“SpinachBasev2: An updated central portal for Spinach genomics tools and information”
Spinach (Spinacia oleracea) is an important agricultural crop because of its nutritional value, popularity, and other potential applications to human health such as being a vector for edible vaccines. In the summer of 2018, a project was undertaken by Fei Lab to build a central database for spinach genomic information and a site, SpinachBase, was created. This site houses data and resources related to the first published spinach genome of cultivar Sp75. In the following years, four more spinach genomes were sequenced of cultivars Monoe-Viroflay, Viroflay, 03-009, and Cornell No.9, creating a need to update the public store of spinach genomic knowledge. The release of these additional genome sequences, along with updates made to the Drupal/Tripal web system upon which the original database is built, necessitated the creation of a new spinach genomic database. Thus, SpinachBasev2 has been constructed and is intended to update and replace the existing SpinachBase site, while continuing to provide helpful tools and analyses relating to spinach genetic and genomic data. These tools include a BLAST similarity search function, a keyword search tool, a synteny viewer, and a genome browser. Various bioinformatics programs were used to format and annotate the genomic data for the database such as NCBI BLAST, Blast2Go, AHRD, InterProScan, and MCScanX. This database will allow spinach researchers and breeders to more easily and efficiently find and investigate data related to spinach genetics and genomics.
Attending a small, liberal arts university has been great, but has not allowed me to work or research in a large laboratory setting during the regular school year. Here at BTI, I have been able to gain a whole new experience of interacting with a PI along with other undergraduates, graduate students, and postdocs. Being able to work on my own bioinformatics project with my mentor has taught me how to use a myriad of different data annotation programs and coding languages, and has helped me to see what a career in bioinformatics really looks like. I have also become a more well-rounded scientist in general through the weekly lectures from diverse plant science researchers and classes dedicated to science ethics and science communication. All in all, this experience has prepared me in many different areas to confidently pursue graduate school and a career in the plant sciences.