The first whole transcriptomic exploration of pre-oviposited early chicken embryos using single and bulked embryonic RNA-sequencing.

Young Sun Hwang,Minseok Seo,Hee Jung Choi,Jae Yong Han,Sang Kyung Kim,Heebal Kim

doi:10.1093/gigascience/giy030

Young Sun Hwang, Minseok Seo + Show 4 more

Open Access

https://doi.org/10.1093/gigascience/giy030

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Abstract

BackgroundThe chicken is a valuable model organism, especially in evolutionary and embryology research because its embryonic development occurs in the egg. However, despite its scientific importance, no transcriptome data have been generated for deciphering the early developmental stages of the chicken because of practical and technical constraints in accessing pre-oviposited embryos.FindingsHere, we determine the entire transcriptome of pre-oviposited avian embryos, including oocyte, zygote, and intrauterine embryos from Eyal-giladi and Kochav stage I (EGK.I) to EGK.X collected using a noninvasive approach for the first time. We also compare RNA-sequencing data obtained using a bulked embryo sequencing and single embryo/cell sequencing technique. The raw sequencing data were preprocessed with two genome builds, Galgal4 and Galgal5, and the expression of 17,108 and 26,102 genes was quantified in the respective builds. There were some differences between the two techniques, as well as between the two genome builds, and these were affected by the emergence of long intergenic noncoding RNA annotations.ConclusionThe first transcriptome datasets of pre-oviposited early chicken embryos based on bulked and single embryo sequencing techniques will serve as a valuable resource for investigating early avian embryogenesis, for comparative studies among vertebrates, and for novel gene annotation in the chicken genome.

Highlights

The chicken is a valuable model organism, especially in evolutionary and embryology research because its embryonic development occurs in the egg
Here, we determine the entire transcriptome of pre-oviposited avian embryos, including oocyte, zygote, and intrauterine embryos from Eyal-giladi and Kochav stage I (EGK.I) to EGK.X collected using a noninvasive approach for the first time
There were some differences between the two techniques, as well as between the two genome builds, and these were affected by the emergence of long intergenic noncoding RNA annotations

Summary

Background

Avian species are valuable animal models in many research areas, especially in embryology, because the avian embryo develops in an egg before hatching. All of the samples in both gene expression matrixes clearly clustered according to their developmental stage, except for the zygote, EGK.I, and EGK.III (Fig.4) This means that there are morphological differences, there is no transcriptome change during the early embryonic development of the chicken for a specific time after zygotic gene activation. Bulked zygote samples were separated from the cluster of EGK.I and EGK.III samples in a MDS analysis based on the Galgal gene matrix, whereas there was no difference in the Galga gene expression matrix (Fig., right panel) This shows that quantifying gene expression using the standard RNA-seq pooled embryo sequencing technique could be affected by the individual gene expression diversity and the difference of gene annotations. Our large dataset should be useful for future studies of avian and comparative genomics because the data were generated using the latest sequencing platform and whole transcriptome sequencing enabling the characterization of all RNA transcripts, including primary transcripts, regardless of polyadenylation

Availability of supporting data

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