conserved chromosomal segments with woody plants, but not with herbaceous plants, of rosids. Overall, the genome sequence data of Japanese chestnut generated in this study is expected to enhance not only its genetics and genomics but also the evolutionary genomics of woody rosids.
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Affiliation(s)
| | - Sogo Nishio
- Institute of Fruit Tree and Tea Science, NARO, Ibaraki 305-8605, Japan
| | - Shingo Terakami
- Institute of Fruit Tree and Tea Science, NARO, Ibaraki 305-8605, Japan
| | - Roberto Botta
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Largo P. Braccini 2, 10095 Grugliasco (TO), Italy
| | - Daniela Torello Marinoni
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, Università degli Studi di Torino, Largo P. Braccini 2, 10095 Grugliasco (TO), Italy
| | - Sachiko Isobe
- Kazusa DNA Research Institute, Chiba 292-0818, Japan
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Spriggs EL, Fertakos ME. Evolution of Castanea in North America: restriction-site-associated DNA sequencing and ecological modeling reveal a history of radiation, range shifts, and disease. AMERICAN JOURNAL OF BOTANY 2021; 108:1692-1704. [PMID: 34519029 DOI: 10.1002/ajb2.1726] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/18/2021] [Accepted: 04/20/2021] [Indexed: 06/13/2023]
Abstract
PREMISE Although chestnuts and chinquapins are some of the best known and most widely loved of any plants in North America, relatively little genomic sequencing has been done, and much is still unknown about their evolution. METHODS We used double-digest restriction-site-associated DNA (ddRAD) sequencing data to infer the species-level phylogeny for Castanea and assess the phylogeography of the North American species using samples collected from populations that span the full extent of the species' ranges. We also constructed species distribution models using digitized herbarium specimens and observational data from field surveys. RESULTS We identified strong population structure within Castanea dentata (American chestnut) that reflects a stepwise northern migration since the last glacial maximum. Our species distribution models further confirmed this scenario and matched closely with the Castanea fossil pollen record. We also found significant structure within the Castanea pumila lineage, most notably a genetic cluster that corresponds to the frequently recognized Castanea pumila var. ozarkensis. CONCLUSIONS The two North American Castanea species have contrasting patterns of population structure, but each is typical of plant phylogeography in North America. Within the C. pumila complex, we found novel genetic structure that provides new insights about C. pumila taxonomy. Our results also identified a series of distinctive populations that will be valuable in ongoing efforts to conserve and restore chestnuts and chinquapins in North America.
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Li S, Shi Z, Zhu Q, Tao L, Liang W, Zhao Z. Transcriptome sequencing and differential expression analysis of seed starch accumulation in Chinese chestnut Metaxenia. BMC Genomics 2021; 22:617. [PMID: 34388974 PMCID: PMC8362260 DOI: 10.1186/s12864-021-07923-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 08/04/2021] [Indexed: 11/21/2022] Open
Abstract
Background Chestnut seeds are important kinds of edible nuts rich in starch and protein. The characteristics and nutrient contents of chestnut have been found to show obvious metaxenia effects in previous studies. To improve the understanding of the effect of metaxenia on chestnut starch and sucrose metabolism, this study used three varieties of chestnut, ‘Yongfeng 1’, ‘YongRen Zao’ and ‘Yimen 1’, as male parents to pollinate the female parent, ‘Yongfeng 1’, and investigated the mechanisms of starch and sucrose metabolism in three starch accumulation stages (70 (S1), 82 (S2), and 94 (S3) days after pollination, DAP) in chestnut seed kernels. Result Most carbohydrate metabolism genes were highly expressed in YFF (self-pollinated ‘Yongfeng 1’) in stage S2 and in YFR (‘Yongfeng 1’ × ‘Yongren Zao’) and YFM (‘Yongfeng 1’ × ‘Yimen 1’) in stage S3. In stage S3, hub genes encoding HSF_DNA-binding, ACT, Pkinase, and LIM proteins and four transcription factors were highly expressed, with YFF showing the highest expression, followed by YFR and YFM. In addition, transcriptome analysis of the kernels at 70, 82 and 94 DAP showed that the starch granule-bound starch synthase (EC 2.4.1.242) and ADP-glucose pyrophosphorylase (EC 2.7 .7.27) genes were actively expressed at 94 DAF. Chestnut seeds regulate the accumulation of soluble sugars, reducing sugars and starch by controlling glycosyl transferase and hydrolysis activity during development. Conclusion These results and resources have important guiding significance for further research on starch and sucrose metabolism and other types of metabolism related to chestnut metaxenia. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07923-5.
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Affiliation(s)
- Shengxing Li
- Guanxi forestry research institute, Nanning, Guanxi, China
| | - Zhuogong Shi
- Guanxi forestry research institute, Nanning, Guanxi, China
| | - Qiurong Zhu
- Guanxi forestry research institute, Nanning, Guanxi, China
| | - Liang Tao
- Guanxi forestry research institute, Nanning, Guanxi, China
| | - Wenhui Liang
- Guanxi forestry research institute, Nanning, Guanxi, China
| | - Zhiheng Zhao
- Guanxi forestry research institute, Nanning, Guanxi, China.
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Comparative Analysis of the Complete Chloroplast Genomes of Four Chestnut Species (Castanea). FORESTS 2021. [DOI: 10.3390/f12070861] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Chloroplast (cp) DNA genomes are traditional workhorses for studying the evolution of species and reconstructing phylogenetic relationships in plants. Species of the genus Castanea (chestnuts and chinquapins) are valued as a source of nuts and timber wherever they grow, and chestnut species hybrids are common. We compared the cp genomes of C. mollissima, C. seguinii, C. henryi, and C. pumila. These cp genomes ranged from 160,805 bp to 161,010 bp in length, comprising a pair of inverted repeat (IR) regions (25,685 to 25,701 bp) separated by a large single-copy (LSC) region (90,440 to 90,560 bp) and a small single-copy (SSC) region (18,970 to 19,049 bp). Each cp genome encoded the same 113 genes; 82–83 protein-coding genes, 30 transfer RNA genes, and four ribosomal RNA genes. There were 18 duplicated genes in the IRs. Comparative analysis of cp genomes revealed that rpl22 was absent in all analyzed species, and the gene ycf1 has been pseudo-genized in all Chinese chestnuts except C. pumlia. We analyzed the repeats and nucleotide substitutions in these plastomes and detected several highly variable regions. The phylogenetic analyses based on plastomes confirmed the monophyly of Castanea species.
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12
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Zamora-Ballesteros C, Pinto G, Amaral J, Valledor L, Alves A, Diez JJ, Martín-García J. Dual RNA-Sequencing Analysis of Resistant ( Pinus pinea) and Susceptible ( Pinus radiata) Hosts during Fusarium circinatum Challenge. Int J Mol Sci 2021; 22:5231. [PMID: 34063405 PMCID: PMC8156185 DOI: 10.3390/ijms22105231] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/11/2021] [Accepted: 05/13/2021] [Indexed: 12/13/2022] Open
Abstract
Fusarium circinatum causes one of the most important diseases of conifers worldwide, the pine pitch canker (PPC). However, no effective field intervention measures aiming to control or eradicate PPC are available. Due to the variation in host genetic resistance, the development of resistant varieties is postulated as a viable and promising strategy. By using an integrated approach, this study aimed to identify differences in the molecular responses and physiological traits of the highly susceptible Pinus radiata and the highly resistant Pinus pinea to F. circinatum at an early stage of infection. Dual RNA-Seq analysis also allowed to evaluate pathogen behavior when infecting each pine species. No significant changes in the physiological analysis were found upon pathogen infection, although transcriptional reprogramming was observed mainly in the resistant species. The transcriptome profiling of P. pinea revealed an early perception of the pathogen infection together with a strong and coordinated defense activation through the reinforcement and lignification of the cell wall, the antioxidant activity, the induction of PR genes, and the biosynthesis of defense hormones. On the contrary, P. radiata had a weaker response, possibly due to impaired perception of the fungal infection that led to a reduced downstream defense signaling. Fusarium circinatum showed a different transcriptomic profile depending on the pine species being infected. While in P. pinea, the pathogen focused on the degradation of plant cell walls, active uptake of the plant nutrients was showed in P. radiata. These findings present useful knowledge for the development of breeding programs to manage PPC.
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Affiliation(s)
- Cristina Zamora-Ballesteros
- Sustainable Forest Management Research Institute, University of Valladolid—INIA, 34004 Palencia, Spain; (J.J.D.); (J.M.-G.)
- Department of Vegetal Production and Forest Resources, University of Valladolid, 34004 Palencia, Spain
| | - Gloria Pinto
- Centre for Environmental and Marine Studies, CESAM, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (G.P.); (J.A.); (A.A.)
| | - Joana Amaral
- Centre for Environmental and Marine Studies, CESAM, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (G.P.); (J.A.); (A.A.)
| | - Luis Valledor
- Department of Organisms and Systems Biology, University of Oviedo, 33071 Oviedo, Spain;
| | - Artur Alves
- Centre for Environmental and Marine Studies, CESAM, Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal; (G.P.); (J.A.); (A.A.)
| | - Julio J. Diez
- Sustainable Forest Management Research Institute, University of Valladolid—INIA, 34004 Palencia, Spain; (J.J.D.); (J.M.-G.)
- Department of Vegetal Production and Forest Resources, University of Valladolid, 34004 Palencia, Spain
| | - Jorge Martín-García
- Sustainable Forest Management Research Institute, University of Valladolid—INIA, 34004 Palencia, Spain; (J.J.D.); (J.M.-G.)
- Department of Vegetal Production and Forest Resources, University of Valladolid, 34004 Palencia, Spain
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Schultes NP, Castañeda-Ruiz RF, Marra RE, Strzalkowski N, De-Wei L. Striatibotrys neoeucylindrosporus sp. nov., a Stachybotrys-like fungus from North America. Int J Syst Evol Microbiol 2021; 71. [PMID: 33886447 DOI: 10.1099/ijsem.0.004778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two isolates from Canada and the USA (UAMH 7122 and UAMH 7211, respectively) previously identified as Stachybotrys eucylindrosporus were studied by morphology and six-locus phylogeny (cmdA, ITS, LSU, rpb2, tef1α and tub2). UAMH 7122 and UAMH 7211 are morphologically related but phylogenetically distinct from Striatibotrys eucylindrosporus (≡Stachybotrys eucylindrosporus) and Str. rhabdosporus. Hence, UAMH 7122 and UAMH 7211 are described as a new species, Striatibotrys neoeucylindrosporus sp. nov. with UAMH 7211 as the holotype. The characters of this species include some phialides proliferating by holoblastic extension of phialides and conidia clavate, subcylindrical or cylindrical ellipsoid, or dumbbell-shaped, dark brown to olivaceous grey when mature, longitudinally striate, 10.3-12.3×3-3.8 µm. A key to the species of Striatibotrys is provided.
