Daily Archives: April 29, 2013

Apr. 28, 2013 From which ancestors have turtles evolved? How did they get their shell? New data provided by the Joint International Turtle Genome Consortium, led by researchers from RIKEN in Japan, BGI in China, and the Wellcome Trust Sanger Institute in the UK provides evidence that turtles are not primitive reptiles but belong to a sister group of birds and crocodiles. The work also sheds light on the evolution of the turtle's intriguing morphology and reveals that the turtle's shell evolved by recruiting genetic information encoding for the limbs.

Turtles are often described as evolutionary monsters, with a unique body plan and a shell that is considered to be one of the most intriguing structures in the animal kingdom.

"Turtles are interesting because they offer an exceptional case to understand the big evolutionary changes that occurred in vertebrate history," explains Dr. Naoki Irie, from the RIKEN Center for Developmental Biology, who led the study.

Using next-generation DNA sequencers, the researchers from 9 international institutions have decoded the genome of the green sea turtle and Chinese soft-shell turtle and studied the expression of genetic information in the developing turtle.

Their results published in Nature Genetics show that turtles are not primitive reptiles as previously thought, but are related to the group comprising birds and crocodilians, which also includes extinct dinosaurs. Based on genomic information, the researchers predict that turtles must have split from this group around 250 million years ago, during one of the largest extinction events ever to take place on this planet.

"We expect that this research will motivate further work to elucidate the possible causal connection between these events," says Dr. Irie.

The study also reveals that despite their unique anatomy, turtles follow the basic embryonic pattern during development. Rather than developing directly into a turtle-specific body shape with a shell, they first establish the vertebrates' basic body plan and then enter a turtle-specific development phase. During this late specialization phase, the group found traces of limb-related gene expression in the embryonic shell, which indicates that the turtle shell evolved by recruiting part of the genetic program used for the limbs.

"The work not only provides insight into how turtles evolved, but also gives hints as to how the vertebrate developmental programs can be changed to produce major evolutionary novelties." explains Dr. Irie.

Another unexpected finding of the study was that turtles possess a large number of olfactory receptors and must therefore have the ability to smell a wide variety of substances. The researchers identified more than 1000 olfactory receptors in the soft-shell turtle, which is one of the largest numbers ever to be found in a non-mammalian vertebrate.

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Turtle genome analysis sheds light on turtle ancestry and shell evolution

Now weve got the book, now weve got the words and the hard part is figuring out the logic and what all the sentences mean.

Howard Lipshitz

the University of Torontos head of molecular genetics

It was like Gods own jigsaw puzzle.

Built up over evolutionary eons, it featured 46 spiralling, ladder-like structures, some three billion pieces, and it took thousands of scientists working around the globe 13 years to complete.

But that, it turned out, was the easy part.

The Human Genome Project which was presented in its final form 10 years ago this month provided a map of mankinds DNA. But it also opened up a Pandoras box of boggling complexity in the biological sciences and medicine that will take decades more to unravel.

Its mind-blowing actually, says Dr. Jeff Wrana, a top cancer researcher at the University of Toronto.

Its one of those things, you know, be careful what you wish for. .

What genome cartographers had wished for at the projects 1990 inception what the genetic tea leaves had led them to expect was something far simpler than what they found.

Excerpt from:
The Human Genome Project: How it changed biology forever

Public release date: 28-Apr-2013 [ | E-mail | Share ]

Contact: Jia Liu liujia@genomics.cn BGI Shenzhen

April 28, 2013, Shenzhen, China- The Joint International Turtle Genomes Consortium, led by investigators from RIKEN, BGI, and Wellcome Trust Sanger Institute, has completed the genome sequencing of soft-shell turtle (Pelodiscus sinensis) and green sea turtle (Chelonia mydas). These achievements shed new light on the origin of turtles and applied the classical evo-devo model to explain the developmental process of their unique body plan. The findings were published online in Nature Genetics.

The evolution of turtles is an enigma in science. Their distinct body design-with a sharp beak and protective hard shell has changed very little over the past 210 million years. As the smallest species of soft-shell turtles, Chinese soft-shell turtle was once commonly sold in pet shops. Green sea turtle is considered as the largest of all the hard-shelled sea turtles and is named because of the green fat beneath its shell. Its population sizes has been drastically reduced recently and it has been listed as an endangered species.

To reveal the evolutionary history of turtles and the mechanisms underlying the development of their unique anatomical features, researchers in this project sequenced and analyzed the genomes of soft-shell turtle and green sea turtle. They found the evidence that turtles are likely to be a sister group with the common ancestor of crocodilians and birds from whole genome phylogenetic analyses. The turtles were diverged from archosaurians approximately between 267.9 and 248.3 million years ago, which coincides with the time range of the Upper Permian to Triassic period that overlapped or followed shortly after the end of Permian extinction.

