Molecular evolution and expression of the CRAL_TRIO protein family in insects

Abstract

a b s t r a c t CRAL_TRIO domain proteins are known to bind small lipophilic molecules such as retinal, inositol and Vitamin E and include such gene family members as PINTA, a-tocopherol transfer (ATT) proteins, retinoid binding proteins, and clavesins. In insects, very little is known about either the molecular evolution of this family of proteins or their ligand specificity. Here we characterize insect CRAL_TRIO domain proteins and present the first insect CRAL_TRIO protein phylogeny constructed by performing reciprocal BLAST searches of the reference genomes of Drosophila melanogaster, Anopheles gambiae, Apis mellifera, Tribolium castaneum, Bombyx mori, Manduca sexta and Danaus plexippus. We find several highly conserved amino acid residues in the CRAL_TRIO domain-containing genes across insects and a gene expansion resulting in more than twice as many gene family members in lepidopterans than in other surveyed insect species, but no lepidopteran homolog of the PINTA gene in Drosophila. In addition, we examined the expression pattern of CRAL_TRIO domain genes in Manduca sexta heads using RNA-Seq data. Of the 42 gene family members found in the M. sexta reference genome, we found 30 expressed in the head tissue with similar expression profiles between males and females. Our results suggest this gene family underwent a large expansion in lepidopteran, making the lepidopteran CRAL_TRIO domain family distinct from other holometabolous insect lineages.

Copy Number Variation and Expression Analysis Reveals a Nonorthologous Pinta Gene Family Member Involved in Butterfly Vision

“…We also investigated the reference genome to search for any CRAL-TRIO domain genes that may be found in the genome but not expressed in the tissues we sampled. We found support for the expansion of the CRAL-TRIO domain gene family in butterflies by identifying 43 CRAL-TRIO domain genes in the H. melpomene genome comparable with the 42 found in Manduca sexta ( Smith and Briscoe 2015 ). We also investigated 18 resequenced H. melpomene genomes ( Martin et al 2013 ) for structural variation (specifically CNV) and found that 32 of the 43 genes in the reference genome had either a large duplication or deletion in at least one of the resequenced genomes.…”

“…The CRAL-TRIO domain gene family is another family that is evolving by lineage-specific duplication in insects and has undergone an expansion in Lepidoptera (moths and butterflies; Smith and Briscoe 2015 ). Lepidoptera thus have almost twice as many CRAL-TRIO domain genes relative to other insects ( Smith and Briscoe 2015 ). The lineage-specific duplications of this gene family make it a candidate to study for CNV ( Zhang 2003 ).…”

Coping with living in the soil: the genome of the parthenogenetic springtail Folsomia candida

“…More recent research [31] indicates that Sec14 proteins are essential in membrane trafficking, connecting lipid metabolism with phosphoinositide signaling through transport of phosphatidylinositol. Sec14 proteins contain a CRAL-TRIO lipid-binding domain, and protein families with this domain also show expansion in lepidopteran species [32]. However, the number of Sec14 proteins in both the F. candida genome and the genome of a related collembolan, O. cincta , exceeds by far the greatest number observed in any hexapod genome (Additional file 1).…”

Multifaceted biological insights from a draft genome sequence of the tobacco hornworm moth, Manduca sexta

“…PINTA , which binds the visual chromophore in Drosophila eyes, appears to be missing in Lepidoptera; however, the M. sexta genome encodes 42 other CRAL-TRIO domain-containing proteins (GenBank Accession Nos. KT943537-KT943566) (Smith and Briscoe, 2015), far more than other insect genomes examined ( D. melanogaster , n = 12; A. gambiae , n = 14; T castaneum , n = 18). Many of the genes in this family have duplicated within Lepidoptera.…”