A New Chicken Genome Assembly Provides Insight into Avian Genome Structure
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...
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Online Access: | http://g3journal.org/lookup/doi/10.1534/g3.116.035923 |
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doaj-707c7ed927fe4217bfe9c7aa6879408b2021-07-02T08:38:20ZengOxford University PressG3: Genes, Genomes, Genetics2160-18362017-01-017110911710.1534/g3.116.03592310A New Chicken Genome Assembly Provides Insight into Avian Genome StructureWesley C. WarrenLaDeana W. HillierChad TomlinsonPatrick MinxMilinn KremitzkiTina GravesChris MarkovicNathan BoukKim D. PruittFrancoise Thibaud-NissenValerie SchneiderTamer A. MansourC. Titus BrownAleksey ZiminRachel HawkenMitch AbrahamsenAlexis B. PyrkoszMireille MorissonValerie FillonAlain VignalWilliam ChowKerstin HoweJanet E. FultonMarcia M. MillerPeter LovellClaudio V. MelloMorgan WirthlinAndrew S. MasonRichard KuoDavid W. BurtJerry B. DodgsonHans H. ChengThe 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.http://g3journal.org/lookup/doi/10.1534/g3.116.035923Gallus gallusgenome assemblyMHC |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Wesley C. Warren LaDeana W. Hillier Chad Tomlinson Patrick Minx Milinn Kremitzki Tina Graves Chris Markovic Nathan Bouk Kim D. Pruitt Francoise Thibaud-Nissen Valerie Schneider Tamer A. Mansour C. Titus Brown Aleksey Zimin Rachel Hawken Mitch Abrahamsen Alexis B. Pyrkosz Mireille Morisson Valerie Fillon Alain Vignal William Chow Kerstin Howe Janet E. Fulton Marcia M. Miller Peter Lovell Claudio V. Mello Morgan Wirthlin Andrew S. Mason Richard Kuo David W. Burt Jerry B. Dodgson Hans H. Cheng |
spellingShingle |
Wesley C. Warren LaDeana W. Hillier Chad Tomlinson Patrick Minx Milinn Kremitzki Tina Graves Chris Markovic Nathan Bouk Kim D. Pruitt Francoise Thibaud-Nissen Valerie Schneider Tamer A. Mansour C. Titus Brown Aleksey Zimin Rachel Hawken Mitch Abrahamsen Alexis B. Pyrkosz Mireille Morisson Valerie Fillon Alain Vignal William Chow Kerstin Howe Janet E. Fulton Marcia M. Miller Peter Lovell Claudio V. Mello Morgan Wirthlin Andrew S. Mason Richard Kuo David W. Burt Jerry B. Dodgson Hans H. Cheng A New Chicken Genome Assembly Provides Insight into Avian Genome Structure G3: Genes, Genomes, Genetics Gallus gallus genome assembly MHC |
author_facet |
Wesley C. Warren LaDeana W. Hillier Chad Tomlinson Patrick Minx Milinn Kremitzki Tina Graves Chris Markovic Nathan Bouk Kim D. Pruitt Francoise Thibaud-Nissen Valerie Schneider Tamer A. Mansour C. Titus Brown Aleksey Zimin Rachel Hawken Mitch Abrahamsen Alexis B. Pyrkosz Mireille Morisson Valerie Fillon Alain Vignal William Chow Kerstin Howe Janet E. Fulton Marcia M. Miller Peter Lovell Claudio V. Mello Morgan Wirthlin Andrew S. Mason Richard Kuo David W. Burt Jerry B. Dodgson Hans H. Cheng |
author_sort |
Wesley C. Warren |
title |
A New Chicken Genome Assembly Provides Insight into Avian Genome Structure |
title_short |
A New Chicken Genome Assembly Provides Insight into Avian Genome Structure |
title_full |
A New Chicken Genome Assembly Provides Insight into Avian Genome Structure |
title_fullStr |
A New Chicken Genome Assembly Provides Insight into Avian Genome Structure |
title_full_unstemmed |
A New Chicken Genome Assembly Provides Insight into Avian Genome Structure |
title_sort |
new chicken genome assembly provides insight into avian genome structure |
publisher |
Oxford University Press |
series |
G3: Genes, Genomes, Genetics |
issn |
2160-1836 |
publishDate |
2017-01-01 |
description |
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. |
topic |
Gallus gallus genome assembly MHC |
url |
http://g3journal.org/lookup/doi/10.1534/g3.116.035923 |
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