Transcriptomes of an Array of Chicken Ovary, Intestinal, and Immune Cells and Tissues

Abstract

While the chicken (Gallus gallus) is the most consumed agricultural animal worldwide, the chicken transcriptome remains understudied. We have characterized the transcriptome of 10 cell and tissue types from the chicken using RNA-seq, spanning intestinal tissues (ileum, jejunum, proximal cecum), immune cells (B cells, bursa, macrophages, monocytes, spleen T cells, thymus), and reproductive tissue (ovary). We detected 17,872 genes and 24,812 transcripts across all cell and tissue types, representing 73% and 63% of the current gene annotation, respectively. Further quantification of RNA transcript biotypes revealed protein-coding and lncRNAs specific to an individual cell/tissue type. Each cell/tissue type also has an average of around 1.2 isoforms per gene, however, they all have at least one gene with at least 11 isoforms. Differential expression analysis revealed a large number of differentially expressed genes between tissues of the same category (immune and intestinal). Many of these differentially expressed genes in immune cells were involved in cellular processes relating to differentiation and cell metabolism as well as basic functions of immune cells such as cell adhesion and signal transduction. The differential expressed genes of the different segments of the chicken intestine (jejunum, ileum, proximal cecum) correlated to the metabolic processes in nutrient digestion and absorption. These data should provide a valuable resource in understanding the chicken genome.

Expression of key genes in the caecum in CM5 and CM9 chickens of the meat cross «Smena 9» against the background of the replacement of fishmeal

“…Доказано также влияние состава рациона на экспрессию генов сельскохозяйственной птицы [9,10]. Известно, что в слепых отростках кишечника птицы экспрессируется множество генов, которые связаны с жизненно важными функциями организма [11]. Благодаря пищеварительной системе происходит взаимодействие организма птицы с окружающей средой, формируется устойчивость к заболеваниям и изменениям условий кормления, что в результате влияет на показатели продуктивности.…”

Microbiome applications for laying hen performance and egg production

“…Host selectivity could also develop in other ways. With the introduction of transcriptomics to the laying hen ovary and other tissues ( Overbey et al, 2021 ; Zhang et al 2021 ), it is may be conceivable in future studies to identify the host defense mechanisms in the laying hen reproductive tract that prevent colonization by certain bacterial groups and, thus, influence microbial community that encounters the eggshell surface.…”

Multiomics uncovers the epigenomic and transcriptomic response to viral and bacterial stimulation in turbot

“…Until recently, functional annotation mainly focused on protein-coding genes using transcriptomics. Transcriptome annotation is now consolidated with robust pipelines (Raghavan et al, 2022) and, throughout the years, transcriptome annotations for human (Frankish et al, 2023), model species (He et al, 2020; Lawson et al, 2020), terrestrial livestock (Summers et al, 2020; Halstead et al, 2021; Overbey et al, 2021) and some aquaculture species (Ramberg et al, 2021; Johnston et al, 2024) have been published.…”