DNA mini barcodes vs full-length barcodes of octocoral museum specimens: a case study of the Okinawa Churaumi Aquarium Zoological Collection
Hakim, A.A.; Ilechukwu, I.; Fourreau, C.J.L.; Nonaka, M.; Gösser, F.; Kajita, T.; Reimer, J.D. (2026). DNA mini barcodes vs full-length barcodes of octocoral museum specimens: a case study of the Okinawa Churaumi Aquarium Zoological Collection. Natural History Collections and Museomics 3: e188052. https://dx.doi.org/10.3897/nhcm.3.188052
In: Natural History Collections and Museomics. Pensoft Publishers: Sofia. ISSN 3033-0955, more
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| Keyword |
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| Author keywords |
ASAP, degraded DNA, mtMutS gene, novel primers, old specimens |
| Authors | | Top |
- Hakim, A.A.
- Ilechukwu, I.
- Fourreau, C.J.L.
- Nonaka, M.
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- Gösser, F.
- Kajita, T.
- Reimer, J.D.
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| Abstract |
Octocorals are noted for their high diversity, with the identification of species and sometimes even genera often difficult based solely on morphological characteristics. Thus, many recent studies have employed DNA barcoding techniques to acquire diversity data. There are many octocoral specimens already deposited within zoological collections that could provide potentially important taxonomic and historical information, but due to their age, often the DNA contained in such specimens has degraded severely. One potential approach to overcome this issue is DNA mini barcoding, amplifying a shorter subset of the original barcode region. This study aimed to utilize a mini barcoding method using novel octocoral-specific primers for validating octocoral species from the Okinawa Churaumi Aquarium Zoological Collection, with specimens dating back to 1982. Based on in silico evaluations using reference sequence data including nucleotide variations and match ratio values of species delimitations, using newly designed primers, mini barcodes performed as well as full-length barcodes. Subsequently, mini barcodes were generated by these novel primers, amplifying a 215 base pairs (bp) fragment of the mitochondrial MutS-like protein (mtMutS), successfully amplifying 92.7% of 166 specimens, and sequences could be used to identify to genus level, while full-length barcoding primers amplified only 45.8% of specimens. Moreover, mini barcodes identified 67 different operational taxonomic units (OTUs) of octocorals within the specimens based on the species delimitation method of Assemble Species by Automatic Partitioning (ASAP) and unique sequences. With most octocoral specimens from the Okinawa Churaumi Aquarium Zoological Collection identified only to genus level, these additional molecular data were significantly beneficial in identifying specimens. Our study shows this DNA mini barcoding approach can cheaply and quickly acquire molecular data from comparatively older octocoral specimens, helping to identify such specimens, and adding further value to historical museum specimen collections. |
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