DNA project to decode 'all complex life' on Earth

By Victoria GillScience correspondent, BBC News

1 November 2018 

A mission to sequence the genome of every known animal, plant, fungus and protozoan - a group of single-celled organisms - is underway.

The Earth BioGenome Project (EBP) has been described as a "moonshot for biology".

A key aim is to use the information in efforts to conserve threatened species.

Scientists say clues about how species adapt to environmental change could be hidden in their DNA code.

As part of the project, the Wellcome Sanger Institute, which played a major part in the human genome project, has committed to sequencing the genomes of all 66,000 UK species.

Dr Jim Smith, director of science at the Wellcome Trust described the mission as timely, adding that it was "incumbent upon human beings to raise awareness of biodiversity".

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Rare feline genetic disorders identified through whole genome sequencing

Findings could help feline preservationists implement breeding strategies for rare species 

Date: May 11, 2017
Source: University of Missouri-Columbia

Whole genome sequencing (WGS), which is the process of determining an organism's complete DNA sequence, can be used to identify DNA anomalies that cause disease. Identifying disease-causing DNA abnormalities allows clinicians to better predict an effective course of treatment for the patient. Now, in a series of recent studies, scientists at the University of Missouri are using whole genome sequencing through the 99 Lives Cat Genome Sequencing Consortium to identify genetic variants that cause rare diseases, such as progressive retinal atrophy and Niemann-Pick type 1, a fatal disorder in domestic cats. Findings from the study could help feline preservationists implement breeding strategies in captivity for rare and endangered species such as the African black-footed cat.

The 99 Lives project was established at Mizzou by Leslie Lyons, the Gilbreath-McLorn Endowed Professor of Comparative Medicine in the College of Veterinary Medicine, to improve health care for cats through research. The database has genetically sequenced more than 50 felines and includes DNA from cats with and without known genetic health problems. The goal of the database is to identify DNA that causes genetic disorders and have a better understanding of how to treat diseases.

In the first study, Lyons and her team used the 99 Lives consortium to identify a genetic mutation that causes blindness in the African black-footed cat, an endangered species often found in U.S. zoos. The team sequenced three cats ? two unaffected parents and an affected offspring ? to determine if the mutation was inherited or spontaneous. The genetic mutation identified was located the IQCB1 gene and is associated with progressive retinal atrophy, an inherited degenerative retinal disorder that leads to blindness. The affected cat had two copies of the genetic mutation, indicating that it was an inherited disorder.



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Scientists sequence the genome of the Iberian lynx, the most endangered feline

Date: December 14, 2016

Source: Centre for Genomic Regulation

Spanish scientists have sequenced the genome of the Iberian lynx (Lynx pardinus), currently one of the world's most endangered felines. They have confirmed the "extreme erosion" suffered by its DNA. The Iberian lynx has one of the least genetically-diverse genomes. It is even less diverse than other endangered mammals, such as the cheetah or Tasmanian devil, or birds, like the crested ibis or osprey.

The study, being published in the scientific journal Genome Biology, has been coordinated by scientists from the Doñana Biological Station (CSIC). The Centre for Genomic Regulation (CRG) contributed to this research project from the very beginning including several groups and facilities. In particular, the laboratories of Roderic Guigó, Cedric Notredame and Toni Gabaldón at the Bioinformatics and Genomics Programme as well as the CRG Bioinformatics unit. This is the first mammal genome of reference generated entirely in Spain.

The project, financed by Banco Santander and managed by the Fundación General CSIC, has integrated the efforts of 50 scientists from research groups of 12 institutions, two of them from outside Spain, that cover a broad range of disciplines, including bioinformatics, genomics, oncology, evolution and conservation.

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Genome sequencing reveals ancient interbreeding between chimpanzees and bonobos

Date: October 27, 2016

Source: Wellcome Trust Sanger Institute

For the first time, scientists have revealed ancient gene mixing between chimpanzees and bonobos, humankind's closest relatives, showing parallels with Neanderthal mixing in human ancestry. Published in the journal Science, the study from scientists at the Wellcome Trust Sanger Institute and their international collaborators showed that one percent of chimpanzee genomes are derived from bonobos.

