PCR primers
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PCR primers
Plants & Algae
chloroplast
nuclear
Fungi & Lichens
- ITS region and 28S rRNA gene (Fungi & Lichens)
- mt SSU (Fungi & Lichens)
- nr RPB2 gene (Fungi & Lichens)
Bacteria
16S rRNA gene
Animal
mitochondria
PCR primers
chloroplast
rbcL (atpB-rbcL-trnR-zfpA)
rps4–trnT–trnL–trnF
matK
| Analyzed region | Forward / Reverse | Primer name | Sequence (5'–3') | References | For |
| trnK intron (including matK) | trnK [tRNA-Lys(UAA)exon1] | CCGACTAGTT CCGGGTTCGA | Demesure et al. (1995) | Bryophytes (Leucobryum, Oguri et al. 2013) | |
| trnK aF | ARWTTCATCC AAACCATTGA CAAGG | Oguri et al. (2013) | Bryophytes (Leucobryum, Oguri et al. 2013) | ||
| matK 410F | TATCAATCTA TTCATTCYGT ATTTCCTTTT | Oguri et al. (2013) | Bryophytes (Leucobryum, Oguri et al. 2013) | ||
| matK 410R | AAAAGGAAAT ACRGAATGAA TAGATTGATA | Oguri et al. (2013) | Bryophytes (Leucobryum, Oguri et al. 2013) | ||
| trnK aR | ATTGCACACG GCTTTCTCTA TGT | Oguri et al. (2013) | Bryophytes (Leucobryum, Oguri et al. 2013) | ||
| trnK [tRNA-Lys(UAA)exon2] | CAACGGTAGA GTACTCGGCT TTTA | Demesure et al. (1995) | Bryophytes (Leucobryum, Oguri et al. 2013) |
rpl16 G2 intron
| Analyzed region | Forward / Reverse | Primer name | Sequence (5'–3') | References | For |
| rpl16 G2 intron | Forward | F71 | GCTATGCTTAGTGTGTGACTCGTTG | Jordan et al. (1996) | Vascular plants, Bryophytes (Jordan et al. 1996, Olsson et al. 2009) |
| rpl16 G2 intron | Forward | F435 | CTCAAAAAGGTAAAGAGCCCTGAGT | Jordan et al. (1996) | Vascular plants (Jordan et al. 1996) |
| rpl16 G2 intron | Reverse | rpl16R | GTAATCCAAGCTGGTTCAAGTGC | Olsson et al. (2009) | Bryophytes (Olsson et al. 2009) |
| rpl16 G2 intron | Reverse | R1661 | CGTACCCATATTTTTCCACCACGAC | Jordan et al. (1996) | Vascular plants (Jordan et al. 1996) |
| rpl16 G2 intron | Reverse | R434 | CTCAGGGCTCTTTACCTTTTTGAGT | Jordan et al. (1996) | Vascular plants (Jordan et al. 1996) |
trnM-trnV [trnM-trnV intergenic region including trnV intron]
| Analyzed region | Forward / Reverse | Primer name | Sequence (5'–3') | References | For |
| trnM-trnV | Forward | trnMF | GCGATACTCTAAACCACTGAG | Werner et al. (2009) | Bryophytes (Werner et al. 2009) |
| trnM-trnV | Reverse | trnVR | TYGAACCGTAGACATTCTCGG | Werner et al. (2009) | Bryophytes (Werner et al. 2009) |
psbA-trnH
trnG(UCC) G2 intron [trnG(UCC) G2 intron]
| Analyzed region | Forward / Reverse | Primer name | Sequence (5'–3') | References | For |
| trnG(UCC) G2 intron | Forward | trnRUCU9Fi | CCTCTGTCCTATCCATTAGACG | Amamoto et al. (2022) | Bryophytes (Amamoto et al. 2022) |
| trnG(UCC) G2 intron | Forward | trnG–F | ACCCGCATCGTTAGCTTG | Pacak & Szweykowska–Kulińska (2000) | Bryophytes (Pacak & Szweykowska–Kulińska 2000) |
| trnG(UCC) G2 intron | Reverse | ycf12_18Ri | TGCACAGCTTACTGCTTTGG | Pacak & Szweykowska–Kulińska (2000) | Bryophytes (Pacak & Szweykowska–Kulińska 2000) |
| trnG(UCC) G2 intron | Reverse | trnG–R | GCGGGTATAGTTTAGTGG | Amamoto et al. (2022) | Bryophytes (Amamoto et al. 2022) |
nuclear
18S rRNA gene and ITS region
References
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- Masuzaki, H., Furuki, T., Dalton, P. J., Tsubota, H., Seppelt, R. D. & Deguchi, H. 2011. The phylogenetic position of Vandiemenia ratkowskiana (Metzgeriales, Marchantiophyta). Hikobia 16: 51–57.
