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A locally funded Puerto Rican parrot (Amazona vittata) genome sequencing project increases avian data and advances young researcher education Oleksyk, Taras K.; Pombert, Jean-Francois; Siu, Daniel; Mazo-Vargas, Anyimilehidi; Ramos, Brian; Guiblet, Wilfried; Afanador, Yashira; Ruiz-Rodriguez, Christina T.; Nickerson, Michael L.; Logue, David M.; Dean, Michael; Figueroa, Luis; Valentin, Ricardo; Martinez-Cruzado, Juan-Carlos Background: Amazona vittata is a critically endangered Puerto Rican endemic bird, the only surviving native parrot species in the United States territory, and the first parrot in the large Neotropical genus Amazona, to be studied on a genomic scale. Findings: In a unique community-based funded project, DNA from an A. vittata female was sequenced using a HiSeq Illumina platform, resulting in a total of ~42.5 billion nucleotide bases. This provided approximately 26.89x average coverage depth at the completion of this funding phase. Filtering followed by assembly resulted in 259,423 contigs (N50=6,983 bp, longest=75,003 bp), which was further scaffolded into 148,255 fragments (N50=19,470, longest=206,462 bp). This provided ~76% coverage of the genome based on an estimated size of 1.58 Gb. The assembled scaffolds allowed basic genomic annotation and comparative analyses with other available avian whole-genome sequences. Conclusions: The current data represents the first genomic information from and work carried out with a unique source of funding. This analysis further provides a means for directed training of young researchers in genetic and bioinformatics analyses and will facilitate progress towards a full assembly and annotation of the Puerto Rican parrot genome. It also adds extensive genomic data to a new branch of the avian tree, making it useful for comparative analyses with other avian species. Ultimately, the knowledge acquired from these data will contribute to an improved understanding of the overall population health of this species and aid in ongoing and future conservation efforts. Sherpa Romeo green journal. Open access article. Creative Commons Attribution 2.0 (CC BY 2.0) applies

I only wrote a chapter in this new book, The HTML and CSS Workshop: A New, Interactive Approach to Learning HTML and CSS, but it is a new book and my name is on it and it’s on Amazon, so it’s still ???? cool. I wrote the chapter on Themes, Colors, and Polish. Here’s what […]

Like many of you I’m working from home for a while. As a mental health strategy, I’m going to do some writing and coding in the hour or so I get back each day from not having to commute. The first post, which will follow today, will be my thoughts on working from home. I […]

While we’re preparing an upcoming release, I didn’t want the day to go by without mentioning that ten years ago today, HTML5 Boilerplate was released. Here’s the story of the project as we wrote it up a few years ago. The History of HTML5 Boilerplate Sometime in 2009… “Wouldn’t it be great if we created […]