Fourth Report on Chicken Genes and Chromosomes 2022

Smith, Jacqueline; Alfieri, James M.; Anthony, Nick; Arensburger, Peter; Athrey, Giridhar; Balacco, Jennifer; Balic, Adam; Bardou, Philippe; Barela, Paul; Bigot, Yves; Blackmon, Heath; Бородин, П. М.; Carroll, Rachel; Casono, Meya C.; Charles, Mathieu; Cheng, Hans H.; Chiodi, Maddie; Cigan, Lacey; Coghill, Lyndon M.; Crooijmans, R.P.M.A.; Das, Neelabja; Davey, Sean; Davidian, Asya; Degalez, Fabien; Dekkers, Jack; Derks, Martijn F.L.; Diack, Abigail B.; Djikeng, Appolinaire; Drechsler, Yvonne; Dyomin, Alexander; Fédrigo, Olivier; Fiddaman, Steven R.; Formenti, Giulio; Frantz, Laurent; Fulton, Janet E.; Gaginskaya, Elena; Galkina, Svetlana; Gallardo, Rodrigo A.; Geibel, Johannes; Gheyas, Almas; Godinez, Cyrill John P; Goodell, Ashton; Graves, Jennifer A. Marshall; Griffin, Daren K.; Haase, Bettina; Han, Jianlin; Hanotte, Olivier; Henderson, Lindsay J.; Hou, Zhuocheng; Howe, Kerstin; Huynh, Lan; Ilatsia, E. D.; Jarvis, Erich D.; Johnson, Sarah M.; Kaufman, Jim; Kelly, T. Ross; Kemp, Stephen J.; Kern, Colin; Keroack, Jacob H.; Klopp, Christophe; Lagarrigue, Sandrine; Lamont, Susan J.; Lange, Margaret J.; Lanke, Anika; Larkin, Denis M.; Larson, Greger; Layos, John King N.; Lebrasseur, Ophélie; Malinovskaya, Lyubov P.; Martin, Rebecca J.; Cerezo, Maria Luisa Martin; Mason, Andrew S.; McCarthy, Fiona M.; McGrew, Michael J.; Mountcastle, Jacquelyn; Muhonja, Christine Kamidi; Muir, William M.; Muret, Kévin; Murphy, Terence; Ng’ang’a, Ismael; Nishibori, Masahide; O'Connor, Rebecca E; Ogugo, Moses; Okimoto, Ron; Ouko, Ochieng; Patel, Hardip R.; Perini, Francesco; Pigozzi, María Inés; Potter, Krista C.; Price, Peter D.; Reimer, Christian; Rice, Edward S.; Rocos, Nicolas I E; Rogers, Thea F; Saelao, Perot; Schauer, Jens; Schnabel, Robert D.; Schneider, Valérie; Simianer, Henner; Smith, Adrian; Stevens, Mark P.; Stiers, Kyle M.; Tiambo, Christian Keambou; Tixier‐Boichard, Michèle; Torgasheva, Anna A.; Tracey, Alan S.; Tregaskes, Clive A.; Vervelde, Lonneke; Wang, Ying; Warren, Wesley C.; Waters, Paul D.; Webb, David J.; Weigend, Steffen; Wolc, Anna; Wright, Alison E.; Wright, Dominic S.; Wu, Zhou; Yamagata, Masahito; Yang, Chentao; Yin, Zhong-Tao; Young, Michelle C.; Zhang, Guojie; Zhao, Bi; Zhou, Huaqiang

doi:10.1159/000529376

Cited by 23 publications

(12 citation statements)

References 801 publications

(1,056 reference statements)

