Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNA-seq of healthy seedling leaf and root tissue of seven legume species

ABSTRACT: Seven closely related species from Hologalegina and Phaseoloid clades were selected: Lathyrus sativus, Pisum sativum (Lathyrus oleraceus), Lens culinaris, Cicer arietinum, Medicago truncatula, Glycine max, and Phaseolus vulgaris, to assess tissue-specific expression in non-inoculated conditions. Plants were cultivated in 0.5 L pots containing growth medium (50% soil, 25% vermiculite, 25% peat) in controlled environment chambers at 22°C with a 12/12-hour photoperiod. At the three fully expanded leaf developmental stage, leaf and root tissues were harvested separately, and RNA was extracted. RNA samples were submitted for Illumina NovaSeq 6000 Sequencing PE150 (40 million paired-end reads per sample) at Novogene (UK) Co. Raw reads were trimmed with cutadapt and gene counts were obtained using StringTie with the respective annotation files of each genome.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Lathyrus sativus

SUBMITTER: Rita Maravilha Marques

PROVIDER: E-MTAB-15524 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Similar Datasets

Project description:Tomato seeds (S. lycopersicum ‘Fl Lanai’) were germinated under greenhouse conditions maintained at 24°C-29°C in flat trays (BWI Apopka, Catalog Number GPPF72S7X) filled with Sungro Horticulture soil (Metro-mix 830, BWI Apopka, Cat# TX830). Two weeks post emergence seedlings were transplanted to 4” pots using the same soil and transferred to a Conviron walk-in growth chamber (CMP6060) for the remainder of the experiment. Conviron conditions include a 14h/10h light/dark cycle maintained at 28°C, and plants were fertilized weekly (20-20-20). To prevent cross contamination, tomato plants were confined to insect proof cages at all times (BioQuip 1450NS68). Four weeks after transplanting, 40 whiteflies (B. tabaci MEAM1) were collected from virus free or Tomato Mottle Virus (ToMoV) established colonies via aspiration and moved into a clip cage placed on the 4th true leaf of each tomato plant as previously described38. Whiteflies were reared cabbage (Brassica oleracea), while viruliferous whiteflies were reared on ToMoV infected tomato from colonies established in the Polston lab. For all plants in this study, feeding was halted after 3 days of whitefly feeding (3 DPI) by gentle removal of clip cages and whitefly termination using insecticidal soap (Garden Safe, 1% of potassium salts of fatty acids). For the samples referred to as “local”, the tomato leaf bound within the clip cages was immediately removed and snap frozen for protein extraction. For the samples designated “systemic”, the plants were allowed to continue growing for 7 additional days after clip cage removal and whitefly termination, at which point the 9th leaf was excised and snap frozen. Plants used for collection of local leaves at 3 DPI were not used for the collection of systemic leaves 10 DPI. For both local and systemic leaves collected, we also included a no treatment control (NTC) that was subjected identically to clip cage and insecticidal soap applications, but without the addition of whitefly or ToMoV. Our experiment therefore consists of a no-treatment control (NTC), a whitefly treatment (+WF), and a viruliferous whitefly (+WFV) treatment for both local (4th true leaf, 3 DPI) and systemic leaves (9th true leaf, 10 DPI). The presence of ToMoV in all infected plants was confirmed via Nanopore sequencing. Briefly, Tomato genomic DNA was extracted from five systemic leaf samples using the PureGene tissue DNA isolation kit (product # 158667; QIAGEN, Valencia, CA, USA), following the manufacturer’s protocol and stored at -80°C until needed. Library preparation was performed using the Rapid Sequencing Kit RBK004 protocol (Oxford Nanopore Technologies) and loaded onto a 9.4.1 flow cell in a MinION connected to a MinIT with live base calling enabled. Resulting sequencing reads for each sample were mapped to both ToMoV A component (GenBank accession: L14460) and ToMoV B component (GenBank accession: L14461) sequences.

Dataset Information

RNA-seq of healthy seedling leaf and root tissue of seven legume species

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets