The overall aim of this project is to gather, collate and present genomic information for echinoderm species including the reference, Strongylocentrotus purpuratus (Sp) through an easily managed web information system (http://spbase.org). These efforts are directly focused to provide the bench scientist with up to date information on the genome sequence, gene structures, expression data and functional information in order to facilitate experiments to study gene regulation in development. Originally a draft sequence for the reference was undertaken by the Baylor College of Medicine, Human Genome Sequencing Center (BCM-HGSC) and published in 2006 (Sea Urchin Genome Sequencing Consortium, 2006). Today efforts in this area are both challenging and interesting in view of the large body of emerging sequence information on the reference and allied species. An entirely new assembly of the Sp genome has been submitted to Genbank and awaits further annotation at SpBase. However, preliminary measurements indicate that this version is so much more complete that it can reveal scientifically interesting elements of genome organization that were unattainable previously. Individual laboratory transcriptome sequencing projects for many species are appearing at a great rate. These datasets are seldom analyzed past the experimental question for which they were originally conducted, yet they can provide genome wide information on gene structure such as tissue specific splicing isoforms. In support of the BCM-HGSC, we have provided material for additional genome sequencing projects including Allocentrotus fragllis, S. franciscanus, Lytechinus variegatus, Eucidaris tribuloides and Patiria miniata. New sequence data for all of these species has been procured and in some cases already posted to Genbank. This is the material that will enrich the offering of SpBase provided it is carefully managed and posted.
Gene regulatory networks are models of the process by which the genome is translated into an organism or through which physiological homeostasis is achieved. Genome sequences and their associated information are crucial to the description of these networks. An easily accessible web information system facilitates the use of genomic information for regulatory network studies.
| Buckley, Katherine M; Dong, Ping; Cameron, R Andrew et al. (2018) Bacterial artificial chromosomes as recombinant reporter constructs to investigate gene expression and regulation in echinoderms. Brief Funct Genomics 17:362-371 |
| Cary, Gregory A; Cameron, R Andrew; Hinman, Veronica F (2018) EchinoBase: Tools for Echinoderm Genome Analyses. Methods Mol Biol 1757:349-369 |
| Kudtarkar, Parul; Cameron, R Andrew (2017) Echinobase: an expanding resource for echinoderm genomic information. Database (Oxford) 2017: |
| Panova, Marina; Aronsson, Henrik; Cameron, R Andrew et al. (2016) DNA Extraction Protocols for Whole-Genome Sequencing in Marine Organisms. Methods Mol Biol 1452:13-44 |
| Cameron, R Andrew; Kudtarkar, Parul; Gordon, Susan M et al. (2015) Do echinoderm genomes measure up? Mar Genomics 22:1-9 |
| Tu, Qiang; Cameron, R Andrew; Davidson, Eric H (2014) Quantitative developmental transcriptomes of the sea urchin Strongylocentrotus purpuratus. Dev Biol 385:160-7 |
| Cameron, R Andrew (2014) Tools for sea urchin genomic analysis. Methods Mol Biol 1128:295-310 |