The study also showed that genomics could help reveal the country of origin of individual chimpanzees, which has strong implications for chimpanzee conservation.

Chimpanzees and bonobos are great apes found only in tropical Africa. They are endangered species and are supposedly fully protected by law, yet many chimpanzees and bonobos are captured and held illegally.

To aid the conservation effort, researchers analysed the whole genome sequences of 75 chimpanzees and bonobos, from 10 African countries, and crucially included 40 new wild-born chimpanzees from known geographic locations. They discovered that there was a strong link between the genetic sequence of a chimpanzee, and their geographic origin.

Dr Chris Tyler Smith, from the Wellcome Trust Sanger Institute, said: "This is the largest analysis of chimpanzee genomes to date and shows that genetics can be used to locate quite precisely where in the wild a chimpanzee comes from. This can aid the release of illegally captured chimpanzees back into the right place in the wild and provide key evidence for action against the captors."

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How did the giraffe get its long neck? Clues now revealed by new genome sequencing

Date: May 17, 2016

Source: Penn State

For the first time, the genomes of the giraffe and its closest living relative, the reclusive okapi of the African rainforest, have been sequenced -- revealing the first clues about the genetic changes that led to the evolution of the giraffe's exceptionally long neck and its record-holding ranking as the world's tallest land species. The research will be published in the scientific journal Nature Communications on May 17, 2016.

"The giraffe's stature, dominated by its long neck and legs and an overall height that can reach 19 feet (~ 6 m), is an extraordinary feat of evolution that has inspired awe and wonder for at least 8,000 years -- as far back as the famous rock carvings at Dabous in the Republic of Niger," said Douglas Cavener of Penn State University, who led the research team with Morris Agaba of the Nelson Mandela African Institute for Science and Technology in Tanzania.

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Corn snake genome sequenced for the first time

Date: November 24, 2015

Source: Université de Genève

Among the 5,000 existing species of mammals, more than 100 have their genome sequenced, whereas the genomes of only 9 species of reptiles (among 10,000 species) are available to the scientific community. This is the reason why a team at the University of Geneva (UNIGE), Swit- zerland, has produced a large database including, among others, the newly-sequenced genome of the corn snake, a species increasingly used to understand the evolution of reptiles. Within the same laboratory, the researchers have discovered the exact mutation that causes albinism in that species, a result published in Scientific Reports.

Genomics allows to better investigate the evolution of the living world. Indeed, describing the function of each gene should enable to understand how the snake lost its limbs or how various skin colorations have evolved. Unfortunately, reptiles are poorly represented in genomic da- tabases. This is why Dr. Athanasia Tzika, researcher in the Department of genetics and evolution of the UNIGE Faculty of Sciences, has built a database including sequenced genomes from the major evolutionary lineages of reptiles: the Reptilian Transcriptomes Database 2.0. "Our aim was to produce ourselves a substantial portion of the missing data by sequencing all genes from several reptilian species. To reach this goal, we used tissues, such as the brain and the kidney, expressing the largest number of genes," says Athanasia Tzika. Multiple other teams also generated sequencing data but each one used different methods for data analysis, making difficult studies of the evolution of reptilian genomes. Hence, another part of Athanasia Tzika's work consisted into gathering these data and developing a bioinformatic approach allowing the pro- duction of a unified database, freely accessible and regularly updated. This tool will become useful for researchers all around the world working on the development and evolution of vertebrates in general and reptiles in particular.

http://www.sciencedaily.com/releases/2015/11/151124081910.htm

How the Eastern tiger swallowtail got 'scary'

Date:

February 12, 2015

Source:

Cell Press

Summary:

Scientists know a lot about Eastern tiger swallowtail -- the state insect in five states -- but they hadn't managed to sequence their genome. Now, researchers have sequenced the complete genome of one wild-caught individual, and they say that it has already told them more than they had anticipated about the butterflies and some of their most intriguing features.

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Reshaping the horse through millennia: Sequencing reveals genes selected by humans in domestication

Date:

December 15, 2014

Source:

Faculty of Science - University of Copenhagen

Summary:

Whole genome sequencing of modern and ancient horses unveils the genes that have been selected by humans in the process of domestication through the last 5,500 years, but also reveals the cost of this domestication. An international research group reports that a significant part of the genetic variation in modern domesticated horses could be attributed to interbreeding with the descendants of a now extinct population of wild horses. This population was distinct from the only surviving wild horse population.

