PCR primers

広島大学 > デジタル自然史博物館 > 植物 > コケ植物（蘚苔類） > 情報

Plants & Algae

chloroplast

• rbcL (atpB-rbcL-trnR-zfpA)
• rps4
• matK
• trnL-F
• psbA-trnH
• trnG(UCC) G2 intron
• rpoC1

nuclear

• 18S rRNA gene and ITS region

Fungi & Lichens

• ITS region and 28S rRNA gene (Fungi & Lichens)
• mt SSU (Fungi & Lichens)
• nr RPB2 gene (Fungi & Lichens)

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PCR primers

chloroplast

rbcL (atpB-rbcL-trnR-zfpA)

• rbcL

rps4–trnT–trnL–trnF

• rps4
• rps4–trnT–trnL–trnF

matK

Table. Primers used for PCR amplification and sequencing

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

Table. Primers used for PCR amplification and sequencing

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]

Table. Primers used for PCR amplification and sequencing

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

• psbA-trnH

trnG(UCC) G2 intron [trnG(UCC) G2 intron]

Table. Primers used for PCR amplification and sequencing

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

• 18S rRNA gene and ITS region

References

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• Nakahara, M., Handa, S., Watanabe, S. & Deguchi, H. 2004a. Choricystis minor as a new symbiont of simultaneous two-species association with Paramecium bursaria and implications for its phylogeny. Symbiosis 36: 127-151.
• 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.
• Olsson, S., Buchbender, V., Enroth, J., Hedenäs, L., Huttunen, S. & Quandt, D. 2009. Evolution of the Neckeraceae (Bryophyta): resolving the backbone phylogeny and identifying ancestral character states. Syst. Biodivers. 7: 419–432.
• Pacak, A. & Szweykowska-Kulińska, Z. 2000. Molecular data concerning the allopolyploid character and the origin of chloroplast and mitochondrial genomes in the liverwort species Pellia borealis. J. Plant Biotechnol. 2: 101–108.
• 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.
• Sang, T., Crawford, D. J. & Stuessy, T. F. 1997. Chloroplast DNA phylogeny, reticulate evolution, and biogeography of Paeonia (Paeoniaceae). Am. J. Bot. 84: 1120–1136.
• Souza-Chies, T. T., Bittar, G., Nadot, S., Carter, L., Besin, E. & Lejeune, B. 1997. Phylogenetic analysis of Iridaceae with parsimony and distance methods using the plastid gene rps4. Plant Syst. Evol. 204: 109–123.
• Taberlet, P., Gielly, L., Pautou, G. & Bouvet, J. 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol. Biol. 17: 1105-1109.
• Taberlet, P., Coissac, E., Pompanon, F., Gielly, L., Miquel, C., Valentini, A., Vermat, T., Corthier, G., Brochmann, C. & Willerslev, E. 2007. Power and limitations of the chloroplast trn L (UAA) intron for plant DNA barcoding. Nucl. Acids Res. 35(3): e14.
• Tate, J. A. & Simpson, B. B. 2003. Paraphyly of Tarasa (Malvaceae) and diverse origins of the polyploid species. Systematic Botany 28: 723-737.
• Tsubota, H., Nakao, N., Arikawa, T., Yamaguchi, T., Higuchi, M., Deguchi, H. & Seki, T. 1999. A preliminary phylogeny of Hypnales (Musci) as inferred from chloroplast rbcL sequence data. Bryol. Res. 7: 233-248.
• Tsubota, H., Nakao, N., Yamaguchi, T., Seki, T. & Deguchi, H. 2000. Preliminary phylogenetic relationships of the genus Brotherella and its allied genera (Hypnales, Musci) based on chloroplast rbcL sequence data. J. Hattori Bot. Lab. 88: 79-99. Abstract
• Tsubota, H., Akiyama, H., Yamaguchi, T. & Deguchi, H. 2001. Molecular phylogeny of the Sematophyllaceae (Hypnales, Musci) based on chloroplast rbcL sequences. J. Hattori Bot. Lab. 90: 221-240.
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• Werner, O., Patiño, J., González-Mancebo, J. M., Gabriel, R. M. A. & Ros, R. M. 2009. The taxonomic status and the geographical relationships of the Macaronesian endemic moss Fissidens luisieri (Fissidentaceae) based on DNA sequence data. Bryologist 112: 315–324.
• White, T. J., Bruns, T., Lee, S. & Taylor, J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In Innis, M. A., Gelfand, D. H., Sninskey, J. J. & White, T. J. (eds.), PCR Protocols: A Guide to Methods and Applications, pp. 315-322. Academic Press, Inc., San Diego.

関連ページ

• Primer
• PCR primers for plants and agae
  • rbcL (atpB-rbcL-trnR-zfpA)
  • rps4 (rps4-trnT-trnL-trnF)
  • matK
  • trnL-F
  • psbA-trnH
  • 18S rRNA gene and ITS region
• PCR primers for lichen
  • mrSSU

• UBC primers
• IUPAC/UBMB codes for nucleic acid bases [Nucleotide base codes (IUPAC)]
• Nucleotide base codes
• pyrimidine
• purine

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