Genetic mechanisms involved in the evolution of the cephalopod camera eye revealed by transcriptomic and developmental studies

Abstract

BackgroundColeoid cephalopods (squids and octopuses) have evolved a camera eye, the structure of which is very similar to that found in vertebrates and which is considered a classic example of convergent evolution. Other molluscs, however, possess mirror, pin-hole, or compound eyes, all of which differ from the camera eye in the degree of complexity of the eye structures and neurons participating in the visual circuit. Therefore, genes expressed in the cephalopod eye after divergence from the common molluscan ancestor could be involved in eye evolution through association with the acquisition of new structural components. To clarify the genetic mechanisms that contributed to the evolution of the cephalopod camera eye, we applied comprehensive transcriptomic analysis and conducted developmental validation of candidate genes involved in coleoid cephalopod eye evolution.ResultsWe compared gene expression in the eyes of 6 molluscan (3 cephalopod and 3 non-cephalopod) species and selected 5,707 genes as cephalopod camera eye-specific candidate genes on the basis of homology searches against 3 molluscan species without camera eyes. First, we confirmed the expression of these 5,707 genes in the cephalopod camera eye formation processes by developmental array analysis. Second, using molecular evolutionary (dN/dS) analysis to detect positive selection in the cephalopod lineage, we identified 156 of these genes in which functions appeared to have changed after the divergence of cephalopods from the molluscan ancestor and which contributed to structural and functional diversification. Third, we selected 1,571 genes, expressed in the camera eyes of both cephalopods and vertebrates, which could have independently acquired a function related to eye development at the expression level. Finally, as experimental validation, we identified three functionally novel cephalopod camera eye genes related to optic lobe formation in cephalopods by in situ hybridization analysis of embryonic pygmy squid.ConclusionWe identified 156 genes positively selected in the cephalopod lineage and 1,571 genes commonly found in the cephalopod and vertebrate camera eyes from the analysis of cephalopod camera eye specificity at the expression level. Experimental validation showed that the cephalopod camera eye-specific candidate genes include those expressed in the outer part of the optic lobes, which unique to coleoid cephalopods. The results of this study suggest that changes in gene expression and in the primary structure of proteins (through positive selection) from those in the common molluscan ancestor could have contributed, at least in part, to cephalopod camera eye acquisition.

Loss of the six3/6 controlling pathways might have resulted in pinhole-eye evolution in Nautilus

“…Predicted Proteins of the pearl oyster were obtained from Marine Genomics Unit, OIST, Japan ( Pinctada fucata Genome Ver 1.00 ). The scallop ESTs were obtained as previously described in Yoshida et al13. Aplysia and Lottia EST sequences were obtained from the NCBI dbEST.…”

“…Even though several transcriptome studies using cephalopods have been reported, only a few papers have used developmental stages of the embryo and none of them have focused on comprehensive transcriptome studies111213. In this study, we compared gene expression in the nautiloid embryonic eye and that in the coleoid cephalopods embryonic eye, to investigate gene regulatory networks involved in eye formation.…”

ESTs library from embryonic stages reveals tubulin and reflectin diversity in Sepia officinalis (Mollusca — Cephalopoda)

“…On the other side, these NRS may also represent specific molecules, not yet characterized in more traditional models. The size of S. officinalis genome was experimentally evaluated as around 4Gb (data not shown) and thus close to the estimations made in few other cephalopod species (Octopus vulgaris: 4.2 Gb, Packard and Albergoni, 1970; L. pealeii: 2.7 Gb, Octopus bimaculatus: 4.2 Gb, Hinegardner, 1974; Idiosepius paradoxus: 2.1 Gb, Nautilus pompilius: 2.8 Gb, Yoshida et al, 2011). A probable wholegenome duplication event in the cephalopod lineage was proposed in two recent molluscan genome structure analysis (Hallinan and Lindberg, 2011;Yoshida et al, 2011).…”

“…ESTs data from different organs have been published or deposited in databases (Table 1): Octopus vulgaris and Nautilus pompilius eye (Ogura et al, 2004;Yoshida and Ogura, 2011), juvenile Euprymna scolopes light organ (Chun et al, 2006), Idiosepius paradoxus brain (Shigeno 2006 unpublished), Sepiella maindroni ink gland (Song 2009 unpublished), Loligo bleekeri liver (Kondo 2010 unpublished) and Loligo pealeii stellate ganglia (DeGiorgis 2011unpublished, cited in Lico et al, 2010. However, none of these ESTs takes into account the developmental aspect of cephalopod genome expression, which is crucial in an evo-devo context.…”

Eye development and photoreceptor differentiation in the cephalopod Doryteuthis pealeii

“…General descriptions of eye development in various cephalopod species have been documented, but an in-depth molecular and cellular understanding of major morphogenetic and cell differentiation events is lacking (Arnold, 1965(Arnold, , 1966(Arnold, , 1967Arnold and Williams-Arnold, 1976;Gilbert et al, 1990;Marthy, 1973;Yamamoto, 1985;Yamamoto et al, 1985;Naef, 1928). Recently, the cephalopod genomic infrastructure was greatly improved by publication of the Octopus bimaculoides genome and a few transcriptomic databases Alon et al, 2015;Yoshida, 2011;Wollesen et al, 2014;Bassaglia et al, 2012). Despite these improvements, however, few sequencing efforts have informed our understanding of embryonic development or organogenesis.…”