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Blind Scottish Centipede Genome Unlocks Evolutionary Secrets

Eric Hopton for redOrbit.com – Your Universe Online

An international group of scientists has completed the first ever genome sequence of a blind myriapod, Strigamia maritima. The species is one of a group of venomous centipedes that are unusual in the way in which they care for their eggs. The research also provides new insights into the biological evolution of Strigamia maritima and its unique absence of vision and circadian rhythm.

The work was partly carried out and the sequencing completed at Baylor College of Medicine in Houston, Texas, and the findings have been published online in the journal PLOS Biology.

“This is the first myriapod and the last of the four classes of arthropods to have its genome sequenced,” said Dr. Stephen Richards, assistant professor in the Human Genome Sequencing Center at Baylor. “Arthropods are particularly interesting for scientific study because they diverged into more species than any other animal group as they adapted in many ways to conquer the planet. The genome of the myriapod in comparison with previously completed genomes of the other arthropod classes gives us an important view of the evolutionary changes of these exciting species.”

Other scientists involved in the study were Dr. Ariel Chipman, of the Hebrew University of Jerusalem in Israel, Dr. David Ferrier, of The University of St. Andrews in the United Kingdom, and Dr. Michael Akam of the University of Cambridge in the UK.

Chipman, associate professor at the Hebrew University, said that “The arthropods have been around for over 500 million years and the relationship between the different groups and early evolution of the species is not really well understood. We have good sampling of insects but this is the first time a centipede, one of the more simple arthropods – simple in terms of body plan, no wings, simple repetitive segments, etc. – has been sequenced. This is a more conservative genome, not necessarily ancient or primitive, but one that has retained ancient features more than other groups.”

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Gibbons Become Last Ape To Have Their Genomes Sequenced

September 12 2014

Chuck Bednar for redOrbit.com – Your Universe Online

New research appearing in Thursday’s edition of the journal Nature details the successful sequencing and annotation of the gibbon genome, meaning that scientists have now mapped the DNA of all of the world’s ape species.

The study authors, which included scientists from Oregon Health & Science University and the Human Genome Sequencing Center at Baylor College of Medicine, explained that the small arboreal apes, which are native to the tropical forests of Southeastern Asia, demonstrate an accelerated rate of chromosomal rearrangement and occupy a key node in the primate phylogeny between Old World monkeys and great apes.

In their paper, they detail the genetic sequence of a northern white-cheeked gibbon (Nomascus leucogenys), including the characterization of a gibbon-specific mobile genetic element known as LAVA. LAVA, which is comprised of known jumping genes and named after its main components (L1, Alu, and the VA section of SVA mobile elements), is only the second type of composite mobile element to ever be discovered in primates.

“Everything we learn about the genome sequence of this particular primate and others analyzed in the recent past helps us to understand human biology in a more detailed and complete way,” lead author Dr. Jeffrey Rogers, associate professor in the Human Genome Sequencing Center at Baylor, said in a statement.

“The gibbon sequence represents a branch of the primate evolutionary tree that spans the gap between the Old World Monkeys and great apes and has not yet been studied in this way. The new genome sequence provides important insight into their unique and rapid chromosomal rearrangements,” Dr. Rogers explained.

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Sequence of water buffalo completed

Date: January 24, 2014

Source: BGI Shenzhen

Summary: Scientists have completed the genome sequencing of water buffalo. The outstanding work lays an important foundation for molecular breeding of water buffalo, and sheds new light on the understanding of its origin and domestication process.

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New Genetic Testing Method Can Determine Whether DNA Comes From Mom Or Dad

redOrbit Staff & Wire Reports – Your Universe Online

In a development expected to improve the process of matching organ donors and help understand how genes contribute to diseases, researchers have devised a method that can help determine whether or not a specific genetic sequence came from an individual’s mother or father.

The technique, which was developed by experts from the Ludwig Institute for Cancer Research and is described in the latest edition of the journal Nature Biotechnology, helps address a longstanding challenge when it comes to genome sequencing – discovering which traits come from which parent. The authors believe that it could improve personalized medicine.

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