In the study, researchers performed the brief research on genes may be associated with the turtle-specific characteristics, and found some olfactory receptor (OR) gene families were highly expanded in both turtles. This finding suggests that turtles have developed superior olfaction ability against a wide variety of hydrophilic substances. In addition, many genes involved in taste perception, hunger-stimulating, and energy homeostasis regulating hormone ghrelin have been uniquely lost in turtles. Researchers suggested that the loss of these genes may be related to their low-metabolic rate.

The consortium also investigated the association of embryonic gene expression profiles (GXP) and their morphological evolution pattern, based on ENSEMBL soft-shell turtle gene-set. By integrating RNA-seq technology, comparative genomics method, and mathematical statistical approaches, researchers confirmed GXP divergence during embryogenesis of soft-shell turtle and chicken indeed follows the developmental hourglass model. They also revealed that the maximal conservation stage occurred at around the vertebrate phylotypic period, rather than at later stage that show the amniote-common pattern.

To clarify the morphological specifications of turtle embryogenesis in late development, especially the formation of the carapacial ridge (CR), researchers investigated into CR-specific miRNA expression, found existence of tissue-specific miRNAs and involvement of Wnt signaling. Also they revealed the Wnt expression involved in the carapacial ridge (CR) formation of the turtle shell, researchers annotated all the Wnt genes in the two turtle genomes, identifying a total of 20 Wnt genes. Intriguingly, they discovered Wnt5a is the only Wnt gene expressed in the turtle CR region, supporting the possible co-option of limb-associated Wnt signaling in the acquisition of this turtle-specific novelty.

Zhuo Wang, Project Manager from BGI, said, "The genome-wide phylogenetic analysis of two turtles in our project, along with two crocodile genomic data additionally, makes clear the evolutionary history of turtles in diverging from other species and settles the disputes about the phylogenetic position of reptiles. The genomic analyses and embryonic gene expression profiles have been combined to reveal the fundamental evo-devo questions on turtle evolution and development. These works have been highly appreciated by the editor and reviewers. Besides the interesting story, the genomic data we released here will provide a platform for more scientists to initialize their genome-wide studies on turtles. "

Dr. Hongyan Zhang, Regional Director of BGI Tech Solutions Co., Ltd. for Japan, said, "The completed genome sequencing of soft-shell turtle and green sea turtle give an important hint to uncover the development and evolution mechanism of turtles. This scientific achievement is a joint effort supported by BGI's advanced sequencing technologies and excellent bioinformatics capabilities, the profound basis research background of developmental biology from RIKEN, and other partners' great contributions. We are looking forward to having more collaboration with other scientists for better exploring the secret of life together in the near future."

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Turtle genome analysis sheds light on the development and evolution of turtle-specific body plan

London, April 29 (ANI): Researchers working under the Joint International Turtle Genomes Consortium have completed the genome sequencing of soft-shell turtle (Pelodiscus sinensis) and green sea turtle (Chelonia mydas).

These achievements shed new light on the origin of turtles and applied the classical evo-devo model to explain the developmental process of their unique body plan.

The evolution of turtles is an enigma in science. Their distinct body design-with a sharp beak and protective hard shell has changed very little over the past 210 million years.

As the smallest species of soft-shell turtles, Chinese soft-shell turtle was once commonly sold in pet shops. Green sea turtle is considered as the largest of all the hard-shelled sea turtles and is named because of the green fat beneath its shell. Its population sizes have been drastically reduced recently and it has been listed as an endangered species.

To reveal the evolutionary history of turtles and the mechanisms underlying the development of their unique anatomical features, researchers in this project sequenced and analyzed the genomes of soft-shell turtle and green sea turtle.

The project, led by investigators from RIKEN, BGI, and Wellcome Trust Sanger Institute, found the evidence that turtles are likely to be a sister group with the common ancestor of crocodilians and birds from whole genome phylogenetic analyses.

The turtles were diverged from archosaurians approximately between 267.9 and 248.3 million years ago, which coincides with the time range of the Upper Permian to Triassic period that overlapped or followed shortly after the end of Permian extinction.

In the study, researchers performed the brief research on genes may be associated with the turtle-specific characteristics, and found some olfactory receptor (OR) gene families were highly expanded in both turtles.

This finding suggests that turtles have developed superior olfaction ability against a wide variety of hydrophilic substances. In addition, many genes involved in taste perception, hunger-stimulating, and energy homeostasis regulating hormone ghrelin have been uniquely lost in turtles. Researchers suggested that the loss of these genes might be related to their low-metabolic rate.

The consortium also investigated the association of embryonic gene expression profiles (GXP) and their morphological evolution pattern, based on ENSEMBL soft-shell turtle gene-set. By integrating RNA-seq technology, comparative genomics method, and mathematical statistical approaches, researchers confirmed GXP divergence during embryogenesis of soft-shell turtle and chicken indeed follows the developmental hourglass model. They also revealed that the maximal conservation stage occurred at around the vertebrate phylotypic period, rather than at later stage that show the amniote-common pattern.

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Genome analysis sheds light on origin of turtles