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Affiliation(s)
- Neil P Schultes
- The Connecticut Agricultural Experiment Station, Department of Plant Pathology and Ecology, 123 Huntington Street, New Haven, CT 06511, USA
| | - Rafael F Castañeda-Ruiz
- Instituto de Investigaciones Fundamentales en Agricultura Tropical 'Alejandro de Humboldt'(INIFAT), Académico Titular de la Academia de Ciencias de Cuba, Calle 1 Esq. 2, Santiago de Las Vegas, C. Habana, Cuba
| | - Robert E Marra
- The Connecticut Agricultural Experiment Station, Department of Plant Pathology and Ecology, 123 Huntington Street, New Haven, CT 06511, USA
| | - Noelle Strzalkowski
- The Connecticut Agricultural Experiment Station, Department of Plant Pathology and Ecology, 123 Huntington Street, New Haven, CT 06511, USA
| | - Li De-Wei
- The Connecticut Agricultural Experiment Station, Valley Laboratory, 153 Cook Hill Road, Windsor, CT 06095, USA
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Pavese V, Moglia A, Gonthier P, Torello Marinoni D, Cavalet-Giorsa E, Botta R. Identification of Susceptibility Genes in Castanea sativa and Their Transcription Dynamics following Pathogen Infection. PLANTS 2021; 10:plants10050913. [PMID: 34063239 PMCID: PMC8147476 DOI: 10.3390/plants10050913] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 02/07/2023]
Abstract
Castanea sativa is one of the main multipurpose tree species valued for its timber and nuts. This species is susceptible to two major diseases, ink disease and chestnut blight, caused by Phytophthora spp. and Cryphonectria parasitica, respectively. The loss-of-function mutations of genes required for the onset of pathogenesis, referred to as plant susceptibility (S) genes, are one mechanism of plant resistance against pathogens. On the basis of sequence homology, functional domain identification, and phylogenetic analyses, we report for the first time on the identification of S-genes (mlo1, dmr6, dnd1, and pmr4) in the Castanea genus. The expression dynamics of S-genes were assessed in C. sativa and C. crenata plants inoculated with P. cinnamomi and C. parasitica. Our results highlighted the upregulation of pmr4 and dmr6 in response to pathogen infection. Pmr4 was strongly expressed at early infection phases of both pathogens in C. sativa, whereas in C. crenata, no significant upregulation was observed. The infection of P. cinnamomi led to a higher increase in the transcript level of dmr6 in C. sativa compared to C. crenata-infected samples. For a better understanding of plant responses, the transcript levels of defense genes gluB and chi3 were also analyzed.
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15
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Transformation of American Chestnut (Castanea dentata (Marsh.) Borkh) Using RITA® Temporary Immersion Bioreactors and We Vitro Containers. FORESTS 2020. [DOI: 10.3390/f11111196] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
American chestnut (Castanea dentata (Marsh.) Borkh) was almost completely wiped out by the fungal pathogen, Cryphonectria parasitica (Murrill) M.E. Barr. Another invasive pathogen, Phytophthora cinnamomi Rands, is devastating American chestnuts in the southern region of the United States. An alternative approach for controlling these pathogens is to use genetic engineering or gene editing. We successfully transformed American chestnut with a detoxifying enzyme, oxalate oxidase, to enhance blight tolerance and more recently with the Cast_Gnk2-like gene, which encodes for an antifungal protein, to be tested for P. cinnamomi putative tolerance. Eight somatic embryo lines were transformed using three methods of selection: semisolid medium in Petri plates, liquid medium in RITA® temporary immersion bioreactors, or liquid medium in We Vitro containers. No significant differences were found between the treatments. These methods will allow for further testing of transgenes and the development of enhanced pathogen resistance in chestnut. It can serve as a model for other tree species threatened by invasive pests and pathogens.
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Integrated Proteomic and Metabolomic Profiling of Phytophthora cinnamomi Attack on Sweet Chestnut ( Castanea sativa) Reveals Distinct Molecular Reprogramming Proximal to the Infection Site and Away from It. Int J Mol Sci 2020; 21:ijms21228525. [PMID: 33198329 PMCID: PMC7697766 DOI: 10.3390/ijms21228525] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/09/2020] [Accepted: 11/10/2020] [Indexed: 01/15/2023] Open
Abstract
Phytophthora cinnamomi is one of the most invasive tree pathogens that devastates wild and cultivated forests. Due to its wide host range, knowledge of the infection process at the molecular level is lacking for most of its tree hosts. To expand the repertoire of studied Phytophthora-woody plant interactions and identify molecular mechanisms that can facilitate discovery of novel ways to control its spread and damaging effects, we focused on the interaction between P. cinnamomi and sweet chestnut (Castanea sativa), an economically important tree for the wood processing industry. By using a combination of proteomics, metabolomics, and targeted hormonal analysis, we mapped the effects of P. cinnamomi attack on stem tissues immediately bordering the infection site and away from it. P. cinnamomi led to a massive reprogramming of the chestnut proteome and accumulation of the stress-related hormones salicylic acid (SA) and jasmonic acid (JA), indicating that stem inoculation can be used as an easily accessible model system to identify novel molecular players in P. cinnamomi pathogenicity.
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Djami-Tchatchou AT, Matsaunyane LBT, Kalu CM, Ntushelo K. Gene expression and evidence of coregulation of the production of some metabolites of chilli pepper inoculated with Pectobacterium carotovorum ssp. carotovorum. FUNCTIONAL PLANT BIOLOGY : FPB 2019; 46:1114-1122. [PMID: 31679560 DOI: 10.1071/fp18244] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 07/12/2019] [Indexed: 06/10/2023]
Abstract
Chilli pepper (Capsicum annuum L.) is susceptible to Pectobacterium carotovorum subsp. carotovorum (Pcc), the causal agent of soft rot disease in crops. Understanding the molecular principles of systemic acquired resistance, which is poorly understood in chilli pepper, represents an important step towards understanding inducible defence responses and can assist in designing appropriate intervention strategies for crop disease management. Accordingly, we investigated (via real-time PCR and metabolomics profiling) the molecular response of chilli pepper to Pcc by characterisation of the crucial metabolic regulators involved in the establishment of defence response. We profiled 13 key inducible defence response genes, which included MYB transcriptor factor, ethylene response element-binding protein, suppressor of the G2 allele of Skp1, cytochrome P450, small Sar1 (GTPase), hydroxycinnamoyl-CoA:quinate hydroxycinnamoyl transferase, pathogenesis-related protein 1a, endo-1,3-β-glucanase, chitinase, proteinase inhibitor, defensin, coiled-coil-nucleotide-binding site-leucine-rich repeat (CC-NBS-LRR) resistance and phenylalanine ammonia lyase. In addition, we determined metabolomic shifts induced by Pcc in pepper. The PCR results revealed a significant induction of the selected plant defence-related genes in response to Pcc inoculation; the metabolomic profiling showed that of 99 primary metabolites profiled the quantities of acetylcarnitine, adenosine, adenosine 3',5' cyclic monophosphate, guanosine 3',5' cyclic monophosphate and inosine decreased in pepper leaves inoculated with Pcc.
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Affiliation(s)
- Arnaud Thierry Djami-Tchatchou
- Department of Agriculture and Animal Health, Science Campus, University of South Africa, Corner Christiaan De Wet and Pioneer Avenue, Private Bag X6, Florida 1710, South Africa
| | | | - Chimdi Mang Kalu
- Department of Agriculture and Animal Health, Science Campus, University of South Africa, Corner Christiaan De Wet and Pioneer Avenue, Private Bag X6, Florida 1710, South Africa
| | - Khayalethu Ntushelo
- Department of Agriculture and Animal Health, Science Campus, University of South Africa, Corner Christiaan De Wet and Pioneer Avenue, Private Bag X6, Florida 1710, South Africa; and Corresponding author.
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18
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Martínez MT, San-José MDC, Arrillaga I, Cano V, Morcillo M, Cernadas MJ, Corredoira E. Holm Oak Somatic Embryogenesis: Current Status and Future Perspectives. FRONTIERS IN PLANT SCIENCE 2019; 10:239. [PMID: 30967881 PMCID: PMC6438927 DOI: 10.3389/fpls.2019.00239] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Accepted: 02/12/2019] [Indexed: 05/11/2023]
Abstract
Quercus ilex (holm oak) is one of the most representative trees in the Mediterranean basin, but now the sustainability of its ecosystems is at serious risk due to the lack of natural regeneration and to the presence of a severe disease called oak decline that has caused the death of thousands of trees. The application of biotechnological tools, such as somatic embryogenesis, allows programs of genetic improvement of the species to be speeded up and helps in the conservation of its ecosystems. Somatic embryogenesis is currently considered one of the main biotechnological techniques that has demonstrated significant benefits when has applied to forest tree species, providing significant advantages such as mass propagation, genetic transformation, application of synthetic seed, and cryopreservation of elite genotypes. In this report, the state of the art of somatic embryogenesis in holm oak is reviewed. Factors affecting the induction (plant donor age, type of explant, or plant growth regulators) and maintenance and proliferation of the embryogenic cultures are summarized. Advances on the conversion of somatic embryos into plants and on the acclimatization of these plantlets, as well as the results obtained on the application of the genetic transformation and the cryopreservation procedures to holm oak embryogenic cultures, are also presented.
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Affiliation(s)
- María Teresa Martínez
- Instituto de Investigaciones Agrobiológicas de Galicia (IIAG-CSIC), Santiago de Compostela, Spain
| | | | - Isabel Arrillaga
- ISIC/ERI Biotec/Med, Departamento de Biología Vegetal, Facultad de Farmacia, Universitat de València, Valencia, Spain
| | - Vanesa Cano
- Instituto de Investigaciones Agrobiológicas de Galicia (IIAG-CSIC), Santiago de Compostela, Spain
| | - Marián Morcillo
- ISIC/ERI Biotec/Med, Departamento de Biología Vegetal, Facultad de Farmacia, Universitat de València, Valencia, Spain
| | - María José Cernadas
- Instituto de Investigaciones Agrobiológicas de Galicia (IIAG-CSIC), Santiago de Compostela, Spain
| | - Elena Corredoira
- Instituto de Investigaciones Agrobiológicas de Galicia (IIAG-CSIC), Santiago de Compostela, Spain
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19
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Zhu C, Shi F, Chen Y, Wang M, Zhao Y, Geng G. Transcriptome Analysis of Chinese Chestnut ( Castanea mollissima Blume) in Response to Dryocosmus kuriphilus Yasumatsu Infestation. Int J Mol Sci 2019; 20:ijms20040855. [PMID: 30781446 PMCID: PMC6412832 DOI: 10.3390/ijms20040855] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/01/2019] [Accepted: 02/10/2019] [Indexed: 12/28/2022] Open
Abstract
Chinese chestnut (Castanea mollissima Blume) can be infested by Dryocosmus kuriphilus Yasumatsu, resulting in gall formation and yield losses. Research on the control of gall wasps using genomics approaches is rarely reported. We used RNA-seq to investigate the dynamic changes in the genes of a chestnut species (C. mollissima B.) during four gall-formation stages caused by D. kuriphilus. A total of 21,306 genes were annotated by BLAST in databases. Transcriptome comparison between different gall-formation stages revealed many genes that were differentially expressed compared to the control. Among these, 2410, 7373, 6294, and 9412 genes were differentially expressed in four gall-formation stages: initiation stage (A), early growth stage (B), late growth stage (C), and maturation stage (D), respectively. Annotation analysis indicated that many metabolic processes (e.g., phenylpropanoid biosynthesis, secondary metabolism, plant⁻pathogen interaction) were affected. Interesting genes encoding putative components of signal transduction, stress response, and transcription factors were also differentially regulated. These genes might play important roles in response to D. kuriphilus gall formation. These new data on the mechanism by which D. kuriphilus infests chestnuts could help improve chestnut resistance.
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Affiliation(s)
- Cancan Zhu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
| | - Fenghou Shi
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China.
| | - Yu Chen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
| | - Min Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
| | - Yuqiang Zhao
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
| | - Guomin Geng
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
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20
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LaBonte NR, Woeste KE. Pooled whole-genome sequencing of interspecific chestnut ( Castanea) hybrids reveals loci associated with differences in caching behavior of fox squirrels ( Sciurus niger L.). Ecol Evol 2018; 8:10638-10654. [PMID: 30519394 PMCID: PMC6262733 DOI: 10.1002/ece3.4336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/07/2018] [Accepted: 06/10/2018] [Indexed: 12/30/2022] Open
Abstract
Dispersal of seeds by scatter-hoarding rodents is common among tropical and temperate tree species, including chestnuts in the genus Castanea. Backcrossed (BC) interspecific hybrid chestnuts exhibit wide variation in seed traits: as the parent species (Castanea dentata and C. mollissima) have distinct seed phenotypes and tend to be handled differently by seed dispersers, phenotypic variation in BC trees is likely due to inheritance of genes that have undergone divergent evolution in the parent species. To identify candidate genomic regions for interspecific differences in seed dispersal, we used tagged seeds to measure average dispersal distance for seeds of third-generation BC chestnuts and sequenced pooled whole genomes of mother trees with contrasting seed dispersal: high caching rate/long distance; low caching rate/short distance; no caching. Candidate regions affecting seed dispersal were identified as loci with more C. mollissima alleles in the high caching rate/ long-distance pool than expected by chance and observed in the other two pools. Functional annotations of candidate regions included predicted lipid metabolism, dormancy regulation, seed development, and carbohydrate metabolism genes. The results support the hypothesis that perception of seed dormancy is a predominant factor in squirrel caching decisions, and also indicate profitable directions for future work on the evolutionary genomics of trees and coevolved seed dispersers.
