Who is sequencing and annotating the papaya genome?

The papaya genome is being sequenced at the University of Hawaii's College of Natural Sciences' Advanced Studies in Genomics, Proteomics, and Bioinformations and directed by Maqsudul Alam. The genome sequencing is led by Shaobin Hou and Maqsudul Alam while the sequence assembly and annotation is lead by Maqsudul Alam, Lei Wang, Steven Salzberg. The team leaders for annotation are Yun Feng at Nakai University, China, Jimmy Saw and Alexandre Dionne-Laporte at the University of Hawaii. Genetic and physical mapping is being carried out at the Hawaii Agriculture Research Center and the University of Illinois at Urbana-Champaign under the direction of Ray Ming and Qingyi Yu. The Hawaii Papaya Genome Project's website can provide more information as to why the papaya genome is being sequenced.

Welcome Brassicales genome researcher!

Thanks to the Hawaii Papaya Genome Project, and the Arabidopsis genomics community, papaya (Cp) and Arabidopsis (At) genomes can now be compared to provide new insight into plant genome evolution. Papaya and Arabidopsis are both in the order of Brassicales. In the time since their divergence, Arabidopsis has undergone two tetraploidy events (followed by fractionation that reduced its genome content to near diploid) while papaya has had none. This phylogenetic relationship allows for better annotation of both papaya and Arabidopsis genomes and genes, to identify conserved non-coding regions that may have a regulatory function on nearby genes, and to identify a variety of genome evolution events such as subfunctionalization, neofunctionalization, fractionation, inversion events, and to reconstruct a good likeness of a Brassicales ancestral genome.

This site gives an overview of some of our research comparing the post-tetraploid Arabidopsis genome to papaya's genome. We have been using our comparative genomics tool, GEvo, to simultaneously compare multiple syntenic regions from Arabidopsis and to the ortholog from papaya. Near the end of this site is a section on how you can use GEvo to comparing papaya and Arabidopsis. However, GEvo is still beta software and our lead programmer, Eric Lyons, is counting on user feedback. Feel free to contact Eric, or any of us in the Freeling lab, using the e-mail addresses on the "Contact Us" page. Thanks.

What's in this site?

Four Arabidopsis genomic regions are syntenic with one papaya region (using GEvo to compare and analyze papaya and Arabidopsis synteny).

Overview of post-tetraploidy evolution.

Examples of using GEvo to find patterns of genome evolution.

Figure 1. This diagram depicts the lineages leading to the modern day genomes of Arabidopsis and papaya. Arabidopsis has had at least two ancient tetraploidy events (most recent and second most recent are called "alpha" and "beta" respectively). Recent work by Freeling's and Patterson's groups have shown that papaya diverged from Arabidopsis prior to its second most recent genome duplication event (beta event).