Transcriptome analysis of root response to citrus blight based on the newly assembled Swingle citrumelo draft genome

Abstract Corynespora cassiicola as a necrotrophic plant pathogenic ascomycetes fungus can infect hundreds of species of plants, and also rarely cause human disease. The pathogen infects cucumber and causes cucumber target spot, which has given rise to great yield loss of cucumber in China recently. Genome sequence and spore germination associated transcriptome analysis will contribute to the understanding of the molecular mechanism of pathogenicity and spore germination of C. cassiicola .Results Firstly, we reported the draft genome sequences of a cucumber-sampled C. cassiicola isolate HGCC with high virulence. Although being conspecific, HGCC had distinct difference with a rubber-sampled isolate (CCP) and a human-sampled isolate (UM591) in genome sequences. The proportion of secreted proteins was 7.4% in HGCC. 28.6% of HGCC predicted genes were highly homologous to experimentally proven virulence-associated genes, which was close to that in CCP, UM591 and some plant fungal pathogens, but far more than 21.9% in Phaeosphaeria nodorum and 19.6% in Botrytis cinerea . Thousands of putative virulence-associated genes in various pathways or families were identified in HGCC. Secondly, a global view of the transcriptome of C. cassiicola spores during germination was evaluated using RNA sequencing (RNA-seq). A total of 3,288 differentially expressed genes (DEGs) were identified. The majority of KEGG annotated DEGs were involved in metabolism, genetic information processing, cellular processes, organismal system, human diseases and environmental information processing.Conclusions These results not only facilitated the exploration of the molecular pathogenic mechanism of C. cassiicola to cucumber and the understanding of molecular and cellular processes during spore germination, but also laid the foundation for the disease control.

Download Full-text

Transcriptome analysis of tobacco root response to different concentrations of nitrate

Agronomy Journal ◽

10.1002/agj2.20102 ◽

2020 ◽

Vol 112 (2) ◽

pp. 1111-1125

Author(s):

Huijuan Yang ◽

Yuning Zhang ◽

Yan Zhou ◽

Jing Wang ◽

Xinqi Geng ◽

...

Keyword(s):

Transcriptome Analysis ◽

Root Response

Download Full-text

Draft Genome of the Korean smelt (Hypomesus nipponensis) and its transcriptomic responses to heat stress in the liver and muscle

10.1101/2021.03.26.437215 ◽

2021 ◽

Author(s):

Biao Xuan ◽

Jongbin Park ◽

Sukjung Choi ◽

Inhwan You ◽

Bo-Hye Nam ◽

...

Keyword(s):

Global Warming ◽

Heat Stress ◽

Transcriptome Analysis ◽

Molecular Mechanisms ◽

Draft Genome ◽

Enrichment Analysis ◽

Economic Resource ◽

Gene Enrichment Analysis ◽

Gene Enrichment ◽

Muscle Tissues

Backgrounds: Hypomesus nipponensis is a cold-freshwater fish species as a winter economic resource of aquaculture in South Korea. Due to its high susceptibility to abnormal water temperature from global warming. Aim of the study: Here, we present the first draft genome of H. nipponensis and transcriptomic changes in molecular mechanisms or intracellular responses under heat stress. Methods: We combined Illumina and PacBio sequencing technologies to generate the draft genome of H. nipponensis. Based on the reference genome, we conducted transcriptome analysis of liver and muscle tissues under normal (NT, 5°C) versus warm (HT, 23°C) conditions, to identify heat stress-induced genes and gene categories. Results: We observed a total of 1,987 contigs, with N50 of 0.46 Gbp with a largest contig (3.03 Mbp) in the assembled genome. A total number of 20,644 protein coding genes were predicted, and 19,224 genes were functionally annotated: 15,955 genes for Gene Ontology (GO) terms; and 11,560 genes for KO (KEGG Orthology). In the missing and gained genes analysis, we detected 4,461 (22.16%), 2,825 (10.62%), and 1,499 (3.09%) genes with coverage less than 10% and for gained genes found from alignment to other species that human, zebrafish and salmon, respectively, we observed 1,133 (5.49%), 1,670 (8.09%), and 229 (1.11%) genes with coverage less than 10% compared with above species, respectively. From transcriptome analysis, a total of 297 and 331 differentially expressed genes (DEGs, adjusted p-value < 0.05) were identified in the liver and muscle tissues, respectively. Gene enrichment analysis of DEGs indicates that up-regulated genes were significantly enriched for lipid biosynthetic process (GO:0008610, P < 0.001) and regulation of apoptotic process (GO:0042981, P < 0.01), and down-regulated genes by immune responses such as myeloid cell differentiation (GO:0030099, P < 0.001) in the liver under heat stress. In muscle tissue, up-regulated genes were enriched for hypoxia (GO:0001666, P < 0.05), transcription regulator activity (GO:0140110, P < 0.001) and calcium-release channel activity (GO:0015278, P < 0.01), and down-regulated genes for nicotinamide nucleotide biosynthetic process (GO:0019359, P < 0.01). The results of KEGG pathway analysis were similar to that of gene enrichment analysis. Conclusion: The draft genome and transcriptomic of H. nipponensis will be used as a useful genetic resource for functional and evolutionary studies. Our findings will improve understanding of the molecular mechanisms and heat responses and be useful for better survival of the smelt and its closely related species under global warming.

