Avian transcriptomics: opportunities and challenges

Abstract

Recent developments in next-generation sequencing technologies have greatly facilitated the study of whole transcriptomes in model and non-model species. Studying the transcriptome and how it changes across a variety of biological conditions has had major implications for our understanding of how the genome is regulated in different contexts, and how to interpret adaptations and the phenotype of an organism. The aim of this review is to highlight the potential of these new technologies for the study of avian transcriptomics, and to summarise how transcriptomics has been applied in ornithology. A total of 81 peer-reviewed scientific articles that used transcriptomics to answer questions within a broad range of study areas in birds are used as examples throughout the review. We further provide a quick guide to highlight the most important points which need to be take into account when planning a transcriptomic study in birds, and discuss how researchers with little background in molecular biology can avoid potential pitfalls. Suggestions for further reading are supplied throughout. We also discuss possible future developments in the technology platforms used for ribonucleic acid sequencing. By summarising how these novel technologies can be used to answer questions that have long been asked by ornithologists, we hope to bridge the gap between traditional ornithology and genomics, and to stimulate more interdisciplinary research.

Avian MHC Evolution in the Era of Genomics: Phase 1.0

“…For example, classical MHC genes can have high or low expression, whereas non-classical MHC genes are defined by having generally low levels of expression [57]. Some basic information on expression, measured as transcription at the level of RNA, of MHC genes in birds beyond chickens is available [11,23,24,29,46,120,140,141,142], but less than a handful of studies have used high-throughput amplicon sequencing to address this question, and few studies have used specific organs, such as spleen [142,143,144,145], to measure expression, likely a more reliable guide to expression than whole blood, although further study is needed. Initial evidence suggests that, even in the case of passerines with numerous MHC genes, a high proportion of MHC-I gene copies are expressed [40,42,43,146], implying that the number of expressed MHC genes correlate with the number of MHC gene copies in the genome.…”

Tissue-specific expression profiles and positive selection analysis in the tree swallow (Tachycineta bicolor) using a de novo transcriptome assembly

“…The rapid increase of available transcriptomes for non-model organisms over the past few years has greatly contributed to ecological and evolutionary advances in natural systems 1–3 . This is particularly true for avian species 4 , yet one key species used in eco-evolutionary and organismal biology has a surprising absence of molecular resources. Tree swallows ( Tachycineta bicolor ) are one of the best-studied, free-living native species in North America 5 .…”

“…A major goal in evolutionary biology is to identify genes that are subject to adaptive evolution (i.e., evolving under positive selection) 18 . Avian transcriptomes have been assembled for a wide range of species 4 , which holds promise for new insights into the molecular processes driving adaptation. For example, research in mammals suggests that genes expressed at low levels and those that are tissue‐specific may evolve more rapidly 19 , and work thus far in birds largely mirrors these findings 20–22 .…”

The physiology of movement

“…Unbiased genome-wide transcriptomics using RNAseq has become very popular in the last couple of years to study movement phenomena [147,152,157,[189][190][191]. In the near future, Next Generation Sequencing (NGS) will allow advanced comparisons of differentially expressed genes across species, movement type, and conditions [192][193][194].…”