Additional file 3: of Comparative transcriptome analysis identified candidate genes involved in mycelium browning in Lentinula edodes

Additional file 9: of Transcriptome analysis reveals pathways facilitating the growth of tobacco powdery mildew in Arabidopsis

Ran Li (57928)
Ling-Li Zhang (482443)
Xue-Mei Yang (3216627)
Xiao-Long Cao (6202820)
Ying-Ge Wang (6202835)
Xian-Feng Ma (6306143)
Viswanathan Chandran (488420)
Jing Fan (149601)
Hui Yang (91136)
Jing Shang (227576)
Ji-Qun Zhao (6202838)
Shunyuan Xiao (722953)
Yan Li (23143)
Wen-Ming Wang (505701)

February 2019

Figure S2. Clustering of deferential expressed genes responsive to tobacco powdery mildew. Hierarchi...

Additional file 2: Table S1. of Transcriptome analysis reveals the complexity of alternative splicing regulation in the fungus Verticillium dahliae

Lirong Jin (3621548)
Guanglin Li (709617)
Dazhao Yu (697557)
Wei Huang (36889)
Chao Cheng (11274)
Shengjie Liao (3721921)
Qijia Wu (3721918)
Yi Zhang (9093)

February 2017

The genic distribution of two sets of transcriptome sequencing reads from the two V. dahliae strains...

Additional file 5: Table S3. of Deciphering common and specific transcriptional immune responses in pea towards the oomycete pathogens Aphanomyces euteiches and Phytophthora pisi

Sara Hosseini (3484100)
Malin Elfstrand (600711)
Fredrik Heyman (2849777)
Dan Funck Jensen (166302)
Magnus Karlsson (150089)

August 2015

List of differentially expressed pea genes during interaction with A. euteiches and P. pisi. Microso...

Additional file 4: of Comparative transcriptome analysis identified candidate genes involved in mycelium browning in Lentinula edodes

Seung-il Yoo (2614858)
Hwa-Yong Lee (511573)
Kesavan Markkandan (2614867)
Suyun Moon (6317828)
Yong Ahn (3063747)
Sumin Ji (5636426)
Junsu Ko (3509726)
Seong-Jin Kim (179277)
Hojin Ryu (6317837)
Chang Hong (3526031)

February 2019

Table S4. List of gene sets enriched in the differentially expressed genes. (XLSX 23 kb

Additional file 2: of Comparative transcriptome analysis identified candidate genes involved in mycelium browning in Lentinula edodes

Seung-il Yoo (2614858)
Hwa-Yong Lee (511573)
Kesavan Markkandan (2614867)
Suyun Moon (6317828)
Yong Ahn (3063747)
Sumin Ji (5636426)
Junsu Ko (3509726)
Seong-Jin Kim (179277)
Hojin Ryu (6317837)
Chang Hong (3526031)

February 2019

Table S2. Summary of the transcriptome annotation and gene expression data. (XLSX 4025 kb

Additional file 6: of Comparative transcriptome analysis identified candidate genes involved in mycelium browning in Lentinula edodes

Seung-il Yoo (2614858)
Hwa-Yong Lee (511573)
Kesavan Markkandan (2614867)
Suyun Moon (6317828)
Yong Ahn (3063747)
Sumin Ji (5636426)
Junsu Ko (3509726)
Seong-Jin Kim (179277)
Hojin Ryu (6317837)
Chang Hong (3526031)

February 2019

Table S6. List of browning-related genes and their respective biological functions. (XLSX 42 kb

Additional file 7: of Comparative transcriptome analysis identified candidate genes involved in mycelium browning in Lentinula edodes

Seung-il Yoo (2614858)
Hwa-Yong Lee (511573)
Kesavan Markkandan (2614867)
Suyun Moon (6317828)
Yong Ahn (3063747)
Sumin Ji (5636426)
Junsu Ko (3509726)
Seong-Jin Kim (179277)
Hojin Ryu (6317837)
Chang Hong (3526031)

February 2019

Table S7. List of differentially expressed carbohydrate-active enzymes (CAZyme) family genes. (XLSX ...

Additional file 10: of Comparative transcriptome analysis identified candidate genes involved in mycelium browning in Lentinula edodes

Seung-il Yoo (2614858)
Hwa-Yong Lee (511573)
Kesavan Markkandan (2614867)
Suyun Moon (6317828)
Yong Ahn (3063747)
Sumin Ji (5636426)
Junsu Ko (3509726)
Seong-Jin Kim (179277)
Hojin Ryu (6317837)
Chang Hong (3526031)

February 2019

Figure S2. Multiple sequence alignment among WC-1 (GenBank no. ESA41977), PHRA (GenBank no. BAF56991...

