Great tit / Parus major genome

Story

Great tits are common, widely distributed, cavity nesting passerines. The range of this super-species spans Europe across Asia to the Pacific, including populations in the Middle East, and North West Africa. From this distribution area four species groups have been identified: major (whole Europe, Siberia and north-west Africa), cinereus (from Iran to India and south-east Asia), minor (China, Japan and eastern Russia) and bokharensis (central Asia). Most studies have concentrated on the north-west European Parus major subspecies and our sequenced bird belongs to this subspecies.

Due to their abundance and ready use of nest boxes, great tit populations have been intensively studied across their range; some ongoing studies have now collected data on tens of thousands of individuals spanning 60 years. As a result they are now one of the most widely studied species in the fields of ecology and evolution.

To provide further insight into the molecular mechanisms behind evolutionary and ecological traits, we de novo assembled a great tit reference genome. A male great tit originating from the Netherlands was sequenced, leveraging a total of 114 Gb of Illumina HiSeq sequence data. After gap-filling and removal of adaptor sequences, the assembly consisted of a total of 2,066 scaffolds with an N50 scaffold length of over 7.7Mb and an N50 contig length of 133kb. Taken together, the assembled contigs span 1.0 Gb. We were able to assign 98% of the assembled bases to a chromosomal location. The total number of chromosomes covered by the assembly is 29 with three additional linkage groups (Chr25LG1, Chr25LG2 and LGE22). The assignment of chromosomal locations to the majority of the assembly resulted in a very high quality reference genome and enabled detailed comparisons with other bird genomes. For the genome annotation step we combined RNA sequencing data from eight different tissues of the reference bird with gene models from chicken (Gallus gallus) and zebra finch (Taeniopygia guttata). The final annotation resulted in a total of 21,057 transcripts for 13,036 high confidence gene predictions. The high-quality genome assembly will play an instrumental role in furthering the integration of ecological, evolutionary, behavioural and genomic approaches in this model species.

Accession Codes: The raw sequences of reference great tit have been deposited to the NCBI Sequence Read Archive (SRA; http://www.ncbi.nlm.nih.gov/sra) under the accession number SRS1185780.

The final assembly (Pmajor1.04) has been deposited in DDBJ/EMBL/GenBank under the accession JRXK00000000. The version described in this paper is version JRXK01000000.1

The RNAseq reads for the eight tissues have been deposited to the NCBI Sequence Read Archive under the accession numbers GT_BoneMarrow SRS863935, GT_Brain SRS866013, GT_BreastFilet SRS866031, GT_HigherIntestine SRS866033, GT_Liver SRS866035, GT_Kidney SRS866036, GT_Lung SRS866044, GT_Testis SRS866048.

The whole-genome bisulfite sequencing reads for the two tissues have been deposited to the NCBI Sequence Read Archive under the accession numbers GT_Brain_BS SRS964344 and GT_Blood_BS SRS964345.

The reads for the 29 re-sequenced birds have been deposited to the NCBI Sequence Read Archive under the accession number SRP066678.

Evolutionary signals of selection on cognition from the great tit genome and methylome. Veronika N. Laine, Toni I. Gossmann, Kyle M. Schachtschneider, Colin J. Garroway, Ole Madsen, Koen J.F. Verhoeven, Victor de Jager, Hendrik-Jan Megens, Wesley C. Warren, Patrick Minx, Richard P.M.A. Crooijmans, Pa´draic Corcoran, The Great Tit Hapmap Consortium, Ben C. Sheldon, Jon Slate, Kai Zeng, Kees van Oers, Marcel E. Visser & Martien A.M. Groenen. Nature Communications, 25 january 2016 online.

http://www.nature.com/ncomms/2016/160125/ncomms10474/full/ncomms10474.html

DOI: 10.1038/NCOMMS10474

http://dx.doi.org/10.1038/NCOMMS10474