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Affiliation(s)
| | - Keith E. Woeste
- USDA Forest ServiceNorthern Research StationHardwood Tree Improvement and Regeneration CenterWest LafayetteIndiana
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21
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Zhang L, Wang Z, Shi G, Yang H, Wang X, Zhao H, Zhao S. Effects of drying methods on the nutritional aspects, flavor, and processing properties of Chinese chestnuts. Journal of Food Science and Technology 2018; 55:3391-3398. [PMID: 30150797 DOI: 10.1007/s13197-018-3227-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 04/09/2018] [Accepted: 05/10/2018] [Indexed: 10/28/2022]
Abstract
To select a suitable drying process for using chestnut products in the food industry, this study investigated the effect of five drying methods, including natural drying, microwave drying (MD), hot air drying (HAD), freeze-vacuum drying (FVD) and microwave-vacuum drying (MVD) on the nutritional composition, flavor, and functional properties of dried chestnuts. The results indicated that the nutritional aspects and functional properties of chestnuts were enhanced by the freeze-drying process compared with the other four drying methods. The quality of the chestnuts dried using the MVD was second to the FVD. The hot-air dried products were quite similar to the naturally dried samples in terms of their functional component content and processability. In terms of the produce texture, the HAD was found to be the best. In total, 45 flavor components were identified in the samples, which comprised the following: 5 aldehydes, 4 alcohols, 4 esters, 8 terpenes, 16 hydrocarbons and, 8 others substances. The highest relative content of the ingredients in microwave-vacuum dried samples was pyrazine and 3-ethyl-2, 5-dimethyl. In the samples treated using the other four drying methods, benzyl alcohol was the ingredient with the highest concentration. Considering the fast drying rate, low energy consumption, and improved quality of chestnut products, MVD is the most suitable dehydration method for commercial production of Chinese chestnuts.
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Affiliation(s)
- Le Zhang
- Agricultural Products Processing Center, Henan Academy of Agricultural Sciences, No. 115 Huayuan Road, Zhengzhou, China
| | - Zhaogai Wang
- Agricultural Products Processing Center, Henan Academy of Agricultural Sciences, No. 115 Huayuan Road, Zhengzhou, China
| | - Guanying Shi
- Agricultural Products Processing Center, Henan Academy of Agricultural Sciences, No. 115 Huayuan Road, Zhengzhou, China
| | - Hui Yang
- Agricultural Products Processing Center, Henan Academy of Agricultural Sciences, No. 115 Huayuan Road, Zhengzhou, China
| | - Xiaomin Wang
- Agricultural Products Processing Center, Henan Academy of Agricultural Sciences, No. 115 Huayuan Road, Zhengzhou, China
| | - Hongyuan Zhao
- Agricultural Products Processing Center, Henan Academy of Agricultural Sciences, No. 115 Huayuan Road, Zhengzhou, China
| | - Shouhuan Zhao
- Agricultural Products Processing Center, Henan Academy of Agricultural Sciences, No. 115 Huayuan Road, Zhengzhou, China
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22
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Zhu S, Wang Y, Xu X, Liu T, Wu D, Zheng X, Tang S, Dai Q. Potential use of high-throughput sequencing of soil microbial communities for estimating the adverse effects of continuous cropping on ramie (Boehmeria nivea L. Gaud). PLoS One 2018; 13:e0197095. [PMID: 29750808 PMCID: PMC5947917 DOI: 10.1371/journal.pone.0197095] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 04/26/2018] [Indexed: 01/09/2023] Open
Abstract
Ramie (Boehmeria nivea L. Gaud) fiber, one of the most important natural fibers, is extracted from stem bark. Continuous cropping is the main obstacle to ramie stem growth and a major cause of reduced yields. Root-associated microbes play crucial roles in plant growth and health. In this study, we investigated differences between microbial communities in the soil of healthy and continuously cropped ramie plants, and sought to identify potential mechanisms whereby these communities could counteract the problems posed by continuous cropping. Paired-end Illumina MiSeq analysis of 16S rRNA and ITS gene amplicons was employed to study bacterial and fungal communities. Long-term monoculture of ramie significantly decreased fiber yields and altered soil microbial communities. Our findings revealed how microbial communities and functional diversity varied according to the planting year and plant health status. Soil bacterial diversity increased with the period of ramie monoculture, whereas no significant differences were observed for fungi. Sequence analyses revealed that Firmicutes, Proteobacteria, and Acidobacteria were the most abundant bacterial phyla. Firmicutes abundance decreased with the period of ramie monoculture and correlated positively with the stem length, stem diameter, and fiber yield. The Actinobacteria, Chloroflexi, and Zygomycota phyla exhibited a significant (P < 0.05) negative correlation with yields during continuous cultivation. Some Actinobacteria members showed reduced microbial diversity, which prevented continuous ramie cropping. Ascomycota, Zygomycota, and Basidiomycota were the main fungal phyla. The relatively high abundance of Bacillus observed in healthy ramie may contribute to disease suppression, thereby promoting ramie growth. In summary, soil weakness and increased disease in ramie plants after long-term continuous cropping can be attributed to changes in soil microbes, a reduction in beneficial microbes, and an accumulation of harmful microbes.
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Affiliation(s)
- Siyuan Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan, P.R. China
- * E-mail: (SZ); (QD)
| | - Yanzhou Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan, P.R. China
| | - Xiaomin Xu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan, P.R. China
| | - Touming Liu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan, P.R. China
| | - Duanqing Wu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan, P.R. China
| | - Xia Zheng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan, P.R. China
| | - Shouwei Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan, P.R. China
| | - Qiuzhong Dai
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, Hunan, P.R. China
- * E-mail: (SZ); (QD)
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23
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Lu X, Kong J, Meng X, Cao B, Luo K, Dai P, Luan S. Identification of SNP markers associated with tolerance to ammonia toxicity by selective genotyping from de novo assembled transcriptome in Litopenaeus vannamei. FISH & SHELLFISH IMMUNOLOGY 2018; 73:158-166. [PMID: 29208499 DOI: 10.1016/j.fsi.2017.12.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 11/26/2017] [Accepted: 12/01/2017] [Indexed: 06/07/2023]
Abstract
The high concentration of ammonia from deteriorated aquaculture environments and the intensive culture system could increase the susceptibility to pathogens and even cause high mortality in Litopenaeus vannamei. In addition, we have revealed that the ammonia-tolerant shrimp also have high disease resistance in L. vannamei. In the present study, in order to identify SNP markers associated with tolerance to ammonia toxicity, we developed and characterized SNPs from our previous transcriptome sequencing data of ammonia-stressed and control groups, and a marker-trait association analysis was performed for marker-assisted selection (MAS) to increase production in L. vannamei. A total of 318,919 SNPs were identified from the transcriptome sequences, and 25,772 SNPs were found from the 1826 ammonia-responsive genes with functional annotation. We selected 49 SNPs from 26 ammonia-responsive genes that had strong homologies to known genes in the shrimp and probably involved in immune function as candidate markers for genotyping, among which 39 SNPs were polymorphic for further marker-trait association analysis with the ammonia-tolerant (AT) and ammonia-sensitive (AS) groups. Finally, 12 out of the 49 SNP markers were identified to be associated with ammonia tolerance, containing 10 loci with significantly different allele frequencies and 10 loci with significantly different genotyping frequencies between the AT and AS groups. Among the associated markers, the G allele of TSP-1 (the first locus from the thrombospondin gene), the A allele of TSP-3, and the C allele of XBP1-5 (the fifth locus from X-box binding protein 1) only presented in the AT groups, but they were absent from the AS groups, which would be the preference of the MAS for the ammonia-tolerant shrimp. In addition, when the 12 associated SNP markers were used for analysis, the genetic diversity of the AT groups were significantly higher than that of the AS groups, but when the 39 loci were used there was no difference. This is the first report for the markers associated with ammonia tolerance in this species, indirectly with disease resistance, which provided important potential for genetic selection to increase survival rate and production in shrimp farming.
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Affiliation(s)
- Xia Lu
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Jie Kong
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Xianhong Meng
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Baoxiang Cao
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Kun Luo
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Ping Dai
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Sheng Luan
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China.
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Rigling D, Prospero S. Cryphonectria parasitica, the causal agent of chestnut blight: invasion history, population biology and disease control. MOLECULAR PLANT PATHOLOGY 2018; 19:7-20. [PMID: 28142223 PMCID: PMC6638123 DOI: 10.1111/mpp.12542] [Citation(s) in RCA: 189] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 12/19/2016] [Accepted: 01/26/2017] [Indexed: 05/25/2023]
Abstract
Chestnut blight, caused by Cryphonectria parasitica, is a devastating disease infecting American and European chestnut trees. The pathogen is native to East Asia and was spread to other continents via infected chestnut plants. This review summarizes the current state of research on this pathogen with a special emphasis on its interaction with a hyperparasitic mycovirus that acts as a biological control agent of chestnut blight. TAXONOMY Cryphonectria parasitica (Murr.) Barr. is a Sordariomycete (ascomycete) fungus in the family Cryphonectriaceae (Order Diaporthales). Closely related species that can also be found on chestnut include Cryphonectria radicalis, Cryphonectria naterciae and Cryphonectria japonica. HOST RANGE Major hosts are species in the genus Castanea (Family Fagaceae), particularly the American chestnut (C. dentata), the European chestnut (C. sativa), the Chinese chestnut (C. mollissima) and the Japanese chestnut (C. crenata). Minor incidental hosts include oaks (Quercus spp.), maples (Acer spp.), European hornbeam (Carpinus betulus) and American chinkapin (Castanea pumila). DISEASE SYMPTOMS Cryphonectria parasitica causes perennial necrotic lesions (so-called cankers) on the bark of stems and branches of susceptible host trees, eventually leading to wilting of the plant part distal to the infection. Chestnut blight cankers are characterized by the presence of mycelial fans and fruiting bodies of the pathogen. Below the canker the tree may react by producing epicormic shoots. Non-lethal, superficial or callusing cankers on susceptible host trees are usually associated with mycovirus-induced hypovirulence. DISEASE CONTROL After the introduction of C. parasitica into a new area, eradication efforts by cutting and burning the infected plants/trees have mostly failed. In Europe, the mycovirus Cryphonectria hypovirus 1 (CHV-1) acts as a successful biological control agent of chestnut blight by causing so-called hypovirulence. CHV-1 infects C. parasitica and reduces its parasitic growth and sporulation capacity. Individual cankers can be therapeutically treated with hypovirus-infected C. parasitica strains. The hypovirus may subsequently spread to untreated cankers and become established in the C. parasitica population. Hypovirulence is present in many chestnut-growing regions of Europe, either resulting naturally or after biological control treatments. In North America, disease management of chestnut blight is mainly focused on breeding with the goal to backcross the Chinese chestnut's blight resistance into the American chestnut genome.
