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.

Genome-Wide Epigenetic Studies in Chicken: A Review

“…The first two versions were assembled using a whole-genome Sanger sequencing [67,69]. The latest version of the chicken genome assembly (Gallus_gallus-5.0; GCA_000002315.3), of 1.2 Gb size, was released in 2015 and was obtained through the combination of short read (Illumina) and long read technologies (PacBio), which significantly improved the contig length and thus the quality of the assembly [70,71]. In the latest version of the chicken genome assembly, the number of assembled chromosomes was improved (from the autosomes GGA1-28 and GGA32 to autosomes GGA1-28 and GGA30-33, [70]).…”

“…The latest version of the chicken genome assembly (Gallus_gallus-5.0; GCA_000002315.3), of 1.2 Gb size, was released in 2015 and was obtained through the combination of short read (Illumina) and long read technologies (PacBio), which significantly improved the contig length and thus the quality of the assembly [70,71]. In the latest version of the chicken genome assembly, the number of assembled chromosomes was improved (from the autosomes GGA1-28 and GGA32 to autosomes GGA1-28 and GGA30-33, [70]). The increased coverage (from 12X to 70X) allowed a more complete chicken genome assembly, but the large amount of data produced also increased the number of scaffolds or unplaced contigs.…”

“…The increased coverage (from 12X to 70X) allowed a more complete chicken genome assembly, but the large amount of data produced also increased the number of scaffolds or unplaced contigs. About 183 Mb of new sequences were added, networks were improved, errors identified and a more complete set of genes was determined [70].…”

Chicken Microchromosomes in the Lampbrush Phase: A Cytogenetic Description

“…Secondly, the approximated values allow assessing the missing part in each chromosome assembly. Telomeric, centromeric, and other regions composed of specific coding and noncoding repeats are omitted in the current version of Gallus_ gallus-5.0 [Warren et al, 2017] due to sequencing and assembling algorithm limitations. DNA reassociation kinetics and S1 nuclease digestion analysis meanwhile reveal about 15% of repetitive DNA in the chicken genome [Epplen et al, 1978].…”

“…According to the image cytometric analysis of Feulgenstained metaphase chromosomes, the mean MI DNA content varies from 2.9 (GGA38) to 25.4 Mb (GGA11) [Mendonça et al, 2016]. Deciphered MI euchromatic fragment lengths vary from 0.024 (GGA30) to 20.22 Mb (GGA11) in the latest version of the assembled chicken genome Gallus_gallus-5.0 [Warren et al, 2017]. The sequences of GGA29 and GGA34-38 have not been published.…”