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- Nakahara, M., Tsubota, H., Handa, S., Watanabe, S. & Deguchi, H. 2004b. Molecular phylogeny of Chlorella-like symbiotic algae in Paramecium bursaria based on 18S rRNA gene sequences. Hikobia 14: 129-142.
- Nakamura, H., Hongo, K., Matsuzaka, K., Nagasaki, R., Ikeda, S., Shioji, T., Shimizu, N. & Tsubota, H. 2022 (2023). Checklist of planted trees on the Higashi-hiroshima Campus of Hiroshima University, Hiroshima Prefecture, SW Japan. Bull. Hiroshima Univ. Museum 14: 75-92. (in Japanese) [中村 創・本郷圭祐・松坂啓佑・長﨑涼平・池田誠慈・塩路恒生・清水則雄・坪田博美. 2022 (2023). 広島大学東広島キャンパスの植栽樹木. 広島大学総合博物館研究報告 14: 75–92.]
- Nakamura, H., Koyama, Y., Phan, Q. C., Nakahara-Tsubota, M. & Tsubota, H. 2023. A note on vascular plants in Miyajima Island, Hiroshima Prefecture, SW Japan: Carpinus japonica and C. laxiflora (Betulaceae), and Lonicera affinis (Caprifoliaceae). Hikobia 19: 37-47. (in Japanese) [中村 創・小山克輝・ファン=クイン=チ・中原-坪田美保・坪田博美. 2023. 広島県宮島の維管束植物：1. クマシデ，アカシデ，ハマニンドウ. Hikobia 19(1): 37-47.]
- Newmaster, S. G. & Ragupathy, S. 2009. Testing plant barcoding in a sister species complex of pantropical Acacias (Mimosoideae, Fabaceae). Mol. Ecol. Resour. 9 (Suppl. 1): 172-180.
- Oguri, E., Yamaguchi, T., Tsubota, H. & Deguchi, H. 2003. A preliminary phylogenetic study of the genus Leucobryum (Leucobryaceae, Musci) in Asia and the Pacific based on ITS and rbcL sequences. Hikobia 14(1): 45-53.
- Oguri, E., Yamaguchi, T., Tsubota, H., Deguchi, H. & Murakami, N. 2013. Geographical origin of Leucobryum boninense Sull. & Lesq. (Leucobryaceae, Musci) endemic to the Bonin Islands, Japan. Ecol. Evol. 3(4): 753–762. DOI: 10.1002/ece3.492.
- Ohyama, K., Fukuzawa, H., Kohchi, T., Shirai, H., Sano, T., Sano, S., Umesono, K., Shiki, Y., Takeuchi, M., Chang, Z., Aota, S., Inokuchi, H. & Ozeki, H. 1986. Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature 322: 572-574.
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- Phan, Q. C., Nakahara-Tsubota, M., Inoue, Y. & Tsubota, H. 2021. New record of Dysphania pumilio (Amaranthaceae) for Hiroshima Prefecture, southwest Japan. Hikobia 18: 145-156.
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- Tsubota, H., Ikeda, S., Inoue, Y., Uchida, S. & Mukai, S. 2015b. Current status of Lysimachia sikokiana Miq. (Primulaceae) in Hiroshima Prefecture, SW Japan. Hikobia 17(1): 81-88. [坪田博美・池田誠慈・井上侑哉・内田慎治・向井誠二. 2015b. 広島県のモロコシソウLysimachia sikokiana Miq.の現状について. Hikobia 17(1): 81-88.]
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関連ページ
- UBC primers
- IUPAC/UBMB codes for nucleic acid bases [Nucleotide base codes (IUPAC)]
- Nucleotide base codes
- pyrimidine
- purine
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