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Affiliation(s)
- Daniel Rigling
- Swiss Federal Institute for ForestSnow and Landscape Research (WSL)Birmensdorf8903Switzerland
| | - Simone Prospero
- Swiss Federal Institute for ForestSnow and Landscape Research (WSL)Birmensdorf8903Switzerland
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25
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Sharma V, Salwan R, Sharma PN, Gulati A. Integrated Translatome and Proteome: Approach for Accurate Portraying of Widespread Multifunctional Aspects of Trichoderma. Front Microbiol 2017; 8:1602. [PMID: 28900417 PMCID: PMC5581810 DOI: 10.3389/fmicb.2017.01602] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/07/2017] [Indexed: 12/31/2022] Open
Abstract
Genome-wide studies of transcripts expression help in systematic monitoring of genes and allow targeting of candidate genes for future research. In contrast to relatively stable genomic data, the expression of genes is dynamic and regulated both at time and space level at different level in. The variation in the rate of translation is specific for each protein. Both the inherent nature of an mRNA molecule to be translated and the external environmental stimuli can affect the efficiency of the translation process. In biocontrol agents (BCAs), the molecular response at translational level may represents noise-like response of absolute transcript level and an adaptive response to physiological and pathological situations representing subset of mRNAs population actively translated in a cell. The molecular responses of biocontrol are complex and involve multistage regulation of number of genes. The use of high-throughput techniques has led to rapid increase in volume of transcriptomics data of Trichoderma. In general, almost half of the variations of transcriptome and protein level are due to translational control. Thus, studies are required to integrate raw information from different “omics” approaches for accurate depiction of translational response of BCAs in interaction with plants and plant pathogens. The studies on translational status of only active mRNAs bridging with proteome data will help in accurate characterization of only a subset of mRNAs actively engaged in translation. This review highlights the associated bottlenecks and use of state-of-the-art procedures in addressing the gap to accelerate future accomplishment of biocontrol mechanisms.
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Affiliation(s)
- Vivek Sharma
- Department of Plant Pathology, Choudhary Sarwan Kumar Himachal Pradesh Agricultural UniversityPalampur, India
| | - Richa Salwan
- Department of Veterinary Microbiology, Choudhary Sarwan Kumar Himachal Pradesh Agricultural UniversityPalampur, India
| | - P N Sharma
- Department of Plant Pathology, Choudhary Sarwan Kumar Himachal Pradesh Agricultural UniversityPalampur, India
| | - Arvind Gulati
- Institute of Himalayan Bioresource TechnologyPalampur, India
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Ćalić I, Koch J, Carey D, Addo-Quaye C, Carlson JE, Neale DB. Genome-wide association study identifies a major gene for beech bark disease resistance in American beech (Fagus grandifolia Ehrh.). BMC Genomics 2017; 18:547. [PMID: 28728575 PMCID: PMC5520234 DOI: 10.1186/s12864-017-3931-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 07/07/2017] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND The American Beech tree (Fagus grandifolia Ehrh.), native to eastern North America, is ecologically important and provides high quality wood products. This species is susceptible to beech bark disease (BBD) and is facing high rates of mortality in North America. The disease occurs from an interaction between the woolly beech scale insect (Cryptococcus fagisuga), one of two species of the fungus Neonectria (N. faginata or N. ditissima), and American Beech trees. METHODS In this case-control genome-wide association study (GWAS), we tested 16 K high quality SNPs using the Affymetrix Axiom 1.5 K - 50 K assay to genotype an association population of 514 individuals. We also conducted linkage analysis in a full-sib family of 115 individuals. Fisher's exact test and logistic regression tests were performed to test associations between SNPs and phenotypes. RESULTS Association tests revealed four highly significant SNPs on chromosome (Chr) 5 for a single gene (Mt), which encodes a mRNA for metallothionein-like protein (metal ion binding) in Fagus sylvatica. Metallothioneins represent Cys-rich metal chelators able to coordinate metal atoms and may play an important role in the resistance mechanisms against beech scale insect. CONCLUSION The GWAS study has identified a single locus of major effect contributing to beech bark disease resistance. Knowledge of this genetic locus contributing to resistance might be used in applied breeding, conservation and restoration programs.
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Affiliation(s)
- Irina Ćalić
- Department of Plant Sciences, University of California, Davis, CA 95616 USA
| | - Jennifer Koch
- USDA Forest Service, Northern Research Station, Forestry Sciences Laboratory, Delaware, OH 43015 USA
| | - David Carey
- USDA Forest Service, Northern Research Station, Forestry Sciences Laboratory, Delaware, OH 43015 USA
| | - Charles Addo-Quaye
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, 47907 USA
- Present address: Division of Natural Sciences and Mathematics, Lewis-Clark State College, 500 8th Avenue, Lewiston, ID 83501 USA
| | - John E. Carlson
- Schatz Center for Tree Molecular Genetics, Department of Ecosystem Science and Management, Pennsylvania State University, University Park, PA 16802 USA
| | - David B. Neale
- Department of Plant Sciences, University of California, Davis, CA 95616 USA
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Ahmed J, Al-Attar H. Structural properties of high-pressure-treated chestnut flour dispersions. INTERNATIONAL JOURNAL OF FOOD PROPERTIES 2017. [DOI: 10.1080/10942912.2017.1311343] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jasim Ahmed
- Food and Nutrition Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
| | - Hasan Al-Attar
- Food and Nutrition Program, Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Safat, Kuwait
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28
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Transcriptome analysis of Cinnamomum longepaniculatum by high-throughput sequencing. ELECTRON J BIOTECHN 2017. [DOI: 10.1016/j.ejbt.2017.05.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
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Li Y, Zhang T, Zhou J, Yang S, Fan M, Sun X, Zhang M, Xu S, Cha M, Hu X, Qi L, Lin S, Liu S, Hu D. Transcriptome analysis of muskrat scented glands degeneration mechanism. PLoS One 2017; 12:e0176935. [PMID: 28472080 PMCID: PMC5417569 DOI: 10.1371/journal.pone.0176935] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 04/19/2017] [Indexed: 12/22/2022] Open
Abstract
The scented gland, a musk-secreting organ of male muskrats, shows clear seasonal changes. When entering the secreting season in March, scented glands gradually increase in size and active secretion starts. In September, scented glands become gradually smaller and secretion decreases. By November, scented glands are gradually replaced by adipose tissue. In this study, six healthy adult male muskrats were analysed: three from the secreting season (March) and three from the non-secreting season (November). Using RNA-Seq analysis, gene expression profiles of scented glands from both seasons were determined. Using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, we found that genes involved in calcium and TGF-beta signalling pathways were significantly more expressed in the non-secreting than in the secreting season. These changes in gene expression correlated with alterations in scented gland size. Both calcium and TGF-beta signalling pathways are important regulators of cell apoptosis, which may thus be involved in muskrat scented gland degeneration.
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Affiliation(s)
- Yimeng Li
- College of Nature Conservation, Beijing Forestry University, Beijing, People’s Republic of China
| | - Tianxiang Zhang
- College of Nature Conservation, Beijing Forestry University, Beijing, People’s Republic of China
| | - Juntong Zhou
- College of Nature Conservation, Beijing Forestry University, Beijing, People’s Republic of China
| | - Shuang Yang
- College of Nature Conservation, Beijing Forestry University, Beijing, People’s Republic of China
| | - Mengyuan Fan
- College of Nature Conservation, Beijing Forestry University, Beijing, People’s Republic of China
| | - Xiaoning Sun
- College of Nature Conservation, Beijing Forestry University, Beijing, People’s Republic of China
| | - Meishan Zhang
- College of Nature Conservation, Beijing Forestry University, Beijing, People’s Republic of China
| | - Shanghua Xu
- College of Nature Conservation, Beijing Forestry University, Beijing, People’s Republic of China
| | - Muha Cha
- College of Nature Conservation, Beijing Forestry University, Beijing, People’s Republic of China
| | - Xiaolong Hu
- College of Nature Conservation, Beijing Forestry University, Beijing, People’s Republic of China
| | - Lei Qi
- College of Nature Conservation, Beijing Forestry University, Beijing, People’s Republic of China
| | - Shaobi Lin
- Research Department, Zhangzhou Pien Tze Huang Pharmaceutical Co., Ltd, Zhangzhou City, Fujian Province, People’s Republic of China
| | - Shuqiang Liu
- College of Nature Conservation, Beijing Forestry University, Beijing, People’s Republic of China
- Research Department, Zhangzhou Pien Tze Huang Pharmaceutical Co., Ltd, Zhangzhou City, Fujian Province, People’s Republic of China
| | - Defu Hu
- College of Nature Conservation, Beijing Forestry University, Beijing, People’s Republic of China
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Ye DY, Qi YH, Cao SF, Wei BQ, Zhang HS. Histopathology combined with transcriptome analyses reveals the mechanism of resistance to Meloidogyne incognita in Cucumis metuliferus. JOURNAL OF PLANT PHYSIOLOGY 2017; 212:115-124. [PMID: 28314173 DOI: 10.1016/j.jplph.2017.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 02/05/2017] [Accepted: 02/07/2017] [Indexed: 05/08/2023]
Abstract
Root-knot nematodes (Meloidogyne spp.) cause serious threat to cucumber production. Cucumis metuliferus, a relative of cucumber, is reported to be resistant to Meloidogyne incognita, yet the underlying resistance mechanism remains unclear. In this study, the response of resistant C. metuliferus accession PI482443 following nematode infection was studied in comparison with susceptible C. sativus cv. Jinlv No.3. Roots of selected Cucumis seedings were analysed using histological and biochemical techniques. Transcriptome changes of the resistance reaction were investigated by RNA-seq. The results showed that penetration and development of the nematode in resistant plants were reduced when compared to susceptible plants. Infection of a resistant genotype with M. incognita resulted in a hypersensitive reaction. The induction of phenylalanine ammonia lyase and peroxidase activities after infection was greater in resistant than susceptible roots. Several of the most relevant genes for phenylpropanoid biosynthesis, plant hormone signal transduction, and the plant-pathogen interaction pathway that are involved in resistance to the nematode were significantly altered. The resistance in C. metuliferus PI482443 to M. incognita was associated with reduced nematode penetration, retardation of nematode development, and hypersensitive necrosis. The expression of genes resulting in the deposition of lignin, toxic compounds synthesis, cell wall reinforcement, suppression of nematode feeding and resistance protein accumulation, and activation of several transcription factors might all contribute to the resistance response to the pest. These results may lead to a better understanding of the resistance mechanism and aid in the identification of potential targets resistant to pests for cucumber improvement.
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Affiliation(s)
- De-You Ye
- Institute of Vegetables, Gansu Academy of Agricultural Sciences, Scientific Observations Experiment Station of Vegetables, Ministry of Agriculture in the Northwest of China, Lanzhou 730070, China.
| | - Yong-Hong Qi
- Institute of Plant Protection, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Su-Fang Cao
- Institute of Fruit and Floriculture Research, Gansu Academy of Agricultural Sciences, Lanzhou 730070, China
| | - Bing-Qiang Wei
- Institute of Vegetables, Gansu Academy of Agricultural Sciences, Scientific Observations Experiment Station of Vegetables, Ministry of Agriculture in the Northwest of China, Lanzhou 730070, China
| | - Hua-Sheng Zhang
- Institute of Vegetables, Gansu Academy of Agricultural Sciences, Scientific Observations Experiment Station of Vegetables, Ministry of Agriculture in the Northwest of China, Lanzhou 730070, China
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Zhao F, Durner J, Winkler JB, Traidl-Hoffmann C, Strom TM, Ernst D, Frank U. Pollen of common ragweed (Ambrosia artemisiifolia L.): Illumina-based de novo sequencing and differential transcript expression upon elevated NO 2/O 3. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 224:503-514. [PMID: 28284545 DOI: 10.1016/j.envpol.2017.02.032] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 12/15/2016] [Accepted: 02/14/2017] [Indexed: 05/28/2023]
Abstract
Common ragweed (Ambrosia artemisiifolia L.) is a highly allergenic annual ruderal plant and native to Northern America, but now also spreading across Europe. Air pollution and climate change will not only affect plant growth, pollen production and duration of the whole pollen season, but also the amount of allergenic encoding transcripts and proteins of the pollen. The objective of this study was to get a better understanding of transcriptional changes in ragweed pollen upon NO2 and O3 fumigation. This will also contribute to a systems biology approach to understand the reaction of the allergenic pollen to air pollution and climate change. Ragweed plants were grown in climate chambers under controlled conditions and fumigated with enhanced levels of NO2 and O3. Illumina sequencing and de novo assembly revealed significant differentially expressed transcripts, belonging to different gene ontology (GO) terms that were grouped into biological process and molecular function. Transcript levels of the known Amb a ragweed encoding allergens were clearly up-regulated under elevated NO2, whereas the amount of allergen encoding transcripts was more variable under elevated O3 conditions. Moreover transcripts encoding allergen known from other plants could be identified. The transcriptional changes in ragweed pollen upon elevated NO2 fumigation indicates that air pollution will alter the transcriptome of the pollen. The changed levels of allergenic encoding transcripts may have an influence on the total allergenic potential of ragweed pollen.