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“…Note that it can be difficult to assess the accuracy of the gene models, particularly in terms of exon/intron structure or gene fusions/splits due to different factors as short-sequencing RNA-seq samples, the variety of bioinformatics analysis methods used for the gene modelling or also the impossibility to gather all the condition-specific RNA-seq samples with an enough high sequencing depth. However, the repeated presence of a model at a specific locus in various databases supports the existence of this gene model, even if the transcript isoforms supporting these models are still badly described in farm species (2, 3, 35). Moreover, the observation of an expression in at least one of the 47 tissues is another argument for the existence of a gene model, especially for lncRNAs, which are weakly expressed and sometimes supported by only a few reads.…”

Section: Discussionmentioning

confidence: 99%

GEGA (Gallus Enriched Gene Annotation): an online tool providing genomics and functional information across 47 tissues for a chicken gene-enriched atlas gathering Ensembl & Refseq genome annotations

Degalez,

Bardou,

Lagarrigue

2024

Preprint

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GEGA is a user-friendly tool to navigate through different genomics and functional information related to an enriched gene atlas in chicken that unifies the gene catalogues from the two reference databases, NCBI-RefSeq & EMBL-Ensembl/GENCODE, and four other additional rich resources as FAANG and NONCODE. Using the latest GRCg7b genome assembly, GEGA offers a total of 78,323 genes, including 24,102 protein-coding genes (PCGs) and 44,428 long non-coding RNAs (lncRNAs), greatly enhancing the number of genes provided by each resource separately. But GEGA is more than just a gene database. It offers a range of features that allow to go deeper into the functional aspects of these genes,e.g., by exploring their expression and co-expression profiles across 47 tissues from 36 datasets and 1400 samples, by discovering tissue-specific variations and their expression as a function of sex or age, by extracting their orthologous genes or their configuration related to the genomics closest gene. For the communities interested in one specific gene, a list of genes or a QTL region in chicken, GEGA’s user-friendly interface enables efficient gene analysis, easy downloading of results and a multitude of graphical representations, from genomic information to detailed visualization of expression levels.GRAPHICAL ABSTRACT

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Section: Discussionmentioning

confidence: 99%

GEGA (Gallus Enriched Gene Annotation): an online tool providing genomics and functional information across 47 tissues for a chicken gene-enriched atlas gathering Ensembl & Refseq genome annotations

Degalez,

Bardou,

Lagarrigue

2024

Preprint

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“…Although multiple improved versions of the RJF genome (galgal2-galgal5 and GRCg6a) [ 2 – 4 ] and commercial chicken genomes (GRCg7b/w) [ 5 , 6 ] have been assembled, understanding of chicken genomes is still far from complete. In particular, the number of protein-coding genes annotated in genomes of different breeds varies widely, and many presumed missing genes in chickens are still not found [ 7 ].…”

Section: Discussionmentioning

confidence: 99%

“…Chicken ( Gallus gallus ) provides us with most protein sources in our daily life and also is a model organism to study the development, immunity and diseases of vertebrates [ 1 ]. As a result, multiple versions of chicken genomes have been assembled, such as those for the red jungle fowl (galgal2-galgal5 and GRCg6a) [ 2 – 4 ], the broiler (GRCg7b) and the layer (GRCg7w) [ 5 , 6 ]. However, the understanding of chicken genetics, egg and meat production, domestication and evolution is still limited due to the incomplete assemblies and annotations of these genome versions.…”

Section: Introductionmentioning

confidence: 99%

Annotations of four high-quality indigenous chicken genomes identify more than one thousand missing genes in subtelomeric regions and micro-chromosomes with high G/C contents

