Journal: BMC Genomics

Article Title: The transcriptome of the NZ endemic sea urchin Kina ( Evechinus chloroticus )

doi: 10.1186/1471-2164-15-45

Figure Lengend Snippet: GO annotations. Top 10 represented GO terms for each of the GO categories; Molecular Function, Biological Process and Cellular Component. GO terms annotated by protein similarity to the NCBI non-redundant database and from InterProScan results.

Article Snippet: Additional GO terms could be retrieved from the InterProScan results and merged with existing GO annotations, 11,478 transcripts had GO terms associated with InterPro results.

Techniques:

Journal: BMC Genomics

Article Title: The transcriptome of the NZ endemic sea urchin Kina ( Evechinus chloroticus )

doi: 10.1186/1471-2164-15-45

Figure Lengend Snippet: InterPro annotations. Top 10 represented InterPro terms from the InterProScan annotations.

Article Snippet: Additional GO terms could be retrieved from the InterProScan results and merged with existing GO annotations, 11,478 transcripts had GO terms associated with InterPro results.

Techniques:

Journal: BMC Genomics

Article Title: Analysis of differentially expressed Sclerotinia sclerotiorum genes during the interaction with moderately resistant and highly susceptible chickpea lines

doi: 10.1186/s12864-021-07655-6

Figure Lengend Snippet: Summary of the Illumina sequence reads generated by RNA – seq obtained from inoculation of a moderately resistant (MR) chickpea line PBA HatTrick and a susceptible (S) chickpea line Kyabra. The values for each time point are the averages of the three biological replicates

Article Snippet: S. sclerotiorum Gene ontology (GO) terms were derived from a previous InterPro annotation [ ].

Techniques: Sequencing, Generated, RNA Sequencing, In Vitro

Journal: BMC Genomics

Article Title: Analysis of differentially expressed Sclerotinia sclerotiorum genes during the interaction with moderately resistant and highly susceptible chickpea lines

doi: 10.1186/s12864-021-07655-6

Figure Lengend Snippet: A multidimensional scaling (MDS) plot showing the relatedness of Sclerotinia sclerotiorum samples used for RNA-Seq analysis. Samples were collected from moderately resistant (MR) and susceptible (S) chickpea lines at 6, 12, 24, 48 and 72 h post inoculation (hpi), as well as samples from an in vitro culture. The symbol ▲represent the MR, ■ the S and ● the in vitro samples. The x and y-axis represent Euclidean dimensions, distinct colours represent each treatment, and individual dots represent each sample

Article Snippet: S. sclerotiorum Gene ontology (GO) terms were derived from a previous InterPro annotation [ ].

Techniques: RNA Sequencing, In Vitro

Journal: BMC Genomics

Article Title: Analysis of differentially expressed Sclerotinia sclerotiorum genes during the interaction with moderately resistant and highly susceptible chickpea lines

doi: 10.1186/s12864-021-07655-6

Figure Lengend Snippet: Reverse transcription - quantitative PCR (RT-qPCR) validation of RNA sequencing (RNA-Seq) data in the moderately resistant (MR) and susceptible (S) chickpea lines following infection with Sclerotinia sclerotiorum . Log 2 (fold change) (LogFC) values were generated for qPCR samples by comparing the expression of genes at each time point of infection vs the in vitro control sample using the 2 -∆∆Ct method ( a ). LogFC values were generated for RNA-Seq samples by comparing the average raw read counts at each time point of infection vs in vitro/vegetative growth culture ( b ). Pairwise contrasts were performed using quasi-likelihood F tests. The data are presented as means ± standard error (SE) from three biological replicates for 12 hpi (early stage of infection) and 48 hpi (late stage of infection)

Article Snippet: S. sclerotiorum Gene ontology (GO) terms were derived from a previous InterPro annotation [ ].

Techniques: Reverse Transcription, Real-time Polymerase Chain Reaction, Quantitative RT-PCR, Biomarker Discovery, RNA Sequencing, Infection, Generated, Expressing, In Vitro, Control

Journal: BMC Genomics

Article Title: Analysis of differentially expressed Sclerotinia sclerotiorum genes during the interaction with moderately resistant and highly susceptible chickpea lines

doi: 10.1186/s12864-021-07655-6

Figure Lengend Snippet: Venn diagram and graph showing upregulated Sclerotinia sclerotiorum genes during interaction with chickpea. Venn diagram shows the number of common and unique genes at time points 6, 12, 24, 48, and 72 hpi in ( a ) moderately resistant (MR), and ( b ) susceptible (S) lines ( c ) Comparison of MR and S genes ( d ). A graph showing expression pattern during the time course of infection of the most highly expressed common gene between MR and S line

Article Snippet: S. sclerotiorum Gene ontology (GO) terms were derived from a previous InterPro annotation [ ].

Techniques: Comparison, Expressing, Infection

Journal: BMC Genomics

Article Title: Analysis of differentially expressed Sclerotinia sclerotiorum genes during the interaction with moderately resistant and highly susceptible chickpea lines

doi: 10.1186/s12864-021-07655-6

Figure Lengend Snippet: The number of in planta upregulated S. sclerotiorum genes involved in the cell wall and cuticle degradation

Article Snippet: S. sclerotiorum Gene ontology (GO) terms were derived from a previous InterPro annotation [ ].

Techniques: Starch

Journal: BMC Genomics

Article Title: Analysis of differentially expressed Sclerotinia sclerotiorum genes during the interaction with moderately resistant and highly susceptible chickpea lines

doi: 10.1186/s12864-021-07655-6

Figure Lengend Snippet: Sclerotinia sclerotiorum detoxification enzymes upregulated (LogFC) in planta relative to in vitro

Article Snippet: S. sclerotiorum Gene ontology (GO) terms were derived from a previous InterPro annotation [ ].

Techniques: In Vitro

Journal: BMC Genomics

Article Title: Analysis of differentially expressed Sclerotinia sclerotiorum genes during the interaction with moderately resistant and highly susceptible chickpea lines

doi: 10.1186/s12864-021-07655-6

Figure Lengend Snippet: Sclerotinia sclerotiorum reactive oxygen scavenging (ROS) enzymes upregulated (LogFC) during chickpea infection relative to in vitro

Article Snippet: S. sclerotiorum Gene ontology (GO) terms were derived from a previous InterPro annotation [ ].

Techniques: Infection, In Vitro