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Affiliation(s)
- Feng Zhao
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.
| | - Jörg Durner
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany; Biochemical Plant Pathology, Technische Universität München, Center of Life and Food Sciences Weihenstephan, Freising-Weihenstephan, Germany.
| | - J Barbro Winkler
- Research Unit Environmental Simulation, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.
| | - Claudia Traidl-Hoffmann
- Institute of Environmental Medicine, UNIKA-T, Augsburg, Germany; CK-CARE, Christine Kühne - Center for Allergy Research and Education, Davos-Wolfgang, Switzerland.
| | - Tim-Matthias Strom
- Institute of Human Genetics, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany.
| | - Dieter Ernst
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany; CK-CARE, Christine Kühne - Center for Allergy Research and Education, Davos-Wolfgang, Switzerland.
| | - Ulrike Frank
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany; CK-CARE, Christine Kühne - Center for Allergy Research and Education, Davos-Wolfgang, Switzerland.
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Cipollini M, Dingley NR, Felch P, Maddox C. Evaluation of phenotypic traits and blight-resistance in an American chestnut backcross orchard in Georgia. Glob Ecol Conserv 2017. [DOI: 10.1016/j.gecco.2017.01.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Lu X, Kong J, Luan S, Dai P, Meng X, Cao B, Luo K. Transcriptome Analysis of the Hepatopancreas in the Pacific White Shrimp (Litopenaeus vannamei) under Acute Ammonia Stress. PLoS One 2016; 11:e0164396. [PMID: 27760162 PMCID: PMC5070816 DOI: 10.1371/journal.pone.0164396] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 09/23/2016] [Indexed: 01/08/2023] Open
Abstract
In the practical farming of Litopenaeus vannamei, the intensive culture system and environmental pollution usually results in a high concentration of ammonia, which usually brings large detrimental effects to shrimp, such as increasing the susceptibility to pathogens, reducing growth, decreasing osmoregulatory capacity, increasing the molting frequency, and even causing high mortality. However, little information is available on the molecular mechanisms of the detrimental effects of ammonia stress in shrimp. In this study, we performed comparative transcriptome analysis between ammonia-challenged and control groups from the same family of L. vannamei to identify the key genes and pathways response to ammonia stress. The comparative transcriptome analysis identified 136 significantly differentially expressed genes that have high homologies with the known proteins in aquatic species, among which 94 genes are reported potentially related to immune function, and the rest of the genes are involved in apoptosis, growth, molting, and osmoregulation. Fourteen GO terms and 6 KEGG pathways were identified to be significantly changed by ammonia stress. In these GO terms, 13 genes have been studied in aquatic species, and 11 of them were reported potentially involved in immune defense and two genes were related to molting. In the significantly changed KEGG pathways, all the 7 significantly changed genes have been reported in shrimp, and four of them were potentially involved in immune defense and the other three were related to molting, defending toxicity, and osmoregulation, respectively. In addition, majority of the significantly changed genes involved in nitrogen metabolisms that play an important role in reducing ammonia toxicity failed to perform the protection function. The present results have supplied molecular level support for the previous founding of the detrimental effects of ammonia stress in shrimp, which is a prerequisite for better understanding the molecular mechanism of the immunosuppression from ammonia stress.
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Affiliation(s)
- Xia Lu
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Jie Kong
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- * E-mail:
| | - Sheng Luan
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Ping Dai
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Xianhong Meng
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Baoxiang Cao
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
| | - Kun Luo
- Key Laboratory of Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
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Khan A, Sovero V, Gemenet D. Genome-assisted Breeding For Drought Resistance. Curr Genomics 2016; 17:330-42. [PMID: 27499682 PMCID: PMC4955035 DOI: 10.2174/1389202917999160211101417] [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: 08/08/2015] [Revised: 09/17/2015] [Accepted: 09/19/2015] [Indexed: 11/30/2022] Open
Abstract
Drought stress caused by unpredictable precipitation poses a major threat to food production worldwide, and its impact is only expected to increase with the further onset of climate change. Understanding the effect of drought stress on crops and plants' response is critical for developing improved varieties with stable high yield to fill a growing food gap from an increasing population depending on decreasing land and water resources. When a plant encounters drought stress, it may use multiple response types, depending on environmental conditions, drought stress intensity and duration, and the physiological stage of the plant. Drought stress responses can be divided into four broad types: drought escape, drought avoidance, drought tolerance, and drought recovery, each characterized by interacting mechanisms, which may together be referred to as drought resistance mechanisms. The complex nature of drought resistance requires a multi-pronged approach to breed new varieties with stable and enhanced yield under drought stress conditions. High throughput genomics and phenomics allow marker-assisted selection (MAS) and genomic selection (GS), which offer rapid and targeted improvement of populations and identification of parents for rapid genetic gains and improved drought-resistant varieties. Using these approaches together with appropriate genetic diversity, databases, analytical tools, and well-characterized drought stress scenarios, weather and soil data, new varieties with improved drought resistance corresponding to grower preferences can be introduced into target regions rapidly.
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Affiliation(s)
- Awais Khan
- International Potato Center (CIP), Avenida La Molina 1895, Lima 12,Peru
| | - Valpuri Sovero
- International Potato Center (CIP), Avenida La Molina 1895, Lima 12,Peru
| | - Dorcus Gemenet
- International Potato Center (CIP), Avenida La Molina 1895, Lima 12,Peru
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Liu T, Li X, Xie S, Wang L, Yang S. RNA-seq analysis of Paris polyphylla var. yunnanensis roots identified candidate genes for saponin synthesis. PLANT DIVERSITY 2016; 38:163-170. [PMID: 30159461 PMCID: PMC6112097 DOI: 10.1016/j.pld.2016.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 04/28/2016] [Accepted: 05/04/2016] [Indexed: 06/08/2023]
Abstract
Paris polyphylla Smith var. yunnanensis (Franch.) Hand.-Mazz. is a rhizomatous, herbaceous, perennial plant that has been used for more than a thousand years in traditional Chinese medicine. It is facing extinction due to overharvesting. Steroids are the major therapeutic components in Paris roots, the commercial value of which increases with age. To date, no genomic data on the species have been available. In this study, transcriptome analysis of an 8-year-old root and a 4-year-old root provided insight into the metabolic pathways that generate the steroids. Using Illumina sequencing technology, we generated a high-quality sequence and demonstrated de novo assembly and annotation of genes in the absence of prior genome information. Approximately 87,577 unique sequences, with an average length of 614 bases, were obtained from the root cells. Using bioinformatics methods, we annotated approximately 65.51% of the unique sequences by conducting a similarity search with known genes in the National Center for Biotechnology Information's non-redundant database. The unique transcripts were functionally classified using the Gene Ontology hierarchy and the Kyoto Encyclopedia of Genes and Genomes database. Of 3082 genes that were identified as significantly differentially expressed between roots of different ages, 1518 (49.25%) were upregulated and 1564 (50.75%) were downregulated in the older root. Metabolic pathway analysis predicted that 25 unigenes were responsible for the biosynthesis of the saponins steroids. These data represent a valuable resource for future genomic studies on this endangered species and will be valuable for efforts to genetically engineer P. polyphylla and facilitate saponin-rich plant development.
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Affiliation(s)
- Tao Liu
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, China
| | - Xiaoxian Li
- Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Shiqing Xie
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, China
| | - Ling Wang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, China
| | - Shengchao Yang
- Yunnan Research Center on Good Agricultural Practice for Dominant Chinese Medicinal Materials, Yunnan Agricultural University, Kunming, 650201, China
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Tsai CC, Wu KM, Chiang TY, Huang CY, Chou CH, Li SJ, Chiang YC. Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes. BMC Genomics 2016; 17:212. [PMID: 26960548 PMCID: PMC4784368 DOI: 10.1186/s12864-016-2508-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 02/22/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Gastrodia elata Blume (Orchidaceae) is an important Chinese medicine with several functional components. In the life cycle of G. elata, the orchid develops a symbiotic relationship with two compatible mycorrhizal fungi Mycena spp. and Armillaria mellea during seed germination to form vegetative propagation corm and vegetative growth to develop tubers, respectively. Gastrodin (p-hydroxymethylphenol-beta-D-glucoside) is the most important functional component in G. elata, and gastrodin significantly increases from vegetative propagation corms to tubers. To address the gene regulation mechanism in gastrodin biosynthesis in G. elata, a comparative analysis of de novo transcriptome sequencing among the vegetative propagation corms and tubers of G. elata and A. mellea was conducted using deep sequencing. RESULTS Transcriptome comparison between the vegetative propagation corms and juvenile tubers of G. elata revealed 703 differentially expressed unigenes, of which 298 and 405 unigenes were, respectively up-regulated (fold-change ≥ 2, q-value < 0.05, the trimmed mean of M-values (TMM)-normalized fragments per kilobase of transcript per Million mapped reads (FPKM) > 10) and down-regulated (fold-change ≤ 0.5, q-value <0.05, TMM-normalized FPKM > 10) in juvenile tubers. After Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, 112 up-regulated unigenes with KEGG Ortholog identifiers (KOids) or enzyme commission (EC) numbers were assigned to 159 isogroups involved in seventy-eight different pathways, and 132 down-regulated unigenes with KOids or EC numbers were assigned to 168 isogroups, involved in eighty different pathways. The analysis of the isogroup genes from all pathways revealed that the two unigenes TRINITY_DN54282_c0_g1 (putative monooxygenases) and TRINITY_DN50323_c0_g1 (putative glycosyltransferases) might participate in hydroxylation and glucosylation in the gastrodin biosynthetic pathway. CONCLUSIONS The gene expression of the two unique unigenes encoding monooxygenase and glycosyltransferase significantly increases from vegetative propagation corms to tubers, and the molecular basis of gastrodin biosynthesis in the tubers of G. elata is proposed.
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Affiliation(s)
- Chi-Chu Tsai
- Crop Improvement Division, Kaohsiung District Agricultural Improvement Station, Pingtung, 900, Taiwan.
- Graduate Institute of Biotechnology, National Pingtung University of Science and Technology, Pingtung, 912, Taiwan.
| | - Keh-Ming Wu
- Welgene Biotech. Co., Ltd., Taipei, 115, Taiwan.
| | - Tzen-Yuh Chiang
- Department of Life Science, Cheng-Kung University, Tainan, 701, Taiwan.
| | - Chun-Yen Huang
- Crop Improvement Division, Kaohsiung District Agricultural Improvement Station, Pingtung, 900, Taiwan.
| | - Chang-Hung Chou
- Research Center for Biodiversity, China Medical University, Taichung, 404, Taiwan.
| | - Shu-Ju Li
- Crop Improvement Division, Kaohsiung District Agricultural Improvement Station, Pingtung, 900, Taiwan.
| | - Yu-Chung Chiang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung, 804, Taiwan.
- Department of Biomedical Science and Environment Biology, Kaohsiung Medical University, Kaohsiung, 807, Taiwan.
