De Novo Transcriptome Assembly of Cucurbita Pepo L. Leaf Tissue Infested by Aphis Gossypii

Abstract

Zucchini (Cucurbita pepo L.), extensively cultivated in temperate areas, belongs to the Cucurbitaceae family and it is a species with great economic value. One major threat related to zucchini cultivation is the damage imposed by the cotton/melon aphid Aphis gossypii Glover (Homoptera: Aphididae). We performed RNA-sequencing on cultivar “San Pasquale” leaves, uninfested and infested by A. gossypii, that were collected at three time points (24, 48, and 96 h post infestation). Then, we combined all high-quality reads for de novo assembly of the transcriptome. This resource was primarily established to be used as a reference for gene expression studies in order to investigate the transcriptome reprogramming of zucchini plants following aphid infestation. In addition, raw reads will be valuable for new experiments based on the latest bioinformatic tools and analytical approaches. The assembled transcripts will serve as an important reference for sequence-based studies and for primer design. Both datasets can be used to support/improve the prediction of protein-coding genes in the zucchini genome, which has been recently released into the public domain.

Zucchini Plants Alter Gene Expression and Emission of (E)-β-Caryophyllene Following Aphis gossypii Infestation

“…Our results describe the timing and dynamics of the zucchini plant responses to aphids and demonstrate that the interaction triggered a deep transcriptome reprogramming that involved more than 700 DEGs ( Figures 1 , 4 and Supplementary Table S2 ). We used the zucchini transcriptome described by Vitiello et al (2018) as it was primarily established to be used as reference for the identification of DEGs. However, all transcripts were mapped onto the available C. pepo genome (see Supplementary Table S2 ) to maintain a link with the zucchini genome released into the public domain ( Montero-Pau et al, 2018 ) and to facilitate comparison and annotation transfer.…”

“…Details on the experimental design of the interaction between the aphid-susceptible C. pepo cultivar “San Pasquale” and A. gossypii , RNA isolation and sequencing, and transcriptome assembly and annotation are described in Vitiello et al (2018) .…”

“…A subset of 42,517 transcripts ( i.e. , the longest transcript for each gene locus) was extracted from the assembled transcriptome (Transcriptome Shotgun Assembly accession GGKS01000000 ; Vitiello et al, 2018 ) and used as reference for read mapping. Bowtie2 ( Langmead and Salzberg, 2012 ) was used to align reads (obtained after sequencing three biological replicates collected for both infested and control plants per time point) onto reference transcripts and was run in “end-to-end” mode using the “very-sensitive” option.…”

Characterization the coding and non-coding RNA components in the transcriptome of invasion weed Alternanthera philoxeroides

“…The bias was also reported in other studies. For example, in the leaf of Cucurbita pepo L. infested by Aphis Gossypii, 25,000 and 8,220 truncated 5'UTR and 3'UTRs were detected, respectively (Vitiello et al, 2018). We speculated that the reasons for this significant bias between incomplete 5'UTR and 3'UTRs may due to: (1) software (e.g.…”

Table_1.XLSX

“…A subset of 42,517 transcripts (i.e., the longest transcript for each gene locus) was extracted from the assembled transcriptome (Transcriptome Shotgun Assembly accession GGKS01000000; Vitiello et al, 2018) and used as reference for read mapping. Bowtie2 (Langmead and Salzberg, 2012) was used to align reads (obtained after sequencing three biological replicates collected for both infested and control plants per time point) onto reference transcripts and was run in "end-to-end" mode using the "verysensitive" option.…”