The Bird 10,000 Genome Project (B10K), an international consortium to sequence the genome of all birds worldwide, has sequenced the genome of 363 bird species in the second phase of this microproject, which started in 2015. This scientific milestone, published in the journal Nature, represents the largest dataset of complete genome for eucaryotes sequenced in a biological group to date.
The study, promoted by B10K, counts on the participation of more than 150 researchers from 125 institutions from 24 countries. Among these are the researchers Marta Riutort, Julio Rozas, Jacob González-Solís, and Joan Ferrer Obiol, from the Faculty of Biology and the Biodiversity Research Institute (IRBio) of the UB.
The article, published in the journal Nature, presents 257 new bird genomes that expand the sequenced genetic material during the first phase and shed light on the evolution of the genomic diversity among bird lineages. It is led by the University of Copenhagen (Denmark), the China National Genebank BGI-Shenzhen (China), the Chinese Academy of Sciences (China), the Smithsonian National Museum of Natural History and the Rockefeller University (United States). The study has used for the first time a method of genome alignment (Cactus) which does not require a reference genome and with which researchers could identify more than twice as many homologous genomic regions (a 149% increase of orthologous coding), compared to previous studies.
The evolutionary history of birds
According to the conclusions, passeriform birds –the order with the highest number of bird species– show the genomic features that differ from other bird groups (for instance, an additional copy of the growth hormone gene). Songbirds –the group with more species within the Passeriformes– has also lost a gen called cornulin, which could contribute to the evolution of their wide vocal repertoire.
“Compared to the other bird groups, Passeriformes –the order that includes species such as sparrows or goldfinches–, have a higher content of guanine-cytosine nucleotide content (GC) in the regions of the genome that code by proteins and use a lower proportion of synonymous codons”, notes the researcher Joan Ferrer-Obiol, from the Department of Genetics, Microbiology and Statistics of the UB. “Moreover –he continues–, the Piciformes –group including woodpeckers–, present a higher number of transposons compared to the other bird orders. Future studies will determine the biological and evolutionary importance of these findings”.
Thanks to the high number of sequenced bird genomes, researches identified 10% more highly conserved nucleotides of the DNA. “These genetic compounds, unknown so far, are largely located in genome regions that are not codifying by proteins, and which could have a great functional importance, specially in the regulation of genes (such as IncRNA, untranslated exons or transcription factor binding sites)”, highlights Professor Julio Rozas, member of the mentioned Department and the Bioinformatics Barcelona platform (BIB).
The genetic study has eased the detection of changes caused by natural selection to a level of just one AND nucleotide. “This detection power is only possible when species are strongly represented in the comparative genomic analyses”, notes Guojie Zhang, principal researcher in B10K and head of the Villum Centre for Genomic Biodiversity of the University of Copenhagen. “These genomes enable us to explore the genomic variations between different bird groups and help us understand their diversification processes”.
The genetic base for Cory’s shearwater migratory behaviour
The UB-IRBio research team focused on the genome sequencing of Cory’s shearwater (Calonectris borealis), a long-distance migratory species that has breeding colonies in the Canary Islands and spends the winter in places such as the coasts of South Africa and Namibia. For more than fifteen years, the group led by Professor Jacob González-Solís studies the migratory behaviour of the species through the use of movement monitoring devices (GPS).
“Moreover, the team actively takes part in one of the projects on compared genomics that are being conducted with the new genomes and which aims to identify the specific regions of the genome associated with the migratory behaviour of birds. In particular, it will search for the molecular print of the evolutionary convergence comparing the genomes from different bird groups in which this behaviour appears independently”, notes Professor Jacob González-Solís, from the Department of Evolutionary Biology, Ecology and Environmental Sciences of the UB.
“The B10K project is not finished yet”, notes Professor Marta Riutort, member of the Department of Genetics, Microbiology and Statistics of the UB. “We are still carrying out many phylogenomic and comparative genomic analyses that will provide new data on the evolutionary history of birds. Having all this genomic data and a phylogeny will enable researchers to conduct a great amount of studies, such as the research on the genetic base of migration. This knowledge will allow us to better understand how the morphological characters and the genomes of birds have evolved, and others such as the migration and social behaviour”.
Field work and museums to preserve an endangered biodiversity
A great part of the genome sequencing has been based on the analysis of tissue samples from museums, which enabled the sequencing of the genome of rare birds and endangered species. Among the collaborating centres are the Smithsonian National Museum of Natural History, the Museum of Natural History of Denmark, the Museum of Natural Science of the Louisiana State University and the National Museum of Natural Sciences (MNCN-CSIC).
For Carsten Rahbek, co-organizer of the B10K project and former bird curator at the Museum of Natural History in Denmark, “this report is also a proof of how science is advancing unpredictably over time. According to Peter Hosner, current bird curator at the Museum of Natural History in Denmark, “the study shows how investing in basic fieldwork provides value to research for decades, an important lesson at a time when nature is disappearing rapidly.
There are still big open questions about the evolutionary relationships of birds. “New genomes play a key role in understanding bird diversification,” said Josefin Stiller, an expert at the University of Copenhagen, who is leading efforts to build a new evolutionary tree for all bird families. Therefore, the new phase of the project is already launched, another scientific challenge to sequence genomes of species representing the 2,250 genera of birds. According to Erich Jarvis, principal co-researcher in the B10K project and professor at Rockefeller University and the Howard Hughes Medical Institute, “being able to access all the genetic diversity of birds will help us decipher the genetics of its various complex traits, such as flight, vocal learning, and the high densities of brain neurons.”
Images: Jon Fjeldså