Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Small RNA-seq on a time series of potato infected with Globodera pallida

ABSTRACT: We explored the sex determination of Globodera pallida. To do so, we grew cuttings of the potato cultivar Desiree on Gamborg B5 medium supplemented with either 1.5 g/L or 20 g/L sucrose. 14-day-old cuttings were inoculated with 100 G. pallida E400 Rookmaker juveniles. Infected root tissue was harvested at 1, 3, 6, and 9 dpi. Also, a subsample of the ppJ2 was kept for each batch. The experiment contains four time-separated batches. Small RNA sequencing was performed by BGI Hong Kong.

INSTRUMENT(S): DNBSEQ-G400, Maxwell 16 LEV-plant RNA kit

ORGANISM(S): Globodera pallida

SUBMITTER: Mark Sterken

PROVIDER: E-MTAB-15069 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Stem cuttings of P. trichocarpa (clone 101-74) were rooted in liquid medium without growth regulators (basal medium). The first emerging roots were observed on cuttings 6 days after the start of culture. The highest average root number per cutting (10 Â± 2 roots/cutting) was obtained after 14 days. The first macroscopic evidence of root initiation was the appearance of root primordia, as lateral bulges observed at the stem surface 3 to 4 days after transfer to basal medium. Stem cross-sections showed intensely dividing cells forming root primordial. One to two days later the bark split and the organized sequence of cell division and differentiation steps in the primordium led to the establishment of the main root tissues, as well as the vascular connections of the incipient root with the pre-existing stem vasculature. Subsequently, the outgrowth and emergence of the adventitious root occurred. We refer to the dormant cutting as stage 0, the organizing primordium as stage 1, the primordium differentiation as stage 2. To examine changes in gene transcription associated with the development of adventitious roots, we monitored the transcript levels in differentiating primordia using microarrays. cDNA was prepared from replicate sets of P. trichocarpa rooted cuttings harvested at stages 0, 1 and 2. The Populus whole-genome expression array version 2.0 manufactured by NimbleGen Systems Limited (Madison, WI) contains in duplicates three independent, non-identical, 60-mer probes per whole gene model plus control probes and labeling controls. Included in the microarray are 65,965 probe sets corresponding to 55,970 gene models predicted on the P. trichocarpa genome sequence version 1.0 and 9,995 aspen cDNA sequences (Populus tremula, Populus tremuloides, and P. tremula x P. tremuloides). NimbleGen whole genome microarray analyses were performed in triplicate as per manufacturers instructions. We carried out nine hybridizations (NimbleGen) with samples derived from three early developmental stages of P. trichocarpa adventitious roots. cDNA was synthesized using CLONTECH Smart cDNA Synthesis kit containing an amplification step on the cDNA level. All samples were labeled with Cy3.

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Small RNA-seq on a time series of potato infected with Globodera pallida

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