The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes

Abstract

Over 95% of all metazoan (animal) species comprise the "invertebrates," but very few genomes from these organisms have been sequenced. We have, therefore, formed a "Global Invertebrate Genomics Alliance" (GIGA). Our intent is to build a collaborative network of diverse scientists to tackle major challenges (e.g., species selection, sample collection and storage, sequence assembly, annotation, analytical tools) associated with genome/transcriptome sequencing across a large taxonomic spectrum. We aim to promote standards that will facilitate comparative approaches to invertebrate genomics and collaborations across the international scientific community. Candidate study taxa include species from Porifera, Ctenophora, Cnidaria, Placozoa, Mollusca, Arthropoda, Echinodermata, Annelida, Bryozoa, and Platyhelminthes, among others. GIGA will target 7000 noninsect/nonnematode species, with an emphasis on marine taxa because of the unrivaled phyletic diversity in the oceans. Priorities for selecting invertebrates for sequencing will include, but are not restricted to, their phylogenetic placement; relevance to organismal, ecological, and conservation research; and their importance to fisheries and human health. We highlight benefits of sequencing both whole genomes (DNA) and transcriptomes and also suggest policies for genomic-level data access and sharing based on transparency and inclusiveness. The GIGA Web site (http://giga.nova.edu) has been launched to facilitate this collaborative venture.

Keywords: GIGA; biodiversity; comparative genomics; consortium; evolution; invertebrates; metazoa.

Figure 1.

Metazoan relationships. This phylogeny of Metazoa is largely based on recent phylogenomic analyses by Dunn et al. (2008) and Hejnol et al. (2009). The basal nodes of the tree are shown as a polytomy based on varying results in recent analyses (Dunn et al. 2008; Hejnol et al. 2009; Philippe et al. 2009; Schierwater et al. 2009; Pick et al. 2010; Ryan et al. 2010; Nosenko et al. 2013). The position of Xenacoelomorpha is uncertain (dashed lines) and is based on recent studies; it could be the sister group to Bilateria (Hejnol et al. 2009), or as part of Deuterostomia (Philippe et al. 2011). There is no phylogenomic data for Mesozoa or Micrognathozoa, and their positions are based on a limited amount of direct sequencing data. Mesozoa (comprising Rhombozoa and Orthonectida) is shown as a single terminal but may not be a clade. The placement of Phoronida is based in the traditional placement of the group as close to Brachiopoda. The estimated numbers for extant described and valid species, indicated in parentheses after the terminal name, are from Zhang (2011a) and for marine groups, from queries of the World Register of Marine Species (June 2013), http://www.marinespecies.org/aphia.php?p=stats. Notes for terminals indicated by *; Mesozoa (comprising Rhombozoa and Orthonectida) is shown as a single terminal but may not be a clade. The species count for Rotifera includes Acanthocephala and for Cnidaria includes Myxozoa.

Figure 2.

Consensus phylogeny of nonbilaterian animals. The Porifera tree and classification is based on Cárdenas et al. (2012), Nosenko et al. (2013), and Wörheide et al. (2012). The Cnidaria tree and classification is based on Collins (2009) and Evans et al. (2008, 2009). Following the terminal name, in parentheses, is the estimated number of extant described and valid species for that group based on the World Register of Marine Species as described in the Figure 1 legend, and Myxozoa estimates stem from Lom and Dyková (2006). When available, common names are written above the branches.

Figure 3.

Consensus phylogeny of the major groups of Arthropoda, based on Regier et al. (2010) and von Reumont et al. (2012). Following the terminal name, in parentheses, is the estimated number of extant described and valid species for that group based on Zhang (2011b) and Ahyong et al. (2011). When available, common names are written above the branches.

Figure 4.

Combined phylogeny of Mollusca and Annelida. The Mollusca tree is drawn from Smith et al. (2011), while the consensus phylogeny of Annelida and Sipuncula is based on Rouse and Pleijel (2001) and Struck et al. (2011). As in Figure 1, following the terminal name, in parentheses, is the estimated number of extant described and valid species for that group based on the World Register of Marine Species. Additional references for groups with nonmarine species are Bivalvia, which also includes many freshwater species (Graf 2013); Gastropoda, which includes numerous freshwater and terrestrial species (Cameron 2013); and Clitellata, which includes many freshwater and terrestrial species (Sket and Trontelj 2007; Wetzel and Reynolds 2011). The species count for the taxon Capitellida includes taxa such as Echiura and polychaetes formerly included in Scolecida, a taxon now shown to be polyphyletic (Struck et al. 2011). When available, common names are written above the branches.

Figure 5.

Phylogeny of Deuterostomia. Note that Xenacoelomorpha is excluded from this figure, but has been proposed to be the sister group to Ambulacraria (see Figure 1). The tree for Hemichordata is from Worsaae et al. (2012), for Echinodermata from Janies et al. (2011), for Chordata from Delsuc et al. (2006), and for Tunicata from Swalla et al. (2000). As in Figure 1, the estimated numbers for extant described and valid species are indicated in parentheses after the terminal name and are from the World Register of Marine Species. When available, common names are written above the branches.