Where do turtles 'fit'?

Green sea turtle. Photo courtesy of RIKEN

Where do turtles fit in the evolutionary tree? Are they reptiles? How did their backbone evolve to form a shell?

To answer these and other questions, researchers in the International Turtle Genome Consortium looked at how the Chinese soft-shell turtle’s genome behaves during different stages of development. Led by Dr Naoki Irie of the RIKEN Centre for Developmental Biology in Japan and with help from nine international institutions including the Ensembl Project at EMBL-EBI and the Wellcome Trust Sanger Institute, the group unearthed several intriguing facts about these unusual creatures.

“Turtles are really exceptional in the way they have evolved, and they can tell us a lot about how vertebrates have changed throughout history,” explains Naoki, who led the study.

The team set out to understand how the turtle embryo develops a shell, a feature that sets it apart from other vertebrates. They used next-generation sequencing techniques to compare the gene expression profile of the Chinese soft-shell turtle embryo with that of another vertebrate – the chicken embryo – focusing on how the turtle’s genes were expressed at different times during development, from an early embryo to a full-grown ‘keeper of secrets’.

“We wanted to see exactly how different tissues in the turtle were influenced by gene expression as they develop – particularly the shell – so we zoomed in on different parts of the genome and analysed the activity over time, as the turtle embryos grew,” says Naoki. “This is a new approach, and has given us fascinating insights into how novel changes occur over the course of development and evolution.”

“This study fits well with Ensembl’s goal of understanding life,” adds Amonida Zadissa, Ensembl team member at EMBL-EBI. “We take these very long DNA sequences, without knowing what any of it means, and label them – for example pointing out which pieces are genes and how or when they are expressed. It’s called “whole genome annotation,” and the whole process is rather like turning a big jumbled bag of content into a book.”

The study showed that, despite their unique anatomy, turtles follow the basic embryonic pattern during development. They first establish the basic vertebrate body plan, same as a chicken would, then get to work on developing a shell and other ‘turtley’ things. The study also uncovered traces of limb-related gene expression in the embryonic shell. This suggests that the shell-building process recruits part of the genetic program used by other vertebrates to make limbs.

To firmly establish where turtles sit on the phylogenetic tree, the researchers decoded the genomes of the green sea turtle and Chinese soft-shell turtle and compared them to other vertebrate genomes. The results of the study, published in Nature Genetics, show that turtles are not primitive reptiles but are related to the group comprising birds and crocodilians, which also includes extinct dinosaurs. They must have split from this group around 250 million years ago, during the Big Extinction.

“I study science because I want to understand the world around me,” says Bronwen Aken of the Ensembl project, who is based at the Sanger Institute. “In Ensembl, we are always trying to find new ways to enable research about different species. Of course we have a lot of information about humans but we also want to know how all vertebrate species are related to one another, to expand the tree of life as much as possible and fill in the gaps in our knowledge.”

One unexpected finding of the study was that turtles must have a keen sense of smell. They possess over 1000 olfactory receptors – more than has ever been found in a non-mammalian vertebrate.

“These smell-related genes are the result of the turtle adapting to its environment,” adds Javier Herrero of the Ensembl team at EMBL-EBI. “We’ve integrated this type of analysis into Ensembl, and are producing these data routinely for every new Ensembl release.”

All of the gene annotation and transcriptome data from the study is freely available in Ensembl, where you can see some of the genes being expressed at different stages of development. www.ensembl.org

Source article

Zhuo Wang, et al. (2013) The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle–specific body plan. Nature Genetics (in press). DOI: 10.1038/ng.2615

About the Joint International Turtle Genome Consortium

The Joint International Turtle Genome Consortium is led by Naoki Irie of RIKEN and Guojie Zhang from BGI. The consortium comprises 34 scientists from nine institutes: RIKEN, BGI, EMBL-EBI, the Wellcome Trust Sanger Institute, Tokyo Medical and Dental University, NIBB Japan, the University of Copenhagen, King Abdulaziz University and China National GeneBank. Researchers from China, Denmark, Japan, Saudia Arabia and the United Kingdom participate in the consortium.

Q&A with the authors

Q: Where do turtles sit on the phylogenetic tree?

A: Turtles are related to birds and crocodiles! The scientists discovered this by sequencing two turtle genomes and comparing them to other vertebrate genomes. Strangely enough, they also have a very large number of olfactory genes, so probably a very good sense of smell.

Q: When does a turtle embryo start developing its shell?

A: Turtle embryos start off looking like any other vertebrate, and at a certain point switch to a very turtle-specific programme. This pattern is called the ‘hourglass model’, and the group confirmed it by comparing gene expression between Chinese softshell turtle embryo and chicken embryos.

Q: How does that happen?

A: Turtles use a number of genes in shell development that are normally used by vertebrates to develop limbs. This finding raises a lot of questions that require further investigation.

Q: Are all genome-sequencing studies done this way?

A: No – each genome study is unique, and this one was special because it used next-generation sequencing to examine the whole transcriptome – all gene expression – during embryo development.

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