Abstract
The whole-genome sequence of watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai), a valuable horticultural crop worldwide, was released in 2013. Here, we compared a de novo-based approach (DBA) to a reference-based approach (RBA) using RNA-seq data, to aid in efforts to improve the annotation of the watermelon reference genome and to obtain biological insight into male-sterility in watermelon. We applied these techniques to available data from two watermelon lines: the male-sterile line DAH3615-MS and the male-fertile line DAH3615. Using DBA, we newly annotated 855 watermelon transcripts, and found gene functional clusters predicted to be related to stimulus responses, nucleic acid binding, transmembrane transport, homeostasis, and Golgi/vesicles. Among the DBA-annotated transcripts, 138 de novo-exclusive differentially-expressed genes (DEDEGs) related to male sterility were detected. Out of 33 randomly selected newly annotated transcripts and DEDEGs, 32 were validated by RT-qPCR. This study demonstrates the usefulness and reliability of the de novo transcriptome assembly in watermelon, and provides new insights for researchers exploring transcriptional blueprints with regard to the male sterility.
Highlights
Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai], a member of the Cucurbitaceae family, is an important crop worldwide, with annual production of approximately 110 million tons in 2013 (FAO, http://faostat.fao.org/)
We identified several previously unreported transcripts including de novo-exclusive differentially-expressed genes (DEDEGs) from the comparison between reference-based approach (RBA) and de novo-based approach (DBA)
Transcriptome/genome analysis through RNA sequencing (RNA-seq) can be effectively accomplished through RBA when a reference genome exists, but RBA is completely dependent on the degree of completion of the reference genome
Summary
Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai], a member of the Cucurbitaceae family, is an important crop worldwide, with annual production of approximately 110 million tons in 2013 (FAO, http://faostat.fao.org/). & Nakai], a member of the Cucurbitaceae family, is an important crop worldwide, with annual production of approximately 110 million tons in 2013 (FAO, http://faostat.fao.org/). The first reference genome sequence of the East Asian watermelon was released in 2013 [1], based on next-generation sequencing (NGS) techniques. Completion of the reference genome has allowed members of the Cucurbitaceae to be analyzed using RNA-seq. Two common RNA-seq assembly methods are widely used: de novo-based approach (DBA) and reference-based approach (RBA) [2,3,4]. Both approaches can be applied to transcriptome
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
