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Transcriptome analysis of candidate genes and signaling pathways associated with light-induced brown film formation in Lentinula edodes

High-throughput Illumina RNA-seq was used for deep sequencing analysis of the transcriptome of poly(A)+ RNA from mycelium grown under three different conditions: 30 days darkness (sample 118), 80 days darkness (313W), and 30 days darkness followed by 50 days in the light (313C), in order to gain ins... Full description

Journal Title: Applied Microbiology and Biotechnology 2013, Vol.97(11), pp.4977-4989
Main Author: Tang, Li-hua
Other Authors: Jian, Hua-hua , Song, Chun-yan , Bao, Da-peng , Shang, Xiao-dong , Wu, Da-qiang , Tan, Qi , Zhang, Xue-hong
Format: Electronic Article Electronic Article
Language: English
Subjects:
ID: ISSN: 0175-7598 ; E-ISSN: 1432-0614 ; DOI: 10.1007/s00253-013-4832-y
Link: http://dx.doi.org/10.1007/s00253-013-4832-y
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recordid: springer_jour10.1007/s00253-013-4832-y
title: Transcriptome analysis of candidate genes and signaling pathways associated with light-induced brown film formation in Lentinula edodes
format: Article
creator:
  • Tang, Li-hua
  • Jian, Hua-hua
  • Song, Chun-yan
  • Bao, Da-peng
  • Shang, Xiao-dong
  • Wu, Da-qiang
  • Tan, Qi
  • Zhang, Xue-hong
subjects:
  • Lentinula edodes
  • Light-induced brown film formation
  • Transcriptome
  • Differential expression
ispartof: Applied Microbiology and Biotechnology, 2013, Vol.97(11), pp.4977-4989
description: High-throughput Illumina RNA-seq was used for deep sequencing analysis of the transcriptome of poly(A)+ RNA from mycelium grown under three different conditions: 30 days darkness (sample 118), 80 days darkness (313W), and 30 days darkness followed by 50 days in the light (313C), in order to gain insight into the molecular mechanisms underlying the process of light-induced brown film (BF) formation in the edible mushroom, Lentinula edodes . Of the three growth conditions, BF formation occurred in 313C samples only. Approximately 159.23 million reads were obtained, trimmed, and de novo assembled into 31,511 contigs with an average length of 1,746 bp and an N 50 of 2,480 bp. Based on sequence orientations determined by a BLASTX search against the NR, Swiss-Prot, COG, and KEGG databases, 24,246 (76.9 %) contigs were assigned putative descriptions. Comparison of 313C/118 and 313C/313W expression profiles revealed 3,958 and 5,651 significantly differentially expressed contigs (DECs), respectively. Annotation using the COG database revealed that candidate genes for light-induced BF formation encoded proteins linked to light reception (e.g., WC-1, WC-2, phytochrome), light signal transduction pathways (e.g., two-component phosphorelay system, mitogen-activated protein kinase pathway), and pigment formation (e.g., polyketide synthase, O -methyltransferase, laccase, P 450 monooxygenase, oxidoreductase). Several DECs were validated using quantitative real-time polymerase chain reaction. Our report is the first to identify genes associated with light-induced BF formation in L. edodes and represents a valuable resource for future genomic studies on this commercially important mushroom.
language: eng
source:
identifier: ISSN: 0175-7598 ; E-ISSN: 1432-0614 ; DOI: 10.1007/s00253-013-4832-y
fulltext: fulltext
issn:
  • 1432-0614
  • 14320614
  • 0175-7598
  • 01757598
url: Link


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titleTranscriptome analysis of candidate genes and signaling pathways associated with light-induced brown film formation in Lentinula edodes
creatorTang, Li-hua ; Jian, Hua-hua ; Song, Chun-yan ; Bao, Da-peng ; Shang, Xiao-dong ; Wu, Da-qiang ; Tan, Qi ; Zhang, Xue-hong
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subjectLentinula edodes ; Light-induced brown film formation ; Transcriptome ; Differential expression
descriptionHigh-throughput Illumina RNA-seq was used for deep sequencing analysis of the transcriptome of poly(A)+ RNA from mycelium grown under three different conditions: 30 days darkness (sample 118), 80 days darkness (313W), and 30 days darkness followed by 50 days in the light (313C), in order to gain insight into the molecular mechanisms underlying the process of light-induced brown film (BF) formation in the edible mushroom, Lentinula edodes . Of the three growth conditions, BF formation occurred in 313C samples only. Approximately 159.23 million reads were obtained, trimmed, and de novo assembled into 31,511 contigs with an average length of 1,746 bp and an N 50 of 2,480 bp. Based on sequence orientations determined by a BLASTX search against the NR, Swiss-Prot, COG, and KEGG databases, 24,246 (76.9 %) contigs were assigned putative descriptions. Comparison of 313C/118 and 313C/313W expression profiles revealed 3,958 and 5,651 significantly differentially expressed contigs (DECs), respectively. Annotation using the COG database revealed that candidate genes for light-induced BF formation encoded proteins linked to light reception (e.g., WC-1, WC-2, phytochrome), light signal transduction pathways (e.g., two-component phosphorelay system, mitogen-activated protein kinase pathway), and pigment formation (e.g., polyketide synthase, O -methyltransferase, laccase, P 450 monooxygenase, oxidoreductase). Several DECs were validated using quantitative real-time polymerase chain reaction. Our report is the first to identify genes associated with light-induced BF formation in L. edodes and represents a valuable resource for future genomic studies on this commercially important mushroom.
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abstractHigh-throughput Illumina RNA-seq was used for deep sequencing analysis of the transcriptome of poly(A)+ RNA from mycelium grown under three different conditions: 30 days darkness (sample 118), 80 days darkness (313W), and 30 days darkness followed by 50 days in the light (313C), in order to gain insight into the molecular mechanisms underlying the process of light-induced brown film (BF) formation in the edible mushroom, Lentinula edodes . Of the three growth conditions, BF formation occurred in 313C samples only. Approximately 159.23 million reads were obtained, trimmed, and de novo assembled into 31,511 contigs with an average length of 1,746 bp and an N 50 of 2,480 bp. Based on sequence orientations determined by a BLASTX search against the NR, Swiss-Prot, COG, and KEGG databases, 24,246 (76.9 %) contigs were assigned putative descriptions. Comparison of 313C/118 and 313C/313W expression profiles revealed 3,958 and 5,651 significantly differentially expressed contigs (DECs), respectively. Annotation using the COG database revealed that candidate genes for light-induced BF formation encoded proteins linked to light reception (e.g., WC-1, WC-2, phytochrome), light signal transduction pathways (e.g., two-component phosphorelay system, mitogen-activated protein kinase pathway), and pigment formation (e.g., polyketide synthase, O -methyltransferase, laccase, P 450 monooxygenase, oxidoreductase). Several DECs were validated using quantitative real-time polymerase chain reaction. Our report is the first to identify genes associated with light-induced BF formation in L. edodes and represents a valuable resource for future genomic studies on this commercially important mushroom.
copBerlin/Heidelberg
pubSpringer-Verlag
doi10.1007/s00253-013-4832-y
pages4977-4989
date2013-06