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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,*
doi:10.6620/ZS.2023.62-25
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 S1丨Table S2丨Table S3
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