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Zhang L, Ming R, Zhang J, Tao A, Fang P, Qi J. De novo transcriptome sequence and identification of major bast-related genes involved in cellulose biosynthesis in jute (Corchorus capsularis L.). BMC Genomics 2015; 16:1062. [PMID: 26666317 PMCID: PMC4678609 DOI: 10.1186/s12864-015-2256-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 11/30/2015] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Jute fiber, extracted from stem bast, is called golden fiber. It is essential for fiber improvement to discover the genes associated with jute development at the vegetative growth stage. However, only 858 EST sequences of jute were deposited in the GenBank database. Obviously, the public available data is far from sufficient to understand the molecular mechanism of the fiber biosynthesis. It is imperative to conduct transcriptomic sequence for jute, which can be used for the discovery of a number of new genes, especially genes involved in cellulose biosynthesis. RESULTS A total of 79,754,600 clean reads (7.98 Gb) were generated using Illumina paired-end sequencing. De novo assembly yielded 48,914 unigenes with an average length of 903 bp. By sequence similarity searching for known proteins, 27,962 (57.16 %) unigenes were annotated for their function. Out of these annotated unigenes, 21,856 and 11,190 unigenes were assigned to gene ontology (GO) and euKaryotic Ortholog Groups (KOG), respectively. Searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG) indicated that 14,216 unigenes were mapped to 268 KEGG pathways. Moreover, 5 Susy, 3 UGPase, 9 CesA, 18 CSL, 2 Kor (Korrigan), and 12 Cobra unigenes involving in cellulose biosynthesis were identified. Among these unigenes, the unigenes of comp11264_c0 (SuSy), comp24568_c0 (UGPase), comp11363_c0 (CesA), comp11363_c1 (CesA), comp24217_c0 (CesA), and comp23531_c0 (CesA), displayed relatively high expression level in stem bast using FPKM and RT-qPCR, indicating that they may have potential value of dissecting mechanism on cellulose biosynthesis in jute. In addition, a total of 12,518 putative gene-associate SNPs were called from these assembled uingenes. CONCLUSION We characterized the transcriptome of jute, discovered a broad survey of unigenes associated with vegetative growth and development, developed large-scale SNPs, and analyzed the expression patterns of genes involved in cellulose biosynthesis for bast fiber. All these provides a valuable genomics resource, which will accelerate the understanding of the mechanism of fiber development in jute.
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Affiliation(s)
- Liwu Zhang
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education / College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- Department of Plant Biology, University of Illlinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Ray Ming
- Department of Plant Biology, University of Illlinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Aifen Tao
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education / College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Pingping Fang
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education / College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Jianmin Qi
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education / College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Bazakos C, Manioudaki ME, Sarropoulou E, Spano T, Kalaitzis P. 454 Pyrosequencing of Olive (Olea europaea L.) Transcriptome in Response to Salinity. PLoS One 2015; 10:e0143000. [PMID: 26576008 PMCID: PMC4648586 DOI: 10.1371/journal.pone.0143000] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 10/29/2015] [Indexed: 11/19/2022] Open
Abstract
Olive (Olea europaea L.) is one of the most important crops in the Mediterranean region. The expansion of cultivation in areas irrigated with low quality and saline water has negative effects on growth and productivity however the investigation of the molecular basis of salt tolerance in olive trees has been only recently initiated. To this end, we investigated the molecular response of cultivar Kalamon to salinity stress using next-generation sequencing technology to explore the transcriptome profile of olive leaves and roots and identify differentially expressed genes that are related to salt tolerance response. Out of 291,958 obtained trimmed reads, 28,270 unique transcripts were identified of which 35% are annotated, a percentage that is comparable to similar reports on non-model plants. Among the 1,624 clusters in roots that comprise more than one read, 24 were differentially expressed comprising 9 down- and 15 up-regulated genes. Respectively, inleaves, among the 2,642 clusters, 70 were identified as differentially expressed, with 14 down- and 56 up-regulated genes. Using next-generation sequencing technology we were able to identify salt-response-related transcripts. Furthermore we provide an annotated transcriptome of olive as well as expression data, which are both significant tools for further molecular studies in olive.
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Affiliation(s)
- Christos Bazakos
- Department of Horticultural Genetics and Biotechnology, Mediterranean Agronomic Institute of Chania (MAICh), Crete, Greece
- Department of Horticulture, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Maria E. Manioudaki
- Department of Horticultural Genetics and Biotechnology, Mediterranean Agronomic Institute of Chania (MAICh), Crete, Greece
| | - Elena Sarropoulou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Crete, Greece
| | - Thodhoraq Spano
- Department of Horticultural Genetics and Biotechnology, Mediterranean Agronomic Institute of Chania (MAICh), Crete, Greece
| | - Panagiotis Kalaitzis
- Department of Horticultural Genetics and Biotechnology, Mediterranean Agronomic Institute of Chania (MAICh), Crete, Greece
- * E-mail:
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Sherman A, Rubinstein M, Eshed R, Benita M, Ish-Shalom M, Sharabi-Schwager M, Rozen A, Saada D, Cohen Y, Ophir R. Mango (Mangifera indica L.) germplasm diversity based on single nucleotide polymorphisms derived from the transcriptome. BMC PLANT BIOLOGY 2015; 15:277. [PMID: 26573148 PMCID: PMC4647706 DOI: 10.1186/s12870-015-0663-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 11/04/2015] [Indexed: 05/29/2023]
Abstract
BACKGROUND Germplasm collections are an important source for plant breeding, especially in fruit trees which have a long duration of juvenile period. Thus, efforts have been made to study the diversity of fruit tree collections. Even though mango is an economically important crop, most of the studies on diversity in mango collections have been conducted with a small number of genetic markers. RESULTS We describe a de novo transcriptome assembly from mango cultivar 'Keitt'. Variation discovery was performed using Illumina resequencing of 'Keitt' and 'Tommy Atkins' cultivars identified 332,016 single-nucleotide polymorphisms (SNPs) and 1903 simple-sequence repeats (SSRs). Most of the SSRs (70.1%) were of trinucleotide with the preponderance of motif (GGA/AAG)n and only 23.5% were di-nucleotide SSRs with the mostly of (AT/AT)n motif. Further investigation of the diversity in the Israeli mango collection was performed based on a subset of 293 SNPs. Those markers have divided the Israeli mango collection into two major groups: one group included mostly mango accessions from Southeast Asia (Malaysia, Thailand, Indonesia) and India and the other with mainly of Floridian and Israeli mango cultivars. The latter group was more polymorphic (FS=-0.1 on the average) and was more of an admixture than the former group. A slight population differentiation was detected (FST=0.03), suggesting that if the mango accessions of the western world apparently was originated from Southeast Asia, as has been previously suggested, the duration of cultivation was not long enough to develop a distinct genetic background. CONCLUSIONS Whole-transcriptome reconstruction was used to significantly broaden the mango's genetic variation resources, i.e., SNPs and SSRs. The set of SNP markers described in this study is novel. A subset of SNPs was sampled to explore the Israeli mango collection and most of them were polymorphic in many mango accessions. Therefore, we believe that these SNPs will be valuable as they recapitulate and strengthen the history of mango diversity.
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Affiliation(s)
- Amir Sherman
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
| | - Mor Rubinstein
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
| | - Ravit Eshed
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
| | - Miri Benita
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
| | - Mazal Ish-Shalom
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
| | - Michal Sharabi-Schwager
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
| | - Ada Rozen
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
| | - David Saada
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
| | - Yuval Cohen
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
| | - Ron Ophir
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel.
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Staton M, Zhebentyayeva T, Olukolu B, Fang GC, Nelson D, Carlson JE, Abbott AG. Substantial genome synteny preservation among woody angiosperm species: comparative genomics of Chinese chestnut (Castanea mollissima) and plant reference genomes. BMC Genomics 2015; 16:744. [PMID: 26438416 PMCID: PMC4595192 DOI: 10.1186/s12864-015-1942-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 09/19/2015] [Indexed: 01/03/2023] Open
Abstract
Background Chinese chestnut (Castanea mollissima) has emerged as a model species for the Fagaceae family with extensive genomic resources including a physical map, a dense genetic map and quantitative trait loci (QTLs) for chestnut blight resistance. These resources enable comparative genomics analyses relative to model plants. We assessed the degree of conservation between the chestnut genome and other well annotated and assembled plant genomic sequences, focusing on the QTL regions of most interest to the chestnut breeding community. Results The integrated physical and genetic map of Chinese chestnut has been improved to now include 858 shared sequence-based markers. The utility of the integrated map has also been improved through the addition of 42,970 BAC (bacterial artificial chromosome) end sequences spanning over 26 million bases of the estimated 800 Mb chestnut genome. Synteny between chestnut and ten model plant species was conducted on a macro-syntenic scale using sequences from both individual probes and BAC end sequences across the chestnut physical map. Blocks of synteny with chestnut were found in all ten reference species, with the percent of the chestnut physical map that could be aligned ranging from 10 to 39 %. The integrated genetic and physical map was utilized to identify BACs that spanned the three previously identified QTL regions conferring blight resistance. The clones were pooled and sequenced, yielding 396 sequence scaffolds covering 13.9 Mbp. Comparative genomic analysis on a microsytenic scale, using the QTL-associated genomic sequence, identified synteny from chestnut to other plant genomes ranging from 5.4 to 12.9 % of the genome sequences aligning. Conclusions On both the macro- and micro-synteny levels, the peach, grape and poplar genomes were found to be the most structurally conserved with chestnut. Interestingly, these results did not strictly follow the expectation that decreased phylogenetic distance would correspond to increased levels of genome preservation, but rather suggest the additional influence of life-history traits on preservation of synteny. The regions of synteny that were detected provide an important tool for defining and cataloging genes in the QTL regions for advancing chestnut blight resistance research. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1942-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Margaret Staton
- Department of Entomology and Plant Pathology, University of Tennessee Institute of Agriculture, Knoxville, TN, USA.
| | | | - Bode Olukolu
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, USA.
| | | | - Dana Nelson
- Southern Institute of Forest Genetics, Southern Research Station, U.S. Forest Service, Saucier, MS, USA.
| | - John E Carlson
- The School of Forest Resources and The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA.
| | - Albert G Abbott
- Department of Forestry, Forest Health Research and Education Center, Lexington, KY, USA.
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Tuan PA, Chung E, Thwe AA, Li X, Kim YB, Mariadhas VA, Al-Dhabi NA, Lee JH, Park SU. Transcriptional Profiling and Molecular Characterization of Astragalosides, Calycosin, and Calycosin-7-O-β-D-glucoside Biosynthesis in the Hairy Roots of Astragalus membranaceus in Response to Methyl Jasmonate. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:6231-6240. [PMID: 26072674 DOI: 10.1021/acs.jafc.5b01822] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We used the next-generation Illumina/Solexa HiSeq2000 platform on RNA analysis to investigate the transcriptome of Astragalus membranaceus hairy roots in response to 100 μM methyl jasmonate (MeJA). In total, 77,758,230 clean reads were assembled into 48,636 transcripts (average length of 1398 bp), which were clustered into 23,658 loci (genes). Of these, 19,940 genes were annotated by BLASTx searches. In addition, DESeq analysis showed that 2127 genes were up-regulated, while 1247 genes were down-regulated by MeJA. Seventeen novel astragaloside (AST) biosynthetic genes and seven novel calycosin and calycosin-7-O-β-D-glucoside (CG) biosynthetic genes were isolated. The accumulation of ASTs, calycosin, and CG increased significantly in MeJA-treated hairy roots compared with control hairy roots. Our findings will provide a valuable resource for molecular characterization of AST, calycosin, and CG biosynthetic pathways and may lead to new approaches to maximize their production and biomass productivity in the hairy roots of A. membranaceus.