Download Full-text

Performance of `Hamlin' Orange on 16 Rootstocks in East-central Florida

HortScience ◽

10.21273/hortsci.30.1.41 ◽

1995 ◽

Vol 30 (1) ◽

pp. 41-43 ◽

Cited By ~ 11

Author(s):

Heinz K. Wutscher ◽

Laura Lee Hill

Keyword(s):

Citrus Sinensis ◽

Poncirus Trifoliata ◽

Trifoliate Orange ◽

Poor Growth ◽

East Central ◽

Central Florida ◽

Citrus Rootstock ◽

Citrus Blight ◽

Freeze Damage ◽

Swingle Citrumelo

`Hamlin' orange (Citrus sinensis L. Osbeck) was grown on 15 rootstocks: four citrumelos [C. paradisi Macf. × Poncirus trifoliata (L.) Raf.], five mandarin × trifoliate orange hybrids (C. reticulata Blanco × P. trifoliata), two pummelo × trifoliate orange hybrids [C. grandis (L.) × P. trifoliata], Vangasay lemon (C. limon Burm. f.), Norton citrange (C. sinensis × P. trifoliata), and two Smooth Flat Seville (C. aurantium L. hybrid?) hybrids. These scion–rootstock combinations were compared to trees on Swingle citrumelo, the most widely used citrus rootstock in Florida. One Smooth Flat Seville hybrid was eliminated early because of poor growth and variability in size, and the Vangasay lemon rootstock was eliminated because of severe freeze damage. At age 5, the trees on Norton citrange developed citrus blight and were eliminated. Remaining in the experiment for 7 years, `Hamlin' trees on six of the 13 rootstocks produced more fruit than trees on Swingle citrumelo. Of these six, HRS 852 (Changsha mandarin × English large-flowered trifoliate orange) was the best overall rootstock, with trees on it producing large quantities of high-quality fruit on medium-sized canopies.

Download Full-text

Lentinula edodes Genome Survey and Postharvest Transcriptome Analysis

Applied and Environmental Microbiology ◽

10.1128/aem.02990-16 ◽

2017 ◽

Vol 83 (10) ◽

Cited By ~ 21

Author(s):

Yuichi Sakamoto ◽

Keiko Nakade ◽

Shiho Sato ◽

Kentaro Yoshida ◽

Kazuhiro Miyazaki ◽

...

Keyword(s):

Cell Wall ◽

Transcriptome Analysis ◽

Fruiting Body ◽

Lentinula Edodes ◽

De Novo ◽

Draft Genome ◽

Postharvest Quality ◽

Content Type ◽

Degrading Enzymes ◽

Whole Life Cycle

ABSTRACT Lentinula edodes is a popular, cultivated edible and medicinal mushroom. Lentinula edodes is susceptible to postharvest problems, such as gill browning, fruiting body softening, and lentinan degradation. We constructed a de novo assembly draft genome sequence and performed gene prediction for Lentinula edodes. De novo assembly was carried out using short reads from paired-end and mate-paired libraries and by using long reads by PacBio, resulting in a contig number of 1,951 and an N50 of 1 Mb. Furthermore, we predicted genes by Augustus using transcriptome sequencing (RNA-seq) data from the whole life cycle of Lentinula edodes, resulting in 12,959 predicted genes. This analysis revealed that Lentinula edodes lacks lignin peroxidase. To reveal genes involved in the loss of quality of Lentinula edodes postharvest fruiting bodies, transcriptome analysis was carried out using serial analysis of gene expression (SuperSAGE). This analysis revealed that many cell wall-related enzymes are upregulated after harvest, such as β-1,3-1,6-glucan-degrading enzymes in glycoside hydrolase (GH) families GH5, GH16, GH30, GH55, and GH128, and thaumatin-like proteins. In addition, we found that several chitin-related genes are upregulated, such as putative chitinases in GH family 18, exochitinases in GH20, and a putative chitosanase in GH family 75. The results suggest that cell wall-degrading enzymes synergistically cooperate for rapid fruiting body autolysis. Many putative transcription factor genes were upregulated postharvest, such as genes containing high-mobility-group (HMG) domains and zinc finger domains. Several cell death-related proteins were also upregulated postharvest. IMPORTANCE Our data collectively suggest that there is a rapid fruiting body autolysis system in Lentinula edodes. The genes for the loss of postharvest quality newly found in this research will be targets for the future breeding of strains that keep fresh longer than present strains. De novo Lentinula edodes genome assembly data will be used for the construction of a complete Lentinula edodes chromosome map for future breeding.