Wu,

Dou,

Yuan

et al. 2024

BMC Genomics

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Background Although multiple chicken genomes have been assembled and annotated, the numbers of protein-coding genes in chicken genomes and their variation among breeds are still uncertain due to the low quality of these genome assemblies and limited resources used in their gene annotations. To fill these gaps, we recently assembled genomes of four indigenous chicken breeds with distinct traits at chromosome-level. In this study, we annotated genes in each of these assembled genomes using a combination of RNA-seq- and homology-based approaches. Results We identified varying numbers (17,497–17,718) of protein-coding genes in the four indigenous chicken genomes, while recovering 51 of the 274 “missing” genes in birds in general, and 36 of the 174 “missing” genes in chickens in particular. Intriguingly, based on deeply sequenced RNA-seq data collected in multiple tissues in the four breeds, we found 571 ~ 627 protein-coding genes in each genome, which were missing in the annotations of the reference chicken genomes (GRCg6a and GRCg7b/w). After removing redundancy, we ended up with a total of 1,420 newly annotated genes (NAGs). The NAGs tend to be found in subtelomeric regions of macro-chromosomes (chr1 to chr5, plus chrZ) and middle chromosomes (chr6 to chr13, plus chrW), as well as in micro-chromosomes (chr14 to chr39) and unplaced contigs, where G/C contents are high. Moreover, the NAGs have elevated quadruplexes G frequencies, while both G/C contents and quadruplexes G frequencies in their surrounding regions are also high. The NAGs showed tissue-specific expression, and we were able to verify 39 (92.9%) of 42 randomly selected ones in various tissues of the four chicken breeds using RT-qPCR experiments. Most of the NAGs were also encoded in the reference chicken genomes, thus, these genomes might harbor more genes than previously thought. Conclusion The NAGs are widely distributed in wild, indigenous and commercial chickens, and they might play critical roles in chicken physiology. Counting these new genes, chicken genomes harbor more genes than originally thought.

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“…These chromosome-level assemblies have contig N50 values ranging from 5.47 to 91.3 Mb (see Table 1). This includes the current species reference assembly on NCBI RefSeq, bGalGal1b, also known as GRCg7b (contig N50 = 18.8 Mb), a haplotype-resolved assembly of a commercial broiler line created using the trio-binning method and an F1 cross between a representative commercial broiler and a white leghorn layer [36]. bGalGal1b, as the current RefSeq reference assembly, is fully annotated, so we use it as the source of annotations in this study.…”

Section: Selection Of Chromosome-level Assembliesmentioning

confidence: 99%

A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants

Rice¹,

Alberdi²,

Alfieri³

et al. 2023

Preprint

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Background. The red junglefowl, the wild progenitor of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of commercial importance. However, the use of a single reference genome does not capture diversity present among modern breeds, many of which have accumulated molecular changes due to drift and selection. While reference-based resequencing is well-suited to cataloging simple variants such as single nucleotide changes and short insertions and deletions, it is mostly inadequate to discover more complex structural variation in the genome. Results. We present a pangenome for the domestic chicken consisting of thirty assemblies of chickens from different breeds and research lines. We demonstrate how this pangenome can be used to catalog structural variants present in modern breeds and untangle complex nested variation. We show that alignment of short reads from 100 diverse wild and domestic chickens to this pangenome reduces reference bias by 38%, which affects downstream genotyping results. This approach also allows for the accurate genotyping of a large and complex pair of structural variants at the K ‘feathering’ locus using short reads, which would not be possible using a linear reference. Conclusions. We expect that this new paradigm of genomic reference will allow better pinpointing of exact mutations responsible for specific phenotypes, which will in turn be necessary for breeding chickens that meet new sustainability criteria and are resilient to quickly evolving pathogen threats.

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Fourth Report on Chicken Genes and Chromosomes 2022

Abstract: none

Cited by 23 publications

References 801 publications

GEGA (Gallus Enriched Gene Annotation): an online tool providing genomics and functional information across 47 tissues for a chicken gene-enriched atlas gathering Ensembl & Refseq genome annotations

GEGA (Gallus Enriched Gene Annotation): an online tool providing genomics and functional information across 47 tissues for a chicken gene-enriched atlas gathering Ensembl & Refseq genome annotations

Annotations of four high-quality indigenous chicken genomes identify more than one thousand missing genes in subtelomeric regions and micro-chromosomes with high G/C contents

A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants

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