Creating reference gene annotation for the mouse C57BL6/J genome assembly

• Published in: Mammalian Genome Vol. 26; no. 9-10; pp. 366 - 378
• Main Authors: Mudge, Jonathan M., Harrow, Jennifer
• Format: Journal Article Book Review
• Language: English
• Published: New York Springer US 01.10.2015; Springer Nature B.V
• Subjects: Amino Acid Sequence - genetics; Animal Genetics and Genomics; Animals; Biomedical and Life Sciences; Cell Biology; Computational Biology - methods; Genome; Genomics; High-Throughput Nucleotide Sequencing; Human Genetics; Life Sciences; Mice; Mice, Inbred C57BL; Molecular Sequence Annotation; Pseudogenes - genetics; Sequence Alignment; Transcript Model; Manual Annotation; Coverage Graph; Computational Annotation; Annotation Project
• ISSN: 0938-8990; 1432-1777
• DOI: 10.1007/s00335-015-9583-x

Annotation on the reference genome of the C57BL6/J mouse has been an ongoing project ever since the draft genome was first published. Initially, the principle focus was on the identification of all protein-coding genes, although today the importance of describing long non-coding RNAs, small RNAs, and pseudogenes is recognized. Here, we describe the progress of the GENCODE mouse annotation project, which combines manual annotation from the HAVANA group with Ensembl computational annotation, alongside experimental and in silico validation pipelines from other members of the consortium. We discuss the more recent incorporation of next-generation sequencing datasets into this workflow, including the usage of mass-spectrometry data to potentially identify novel protein-coding genes. Finally, we will outline how the C57BL6/J genebuild can be used to gain insights into the variant sites that distinguish different mouse strains and species.