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Affiliation(s)
- Pham Anh Tuan
- †Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 305-764, Korea
| | - Eunsook Chung
- ‡Department of Genetic Engineering, Dong-A University, Busan 604-714, Korea
| | - Aye Aye Thwe
- †Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 305-764, Korea
| | - Xiaohua Li
- †Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 305-764, Korea
| | | | - Valan Arasu Mariadhas
- §Department of Botany and Microbiology, Addiriyah Chair for Environmental Studies, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Naif Abdullah Al-Dhabi
- §Department of Botany and Microbiology, Addiriyah Chair for Environmental Studies, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Jai-Heon Lee
- ‡Department of Genetic Engineering, Dong-A University, Busan 604-714, Korea
| | - Sang Un Park
- †Department of Crop Science, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 305-764, Korea
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Plomion C, Aury JM, Amselem J, Alaeitabar T, Barbe V, Belser C, Bergès H, Bodénès C, Boudet N, Boury C, Canaguier A, Couloux A, Da Silva C, Duplessis S, Ehrenmann F, Estrada-Mairey B, Fouteau S, Francillonne N, Gaspin C, Guichard C, Klopp C, Labadie K, Lalanne C, Le Clainche I, Leplé JC, Le Provost G, Leroy T, Lesur I, Martin F, Mercier J, Michotey C, Murat F, Salin F, Steinbach D, Faivre-Rampant P, Wincker P, Salse J, Quesneville H, Kremer A. Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies. Mol Ecol Resour 2015; 16:254-65. [PMID: 25944057 DOI: 10.1111/1755-0998.12425] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/27/2015] [Accepted: 04/30/2015] [Indexed: 12/31/2022]
Abstract
The 1.5 Gbp/2C genome of pedunculate oak (Quercus robur) has been sequenced. A strategy was established for dealing with the challenges imposed by the sequencing of such a large, complex and highly heterozygous genome by a whole-genome shotgun (WGS) approach, without the use of costly and time-consuming methods, such as fosmid or BAC clone-based hierarchical sequencing methods. The sequencing strategy combined short and long reads. Over 49 million reads provided by Roche 454 GS-FLX technology were assembled into contigs and combined with shorter Illumina sequence reads from paired-end and mate-pair libraries of different insert sizes, to build scaffolds. Errors were corrected and gaps filled with Illumina paired-end reads and contaminants detected, resulting in a total of 17,910 scaffolds (>2 kb) corresponding to 1.34 Gb. Fifty per cent of the assembly was accounted for by 1468 scaffolds (N50 of 260 kb). Initial comparison with the phylogenetically related Prunus persica gene model indicated that genes for 84.6% of the proteins present in peach (mean protein coverage of 90.5%) were present in our assembly. The second and third steps in this project are genome annotation and the assignment of scaffolds to the oak genetic linkage map. In accordance with the Bermuda and Fort Lauderdale agreements and the more recent Toronto Statement, the oak genome data have been released into public sequence repositories in advance of publication. In this presubmission paper, the oak genome consortium describes its principal lines of work and future directions for analyses of the nature, function and evolution of the oak genome.
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Affiliation(s)
- Christophe Plomion
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | - Jean-Marc Aury
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | - Joëlle Amselem
- INRA, Unité de Recherche Génomique Info (URGI), Versailles, F78026, France
| | - Tina Alaeitabar
- INRA, Unité de Recherche Génomique Info (URGI), Versailles, F78026, France
| | - Valérie Barbe
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | - Caroline Belser
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | | | - Catherine Bodénès
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | | | - Christophe Boury
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | | | - Arnaud Couloux
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | - Corinne Da Silva
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | - Sébastien Duplessis
- INRA, UMR1136 INRA-Université de Lorraine, Interactions Arbres/Micro-organismes, Laboratoire d'Excellence ARBRE, Champenoux, F-54280, France
| | - François Ehrenmann
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | - Barbara Estrada-Mairey
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | - Stéphanie Fouteau
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | | | - Christine Gaspin
- Plateforme bioinformatique Toulouse Midi-Pyrénées, UBIA, INRA, Castanet-Tolosan, F-31326, France
| | | | - Christophe Klopp
- Plateforme bioinformatique Toulouse Midi-Pyrénées, UBIA, INRA, Castanet-Tolosan, F-31326, France
| | - Karine Labadie
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | - Céline Lalanne
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | | | - Jean-Charles Leplé
- INRA, UR0588 Amélioration Génétique et Physiologie Forestières, Orléans, F-45075, France
| | - Grégoire Le Provost
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | - Thibault Leroy
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | - Isabelle Lesur
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | - Francis Martin
- INRA, UMR1136 INRA-Université de Lorraine, Interactions Arbres/Micro-organismes, Laboratoire d'Excellence ARBRE, Champenoux, F-54280, France
| | - Jonathan Mercier
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France
| | - Célia Michotey
- INRA, Unité de Recherche Génomique Info (URGI), Versailles, F78026, France
| | - Florent Murat
- INRA/UBP UMR 1095, Laboratoire Génétique, Diversité et Ecophysiologie des Céréales, Clermont-Ferrand, F-63039, France
| | - Franck Salin
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
| | - Delphine Steinbach
- INRA, Unité de Recherche Génomique Info (URGI), Versailles, F78026, France
| | | | - Patrick Wincker
- Commissariat à l'Energie Atomique (CEA), Institut de Génomique (IG), Genoscope, Evry, 91057, France.,Université d'Evry Val d'Essone, UMR 8030, Evry, CP5706, France.,Centre National de Recherche Scientifique (CNRS), UMR 8030, Evry, CP5706, France
| | - Jérôme Salse
- INRA/UBP UMR 1095, Laboratoire Génétique, Diversité et Ecophysiologie des Céréales, Clermont-Ferrand, F-63039, France
| | - Hadi Quesneville
- INRA, Unité de Recherche Génomique Info (URGI), Versailles, F78026, France
| | - Antoine Kremer
- INRA, UMR1202, BIOGECO, Cestas, F-33610, France.,University of Bordeaux, BIOGECO, UMR1202, Talence, F-33170, France
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Zou LQ, Kuang XJ, Sun C. Advances in Transcriptomic Studies and Ginsenoside Biosynthesis of American Ginseng. CHINESE HERBAL MEDICINES 2015. [DOI: 10.1016/s1674-6384(15)60028-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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44
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Nejat N, Cahill DM, Vadamalai G, Ziemann M, Rookes J, Naderali N. Transcriptomics-based analysis using RNA-Seq of the coconut (Cocos nucifera) leaf in response to yellow decline phytoplasma infection. Mol Genet Genomics 2015; 290:1899-910. [PMID: 25893418 DOI: 10.1007/s00438-015-1046-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 04/06/2015] [Indexed: 12/25/2022]
Abstract
Invasive phytoplasmas wreak havoc on coconut palms worldwide, leading to high loss of income, food insecurity and extreme poverty of farmers in producing countries. Phytoplasmas as strictly biotrophic insect-transmitted bacterial pathogens instigate distinct changes in developmental processes and defence responses of the infected plants and manipulate plants to their own advantage; however, little is known about the cellular and molecular mechanisms underlying host-phytoplasma interactions. Further, phytoplasma-mediated transcriptional alterations in coconut palm genes have not yet been identified. This study evaluated the whole transcriptome profiles of naturally infected leaves of Cocos nucifera ecotype Malayan Red Dwarf in response to yellow decline phytoplasma from group 16SrXIV, using RNA-Seq technique. Transcriptomics-based analysis reported here identified genes involved in coconut innate immunity. The number of down-regulated genes in response to phytoplasma infection exceeded the number of genes up-regulated. Of the 39,873 differentially expressed unigenes, 21,860 unigenes were suppressed and 18,013 were induced following infection. Comparative analysis revealed that genes associated with defence signalling against biotic stimuli were significantly overexpressed in phytoplasma-infected leaves versus healthy coconut leaves. Genes involving cell rescue and defence, cellular transport, oxidative stress, hormone stimulus and metabolism, photosynthesis reduction, transcription and biosynthesis of secondary metabolites were differentially represented. Our transcriptome analysis unveiled a core set of genes associated with defence of coconut in response to phytoplasma attack, although several novel defence response candidate genes with unknown function have also been identified. This study constitutes valuable sequence resource for uncovering the resistance genes and/or susceptibility genes which can be used as genetic tools in disease resistance breeding.
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Affiliation(s)
- Naghmeh Nejat
- Institute of Tropical Agriculture, University of Putra Malaysia, Serdang, Malaysia.
| | - David M Cahill
- School of Life and Environmental Sciences, Faculty of Science Engineering and Built Environment, Deakin University, Geelong, Australia
| | - Ganesan Vadamalai
- Institute of Tropical Agriculture, University of Putra Malaysia, Serdang, Malaysia
| | - Mark Ziemann
- Baker IDI Heart and Diabetes Institute, Melbourne, Australia
| | - James Rookes
- School of Life and Environmental Sciences, Faculty of Science Engineering and Built Environment, Deakin University, Geelong, Australia
| | - Neda Naderali
- Institute of Tropical Agriculture, University of Putra Malaysia, Serdang, Malaysia
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Huang S, Liu Z, Yao R, Li D, Feng H. Comparative transcriptome analysis of the petal degeneration mutant pdm in Chinese cabbage (Brassica campestris ssp. pekinensis) using RNA-Seq. Mol Genet Genomics 2015; 290:1833-47. [PMID: 25860116 DOI: 10.1007/s00438-015-1041-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 03/27/2015] [Indexed: 10/23/2022]
Abstract
Flowering, which plays a crucial role in the growth and development of flowering plants, is a crucial point from vegetative growth to reproductive growth. The goal of this study was to examine the differences between the transcriptomes of the Chinese cabbage mutant pdm and the corresponding wild-type line 'FT'. We performed transcriptome analysis on mRNA isolated from flower buds of pdm and 'FT' using Illumina RNA sequencing (RNA-Seq) data. A total of 117 differentially expressed genes (DEGs) were detected. Among the DEGs, we identified a number of genes involved in floral development and flowering, including an F-box protein gene, EARLY FLOWERING 4 (ELF4), and transcription factors BIGPETAL (BPE) and MYB21 (v-myb avian myeloblastosis viral oncogene homolog); differential expression of these genes could potentially explain the difference in the flowers between pdm and 'FT'. In addition, the expression patterns of 20 DEGs, including 12 floral development and flowering-related genes and eight randomly selected genes, were validated by qRT-PCR, and the results were highly concordant with the RNA-Seq results. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed to better understand the functions of these DEGs. We also identified a large number of single nucleotide polymorphism and insertion/deletion markers, which will be a rich resource for future marker development and breeding research in Chinese cabbage. Also, our analysis revealed numerous novel transcripts and alternative splicing events. The transcriptome analysis provides valuable information for furthering our understanding of the molecular mechanisms that regulate the flowering process, and establishes a solid foundation for future genetic and functional genomic studies in Chinese cabbage.
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Affiliation(s)
- Shengnan Huang
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, 110866, People's Republic of China
| | - Zhiyong Liu
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, 110866, People's Republic of China
| | - Runpeng Yao
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, 110866, People's Republic of China
| | - Danyang Li
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, 110866, People's Republic of China
| | - Hui Feng
- Department of Horticulture, Shenyang Agricultural University, 120 Dongling Road, Shenyang, 110866, People's Republic of China.
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46
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Liang M, Yang X, Li H, Su S, Yi H, Chai L, Deng X. De novo transcriptome assembly of pummelo and molecular marker development. PLoS One 2015; 10:e0120615. [PMID: 25799271 PMCID: PMC4370633 DOI: 10.1371/journal.pone.0120615] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/24/2015] [Indexed: 11/19/2022] Open
Abstract
Pummelo (Citrus grandis) is an important fruit crop worldwide because of its nutritional value. To accelerate the pummelo breeding program, it is essential to obtain extensive genetic information and develop relative molecular markers. Here, we obtained a 12-Gb transcriptome dataset of pummelo through a mixture of RNA from seven tissues using Illumina pair-end sequencing, assembled into 57,212 unigenes with an average length of 1010 bp. The annotation and classification results showed that a total of 39,584 unigenes had similar hits to the known proteins of four public databases, and 31,501 were classified into 55 Gene Ontology (GO) functional sub-categories. The search for putative molecular markers among 57,212 unigenes identified 10,276 simple sequence repeats (SSRs) and 64,720 single nucleotide polymorphisms (SNPs). High-quality primers of 1174 SSR loci were designed, of which 88.16% were localized to nine chromosomes of sweet orange. Of 100 SSR primers that were randomly selected for testing, 87 successfully amplified clear banding patterns. Of these primers, 29 with a mean PIC (polymorphic information content) value of 0.52 were effectively applied for phylogenetic analysis. Of the 20 SNP primers, 14 primers, including 54 potential SNPs, yielded target amplifications, and 46 loci were verified via Sanger sequencing. This new dataset will be a valuable resource for molecular biology studies of pummelo and provides reliable information regarding SNP and SSR marker development, thus expediting the breeding program of pummelo.
