Daily Archives: September 18, 2014

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SraTailor (Preparation of genome libraries)
Preparation of genome library files for SraTailor. SraTailor requires library files from the genome assemblies of your interest. The library files are used f...

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A team of Spanish researchers have obtained the first partial genome sequence of an ancient pig. Extracted from a sixteenth century pig found at the site of the Montsoriu Castle in Girona, the data obtained indicates that this ancient pig is closely related to today's Iberian pig. Researchers also discard the hypothesis that Asian pigs were crossed with modern Iberian pigs.

The study, published in Heredity, sheds new light on evolutionary aspects of pig species, and particularly on that of the Iberian breed, considered to be representative of original European Mediterranean populations. The study was led by Miguel Prez-Enciso, ICREA researcher at Universitat Autnoma de Barcelona (UAB) and at the Centre for Research in Agrigenomics (CRAG). Researchers from the Institute of Evolutionary Biology (CSIC-Pompeu Fabra University) and the National Centre for Genome Analysis (CNAG) also participated in the study.

The sample dates approximately from the years 1520 to 1550 and is previous to the introduction of Asian pigs in Europe, which were later crossed with local European breeds which are the origin of today's international pig species. The sample pig is contemporary to the beginning of America's colonisation.

"Although it is a very fragmented sample, the gene sequence offers very interesting information," Miguel Prez-Enciso says. "First of all, we know it is not a white pig because it is missing a duplicated KIT gene which would make it this colour. This coincides with the majority of paintings from that period, in which the animal was always painted black or in reddish tones. We were also able to establish that it is very closely related to today's Iberian pig species, and specifically to the 'Lampio del Guadiana' strain. We could say that the Iberian pig is very similar to the pigs which existed in the sixteenth century and no great changes have been registered in this genome. Therefore, more studies will be needed before we are able to distinguish the modern species from the older ones."

The study indicates that the pig was a domestic pig, given that the sequence presents a series of markers typical of domestic pigs and which are very rare or absent in wild boars (the precursor animals to the domestic pig); moreover, this coincides with the historical registers of the castle, which clearly indicates that pig breeding was an important castle activity. Nevertheless, there is also evidence of occasional crossbreeding between wild boars and ancient pigs, as has happened between wild boars and Iberian pigs.

"This close relation between the Iberian pig, the European boar and the ancient pig confirms, as stated in previous studies, that crossbreeding between the Asian pig and modern Iberian pigs did not exist or was insignificant," Miguel Prez-Enciso points out.

The study also compared the ancient pig sample with the genome of modern pigs of different breeds, including 'Creole' pigs, which are presumably the descendents of the animals Spanish colonizers brought to America. Researchers demonstrate that this hypothesis is incorrect and that there is very little remaining of those first Spanish animals in today's creole pigs, which were crossbred mainly with international pig breeds.

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The above story is based on materials provided by Universitat Autnoma de Barcelona. Note: Materials may be edited for content and length.

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Iberian pig genome remains unchanged after five centuries

PUBLIC RELEASE DATE:

17-Sep-2014

Contact: Maria Jesus Delgado MariaJesus.Delgado@uab.cat 34-935-814-049 Universitat Autonoma de Barcelona

A team of Spanish researchers have obtained the first partial genome sequence of an ancient pig. Extracted from a sixteenth century pig found at the site of the Montsoriu Castle in Girona, the data obtained indicates that this ancient pig is closely related to today's Iberian pig. Researchers also discard the hypothesis that Asian pigs were crossed with modern Iberian pigs.

The study, published in Heredity, sheds new light on evolutionary aspects of pig species, and particularly on that of the Iberian breed, considered to be representative of original European Mediterranean populations. The study was led by Miguel Prez-Enciso, ICREA researcher at Universitat Autnoma de Barcelona (UAB) and at the Centre for Research in Agrigenomics (CRAG). Researchers from the Institute of Evolutionary Biology (CSIC-Pompeu Fabra University) and the National Centre for Genome Analysis (CNAG) also participated in the study.

