A New Chicken Genome Assembly Provides Insight into Avian Genome Structure

Abstract

The importance of the Gallus gallus (chicken) as a model organism and agricultural animal merits a continuation of sequence assembly improvement efforts. We present a new version of the chicken genome assembly (Gallus_gallus-5.0; GCA_000002315.3), built from combined long single molecule sequencing technology, finished BACs, and improved physical maps. In overall assembled bases, we see a gain of 183 Mb, including 16.4 Mb in placed chromosomes with a corresponding gain in the percentage of intact repeat elements characterized. Of the 1.21 Gb genome, we include three previously missing autosomes, GGA30, 31, and 33, and improve sequence contig length 10-fold over the previous Gallus_gallus-4.0. Despite the significant base representation improvements made, 138 Mb of sequence is not yet located to chromosomes. When annotated for gene content, Gallus_gallus-5.0 shows an increase of 4679 annotated genes (2768 noncoding and 1911 protein-coding) over those in Gallus_gallus-4.0. We also revisited the question of what genes are missing in the avian lineage, as assessed by the highest quality avian genome assembly to date, and found that a large fraction of the original set of missing genes are still absent in sequenced bird species. Finally, our new data support a detailed map of MHC-B, encompassing two segments: one with a highly stable gene copy number and another in which the gene copy number is highly variable. The chicken model has been a critical resource for many other fields of study, and this new reference assembly will substantially further these efforts.

Keywords: Gallus gallus; MHC; genome assembly.

Figure 1

Chromosome synteny alignments of GGA9 and GGA16 derived from Gallus_gallus-4.0 and Gallus_gallus-5.0. Each assembly chromosome file was aligned by BLAT to the other in 1 kb blocks, then parsed by base location.

Figure 2

A summary of gene representation within each assembled version. (A) Gene counts derived from the NCBI RefSeq database are parsed by defined gene categories for each assembled version of the chicken genome. Green and blue bars are Gallus_gallus-4.0 and Gallus_gallus-5.0, respectively. (B) Gene model build comparison of the citrate synthase gene (gene ID 100858903) in each assembled version of the chicken genome.

Figure 3

Map for chicken chromosome 16 (GGA16) p- and q-arms. Genes currently mapped to GGA16 are described in four regions: (1) the olfactory and scavenger receptor gene region, (2) the nucleolar organizer region containing ribosomal RNA genes, (3) the MHC-Y region containing mainly MHC class I-like and c-type lectin-like genes, and (4) the MHC-B and CD1 gene region. Intervening between MHC-Y and the MHC-B and CD1 region is a region known to contain repeat sequences. Currently available haplotype sequences suggest that in one portion of the MHC-B and CD1 region the gene number is stable and in the other the copy number is variable. Asterisk indicates that whether the copy number variable subregion is proximal (as drawn) or the copy number stable region of MHC-B and CD1 is proximal remains to be determined.