Phytophthora palmivora

RNA-seq of Phytophthora palmivora: Mycelia rep2

We employed dual transcriptomic approach to study Cocos nucifera-Phytophthora palmivora interactions at the cellular and molecular levels. Time-resolved dual transcriptomics revealed different pathogen and host transcriptome dynamics.

{'host': 'Cocos nucifera', 'isolate': 'TR-PP-2 r2', 'lat_lon': '12.52 N 74.96 E', 'env_medium': 'bud rot affected tissue from coconut', 'collected_by': 'Gangaraj K P', 'geo_loc_name': 'India: Kasaragod', 'host_disease': 'Bud rot', 'biosamplemodel': 'MIGS/MIMS/MIMARKS.plant-associated', 'collection_date': '2019-01-05', 'isolation_source': 'bud rot affected tissue from coconut', 'isol_growth_condt': 'PMC7150523'}

De novo transcriptome dataset of gene expression in Durio zibethinus during the infection of Phytophthora palmivora

Total RNA of P. palmivora were isolated from infected D. zibethinus leave using Rneasy Plant Mini kit (Qiagen). RNA is converted to cDNA by reverse transcription. Fragments are converted into the library by ligation to sequencing adapters containing specific sequences by Illumina. Next step involve clonal amplification of the library through cluster generation and finally generating sequence.

{'host': 'Durio zibethinus', 'lat_lon': '3.853 N 103.312 E', 'description': 'Young and healthy durian leave samples were detached from 3-months-old durian seedling and treated with sterile distilled water. Treated samples were collected after 3 days post treatment.', 'sample_type': 'Leave tissue sample', 'collected_by': 'Nur Sabrina Ahmad Azmi', 'geo_loc_name': 'Malaysia: Glasshouse and Nursery Complex IIUM, Kuantan', 'biosamplemodel': 'Microbe, viral or environmental', 'collection_date': '2021-09-27', 'isolation_source': 'Healthy durian leaves', 'biomaterial_provider': 'Microbe preparation room, IIUM Kuantan campus'}

De novo transcriptome dataset of gene expression in Durio zibethinus during the infection of Phytophthora palmivora

Total RNA of P. palmivora were isolated from infected D. zibethinus leave using Rneasy Plant Mini kit (Qiagen). RNA is converted to cDNA by reverse transcription. Fragments are converted into the library by ligation to sequencing adapters containing specific sequences by Illumina. Next step involve clonal amplification of the library through cluster generation and finally generating sequence.

{'host': 'Durio zibethinus', 'strain': 'PPUIA-4', 'isolate': 'Isolate 4', 'lat_lon': '3.853 N 103.312 E', 'description': 'Young and healthy durian leave samples were detached from 3-months-old durian seedling and inoculated with P. palmivora zoospores. Infected samples were collected at 3 days post inoculation (3 dpi).', 'sample_type': 'Leave tissue sample', 'collected_by': 'Nur Sabrina Ahmad Azmi', 'geo_loc_name': 'Malaysia: Glasshouse and Nursery Complex IIUM, Kuantan', 'biosamplemodel': 'Microbe, viral or environmental', 'collection_date': '2021-09-27', 'isolation_source': 'Infected durian leaves', 'biomaterial_provider': 'Microbe preparation room, IIUM Kuantan campus'}

RNA-seq of Marchantia polymorpha thallus infetced with Phytophthora palmivora, 4 dpi

mRNAs from M.polymorpha plants infected with P. palmivora at 3 dpi and 4 dpi, and P. palmivora mRNAs from the mycelium sample were purified using Poly(A) selection from total RNA sample, and then fragmented. cDNA library preparation was performed with the TruSeq® RNA Sample Preparation Kit (Illumina, US) according to the manufacturer’s protocol. cDNA sequencing of the 9 samples (3 dpi, 4 dpi and mycelium sample, all in triplicates) was performed with Illumina NextSeq 2500 in 100 paired end mode. Samples were de-multiplexed and analyzed further.

{'host': 'Marchantia polymorpha', 'strain': 'ARI', 'sample_type': 'mixed plant-pathogen sample', 'collected_by': 'Philip Carella', 'biosamplemodel': 'Microbe, viral or environmental', 'collection_date': '2016-12', 'isolation_source': '4-week old M. polymorpha thallus 3 days after infection', 'host_tissue_sampled': 'thallus', 'biomaterial_provider': 'Sebastian Schornack SLCU'}

RNA-seq of Marchantia polymorpha thallus infetced with Phytophthora palmivora, 4 dpi

mRNAs from M.polymorpha plants infected with P. palmivora at 3 dpi and 4 dpi, and P. palmivora mRNAs from the mycelium sample were purified using Poly(A) selection from total RNA sample, and then fragmented. cDNA library preparation was performed with the TruSeq® RNA Sample Preparation Kit (Illumina, US) according to the manufacturer’s protocol. cDNA sequencing of the 9 samples (3 dpi, 4 dpi and mycelium sample, all in triplicates) was performed with Illumina NextSeq 2500 in 100 paired end mode. Samples were de-multiplexed and analyzed further.

{'host': 'Marchantia polymorpha', 'strain': 'ARI', 'sample_type': 'mixed plant-pathogen sample', 'collected_by': 'Philip Carella', 'biosamplemodel': 'Microbe, viral or environmental', 'collection_date': '2016-12', 'isolation_source': '4-week old M. polymorpha thallus 3 days after infection', 'host_tissue_sampled': 'thallus', 'biomaterial_provider': 'Sebastian Schornack SLCU'}

RNA-seq of Phytophthora palmivora axenically grown mycelium and zoospores

mRNAs from M.polymorpha plants infected with P. palmivora at 3 dpi and 4 dpi, and P. palmivora mRNAs from the mycelium sample were purified using Poly(A) selection from total RNA sample, and then fragmented. cDNA library preparation was performed with the TruSeq® RNA Sample Preparation Kit (Illumina, US) according to the manufacturer’s protocol. cDNA sequencing of the 9 samples (3 dpi, 4 dpi and mycelium sample, all in triplicates) was performed with Illumina NextSeq 2500 in 100 paired end mode. Samples were de-multiplexed and analyzed further.

{'host': 'NA', 'strain': 'ARI', 'sample_type': 'axenically grown mycelium and zoospores', 'collected_by': 'Philip Carella', 'biosamplemodel': 'Microbe, viral or environmental', 'collection_date': '2016-12', 'isolation_source': 'axenically grown mycelium and zoospores', 'biomaterial_provider': 'Sebastian Schornack SLCU'}