Additional file 9: of Comparative transcriptome analysis identified candidate genes involved in mycelium browning in Lentinula edodes

Seung-il Yoo (2614858)
Hwa-Yong Lee (511573)
Kesavan Markkandan (2614867)
Suyun Moon (6317828)
Yong Ahn (3063747)
Sumin Ji (5636426)
Junsu Ko (3509726)
Seong-Jin Kim (179277)
Hojin Ryu (6317837)
Chang Hong (3526031)

February 2019

Figure S1. Comparison of expression patterns by RNA-seq and qRT-PCR. The qRT-PCR log2 values (y-axis...

Additional file 11: of Comparative transcriptome analysis identified candidate genes involved in mycelium browning in Lentinula edodes

Seung-il Yoo (2614858)
Hwa-Yong Lee (511573)
Kesavan Markkandan (2614867)
Suyun Moon (6317828)
Yong Ahn (3063747)
Sumin Ji (5636426)
Junsu Ko (3509726)
Seong-Jin Kim (179277)
Hojin Ryu (6317837)
Chang Hong (3526031)

February 2019

Figure S3. Expression of tryrosinases (A) and PHRA (B) in white (W), normal brown (B), and partial b...

Additional file 3: of Transcriptome analysis reveals pathways facilitating the growth of tobacco powdery mildew in Arabidopsis

Ran Li (57928)
Ling-Li Zhang (482443)
Xue-Mei Yang (3216627)
Xiao-Long Cao (6202820)
Ying-Ge Wang (6202835)
Xian-Feng Ma (6306143)
Viswanathan Chandran (488420)
Jing Fan (149601)
Hui Yang (91136)
Jing Shang (227576)
Ji-Qun Zhao (6202838)
Shunyuan Xiao (722953)
Yan Li (23143)
Wen-Ming Wang (505701)

February 2019

Table S2. List of differentially expressed genes with more than 4-fold change between any two sample...

Additional file 1 of Transcriptomic analysis reveals candidate genes regulating development and host interactions of Colletotrichum fructicola

Xiaofei Liang (843086)
Shengping Shang (5568197)
Qiuyue Dong (3751315)
Bo Wang (86769)
Rong Zhang (44942)
Mark Gleason (3751306)
Guangyu Sun (429231)

July 2018

Table S1. Bioinformatic command lines used in this study. Table S2. qRT-PCR primers used in this stu...

Comparative transcriptome analysis identified candidate genes involved in mycelium browning in Lentinula edodes

Seung-il Yoo
Hwa-Yong Lee
Kesavan Markkandan
Suyun Moon
Yong Ju Ahn
Sumin Ji
Junsu Ko
Seong-Jin Kim
Hojin Ryu
Chang Pyo Hong

February 2019

Abstract Background Lentinula edodes is one of the most popular edible mushroom species in the world...

Additional file 7: of Comparative transcriptome analysis and identification of candidate effectors in two related rust species (Gymnosporangium yamadae and Gymnosporangium asiaticum)

Si-Qi Tao (4384186)
Bin Cao (186972)
Cheng-Ming Tian (838397)
Ying-Mei Liang (4384189)

August 2017

Analysis of orthologous genes. This file provides the orthologous genes identified by OrthoMCL as we...

Additional file 3: of Transcriptomic analysis of genes in soybean in response to Peronospora manshurica infection

Hang Dong (4754823)
Shuangfeng Shi (5237513)
Chong Zhang (418677)
Sihui Zhu (5237516)
Mei Li (217363)
Jie Tan (339881)
Yue Yu (260119)
Liping Lin (213510)
Shirong Jia (131035)
Xujing Wang (21247)
Yuanhua Wu (5237519)
Yuhui Liu (669854)

May 2018

Table S3. GO terms identified in soybean HR (JL1i vs. JL1ni) and HS (KF1i vs. KF1ni). Note: A total ...

Additional file 9: of Transcriptome analysis reveals pathways facilitating the growth of tobacco powdery mildew in Arabidopsis

Ran Li (57928)
Ling-Li Zhang (482443)
Xue-Mei Yang (3216627)
Xiao-Long Cao (6202820)
Ying-Ge Wang (6202835)
Xian-Feng Ma (6306143)
Viswanathan Chandran (488420)
Jing Fan (149601)
Hui Yang (91136)
Jing Shang (227576)
Ji-Qun Zhao (6202838)
Shunyuan Xiao (722953)
Yan Li (23143)
Wen-Ming Wang (505701)

February 2019

Figure S2. Clustering of deferential expressed genes responsive to tobacco powdery mildew. Hierarchi...

