The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan

Abstract

The unique anatomical features of turtles have raised unanswered questions about the origin of their unique body plan. We generated and analyzed draft genomes of the soft-shell turtle (Pelodiscus sinensis) and the green sea turtle (Chelonia mydas); our results indicated the close relationship of the turtles to the bird-crocodilian lineage, from which they split ~267.9–248.3 million years ago (Upper Permian to Triassic). We also found extensive expansion of olfactory receptor genes in these turtles. Embryonic gene expression analysis identified an hourglass-like divergence of turtle and chicken embryogenesis, with maximal conservation around the vertebrate phylotypic period, rather than at later stages that show the amniote-common pattern. Wnt5a expression was found in the growth zone of the dorsal shell, supporting the possible co-option of limb-associated Wnt signaling in the acquisition of this turtle-specific novelty. Our results suggest that turtle evolution was accompanied by an unexpectedly conservative vertebrate phylotypic period, followed by turtle-specific repatterning of development to yield the novel structure of the shell.

Sensory Evolution and Ecology of Early Turtles Revealed by Digital Endocranial Reconstructions

“…Unique morphological characters, including the anapsid cranial configuration, which lacks temporal fenestrations, and the presence of a bony shell formed by a dorsal carapace and a ventral plastron have long obfuscated the phylogenetic affinities of turtles (Rieppel, 2007;Lyson et al, 2010). While most molecular studies have recovered turtles nested within diapsid reptiles and often as a sister-group to Archosauria (birds and crocodiles) (Hedges and Poling, 1999;Wang et al, 2013;Field et al, 2014), most studies based on comparative anatomy have placed turtles outside of Diapsida (Gauthier et al, 1988;Lee, 1997;Werneburg and Sánchez-Villagra, 2009;Neenan et al, 2013;Scheyer et al, 2017) or alternatively inside Lepidosauromorpha (deBraga and Rieppel, 1997;Rieppel and Reisz, 1999;Li et al, 2008;Liu et al, 2011). The scant fossil record of stem-turtles (i.e., non-Testudines Testudinata) has further obscured the evolutionary origin of this group.…”

Similar ratios of introns to intergenic sequence across animal genomes

“…Builds of Homo sapiens, Pan troglodytes, Mus musculus, Canis lupus (Kirkness 2003), Monodelphis domestica (Mikkelsen et al 2007), Ornithorhynchus anatinus (Warren et al 2008), Xenopus tropicalis (Hellsten et al 2010), Struthio camelus (Zhang et al 2014), Gallus gallus, Taeniopygia guttata (Warren et al 2010), Aptenodytes forsteri (Zhang et al 2014), Anas platyrhynchos (Huang et al 2013), Melopsittacus undulatus (Ganapathy et al 2014), Alligator mississippiensis (Green et al 2014), Anolis carolinensis (Alfö ldi et al 2011), Chrysemys picta bellii (Shaffer et al 2013), Chelonia mydas (Wang et al 2013), Pelodiscus sinensis (Wang et al 2013), Python bivittatus (Koning et al 2013), Salmo salar, Danio rerio (Howe et al 2013), Latimeria chalumnae (Amemiya et al 2013), Petromyzon marinus (Smith et al 2013), Callorhinchus milii (Venkatesh et al 2014), Crassostrea gigas , Dendroctonus ponderosae (Keeling et al 2013), Tribolium castaneum (Richards et al 2008), Bombyx mori (Mita et al 2004), Limulus polyphemus (Nossa et al 2014) were downloaded from the NCBI Genome server.…”

Effects of Dietary Soy Protein Concentrate on Growth, Digestive Enzymes Activities and Target of Rapamycin Signaling Pathway Regulation in Juvenile Soft-Shelled Turtle, <i>Pelodiscus sinensis</i>

“…Jian [12]- [14], cobia, Rachycentron canadum [15] and Chinese shrimp, Fenneropenaeus chinensis [16] have indicated that nutrition status could possibly regulate the TOR signaling pathway in aquatic animals as in mammals. Recently, the whole genome shotgun sequence of soft-shelled turtle has been projected by Wang et al [17], and the TOR, S6K1 and 4E-BP1 gene sequences were reported, meanwhile, the potential of dietary FM protein replacing by SPC in soft-shelled turtle diet has been evaluated in our laboratory [18]. In view of the foregoing, the present research was designed to study the effects of dietary SPC on digestive enzyme activities and TOR signaling pathway regulation in juvenile soft-shelled turtle, for which could provide further theoretical evidence for SPC application in its commercial feeds.…”