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.

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References 52

1. 1.

   Afanassieff M. Goto R. M. Ha J. Sherman M. A. Zhong L., 2001 At least one class I gene in restriction fragment pattern-Y (Rfp-Y), the second MHC gene cluster in the chicken, is transcribed, polymorphic, and shows divergent specialization in antigen binding region. J. Immunol. 166: 3324–3333.

   Not in our library10.4049/jimmunol.166.5.3324

2. 2.

   Bellott D. W. Skaletsky H. Pyntikova T. Mardis E. R. Graves T., 2010 Convergent evolution of chicken Z and human X chromosomes by expansion and gene acquisition. Nature 466: 612–616.

   Not in our library10.1038/nature09172

3. 3.

   Berlin K. Koren S. Chin C. Drake J. Landolin J. M., 2014 Assembling large genomes with single-molecule sequencing and locality sensitive hashing. bioRxiv 1: 1–35.

   Not in our library10.1038/nbt.3238

4. 4.
   SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information · 2014

   No notice
5. 5.

   Boutet E. Lieberherr D. Tognolli M. Schneider M. Bansal P., 2016 UniProtKB/Swiss-Prot, the manually annotated section of the UniProt KnowledgeBase: how to use the entry view. Methods Mol. Biol. 1374: 23–54.

   Not in our library10.1007/978-1-4939-3167-5_2

6. 6.

   Brown G. R. Hem V. Katz K. S. Ovetsky M. Wallin C., 2015 Gene: a gene-centered information resource at NCBI. Nucleic Acids Res. 43: D36–D42.

   Not in our library10.1093/nar/gku1055

7. 7.

   Chaisson M. J. Huddleston J. Dennis M. Y. Sudmant P. H. Malig M., 2015 Resolving the complexity of the human genome using single-molecule sequencing. Nature 517: 608–611.

   Not in our library10.1038/nature13907

8. 8.
   High speed BLASTN: an accelerated MegaBLAST search tool · 2015

   No notice
9. 9.

   Cheng H. H. Levin I. Vallejo R. L. Khatib H. Dodgson J. B., 1995 Development of a genetic map of the chicken with markers of high utility. Poult. Sci. 74: 1855–1874.

   Not in our library10.3382/ps.0741855

10. 10.
    LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons · 2008

    No notice
11. 11.

    Fulton J. E. McCarron A. M. Lund A. R. Pinegar K. N. Wolc A., 2016 A high-density SNP panel reveals extensive diversity, frequent recombination and multiple recombination hotspots within the chicken major histocompatibility complex B region between BG2 and CD1A1. Genet. Sel. Evol. 48: 1.

    Not in our library10.1186/s12711-015-0181-x

12. 12.

    Gordon L. Yang S. Tran-Gyamfi M. Baggott D. Christensen M., 2007 Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions. Genome Res. 17: 1603–1613.

    Not in our library10.1101/gr.6775107

13. 13.

    Gotz S. Garcia-Gomez J. M. Terol J. Williams T. D. Nagaraj S. H., 2008 High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res. 36: 3420–3435.

    Not in our library10.1093/nar/gkn176

14. 14.

    Groenen M. A. Wahlberg P. Foglio M. Cheng H. H. Megens H. J., 2009 A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate. Genome Res. 19: 510–519.

    Not in our library10.1101/gr.086538.108

15. 15.

    Huntley R. P. Sawford T. Mutowo-Meullenet P. Shypitsyna A. Bonilla C., 2015 The GOA database: gene ontology annotation updates for 2015. Nucleic Acids Res. 43: D1057–D1063.

    Not in our library10.1093/nar/gku1113

16. 16.

    International Chicken Genome Sequencing Consortium, 2004 Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695–716.

    Not in our library10.1038/nature03154

17. 17.

    Johnson M. Zaretskaya I. Raytselis Y. Merezhuk Y. McGinnis S., 2008 NCBI BLAST: a better web interface. Nucleic Acids Res. 36: W5–W9.

    Not in our library10.1093/nar/gkn201

18. 18.
    InterProScan 5: genome-scale protein function classification · 2014

    No notice
19. 19.
    Splign: algorithms for computing spliced alignments with identification of paralogs · 2008

    No notice
20. 20.

    Kent W. J., 2002 BLAT–the BLAST-like alignment tool. Genome Res. 12: 656–664.

    Not in our library10.1101/gr.229202

21. 21.

    Koboldt DC Larson DE Wilson RK, 2013 Using VarScan 2 for germline variant calling and somatic mutation detection. Curr. Protoc. Bioinformatics 44: 15 14 1–15 14 17.

    Not in our library10.1002/0471250953.bi1504s44

22. 22.

