Characterization of transcriptome dynamics during watermelon fruit development: sequencing, assembly, annotation and gene expression profiles

Abstract

BackgroundCultivated watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai var. lanatus] is an important agriculture crop world-wide. The fruit of watermelon undergoes distinct stages of development with dramatic changes in its size, color, sweetness, texture and aroma. In order to better understand the genetic and molecular basis of these changes and significantly expand the watermelon transcript catalog, we have selected four critical stages of watermelon fruit development and used Roche/454 next-generation sequencing technology to generate a large expressed sequence tag (EST) dataset and a comprehensive transcriptome profile for watermelon fruit flesh tissues.ResultsWe performed half Roche/454 GS-FLX run for each of the four watermelon fruit developmental stages (immature white, white-pink flesh, red flesh and over-ripe) and obtained 577,023 high quality ESTs with an average length of 302.8 bp. De novo assembly of these ESTs together with 11,786 watermelon ESTs collected from GenBank produced 75,068 unigenes with a total length of approximately 31.8 Mb. Overall 54.9% of the unigenes showed significant similarities to known sequences in GenBank non-redundant (nr) protein database and around two-thirds of them matched proteins of cucumber, the most closely-related species with a sequenced genome. The unigenes were further assigned with gene ontology (GO) terms and mapped to biochemical pathways. More than 5,000 SSRs were identified from the EST collection. Furthermore we carried out digital gene expression analysis of these ESTs and identified 3,023 genes that were differentially expressed during watermelon fruit development and ripening, which provided novel insights into watermelon fruit biology and a comprehensive resource of candidate genes for future functional analysis. We then generated profiles of several interesting metabolites that are important to fruit quality including pigmentation and sweetness. Integrative analysis of metabolite and digital gene expression profiles helped elucidating molecular mechanisms governing these important quality-related traits during watermelon fruit development.ConclusionWe have generated a large collection of watermelon ESTs, which represents a significant expansion of the current transcript catalog of watermelon and a valuable resource for future studies on the genomics of watermelon and other closely-related species. Digital expression analysis of this EST collection allowed us to identify a large set of genes that were differentially expressed during watermelon fruit development and ripening, which provide a rich source of candidates for future functional analysis and represent a valuable increase in our knowledge base of watermelon fruit biology.

Estrogen alters the profile of the transcriptome in river snail Bellamya aeruginosa

“…For example, only 17.85 % of the unigenes were annotated using the GO tool, and only 36.85 % were annotated in the Nr database. This is consistent with previous reports of 20-40 % annotation efficiency in eukaryotes (Meyer et al 2009;Wang et al 2010a, b), although lower than some studies (Guo et al 2011;Ji et al 2012).…”

Discovery of clubroot-resistant genes in Brassica napus by transcriptome sequencing

“…The rate of reads with Q20-value reached 98.68%. Based on these reads, 96,149 unigenes were assembled with an average length of 973 bp, which was larger than the mean unigene lengths found in butterfly (197 bp;Vera et al, 2008), sweet potato (581 bp; Guo et al, 2011), Salvia miltiorrhiza (331 bp; Zhang et al, 2012), safflower (446 bp; Lulin et al, 2012), and wax gourd (709 bp; Jiang et al, 2013). We aligned the unigene sequences to the Nr, Swiss-Prot, GO, COG, and KEGG protein databases and found that most unigene sequences could be matched to unique protein sequences in the various databases.…”

The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions

“…Paired-end Illumina libraries were prepared following the manufacturer's instructions and sequenced on an Illumina GAII system. We sequenced 44,75 or 90 bp at each end. The Illumina paired-end reads from each watermelon accession were aligned to the reference 97103 genome sequences using BWA 67 .…”

“…Fruit flesh and rind tissues of 97103 were collected at four developmental stages: 10, 18, 26 and 34 days after pollination 75 . RNA extraction and strand-specific RNA-Seq library preparations were performed as described 44 , and RNA-Seq libraries were sequenced on the Illumina HiSeq 2000 system.…”