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Bioinformatics. 2018 Feb 1;34(3):361-366. doi: 10.1093/bioinformatics/btx619.

The systematic analysis of ultraconserved genomic regions in the budding yeast.

Yang ZK1,2, Gao F1,3,4.

Author information

1
Department of Physics, Tianjin University, Tianjin 300072, China.
2
SinoGenoMax Co., Ltd./Chinese National Human Genome Center, Beijing 100176, China.
3
Key Laboratory of Systems Bioengineering (Ministry of Education).
4
SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, China.

Abstract

Motivation:

In the evolution of species, a kind of special sequences, termed ultraconserved sequences (UCSs), have been inherited without any change, which strongly suggests those sequences should be crucial for the species to survive or adapt to the environment. However, the UCSs are still regarded as mysterious genetic sequences so far. Here, we present a systematic study of ultraconserved genomic regions in the budding yeast based on the publicly available genome sequences, in order to reveal their relationship with the adaptability or fitness advantages of the budding yeast.

Results:

Our results indicate that, in addition to some fundamental biological functions, the UCSs play an important role in the adaptation of Saccharomyces cerevisiae to the acidic environment, which is backed up by the previous observation. Besides that, we also find the highly unchanged genes are enriched in some other pathways, such as the nutrient-sensitive signaling pathway. To facilitate the investigation of unique UCSs, the UCSC Genome Browser was utilized to visualize the chromosomal position and related annotations of UCSs in S.cerevisiae genome.

Availability and implementation:

For more details on UCSs, please refer to the Supplementary information online, and the custom code is available on request.

Contact:

fgao@tju.edu.cn.

Supplementary information:

Supplementary data are available at Bioinformatics online.

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