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The barn swallow genome has been sequenced04-12-2018

Gigascience published the research conducted by the University of Milan that led to the sequencing of the barn swallow genome. The Study involves scientists from California State Polytechnic University, and the University of Pavia.

By using the most advanced genomics technologies available, scientists form the Departments of Environmental Sciences and Policies (Giulio Formenti and Nicola Saino) and of Biosciences (Matteo Chiara and David Horner) of the University of Milan, sequenced the barn swallow genome.

The study, published by the international journal Gigascience, involves researchers from California State Polytechnic University and the University of Pavia, and was funded by the Banking Foundation of Lodi.

The result represents one of the highest quality animal genome sequences ever produced, and the entire sequence has been made freely available to the entire scientific community. The knowledge of the DNA sequence of the barn swallow will boost the conservation efforts for this species and the study of the most fundamental aspects of the biology of this and of many other bird species, including migration, sexual behavior and adaptation to climate change.

Despite the limited availability of high-quality whole genome sequences, previous studies on the barn swallow and other bird species have already demonstrated a strong genetic component to key survival traits, such as migration and reproductive behavior. The knowledge of the barn swallow genome sequence will be pivotal to identifying the genes that control key life history characters as well as individual variability. The barn swallow has been intensely studied by scientists, but it also has highly iconic cultural value due both to its ‘philopatry’, bringing individuals back to their homes even after a long migration, and its demographic decline - partly associated with climate change. The availability of a high-quality genome sequence will accelerate researchers’ efforts to understand how environmental changes interact with genetic factors to determine decline in numbers as well as allowing insights into the adaptive processes that could assist in the adaptation of populations to rapidly changing environmental conditions.

The physiology, morphology and behavior of an organism (i.e. its 'phenotype') depends on environmental conditioning and genetic material. The study of genetic control of the phenotype is greatly facilitated by detailed knowledge of the genome sequence. The researchers' ability to 'assemble' genomes, i.e. to reconstruct the entire genetic information on each chromosome without gaps and without errors, took a leap forward this year with improvements to a technique called ‘optical mapping’ by Bionano Genomics (San Diego, CA). This approach allowed them to visualize individual megabase size DNA molecules while they flow inside silicon nanochannels, and use this long range data to build chromosome-arm length maps of the genome. The technology, available at the Functional Genomics Center in Zurich, coupled with long-read DNA sequencing from Pacific Biosciences allowed the production of a genome assembly of unprecedented quality for a wild species. Indeed, the quality of the barn swallow genome assembly is, in many respects, comparable to those of the intensively studied human and mouse genomes.

A global project. The barn swallow genome project contributes to the Vertebrate Genomes Project, a colossal international effort to sequence, in the coming years, the genomes of all living vertebrate species (over 66,000). The Vertebrate Genomes Project, a project of the G10K consortium, will construct a genomic ark, containing the genetic information of all these species, many of which are in decline or endangered. This project brings together several renowned research centers in the world, including the Vertebrate Genome Laboratory (VGL) at Rockefeller University in New York and the Wellcome Sanger Institute in England and, the University of Milan, in Italy, with a study coordinated by Giulio Formenti and Nicola Saino. The G10K consortium has an open-door policy for scientists and others to join their international effort.

Contacts
The University of Milan
Departments of Environmental Sciences and Policies

Nicola Michele Francesco Saino
nicola.saino@unimi.it

Giulio Formenti
giulio.formenti@unimi.it