「PCR primers nr 18SrRNA ITSs」の版間の差分
提供: 広島大学デジタル博物館
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1行目: | 1行目: | ||
− | <span style="font-size:10">[ | + | <span style="font-size:10">[https://www.hiroshima-u.ac.jp/index-j.html 広島大学] > [https://www.digital-museum.hiroshima-u.ac.jp/~museum/ デジタル自然史博物館] > [https://www.digital-museum.hiroshima-u.ac.jp/~museum/plant/ 植物] > [[コケ|コケ植物(蘚苔類)]] > [[コケ/情報|情報]]</span> |
= [[PCR_primers|PCR primers]] = | = [[PCR_primers|PCR primers]] = | ||
== nuclear == | == nuclear == | ||
− | === 18S rRNA gene and ITS region === | + | === 18S rRNA gene and [[ITS]] region === |
{| class="wikitable" style="width:90%; margin:0 2em 0 2em; background-color:#d1d1a5; text-align:left" | {| class="wikitable" style="width:90%; margin:0 2em 0 2em; background-color:#d1d1a5; text-align:left" | ||
− | |+ style="text-align:left" | Table. Primers used for PCR amplification and sequencing | + | |+ style="text-align:left" | Table. Primers used for PCR amplification and sequencing of the nr 18S rRNA gene and ITS regions. The numbers within the primer name correspond to positions in the 18S rRNA gene of [http://getentry.ddbj.nig.ac.jp/getentry/na/X13688/?format=flatfile&filetype=html&trace=true&show_suppressed=false&limit=10 ''Chlorella vulgaris'' (X13688)] and the 5.8S rRNA gene of [http://getentry.ddbj.nig.ac.jp/getentry/na/AB004866/?format=flatfile&filetype=html&trace=true&show_suppressed=false&limit=10 ''Chlamydomonas tetragama'' (AB004866).] |
|- | |- | ||
| Analyzed region | | Analyzed region | ||
18行目: | 18行目: | ||
| 18SPrimer A | | 18SPrimer A | ||
| <tt>CCGAATTCGT CGACAACCTG GTTGATCCTG CCAGT</tt> | | <tt>CCGAATTCGT CGACAACCTG GTTGATCCTG CCAGT</tt> | ||
− | | Medlin et al. (1988) | + | | [[Medlin_Elwood_Stickel_Sogin_1988|Medlin et al. (1988)]] |
| Algae (''Stichococcus'' etc.) | | Algae (''Stichococcus'' etc.) | ||
|- | |- | ||
25行目: | 25行目: | ||
| 18S1Fh | | 18S1Fh | ||
| <tt>AACCTGGTTG ATCCTGCC</tt> | | <tt>AACCTGGTTG ATCCTGCC</tt> | ||
− | | Nakahara et al. ( | + | | [[Nakahara_Handa_Watanabe_Deguchi_2004|Nakahara et al. (2004a)]] |
− | | Algae, Vascular plants (''Lactuca'' etc.) | + | | Algae, Vascular plants (''Lactuca'', ''Sisymbrium'' etc.) |
|- | |- | ||
| 18S rRNA gene | | 18S rRNA gene | ||
32行目: | 32行目: | ||
| 18S2Fh | | 18S2Fh | ||
| <tt>GTTGATCCTG CCAGTAGTCA</tt> | | <tt>GTTGATCCTG CCAGTAGTCA</tt> | ||
− | | Nakahara et al. ( | + | | [[Nakahara_Handa_Watanabe_Deguchi_2004|Nakahara et al. (2004a)]] |
| Algae | | Algae | ||
|- | |- | ||
39行目: | 39行目: | ||
| 18SNS1 | | 18SNS1 | ||
| <tt>GTAGTCATAT GCTTGTCTC</tt> | | <tt>GTAGTCATAT GCTTGTCTC</tt> | ||
− | | White et al. (1990); Kocher & White (1992) | + | | [[White_et_al_1990|White et al. (1990)]]; [[Kocher_White_1992|Kocher & White (1992)]] |
| Fungi, Algae (''Stichococcus'' etc.), Vascular plants (''Lactuca'' etc.) | | Fungi, Algae (''Stichococcus'' etc.), Vascular plants (''Lactuca'' etc.) | ||
+ | |- | ||
+ | | 18S rRNA gene | ||
+ | | Forward | ||
+ | | 18S156 | ||
+ | | <tt>TCTAGAGCTA ATACGTGCG</tt> | ||
+ | | [[Nakahara_Tsubota_Handa_Watanabe_Deguchi_2004|Nakahara et al. (2004b)]] | ||
+ | | Algae | ||
+ | |- | ||
+ | | 18S rRNA gene | ||
+ | | Forward | ||
+ | | 18S325R | ||
+ | | <tt>CTGCCCTATC AACTTTCG</tt> | ||
+ | | [[Nakahara_Tsubota_Handa_Watanabe_Deguchi_2004|Nakahara et al. (2004b)]] | ||
+ | | Algae ([http://getentry.ddbj.nig.ac.jp/getentry/na/AB191205/?format=flatfile&filetype=html&trace=true&show_suppressed=false&limit=10 ''Chlorella''] etc.) | ||
|- | |- | ||
| 18S rRNA gene | | 18S rRNA gene | ||
46行目: | 60行目: | ||
| 18S323 | | 18S323 | ||