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Affiliation(s)
- Mei Liang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Xiaoming Yang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Hang Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Shiying Su
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Hualin Yi
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Lijun Chai
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Horticultural Crop Biology and Genetic improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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Lesur I, Le Provost G, Bento P, Da Silva C, Leplé JC, Murat F, Ueno S, Bartholomé J, Lalanne C, Ehrenmann F, Noirot C, Burban C, Léger V, Amselem J, Belser C, Quesneville H, Stierschneider M, Fluch S, Feldhahn L, Tarkka M, Herrmann S, Buscot F, Klopp C, Kremer A, Salse J, Aury JM, Plomion C. The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release. BMC Genomics 2015; 16:112. [PMID: 25765701 PMCID: PMC4350297 DOI: 10.1186/s12864-015-1331-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Accepted: 02/09/2015] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Many northern-hemisphere forests are dominated by oaks. These species extend over diverse environmental conditions and are thus interesting models for studies of plant adaptation and speciation. The genomic toolbox is an important asset for exploring the functional variation associated with natural selection. RESULTS The assembly of previously available and newly developed long and short sequence reads for two sympatric oak species, Quercus robur and Quercus petraea, generated a comprehensive catalog of transcripts for oak. The functional annotation of 91 k contigs demonstrated the presence of a large proportion of plant genes in this unigene set. Comparisons with SwissProt accessions and five plant gene models revealed orthologous relationships, making it possible to decipher the evolution of the oak genome. In particular, it was possible to align 9.5 thousand oak coding sequences with the equivalent sequences on peach chromosomes. Finally, RNA-seq data shed new light on the gene networks underlying vegetative bud dormancy release, a key stage in development allowing plants to adapt their phenology to the environment. CONCLUSION In addition to providing a vast array of expressed genes, this study generated essential information about oak genome evolution and the regulation of genes associated with vegetative bud phenology, an important adaptive traits in trees. This resource contributes to the annotation of the oak genome sequence and will provide support for forward genetics approaches aiming to link genotypes with adaptive phenotypes.
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Affiliation(s)
- Isabelle Lesur
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.
- HelixVenture, F-33700, Mérignac, France.
| | - Grégoire Le Provost
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.
- University Bordeaux, BIOGECO, UMR1202, F-33170, Talence, France.
| | - Pascal Bento
- CEA-Institut de Génomique, GENOSCOPE, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, F-91057, Evry Cedex, France.
| | - Corinne Da Silva
- CEA-Institut de Génomique, GENOSCOPE, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, F-91057, Evry Cedex, France.
| | - Jean-Charles Leplé
- INRA, UR0588 Amélioration Génétique et Physiologie Forestières, F-45075, Orléans, France.
| | - Florent Murat
- INRA/UBP UMR 1095, Laboratoire Génétique, Diversité et Ecophysiologie des Céréales, F-63039, Clermont-Ferrand, France.
| | - Saneyoshi Ueno
- Forestry and Forest Products Research Institute, Department of Forest Genetics, Tree Genetics Laboratory, 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan.
| | - Jerôme Bartholomé
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.
- CIRAD, UMR AGAP, F-34398, Montpellier, France.
| | - Céline Lalanne
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.
- University Bordeaux, BIOGECO, UMR1202, F-33170, Talence, France.
| | - François Ehrenmann
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.
- University Bordeaux, BIOGECO, UMR1202, F-33170, Talence, France.
| | - Céline Noirot
- Plateforme bioinformatique Toulouse Midi-Pyrénées, UBIA, INRA, F-31326, Auzeville Castanet-Tolosan, France.
| | - Christian Burban
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.
- University Bordeaux, BIOGECO, UMR1202, F-33170, Talence, France.
| | - Valérie Léger
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.
- University Bordeaux, BIOGECO, UMR1202, F-33170, Talence, France.
| | - Joelle Amselem
- INRA, Unité de Recherche Génomique Info (URGI), F78026, Versailles, France.
| | - Caroline Belser
- CEA-Institut de Génomique, GENOSCOPE, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, F-91057, Evry Cedex, France.
| | - Hadi Quesneville
- INRA, Unité de Recherche Génomique Info (URGI), F78026, Versailles, France.
| | | | - Silvia Fluch
- AIT Austrian Institute of Technology GmbH, Konrad-Lorenz Str 24, 3430, Tulln, Austria.
| | - Lasse Feldhahn
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, DE-06120, Halle/Saale, Germany.
| | - Mika Tarkka
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, DE-06120, Halle/Saale, Germany.
- iDiv - German Centre for Integrative Biodiversity Research, Halle Jena Leipzig, DE-04103, Leipzig, Germany.
| | - Sylvie Herrmann
- iDiv - German Centre for Integrative Biodiversity Research, Halle Jena Leipzig, DE-04103, Leipzig, Germany.
- Department of Community Ecology, UFZ - Helmholtz Centre for Environmental Research, 06120, Halle/Saale, Germany.
| | - François Buscot
- Department of Soil Ecology, UFZ - Helmholtz Centre for Environmental Research, DE-06120, Halle/Saale, Germany.
- iDiv - German Centre for Integrative Biodiversity Research, Halle Jena Leipzig, DE-04103, Leipzig, Germany.
| | - Christophe Klopp
- Plateforme bioinformatique Toulouse Midi-Pyrénées, UBIA, INRA, F-31326, Auzeville Castanet-Tolosan, France.
| | - Antoine Kremer
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.
- University Bordeaux, BIOGECO, UMR1202, F-33170, Talence, France.
| | - Jérôme Salse
- INRA/UBP UMR 1095, Laboratoire Génétique, Diversité et Ecophysiologie des Céréales, F-63039, Clermont-Ferrand, France.
| | - Jean-Marc Aury
- CEA-Institut de Génomique, GENOSCOPE, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, F-91057, Evry Cedex, France.
| | - Christophe Plomion
- INRA, UMR1202, BIOGECO, F-33610, Cestas, France.
- University Bordeaux, BIOGECO, UMR1202, F-33170, Talence, France.
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48
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Zhang L, Lin Q, Feng Y, Fan X, Zou F, Yuan DY, Zeng X, Cao H. Transcriptomic identification and expression of starch and sucrose metabolism genes in the seeds of Chinese chestnut (Castanea mollissima). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:929-42. [PMID: 25537355 DOI: 10.1021/jf505247d] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The Chinese chestnut (Castanea mollissima) seed provides a rich source of carbohydrates as food and feed. However, little is known about starch biosynthesis in the seeds. The objectives of this study were to determine seed composition profiles and identify genes involved in starch and sucrose metabolism. Metabolite analysis showed that starch was the major component and rapidly accumulated during seed endosperm development. Amylopectin was approximately 3-fold of amylose content in chestnut starch. Illumina platform-based transcriptome sequencing generated 56671 unigenes in two cDNA libraries from seed endosperms collected at 45 and 75 days after flowering (DAF). A total of 1537 unigenes showed expression differences ≥2-fold in the two stages of seeds including 570 up-regulated and 967 down-regulated unigenes. One hundred and fifty-two unigenes were identified as involved in starch and sucrose metabolism, including 1 for glycogenin glucosyltransferase, 4 for adenylate transporter (brittle1-type), 3 for ADP-glucose pyrophosphorylase (AGP, not brittle2- or shrunken2-type), 3 for starch synthase (SS), 2 for starch branching enzyme, 5 for starch debranching enzyme, 11 for sucrose synthase, and 3 for sucrose-phosphate synthase. Among them, 58 unigenes showed a ≥2-fold expression difference between the 45 and 75 DAF seeds including 11 up- and 47 down-regulated unigenes. The expression of 21 unigenes putatively coding for major enzymes in starch and sucrose metabolism was validated by qPCR using RNA from five seed stages. Expression profiles and correlation analysis indicated that the mRNA levels of AGP (large and small subunits), granule-bound SS2, and soluble SS1 and SS4 were well-correlated with starch accumulation in the seeds. This study suggests that the starch biosynthesis pathway in Chinese chestnut is similar to that of potato tuber/Arabidopsis leaf and differs from that of maize endosperm. The information provides valuable metabolite and genetic resources for future research in starch and sucrose metabolism in Chinese chestnut tree.
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Affiliation(s)
- Lin Zhang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology , 498 South Shaoshan Road, Changsha, Hunan Province 410004, People's Republic of China
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Vijayakumar P, Raut AA, Kumar P, Sharma D, Mishra A. De novo assembly and analysis of crow lungs transcriptome. Genome 2015; 57:499-506. [PMID: 25633965 DOI: 10.1139/gen-2014-0122] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The jungle crow (Corvus macrorhynchos) belongs to the order Passeriformes of bird species and is important for avian ecological and evolutionary genetics studies. However, there is limited information on the transcriptome data of this species. In the present study, we report the characterization of the lung transcriptome of the jungle crow using GS FLX Titanium XLR70. Altogether, 1,510,303 high-quality sequence reads with 581,198,230 bases was de novo assembled into 22,169 isotigs (isotig represents an individual transcript) and 784,009 singletons. Using these isotigs and 581,681 length-filtered (greater than 300 bp) singletons, 20,010 unique protein-coding genes were identified by BLASTx comparison against a nonredundant (nr) protein sequence database. Comparative analysis revealed that 46,604 (70.29%) and 51,642 (72.48%) of the assembled transcripts have significant similarity to zebra finch and chicken RefSeq proteins, respectively. As determined by GO annotation and KEGG pathway mapping, functional annotation of the unigenes recovered diverse biological functions and processes. Transcripts putatively involved in the immune response were identified. Furthermore, 20,599 single nucleotide polymorphisms (SNPs) and 7525 simple sequence repeats (SSRs) were retrieved from the assembled transcript database. This resource should lay an important base for future ecological, evolutionary, and conservation genetic studies on this species and in other related species.
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Affiliation(s)
- Periyasamy Vijayakumar
- a High Security Animal Disease Laboratory, Indian Veterinary Research Institute, Anand Nagar, Bhopal-462021, Madhya Pradesh, India
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50
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Transcriptome sequencing in a Tibetan barley landrace with high resistance to powdery mildew. ScientificWorldJournal 2014; 2014:594579. [PMID: 25587568 PMCID: PMC4284937 DOI: 10.1155/2014/594579] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/01/2014] [Accepted: 12/01/2014] [Indexed: 12/01/2022] Open
Abstract
Hulless barley is an important cereal crop worldwide, especially in Tibet of China. However, this crop is usually susceptible to powdery mildew caused by Blumeria graminis f. sp. hordei. In this study, we aimed to understand the functions and pathways of genes involved in the disease resistance by transcriptome sequencing of a Tibetan barley landrace with high resistance to powdery mildew. A total of 831 significant differentially expressed genes were found in the infected seedlings, covering 19 functions. Either “cell,” “cell part,” and “extracellular region” in the cellular component category or “binding” and “catalytic” in the category of molecular function as well as “metabolic process” and “cellular process” in the biological process category together demonstrated that these functions may be involved in the resistance to powdery mildew of the hulless barley. In addition, 330 KEGG pathways were found using BLASTx with an E-value cut-off of <10−5. Among them, three pathways, namely, “photosynthesis,” “plant-pathogen interaction,” and “photosynthesis-antenna proteins” had significant matches in the database. Significant expressions of the three pathways were detected at 24 h, 48 h, and 96 h after infection, respectively. These results indicated a complex process of barley response to powdery mildew infection.
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