Cover Image
QR Code

Expanding the cattle reference graph genome

Recent studies have highlighted several key advantages of graph genomes over standard linear reference genomes. These advantages include improvements in read mapping rates at divergent loci and the ability to more accurately call structural variants. However, the availability of graph genomes that r...

Full description

Main Authors: Talenti, A., Powell, J., Wragg, D., Paxton, E., Chepkwony, M., Miyunga, Antoinette, Njeru, R., Hemmink, Johanneke D., Fisch, A., Ferreira, B.R., Hammond, J.A., Archibald, A.L., Toye, Philip G., Connelley, T., Morrison, L., Prendergast, J.
Format: Book Chapter
Language:Inglés
Published: Wageningen University & Research 2022
Subjects:
genetics
animal breeding
Online Access:https://hdl.handle.net/10568/128741
_version_ 1855520178533564416
author Talenti, A.
Powell, J.
Wragg, D.
Paxton, E.
Chepkwony, M.
Miyunga, Antoinette
Njeru, R.
Hemmink, Johanneke D.
Fisch, A.
Ferreira, B.R.
Hammond, J.A.
Archibald, A.L.
Toye, Philip G.
Connelley, T.
Morrison, L.
Prendergast, J.
author_browse Archibald, A.L.
Chepkwony, M.
Connelley, T.
Ferreira, B.R.
Fisch, A.
Hammond, J.A.
Hemmink, Johanneke D.
Miyunga, Antoinette
Morrison, L.
Njeru, R.
Paxton, E.
Powell, J.
Prendergast, J.
Talenti, A.
Toye, Philip G.
Wragg, D.
author_facet Talenti, A.
Powell, J.
Wragg, D.
Paxton, E.
Chepkwony, M.
Miyunga, Antoinette
Njeru, R.
Hemmink, Johanneke D.
Fisch, A.
Ferreira, B.R.
Hammond, J.A.
Archibald, A.L.
Toye, Philip G.
Connelley, T.
Morrison, L.
Prendergast, J.
author_sort Talenti, A.
collection Repository of Agricultural Research Outputs (CGSpace)
description Recent studies have highlighted several key advantages of graph genomes over standard linear reference genomes. These advantages include improvements in read mapping rates at divergent loci and the ability to more accurately call structural variants. However, the availability of graph genomes that represent the extensive diversity of livestock species remain limited. To address this limitation, we have incorporated 15 cattle genomes into an expanded cattle graph genome, including 8 completely novel high-quality cattle assemblies from 4 divergent breeds (Holstein-Friesian, N'Dama, Boran and Nelore), each with high contiguity (N50>10 Mb). This graph genome incorporates over 250 Mb (9.5%) of novel sequence across the primary chromosomes, providing a better reference representation of the bovine pangenome and a key resource for the livestock community.
format Book Chapter
id CGSpace128741
institution CGIAR Consortium
language Inglés
publishDate 2022
publishDateRange 2022
publishDateSort 2022
publisher Wageningen University & Research
publisherStr Wageningen University & Research
record_format dspace
spelling CGSpace1287412026-01-26T06:49:14Z Expanding the cattle reference graph genome Talenti, A. Powell, J. Wragg, D. Paxton, E. Chepkwony, M. Miyunga, Antoinette Njeru, R. Hemmink, Johanneke D. Fisch, A. Ferreira, B.R. Hammond, J.A. Archibald, A.L. Toye, Philip G. Connelley, T. Morrison, L. Prendergast, J. genetics animal breeding Recent studies have highlighted several key advantages of graph genomes over standard linear reference genomes. These advantages include improvements in read mapping rates at divergent loci and the ability to more accurately call structural variants. However, the availability of graph genomes that represent the extensive diversity of livestock species remain limited. To address this limitation, we have incorporated 15 cattle genomes into an expanded cattle graph genome, including 8 completely novel high-quality cattle assemblies from 4 divergent breeds (Holstein-Friesian, N'Dama, Boran and Nelore), each with high contiguity (N50>10 Mb). This graph genome incorporates over 250 Mb (9.5%) of novel sequence across the primary chromosomes, providing a better reference representation of the bovine pangenome and a key resource for the livestock community. 2022-12-31 2023-02-20T11:13:45Z 2023-02-20T11:13:45Z Book Chapter https://hdl.handle.net/10568/128741 en Open Access Wageningen University & Research Talenti, A., Powell, J., Wragg, D., Paxton, E., Chepkwony, M., Miyunga, A., Njeru, R., Hemmink, J.D., Fisch, A., Ferreira, B.R., Hammond, J.A., Archibald, A.L., Toye, P., Connelley, T., Morrison, L. and Prendergast, J. 2023. Expanding the cattle reference graph genome. IN: Veerkamp, R.F. and Haas, Y. de. (eds), Proceedings of the 12th World Congress on Genetics Applied to Livestock Production (WCGALP): Technical and species orientated innovations in animal breeding, and contribution of genetics to solving societal challenges. Wageningen, the Netherlands: Wageningen Academic Publishers: 1737-1740.
spellingShingle genetics
animal breeding
Talenti, A.
Powell, J.
Wragg, D.
Paxton, E.
Chepkwony, M.
Miyunga, Antoinette
Njeru, R.
Hemmink, Johanneke D.
Fisch, A.
Ferreira, B.R.
Hammond, J.A.
Archibald, A.L.
Toye, Philip G.
Connelley, T.
Morrison, L.
Prendergast, J.
Expanding the cattle reference graph genome
title Expanding the cattle reference graph genome
title_full Expanding the cattle reference graph genome
title_fullStr Expanding the cattle reference graph genome
title_full_unstemmed Expanding the cattle reference graph genome
title_short Expanding the cattle reference graph genome
title_sort expanding the cattle reference graph genome
topic genetics
animal breeding
url https://hdl.handle.net/10568/128741
work_keys_str_mv AT talentia expandingthecattlereferencegraphgenome
AT powellj expandingthecattlereferencegraphgenome
AT wraggd expandingthecattlereferencegraphgenome
AT paxtone expandingthecattlereferencegraphgenome
AT chepkwonym expandingthecattlereferencegraphgenome
AT miyungaantoinette expandingthecattlereferencegraphgenome
AT njerur expandingthecattlereferencegraphgenome
AT hemminkjohanneked expandingthecattlereferencegraphgenome
AT fischa expandingthecattlereferencegraphgenome
AT ferreirabr expandingthecattlereferencegraphgenome
AT hammondja expandingthecattlereferencegraphgenome
AT archibaldal expandingthecattlereferencegraphgenome
AT toyephilipg expandingthecattlereferencegraphgenome
AT connelleyt expandingthecattlereferencegraphgenome
AT morrisonl expandingthecattlereferencegraphgenome
AT prendergastj expandingthecattlereferencegraphgenome

Similar Items