Download Full-text

Transcriptome analysis provides genome annotation and expression profiles in the central nervous system of Lymnaea stagnalis at different ages

10.1101/2021.05.17.444496 ◽

2021 ◽

Author(s):

Martina Rosato ◽

Brittany A. Hoelscher ◽

Zhenguo Lin ◽

Chidera Agwu ◽

Fenglian Xu

Keyword(s):

Central Nervous System ◽

Nervous System ◽

Young Adult ◽

Transcriptome Analysis ◽

Developmental Stages ◽

Lymnaea Stagnalis ◽

Gene Annotation ◽

Expression Profiles ◽

Draft Genome ◽

Model Organism

Molecular studies of the freshwater snail Lymnaea stagnalis, a unique model organism for neurobiology research, has been severely hindered by the lack of sufficient genomic information. As part of our ongoing effort studying L. stagnalis neuronal growth and connectivity at various developmental stages, we provide the first age-specific transcriptome analysis and gene annotation of young, adult, and old L. stagnalis central nervous system (CNS). RNA sequencing using Illumina NovaSeq 6000 platform produced 56-69 millions of 150 bp paired-end reads, and 74% of these reads were mapped to the draft genome of L. stagnalis. We provide gene annotations for 32,288 coding sequences with a minimum of 100 codons, contributing to the largest number of annotated genes for the L. stagnalis genome to date. Lastly, transcriptomic analyses reveal age-specific differentially expressed genes and enriched pathways in young, adult, and old CNS. These datasets represent the largest and most updated L. stagnalis CNS transcriptomes.

Download Full-text

Draft Genome of the Korean smelt Hypomesus nipponensis and its transcriptomic responses to heat stress in the liver and muscle

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkab147 ◽

2021 ◽

Author(s):

Biao Xuan ◽

Jongbin Park ◽

Sukjung Choi ◽

Inhwan You ◽

Bo-Hye Nam ◽

...

Keyword(s):

Global Warming ◽

Heat Stress ◽

Transcriptome Analysis ◽

Molecular Mechanisms ◽

Draft Genome ◽

Enrichment Analysis ◽

Economic Resource ◽

Gene Enrichment Analysis ◽

Gene Enrichment ◽

Muscle Tissues

Abstract Pond smelt (Hypomesus nipponensis) is a cold-freshwater fish species as a winter economic resource of aquaculture in South Korea. Due to its high susceptibility to abnormal water temperature from global warming, a large number of smelt die in hot summer. Here, we present the first draft genome of H. nipponensis and transcriptomic changes in molecular mechanisms or intracellular responses under heat stress. We combined Illumina and PacBio sequencing technologies to generate the draft genome of H. nipponensis. Based on the reference genome, we conducted transcriptome analysis of liver and muscle tissues under normal (NT, 5 °C) versus warm (HT, 23 °C) conditions, to identify heat stress-induced genes and gene categories. We observed a total of 1,987 contigs, with N50 of 0.46 Mbp with a largest contig (3.03 Mbp) in the assembled genome. A total number of 20,644 protein coding genes were predicted, and 19,224 genes were functionally annotated: 15,955 genes for Gene Ontology (GO) terms; and 11,560 genes for KEGG Orthology (KO). We conducted the lost and gained genes analysis compared with three species that human, zebrafish and salmon. In the lost genes analysis, we detected smelt lost 4,461 (22.16%), 2,825 (10.62%), and 1,499 (3.09%) genes compare with above three species, respectively. In the gained genes analysis, we observed smelt gain 1,133 (5.49%), 1,670 (8.09%), and 229 (1.11%) genes compare with above species, respectively. From transcriptome analysis, a total of 297 and 331 differentially expressed genes (DEGs) with False discovery rate (FDR) < 0.05 were identified in the liver and muscle tissues, respectively. Gene enrichment analysis of DEGs indicates that up-regulated genes were significantly enriched for lipid biosynthetic process (GO : 0008610, P < 0.001) and regulation of apoptotic process (GO : 0042981, P < 0.01), and down-regulated genes by immune responses such as myeloid cell differentiation (GO : 0030099, P < 0.001) in the liver under heat stress. In muscle tissue, up-regulated genes were enriched for hypoxia (GO : 0001666, P < 0.05), transcription regulator activity (GO : 0140110, P < 0.001) and calcium-release channel activity (GO : 0015278, P < 0.01), and down-regulated genes for nicotinamide nucleotide biosynthetic process (GO : 0019359, P < 0.01). The results of KEGG pathway analysis were similar to that of gene enrichment analysis. The draft genome and transcriptomic of H. nipponensis will be used as a useful genetic resource for functional and evolutionary studies. Our findings will improve understanding of the molecular mechanisms and heat responses and will be useful for predicting survival of the smelt and its closely related species under global warming.

Download Full-text