    Koren S. Schatz M. C. Walenz B. P. Martin J. Howard J. T., 2012 Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat. Biotechnol. 30: 693–700.

    Not in our library10.1038/nbt.2280

23. 23.
    Versatile and open software for comparing large genomes · 2004

    No notice
24. 24.

    Laun K. Coggill P. Palmer S. Sims S. Ning Z., 2006 The leukocyte receptor complex in chicken is characterized by massive expansion and diversification of immunoglobulin-like loci. PLoS Genet. 2: e73.

    Not in our library10.1371/journal.pgen.0020073

25. 25.

    Li H. Durbin R., 2009 Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754–1760.

    Not in our library10.1093/bioinformatics/btp324

26. 26.

    Lovell P. V. Wirthlin M. Wilhelm L. Minx P. Lazar N. H., 2014 Conserved syntenic clusters of protein coding genes are missing in birds. Genome Biol. 15: 565.

    Not in our library10.1186/s13059-014-0565-1

27. 27.

    Manly K. F. Cudmore R. H. Jr Meer J. M., 2001 Map manager QTX, cross-platform software for genetic mapping. Mamm. Genome 12: 930–932.

    Not in our library10.1007/s00335-001-1016-3

28. 28.

    Mason A. S. Fulton J. E. Hocking P. M. Burt D. W., 2016 A new look at the LTR retrotransposon content of the chicken genome. BMC Genomics 17: 688.

    Not in our library10.1186/s12864-016-3043-1

29. 29.

    McCarthy E. M. McDonald J. F., 2003 LTR_STRUC: a novel search and identification program for LTR retrotransposons. Bioinformatics 19: 362–367.

    Not in our library10.1093/bioinformatics/btf878

30. 30.

    Miller M. M. Taylor R. L. Jr, 2016 Brief review of the chicken major histocompatibility complex: the genes, their distribution on chromosome 16, and their contributions to disease resistance. Poult. Sci. 95: 375–392.

    Not in our library10.3382/ps/pev379

31. 31.
    The InterPro protein families database: the classification resource after 15 years · 2014

    No notice
32. 32.

    Montague M. J. Li G. Gandolfi B. Khan R. Aken B. L., 2014 Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication. Proc. Natl. Acad. Sci. USA 111: 17230–17235.

    Not in our library10.1073/pnas.1410083111

33. 33.

    Morgulis A. Gertz E. M. Schaffer A. A. Agarwala R., 2006 WindowMasker: window-based masker for sequenced genomes. Bioinformatics 22: 134–141.

    Not in our library10.1093/bioinformatics/bti774

34. 34.

    Myhre S. Tveit H. Mollestad T. Laegreid A., 2006 Additional gene ontology structure for improved biological reasoning. Bioinformatics 22: 2020–2027.

    Not in our library10.1093/bioinformatics/btl334

35. 35.
    Chromosome-scale shotgun assembly using an in vitro method for long-range linkage · 2016

    No notice
36. 36.

    Qanbari S. Seidel M. Strom T. M. Mayer K. F. Preisinger R., 2015 Parallel selection revealed by population sequencing in chicken. Genome Biol. Evol. 7: 3299–3306.

    Not in our library10.1093/gbe/evv222

37. 37.

    Reyer H. Hawken R. Murani E. Ponsuksili S. Wimmers K., 2015 The genetics of feed conversion efficiency traits in a commercial broiler line. Sci. Rep. 5: 16387.

    Not in our library10.1038/srep16387

38. 38.

    Rho M. Choi J. H. Kim S. Lynch M. Tang H., 2007 De novo identification of LTR retrotransposons in eukaryotic genomes. BMC Genomics 8: 90.

    Not in our library10.1186/1471-2164-8-90

39. 39.

    Rubin C. J. Zody M. C. Eriksson J. Meadows J. R. Sherwood E., 2010 Whole-genome resequencing reveals loci under selection during chicken domestication. Nature 464: 587–591.

    Not in our library10.1038/nature08832

40. 40.

    Salomonsen J. Chattaway J. A. Chan A. C. Parker A. Huguet S., 2014 Sequence of a complete chicken BG haplotype shows dynamic expansion and contraction of two gene lineages with particular expression patterns. PLoS Genet. 10: e1004417.

    Not in our library10.1371/journal.pgen.1004417

Cited by papers we hold 6

• Evolutionary analysis of a complete chicken genome · 2023
  No notice
• False gene and chromosome losses in genome assemblies caused by GC content variation and repeats · 2022
  Not checked
• Towards complete and error-free genome assemblies of all vertebrate species · 2021
  No notice
• Reliability of genomic evaluation for egg quality traits in layers · 2020
  Not checked
• Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise · 2020
  No notice
• BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics · 2017
  No notice

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