Additional file 2: Table S1. of Transcriptome analysis reveals the complexity of alternative splicing regulation in the fungus Verticillium dahliae

Lirong Jin (3621548)
Guanglin Li (709617)
Dazhao Yu (697557)
Wei Huang (36889)
Chao Cheng (11274)
Shengjie Liao (3721921)
Qijia Wu (3721918)
Yi Zhang (9093)

February 2017

The genic distribution of two sets of transcriptome sequencing reads from the two V. dahliae strains...

Additional file 5: Table S3. of Deciphering common and specific transcriptional immune responses in pea towards the oomycete pathogens Aphanomyces euteiches and Phytophthora pisi

Sara Hosseini (3484100)
Malin Elfstrand (600711)
Fredrik Heyman (2849777)
Dan Funck Jensen (166302)
Magnus Karlsson (150089)

August 2015

List of differentially expressed pea genes during interaction with A. euteiches and P. pisi. Microso...

Additional file 4: of Comparative transcriptome analysis identified candidate genes involved in mycelium browning in Lentinula edodes

Seung-il Yoo (2614858)
Hwa-Yong Lee (511573)
Kesavan Markkandan (2614867)
Suyun Moon (6317828)
Yong Ahn (3063747)
Sumin Ji (5636426)
Junsu Ko (3509726)
Seong-Jin Kim (179277)
Hojin Ryu (6317837)
Chang Hong (3526031)

February 2019

Table S4. List of gene sets enriched in the differentially expressed genes. (XLSX 23 kb

Additional file 2: of Comparative transcriptome analysis identified candidate genes involved in mycelium browning in Lentinula edodes

Seung-il Yoo (2614858)
Hwa-Yong Lee (511573)
Kesavan Markkandan (2614867)
Suyun Moon (6317828)
Yong Ahn (3063747)
Sumin Ji (5636426)
Junsu Ko (3509726)
Seong-Jin Kim (179277)
Hojin Ryu (6317837)
Chang Hong (3526031)

February 2019

Table S2. Summary of the transcriptome annotation and gene expression data. (XLSX 4025 kb

Additional file 6: of Comparative transcriptome analysis identified candidate genes involved in mycelium browning in Lentinula edodes

Seung-il Yoo (2614858)
Hwa-Yong Lee (511573)
Kesavan Markkandan (2614867)
Suyun Moon (6317828)
Yong Ahn (3063747)
Sumin Ji (5636426)
Junsu Ko (3509726)
Seong-Jin Kim (179277)
Hojin Ryu (6317837)
Chang Hong (3526031)

February 2019

Table S6. List of browning-related genes and their respective biological functions. (XLSX 42 kb

Additional file 7: of Comparative transcriptome analysis identified candidate genes involved in mycelium browning in Lentinula edodes

Seung-il Yoo (2614858)
Hwa-Yong Lee (511573)
Kesavan Markkandan (2614867)
Suyun Moon (6317828)
Yong Ahn (3063747)
Sumin Ji (5636426)
Junsu Ko (3509726)
Seong-Jin Kim (179277)
Hojin Ryu (6317837)
Chang Hong (3526031)

February 2019

Table S7. List of differentially expressed carbohydrate-active enzymes (CAZyme) family genes. (XLSX ...

Additional file 10: of Comparative transcriptome analysis identified candidate genes involved in mycelium browning in Lentinula edodes

Seung-il Yoo (2614858)
Hwa-Yong Lee (511573)
Kesavan Markkandan (2614867)
Suyun Moon (6317828)
Yong Ahn (3063747)
Sumin Ji (5636426)
Junsu Ko (3509726)
Seong-Jin Kim (179277)
Hojin Ryu (6317837)
Chang Hong (3526031)

February 2019

Figure S2. Multiple sequence alignment among WC-1 (GenBank no. ESA41977), PHRA (GenBank no. BAF56991...

Additional file 9: of Comparative transcriptome analysis identified candidate genes involved in mycelium browning in Lentinula edodes

Seung-il Yoo (2614858)
Hwa-Yong Lee (511573)
Kesavan Markkandan (2614867)
Suyun Moon (6317828)
Yong Ahn (3063747)
Sumin Ji (5636426)
Junsu Ko (3509726)
Seong-Jin Kim (179277)
Hojin Ryu (6317837)
Chang Hong (3526031)

February 2019

Figure S1. Comparison of expression patterns by RNA-seq and qRT-PCR. The qRT-PCR log2 values (y-axis...

Additional file 11: of Comparative transcriptome analysis identified candidate genes involved in mycelium browning in Lentinula edodes

Seung-il Yoo (2614858)
Hwa-Yong Lee (511573)
Kesavan Markkandan (2614867)
Suyun Moon (6317828)
Yong Ahn (3063747)
Sumin Ji (5636426)
Junsu Ko (3509726)
Seong-Jin Kim (179277)
Hojin Ryu (6317837)
Chang Hong (3526031)

February 2019

Figure S3. Expression of tryrosinases (A) and PHRA (B) in white (W), normal brown (B), and partial b...

