IPARUS: Genomic Resources for the Parus genus

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

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. The scientific contact person and project coordinator is Nikolas Vellnow.

The web portal and technical implementation are developed by student assistant Mohammadmoein Hajihoseinigazestani (Moein Gazestani).