The sample dates approximately from the years 1520 to 1550 and is previous to the introduction of Asian pigs in Europe, which were later crossed with local European breeds which are the origin of today's international pig species. The sample pig is contemporary to the beginning of America's colonisation.

"Although it is a very fragmented sample, the gene sequence offers very interesting information", Miguel Prez-Enciso says. "First of all, we know it is not a white pig because it is missing a duplicated KIT gene which would make it this colour. This coincides with the majority of paintings from that period, in which the animal was always painted black or in reddish tones. We were also able to establish that it is very closely related to today's Iberian pig species, and specifically to the 'Lampio del Guadiana' strain. We could say that the Iberian pig is very similar to the pigs which existed in the sixteenth century and no great changes have been registered in this genome. Therefore, more studies will be needed before we are able to distinguish the modern species from the older ones".

The study indicates that the pig was a domestic pig, given that the sequence presents a series of markers typical of domestic pigs and which are very rare or absent in wild boars (the precursor animals to the domestic pig); moreover, this coincides with the historical registers of the castle, which clearly indicates that pig breeding was an important castle activity. Nevertheless, there is also evidence of occasional crossbreeding between wild boars and ancient pigs, as has happened between wild boars and Iberian pigs.

"This close relation between the Iberian pig, the European boar and the ancient pig confirms, as stated in previous studies, that crossbreeding between the Asian pig and modern Iberian pigs did not exist or was insignificant", Miguel Prez-Enciso points out.

The study also compared the ancient pig sample with the genome of modern pigs of different breeds, including 'Creole' pigs, which are presumably the descendents of the animals Spanish colonizers brought to America. Researchers demonstrate that this hypothesis is incorrect and that there is very little remaining of those first Spanish animals in today's creole pigs, which were crossbred mainly with international pig breeds.

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Iberian pig genome remains unchanged after 5 centuries

Researchers in Biomedical Informatics at IMIM (Hospital del Mar Medical Research Institute) and at the Universitat Politcnica de Catalunya (UPC) have recently published a study in eLife showing that RNA called non-coding (IncRNA) plays an important role in the evolution of new proteins, some of which could have important cell functions yet to be discovered.

Ribosomes produce proteins from the instructions found in an RNA molecule. However, only 2% of the human genome is RNA containing information for the synthesis of proteins, meaning it is coding. Other parts of the genome that are transcribed could be "evolutionary noise," parts of the DNA that are copied to RNA randomly but with no concrete biological function. Now, a new sequencing technique has revealed that many of these transcripts (IncRNAs) may also translate into proteins, leading to an intense debate.

"We have confirmed that in all six species that were studied -human beings, mice, fish, flies, yeast and a plant- many of the IncRNAs were associated to ribosomes and seemed to be ready to translate RNA into proteins. This suggests that they could act as a repository for the synthesis of new proteins" explains Mar Alb, a professor at ICREA and the coordinator for the research group on Evolutionary Genomics at IMIM.

The study has found almost 2,500 IncRNAs that had not been studied, besides those identified previously, and has shown that very few IncRNAs are in more than one species. This would suggest that they have evolved recently. This hypothesis is backed by the fact that the properties of the IncRNA molecules show many similarities with the properties of "young" genes that are known to produce proteins.

"The birth of a new functional protein is a trial and error process that probably requires the production of many transcripts that will not survive the test of time, and IncRNA seems to fit this role. The study of closely related species will allow us to better understand how new coding genes are formed and identify those that can be functional. It will also be interesting to study the link between the alteration of IncRNA expression patterns and certain diseases" concludes Mar Alb.

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The above story is based on materials provided by IMIM (Hospital del Mar Medical Research Institute). Note: Materials may be edited for content and length.

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Parts of genome without a known function may play a key role in the birth of new proteins