IPARUS: Genomic Resources for the Parus genus

This website hosts the IPARUS (Integrated Platform for Parus Alignments, Resources and Useful Sequences) project, providing public access to genomic resources from birds of the Parus genus. The great tit (Parus major) is currently the most represented species, with data from other Parus species and subspecies potentially added in the future.

The platform provides sequence data and sample metadata, along with an embedded IGV browser for interactive genomic visualization, supporting research collaboration and open access to genomic data.

0 WGS Samples
0 SNP-Chip Samples
0 Locations
0 Publications

📜 References

  • Robinson, J. T., Turner, D., Durand, N. C., Thorvaldsdóttir, H., and Mesirov, J. P. 2023. igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV). Bioinformatics 39(1): btac830. View Article (DOI)

Bioinformatic Pipeline & Reference Genome

The bioinformatic pipeline to map the reads to the reference was the same as described in Chen et al. (2025). Briefly, the quality of the Illumina sequencing reads was assessed using FastQC v0.12.1 and trimmed using Trimmomatic v0.39 (Bolger et al. 2014). Trimmed reads were then aligned to the Parus major reference genome (GCF_001522545.3) with the BWA-MEM2 v2.2.1 algorithm (Li 2013) with default parameters. After converting SAM to BAM files and indexing with SAMtools v1.2 (Li et al. 2009) duplicated reads were marked using MarkDuplicatesSpark implemented in GATK v4.5.0 (Auwera and O’Connor 2020). This pipeline was developed and executed by Yu-Chi Chen during her PHD at the Gossmann lab. It is the same pipeline used in Chen et al. 2025.

📥 Download Reference Genome

You can download the Parus major reference genome from our database here:

⬇️ Download GCF_001522545.3
Bioinformatic Pipeline Diagram

📜 References

  • Auwera, G. A. V. der, and B. D. O’Connor. 2020. Genomics in the Cloud: Using Docker, GATK, and WDL in Terra. 1st ed. O’Reilly Media, Inc.
  • Bolger, A. M., M. Lohse, and B. Usadel. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120.
  • Chen, Y.-C., N. Vellnow, J. J. S. Wilcox, S. Javaheri Tehrani, and T. I. Gossmann. 2025. Opinion: Why Sex-Based Genomic Differentiation Should Not Be Overlooked in Population Genetics. Mol. Ecol. e70061.
  • Li, H. 2013. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv.
  • Li, H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin, and 1000 Genome Project Data Processing Subgroup. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078–2079.

List of publications in which the samples on this website were analyzed:

  • Opinion: Why Sex-Based Genomic Differentiation Should Not Be Overlooked in Population Genetics.
    Chen, Y.-C., Vellnow, N., Wilcox, J.J.S., Javaheri Tehrani, S., Gossmann, T.I. (2025) | Mol. Ecol. e70061
    View Article (DOI)
  • Comparative Genomics Reveals Evolution of a Beak Morphology Locus in a High-Altitude Songbird.
    Cheng, Y., Miller, M.J., Zhang, D., Song, G., Jia, C., Qu, Y., Lei, F. (2020) | Mol. Biol. Evol. 37, 2983–2988
    View Article (DOI)
  • Parallel genomic responses to historical climate change and high elevation in East Asian songbirds.
    Cheng, Y., Miller, M.J., Zhang, D., Xiong, Y., Hao, Y., Jia, C., Cai, T., Li, S.-H., Johansson, U.S., Liu, Y., Chang, Y., Song, G., Qu, Y., Lei, F. (2021) | Proc. Natl. Acad. Sci. 118, e2023918118
    View Article (DOI)
  • Determinants of the Efficacy of Natural Selection on Coding and Noncoding Variability in Two Passerine Species.
    Corcoran, P., Gossmann, T.I., Barton, H.J., The Great Tit HapMap Consortium, Slate, J., Zeng, K. (2017) | Genome Biol. Evol. 9, 2987–3007
    View Article (DOI)
  • Evolutionary signals of selection on cognition from the great tit genome and methylome.
    Laine, V.N., Gossmann, T.I., Schachtschneider, K.M., Garroway, C.J., Madsen, O., Verhoeven, K.J.F., de Jager, V., Megens, H.-J., Warren, W.C., Minx, P., Crooijmans, R.P.M.A., Corcoran, P., Sheldon, B.C., Slate, J., Zeng, K., van Oers, K., Visser, M.E., Groenen, M.A.M. (2016) | Nat. Commun. 7, 10474
    View Article (DOI)
  • Genetic responses to seasonal variation in altitudinal stress: whole-genome resequencing of great tit in eastern Himalayas.
    Qu, Y., Tian, S., Han, N., Zhao, H., Gao, B., Fu, J., Cheng, Y., Song, G., Ericson, P.G.P., Zhang, Y.E., Wang, D., Quan, Q., Jiang, Z., Li, R., Lei, F. (2015) | Sci. Rep. 5, 14256
    View Article (DOI)
  • Ground tit genome reveals avian adaptation to living at high altitudes in the Tibetan plateau.
    Qu, Y., Zhao, H., Han, N., Zhou, G., Song, G., Gao, B., Tian, S., Zhang, J., Zhang, R., Meng, X., Zhang, Yuan, Zhang, Yong, Zhu, X., Wang, W., Lambert, D., Ericson, P.G.P., Subramanian, S., Yeung, C., Zhu, H., Jiang, Z., Li, R., Lei, F. (2013) | Nat. Commun. 4, 2071
    View Article (DOI)

The IPARUS database and this website are maintained by the Gossmann lab at TU Dortmund University.

Prof. Dr. Toni Gossmann

Prof. Dr. Toni Gossmann

Principal Investigator
toni.gossmann@tu-dortmund.de
+49 231 755 6857
Nikolas Vellnow

Dr. Nikolas Vellnow

Scientific Coordinator
nikolas.vellnow@tu-dortmund.de
+49 231 755 6863
Mohammadmoein Hajihoseinigazestani

MSc. Moein Gazestani

Web Developer & Student Assistant
mohammadmoein.hajihoseinigazestani@tu-dortmund.de
+49 231 755 6863