The transcriptome of the veiled chameleon (Chamaeleo calyptratus): A resource for studying the evolution and development of vertebrates

Abstract

Purpose The veiled chameleon (Chamaeleo calyptratus) is an emerging model system for studying functional morphology and evolutionary developmental biology (evo‐devo). Chameleons possess body plans that are highly adapted to an arboreal life style, featuring laterally compressed bodies, split hands/ft for grasping, a projectile tongue, turreted independently moving eyes, and a prehensile tail. Despite being one of the most phenotypically divergent clades of tetrapods, genomic resources for chameleons are severely lacking. Methods To address this lack of resources, we used RNAseq to generate 288 million raw Illumina sequence reads from four adult tissues (male and female eyes and gonads) and whole embryos at three distinct developmental stages. We used these data to assemble a largely complete de novo transcriptome consisting of only 82 952 transcripts. In addition, a majority of assembled transcripts (67%) were successfully annotated. Results We then demonstrated the utility of these data in the context of studying visual system evolution by examining the content of veiled chameleon opsin genes to show that chameleons possess all five ancestral tetrapod opsins. Conclusion We present this de novo, annotated, multi‐tissue transcriptome assembly for the Veiled Chameleon, Chamaeleo calyptratus, as a resource to address a range of evolutionary and developmental questions. The associated raw reads and final annotated transcriptome assembly are freely available for use on NCBI and Figshare, respectively.

Filling in the phylogenetic gaps: Induction, migration, and differentiation of neural crest cells in a squamate reptile, the veiled chameleon (Chamaeleo calyptratus)

“…While static snapshots of neural crest cell formation and migration can be identified by means of HNK1 immunostaining in chameleons, it will be critical in the future to conduct extensive molecular analyses with a repertoire of standard neural crest cell markers including TFAP2a , FoxD3 , Snail1/2 , Zfhx1b , Sox9 , and Sox10 . The production of a veiled chameleon transcriptome will enable the dynamics of gene expression in neural crest cells in a squamate to be explored . As a proof of principle, this transcriptome has already been used to demonstrate that the sex of veiled chameleons is genetically determined .…”

Embryonic development of a parthenogenetic vertebrate, the mourning gecko (Lepidodactylus lugubris)

“…We extracted RNA from a whole L. lugubris embryo (specimen ID: “BJP18”) at 59 dpo (stage 42) and followed a modified protocol for extracting RNA from TRIzol preserved tissue . RNAseq library preparation was identical to methods used by Pinto et al Briefly, we used the KAPA Stranded mRNA‐Seq Kit for Illumina (KR0960 [v5.17]) using oligo‐dT beads for mRNA enrichment. We sequenced this RNAseq library on an Illumina HiSeq 2500 at the Medical College of Wisconsin (Milwaukee, Wisconsin; paired‐end 125 bp reads).…”

“…We then used these Gekko sequences to query the de novo Lepidodactylus transcriptome, the P. picta genome, and the E. macularius genome . To further increase the sampling of squamate reptiles, we also incorporated Chamaeleo calyptratus BMP sequences . We aligned each BMP molecule separately using MAFFT [v7.388] implemented in Geneious [v11.1.2] .…”

“…24 To further increase the sampling of squamate reptiles, we also incorporated Chamaeleo calyptratus BMP sequences. 110 We aligned each BMP molecule separately using MAFFT [v7.388] implemented in Geneious [v11.1.2]. 123,124 Then, used the Geneious consensus alignment function to generate an alignment of all six BMP paralogs.…”

Non‐model organisms and unique approaches are needed for the future of evo‐devo

“…In addition to genetic tools, genomic resources are key for advancing studies in non‐model systems. Here, Pinto et al present a new multi‐tissue transcriptome for the veiled chameleon. This invaluable resource will greatly expand the reach of this emerging model system by facilitating the design of probes for future gene expression analyses, allowing comparative genomic studies with other vertebrate transcriptomes and even serving as a resource for genomic resources to come, such as the annotation of a genome assembly.…”