Gecko as reptilian 'model'
Since the era before our lab got its current shape at NIG in Mishima, one of our interests has been tracing vertebrate genome evolution. To facilitate unbiased comparisons, we have also worked on generating sequence data for underrepresented taxa, taking advantage of the technical expertise in sequence data production and analysis.
Here is a brief summary of our original genomic and transcriptomic resources for the Madagascar ground gecko (Paroedura picta).
Genome Assemblies
(Background details are documented on this page associated with the Squalomix consortium)
Latest: Ppicta_v3.0 (NCBI BioProject ID: GCF_049243985.1; released April 2025)
Chromosome-scale scaffolds generated using PacBio HiFi long reads, the iconHi-C protocol, and Bionano Saphyr optical mapping.
Publication:
Yamaguchi, K., Kadota, M., Nishimura, O., Ohishi, Y., Naito, Y., & Kuraku, S. (2021) Molecular Ecology, 30, 5923–5934.
Ppicta_v2.0 (Released September 2021)
Chromosome-scale scaffolds built with 10x Genomics Chromium Linked-Reads and the iconHi-C protocol.
First Version (Ppicta_v1.0)**
Scaffolds assembled using Illumina short reads and the iMate protocol.
Publication:
Hara, Y., Takeuchi, M., Kageyama, Y., Tatsumi, K., Hibi, M., Kiyonari, H., & Kuraku, S. (2018) BMC Biol. 16:40.
These assemblies can also be utilized via the guide RNA design tool CRISPRdirect (support for v3.0 is currently in preparation).
Transcriptomes
De novo assembly of RNA-seq reads using Illumina short-read platforms.
Publication:
Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation.
Hara, Y., Tatsumi, K., Yoshida, M., Kajikawa, E., Kiyonari, H., & Kuraku, S. (2015) BMC Genomics, 16:977.
(This paper also details our Core Vertebrate Genes (CVG) set for completeness assessment and discusses optimizing library insert lengths for short-read sequencing.)
All of these resources were made possible thanks to our lab members' dedication to both wet-lab techniques and bioinformatics. As a side note, for anyone working with live specimens, please be mindful of international ABS (Access and Benefit-Sharing) compliance.
