Tissue Resources for the Functional Annotation of Animal Genomes

Abstract

In order to generate an atlas of the functional elements driving genome expression in domestic animals, the Functional Annotation of Animal Genome (FAANG) strategy was to sample many tissues from a few animals of different species, sexes, ages, and production stages. This article presents the collection of tissue samples for four species produced by two pilot projects, at INRAE (National Research Institute for Agriculture, Food and Environment) and the University of California, Davis. There were three mammals (cattle, goat, and pig) and one bird (chicken). It describes the metadata characterizing these reference sets (1) for animals with origin and selection history, physiological status, and environmental conditions; (2) for samples with collection site and tissue/cell processing; (3) for quality control; and (4) for storage and further distribution. Three sets are identified: set 1 comprises tissues for which collection can be standardized and for which representative aliquots can be easily distributed (liver, spleen, lung, heart, fat depot, skin, muscle, and peripheral blood mononuclear cells); set 2 comprises tissues requiring special protocols because of their cellular heterogeneity (brain, digestive tract, secretory organs, gonads and gametes, reproductive tract, immune tissues, cartilage); set 3 comprises specific cell preparations (immune cells, tracheal epithelial cells). Dedicated sampling protocols were established and uploaded in https://data.faang.org/protocol/samples. Specificities between mammals and chicken are described when relevant. A total of 73 different tissues or tissue sections were collected, and 21 are common to the four species. Having a common set of tissues will facilitate the transfer of knowledge within and between species and will contribute to decrease animal experimentation. Combining data on the same samples will facilitate data integration. Quality control was performed on some tissues with RNA extraction and RNA quality control. More than 5,000 samples have been stored with unique identifiers, and more than 4,000 were uploaded onto the Biosamples database, provided that standard ontologies were available to describe the sample. Many tissues have already been used to implement FAANG assays, with published results. All samples are available without restriction for further assays. The requesting procedure is described. Members of FAANG are encouraged to apply a range of molecular assays to characterize the functional status of collected samples and share their results, in line with the FAIR (Findable, Accessible, Interoperable, and Reusable) data principles.

Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues

“…Gene models used to build the enriched genome annotation come from 6 genome annotations, all based on multi-tissue resources: (i) both reference genome annotations according to the GRCg7b assembly: “RefSeq” v106 67 and “ Ensembl” v107 68 , this latter has integrated the GENESWitCH project data; (ii) both gene model datasets from FAANG pilot projects 69 , 70 according to the GRCg6a assembly (GCF_.5): the FR-AgENCODE project 71 involving 11 tissues represented by 2 males and 2 females by tissue and the FarmENCODE proect including 15 tissues with 1 male and 1 female; (iii) and two other datasets including gene models from the previous atlas as presented in Jehl et al 13 produced according to the galgal5 assembly (GCF_000002315.4) and NONCODE v6.0 72 including only non-coding gene models from the literature and other public databases according to the galgal4 assembly (GCF_000002315.2). Contrary to all projects which used short-read sequencing, FarmENCODE includes samples sequenced with Oxford Nanopore long read Technology as presented in Guan et al 73 .…”

Livestock species as emerging models for genomic imprinting

“…Following the path taken by the biomedical research community, international initiatives promote the generation of increasingly comprehensive and accessible tools and resources in epigenomics and transcriptomics ( Giuffra et al, 2019 ; Tixier-Boichard et al, 2021 ). Recent large-scale cattle studies show the interest of multi-omics not limited to coding regions to capture large proportions of heritability and better predict the phenome ( Xiang et al, 2019 ; Xiang et al, 2023 ).…”

De novo transcriptome assembly database for 100 tissues from each of seven species of domestic herbivore

“…Using a combination of genomics and transcriptomics was first proposed by the Functional Annotation of Animal Genomes (FFANG) Consortium to identify the genes that code for proteins that are involved in critical production traits in farm animals 5 . Transcriptomic atlases were generated for common domestic animals such as pigs, cattle, sheep, and chickens [6][7][8][9][10] as well as other species of herbivores such as donkey 11 , water buffalo 12 , and goat 13 . While these published transcriptomic atlases of herbivores are valuable, they are published in independent databases, with no standard protocols for sample collection, RNA sequencing, or data processing.…”