Zoological Studies

Vol. 62, 2023

(update: 2023.5.26)

Long-Read Genome Sequencing of Abscondita cerata (Coleoptera: Lampyridae), the Endemic Firefly of Taiwan

Tzi-Yuan Wang1, King-Siang Goh2, Liang-Jong Wang3, Li-Ling Wu4, Feng-Yu Wang3,*, and Yu-Wei Wu6,7,8,* 

1Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan. E-mail: tziyuan@gmail.com (TY Wang)
2Genomics Research Center, Academia Sinica, Taipei 115, Taiwan. E-mail: gohks0505@gmail.com (Goh)
3Forest Protection Division, Taiwan Forestry Research Institute, Taipei 100, Taiwan. E-mail: josephwang23@tfri.gov.tw (LJ Wang)
4Department and Institute of Physiology, College of Medicine, National Yang Ming Chiao Tung University, Taipei 112, Taiwan. E-mail: wuliling@nycu.edu.tw (LL Wu)
5Taiwan Ocean Research Institute, National Applied Research Laboratories, Kaohsiung 852, Taiwan. *Correspondence: E-mail: hitachiwang@gmail.com (FY Wang)
6Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei 106, Taiwan. *Correspondence: Email: yuwei.wu@tmu.edu.tw (YW Wu)
7Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei 235, Taiwan
8TMU Research Center for Digestive Medicine, Taipei Medical University Taipei 110, Taiwan

(Received 27 August 2022 / Accepted 17 February 2023 / Published -- 2023)
Communicated by Chih-Ming Hung

Abscondita cerata is the most abundant and widely distributed endemic firefly species in Taiwan and is considered a key environmental and ecological indicator organism. In this study, we report the first longread genome sequencing of Abs. cerata sequenced by Nanopore technology. The draft genome size, 967 Mb, was measured through a hybrid approach that consisted of assembling using 11.25-Gb Nanopore long reads and polishing using 9.47-Gb BGI PE100 short reads. The drafted genome was assembled into 4,855 contigs, with the N50 reaching 325.269 kb length. The assembled genome was predicted to possess 55,206 protein-coding genes, of which 20,862 (37.78%) were functionally annotated with public databases. 47.11% of the genome sequences consisted of repeat elements; among them DNA transposons accounted for the largest proportion (26.79%). A BUSCO (Benchmarking Universal Single Copy Orthologs) evaluation demonstrated that the genome and gene completeness were 84.8% and 79%, respectively. The phylogeny constructed using 1,792 single copy genes was consistent with previous studies. The comparative transcriptome between adult male head and lantern tissues revealed (1) the vision of Abs. cerata is primarily UV-sensitive to environmental twilight, which determines when it begins its nocturnal activity, (2) the major expressed OR56d receptor may be correlated to suitable humidity sensing, and (3) Luc1-type luciferase is responsible for Abs. cerata’s luminescent spectrum.

Key words: Nanopore, firefly, Lampyridae, Abscondita, Genome, Vision, Olfaction, Luciferase.

Citation: Wang TY, Goh KS, Wang LJ, Lee CM, Wu LL, Wang FY, Wu YW. 2023. Long-Read Genome Sequencing of Abscondita cerata (Coleoptera: Lampyridae), the endemic firefly of Taiwan. Zool Stud 62:25. doi:10.6620/ZS.2023.62-25. doi:10.6620/ZS.2023.62-25.

Supplementary materials: Table S1Table S2Table S3