Additional file 3: of Transcriptome analysis reveals pathways facilitating the growth of tobacco powdery mildew in Arabidopsis

Ran Li (57928)
Ling-Li Zhang (482443)
Xue-Mei Yang (3216627)
Xiao-Long Cao (6202820)
Ying-Ge Wang (6202835)
Xian-Feng Ma (6306143)
Viswanathan Chandran (488420)
Jing Fan (149601)
Hui Yang (91136)
Jing Shang (227576)
Ji-Qun Zhao (6202838)
Shunyuan Xiao (722953)
Yan Li (23143)
Wen-Ming Wang (505701)

February 2019

Table S2. List of differentially expressed genes with more than 4-fold change between any two sample...

Additional file 1 of Transcriptomic analysis reveals candidate genes regulating development and host interactions of Colletotrichum fructicola

Xiaofei Liang (843086)
Shengping Shang (5568197)
Qiuyue Dong (3751315)
Bo Wang (86769)
Rong Zhang (44942)
Mark Gleason (3751306)
Guangyu Sun (429231)

July 2018

Table S1. Bioinformatic command lines used in this study. Table S2. qRT-PCR primers used in this stu...

Comparative transcriptome analysis identified candidate genes involved in mycelium browning in Lentinula edodes

Seung-il Yoo
Hwa-Yong Lee
Kesavan Markkandan
Suyun Moon
Yong Ju Ahn
Sumin Ji
Junsu Ko
Seong-Jin Kim
Hojin Ryu
Chang Pyo Hong

February 2019

Abstract Background Lentinula edodes is one of the most popular edible mushroom species in the world...

Additional file 7: of Comparative transcriptome analysis and identification of candidate effectors in two related rust species (Gymnosporangium yamadae and Gymnosporangium asiaticum)

Si-Qi Tao (4384186)
Bin Cao (186972)
Cheng-Ming Tian (838397)
Ying-Mei Liang (4384189)

August 2017

Analysis of orthologous genes. This file provides the orthologous genes identified by OrthoMCL as we...

Additional file 3: of Transcriptomic analysis of genes in soybean in response to Peronospora manshurica infection

Hang Dong (4754823)
Shuangfeng Shi (5237513)
Chong Zhang (418677)
Sihui Zhu (5237516)
Mei Li (217363)
Jie Tan (339881)
Yue Yu (260119)
Liping Lin (213510)
Shirong Jia (131035)
Xujing Wang (21247)
Yuanhua Wu (5237519)
Yuhui Liu (669854)

May 2018

Table S3. GO terms identified in soybean HR (JL1i vs. JL1ni) and HS (KF1i vs. KF1ni). Note: A total ...

Additional file 9: of Transcriptome analysis reveals pathways facilitating the growth of tobacco powdery mildew in Arabidopsis

Ran Li (57928)
Ling-Li Zhang (482443)
Xue-Mei Yang (3216627)
Xiao-Long Cao (6202820)
Ying-Ge Wang (6202835)
Xian-Feng Ma (6306143)
Viswanathan Chandran (488420)
Jing Fan (149601)
Hui Yang (91136)
Jing Shang (227576)
Ji-Qun Zhao (6202838)
Shunyuan Xiao (722953)
Yan Li (23143)
Wen-Ming Wang (505701)

February 2019

Figure S2. Clustering of deferential expressed genes responsive to tobacco powdery mildew. Hierarchi...

Additional file 2: Table S1. of Transcriptome analysis reveals the complexity of alternative splicing regulation in the fungus Verticillium dahliae

Lirong Jin (3621548)
Guanglin Li (709617)
Dazhao Yu (697557)
Wei Huang (36889)
Chao Cheng (11274)
Shengjie Liao (3721921)
Qijia Wu (3721918)
Yi Zhang (9093)

February 2017

The genic distribution of two sets of transcriptome sequencing reads from the two V. dahliae strains...

Additional file 5: Table S3. of Deciphering common and specific transcriptional immune responses in pea towards the oomycete pathogens Aphanomyces euteiches and Phytophthora pisi

Sara Hosseini (3484100)
Malin Elfstrand (600711)
Fredrik Heyman (2849777)
Dan Funck Jensen (166302)
Magnus Karlsson (150089)

August 2015

List of differentially expressed pea genes during interaction with A. euteiches and P. pisi. Microso...

Additional file 3: of Comparative transcriptome analysis identified candidate genes involved in mycelium browning in Lentinula edodes

Abstract

Extracted data

Additional file 3: of Comparative transcriptome analysis identified candidate genes involved in mycelium browning in Lentinula edodes

Abstract

Extracted data

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