Cephalopod genomics: A plan of strategies and organization

Abstract

The Cephalopod Sequencing Consortium (CephSeq Consortium) was established at a NESCent Catalysis Group Meeting, “Paths to Cephalopod Genomics- Strategies, Choices, Organization,” held in Durham, North Carolina, USA on May 24-27, 2012. Twenty-eight participants representing nine countries (Austria, Australia, China, Denmark, France, Italy, Japan, Spain and the USA) met to address the pressing need for genome sequencing of cephalopod mollusks. This group, drawn from cephalopod biologists, neuroscientists, developmental and evolutionary biologists, materials scientists, bioinformaticians and researchers active in sequencing, assembling and annotating genomes, agreed on a set of cephalopod species of particular importance for initial sequencing and developed strategies and an organization (CephSeq Consortium) to promote this sequencing. The conclusions and recommendations of this meeting are described in this white paper.

The contribution of molecular data to our understanding of cephalopod evolution and systematics: a review

“…Cephalopod genomes appear to be large in comparison with many other metazoan genomes and also rich in repeated regions (Yoshida et al 2011;Albertin et al 2012). Size may not be directly related to whole genome duplication events, as the increase can also be the result of lineage-specific increases in smaller repeat elements (Yoshida et al 2011 Reported as a haploid number in various secondary sources (e.g.…”

“…The move towards cephalopod genomics will likely contribute enormously towards our understanding of cephalopod evolution, even though the reasons that particular taxa are targeted are likely to vary widely (e.g. Albertin et al 2012). Genomic approaches solved major evolutionary conundrums in Mollusca as a whole, but several efforts to obtain funding for a similar approach in Cephalopoda have not been successful.…”

“…Some information has been gathered on cephalopod genome size (Albertin et al 2012), which may also give an indication of duplication events. Cephalopod genomes appear to be large in comparison with many other metazoan genomes and also rich in repeated regions (Yoshida et al 2011;Albertin et al 2012).…”

Cytogenetic studies in three octopods, Octopus minor, Amphioctopus fangsiao, and Cistopus chinensis from the coast of China

“…Regardless of the cephalopod species, the obtained genome size by complete genome sequencing is generally larger than other testing methods. For example, using biochemical analysis method to get O.vulgaris genome size is 5.15 pg (Packard and Albergoni 1970), and the result of genome sequencing is 2.5 to 5.0 Gb, about 2.62 to 5.24 pg (Albertin et al 2012). The O.bimaculoides genome size is 2.93 pg/3.2 Gb (about 3.35 pg) by bulk fluorometric assay (Albertin et al 2012) and genome sequencing (Albertin et al 2015), respectively.…”

“…These C values were estimated based on bulk fluorometric assay and feulgen image analysis densitometry. As genomic and transcriptomic sequencing is carried out in cephalopods, more and more cephalopod genome sizes have been revealed by complete genome sequencing such as N.pompilius , Architeuthisdux , Hapalochlaenamaculosa , E.scolopes , Idiosepiusparadoxus , L.pealeii , S.officinalis , etc (Yoshida et al 2011, Albertin et al 2012) (Table 1). Besides, Adachi et al (2014) examined the C values of O.ocellatus and O.vulgaris based on flow cytometry.…”