The i5K Pilot Genome Sequencing at the Baylor College of Medicine Human Genome Sequencing Center

The i5K is an initiative to sequence the genomes of 5,000 arthropods of medical, agricultural and scientific importance. As a pilot project to identify potential problems and challenges in species selection, identification and acquisition, DNA isolation, sequencing strategies and assembly, automated and manual annotation, analysis and publication, the BCM-HGSC is sequencing ~30 arthropods, selected by the i5K species selection committee.

Our extensive experience in arthropod genomics, has allowed us to quickly identify new challenges in scaling the number of de-novo genome projects. For example, many arthropod species have much larger genome sizes than initially expected (e.g. the Preying Mantis has a 5Gb genome, the American Cockroach’s is 3Gb genome, the Velvet worm - a living fossil out-group to the arthropods ~ 5Gb, most Crustacea are 3Gb+). For a number of arthropod orders, small body sizes yield tiny amounts of DNA, for example sand flies, thrips and protura – an out-group to the insects with no wings. Other challenges include the inability to inbreed, a common situation for most arthropods (extreme examples are the cicadas with life cycles of 13 and 17 years) or inability to sex individuals – for example arthropods where only larvae can be easily collected. An additional challenge is to identify ongoing genome projects to avoid replication of work. This challenge will become increasingly important as the reduction in sequencing cost leads to a rapid increase in genome sequencing projects.

We present our success in working with community groups to select appropriate species for sequencing, our Illumina sequencing plans, and initial assembly demonstration results, our proposed modifications for extremely low quantities of DNA, and our automated analysis plans. Also we present an outline of the i5K community annotation and analysis process.

Perhaps the biggest contribution of this project will be bringing the genomics revolution to the field of arthropod biology, establishing a molecular baseline to the study of animals that affect our society so greatly.