| <tt>CGATGGTAGG ATAGAGG</tt> | | <tt>CGATGGTAGG ATAGAGG</tt> | ||
− | | Handa et al. (2003) | + | | [[Handa_et_al_2003|Handa et al. (2003)]] |
| Algae (''Stichococcus'' etc.) | | Algae (''Stichococcus'' etc.) | ||
|- | |- | ||
53行目: | 67行目: | ||
| 18S410 | | 18S410 | ||
| <tt>CCACATCCAA GGAAGGCAGC</tt> | | <tt>CCACATCCAA GGAAGGCAGC</tt> | ||
− | | Handa et al. (2003) | + | | [[Handa_et_al_2003|Handa et al. (2003)]] |
− | | Algae (''Stichococcus'' etc.), Vascular plants (''Lactuca'' etc.) | + | | Algae (''Stichococcus'' etc.), Vascular plants (''Lactuca'', ''Sisymbrium'' etc.) |
|- | |- | ||
| 18S rRNA gene | | 18S rRNA gene | ||
60行目: | 74行目: | ||
| 18S575 | | 18S575 | ||
| <tt>CGGTAATTCC AGCTCCA</tt> | | <tt>CGGTAATTCC AGCTCCA</tt> | ||
− | | Handa et al. (2003 | + | | [[Handa_et_al_2003|Handa et al. (2003)]] |
| Algae (''Stichococcus'' etc.), Vascular plants (''Lactuca'' etc.) | | Algae (''Stichococcus'' etc.), Vascular plants (''Lactuca'' etc.) | ||
+ | |- | ||
+ | | 18S rRNA gene | ||
+ | | Forward | ||
+ | | 18S578 | ||
+ | | <tt>CCAGCTCCAA TAGCGTATAT TT</tt> | ||
+ | | [[Nakahara_Tsubota_Handa_Watanabe_Deguchi_2004|Nakahara et al. (2004b)]] | ||
+ | | Algae | ||
|- | |- | ||
| 18S rRNA gene | | 18S rRNA gene | ||
67行目: | 88行目: | ||
| 18S705 | | 18S705 | ||
| <tt>GGCTCCTGGG CTTCACTG</tt> | | <tt>GGCTCCTGGG CTTCACTG</tt> | ||
− | | Handa et al. (2003) | + | | [[Handa_et_al_2003|Handa et al. (2003)]] |
| Algae (''Stichococcus'' etc.) | | Algae (''Stichococcus'' etc.) | ||
+ | |- | ||
+ | | 18S rRNA gene | ||
+ | | Forward | ||
+ | | 18S791 | ||
+ | | <tt>AGCATGGGAT AACACGATAG GA</tt> | ||
+ | | [[Nakahara_Tsubota_Handa_Watanabe_Deguchi_2004|Nakahara et al. (2004b)]] | ||
+ | | Algae | ||
|- | |- | ||
| 18S rRNA gene | | 18S rRNA gene | ||
74行目: | 102行目: | ||
| 18S921 | | 18S921 | ||
| <tt>GAAAGACGAA CTACTGCGA</tt> | | <tt>GAAAGACGAA CTACTGCGA</tt> | ||
− | | Handa et al. (2003) | + | | [[Handa_et_al_2003|Handa et al. (2003)]] |
− | | Algae (''Stichococcus'' etc.), Vascular plants (''Lactuca'' etc.) | + | | Algae (''Stichococcus'' etc.), Vascular plants (''Lactuca'', ''Sisymbrium'' etc.) |
|- | |- | ||
| 18S rRNA gene | | 18S rRNA gene | ||
81行目: | 109行目: | ||
| 18S1171 | | 18S1171 | ||
| <tt>GCTTAATTTG ACTCAACAC</tt> | | <tt>GCTTAATTTG ACTCAACAC</tt> | ||
− | | Tsubota et al. (2012) | + | | [[Tsubota_Kubo_Takeuchi_Nakahara-Tsubota_Inoue_Uchida_Mukai_2012|Tsubota et al. (2012)]] |
| Algae, Vascular plants (''Lactuca'' etc.) | | Algae, Vascular plants (''Lactuca'' etc.) | ||
|- | |- | ||
88行目: | 116行目: | ||
| 18S1208 | | 18S1208 | ||
| <tt>TACCAGGTCC AGACATAGTG AGG</tt> | | <tt>TACCAGGTCC AGACATAGTG AGG</tt> | ||
− | | Handa et al. (2003) | + | | [[Handa_et_al_2003|Handa et al. (2003)]] |
| Algae (''Stichococcus'' etc.) | | Algae (''Stichococcus'' etc.) | ||
|- | |- | ||
95行目: | 123行目: | ||
| 18S1288 | | 18S1288 | ||
| <tt>TGGGTTGCCT TGTCA</tt> | | <tt>TGGGTTGCCT TGTCA</tt> | ||
− | | Nakahara et al. ( | + | | [[Nakahara_Handa_Watanabe_Deguchi_2004|Nakahara et al. (2004a)]] |
| Algae | | Algae | ||
|- | |- | ||
102行目: | 130行目: | ||
| 18S1307 | | 18S1307 | ||
| <tt>ACGAGACCTC AGCCTGCT</tt> | | <tt>ACGAGACCTC AGCCTGCT</tt> | ||
− | | Nakahara et al. ( | + | | [[Nakahara_Handa_Watanabe_Deguchi_2004|Nakahara et al. (2004a)]] |
| Algae | | Algae | ||
|- | |- | ||
109行目: | 137行目: | ||
| 18S1421 | | 18S1421 | ||
| <tt>CAGGTCTGTG ATGCCCTTAG A</tt> | | <tt>CAGGTCTGTG ATGCCCTTAG A</tt> | ||
− | | Nakahara et al. ( | + | | [[Nakahara_Handa_Watanabe_Deguchi_2004|Nakahara et al. (2004a)]] |
− | | Algae, Vascular plants (''Lactuca'' etc.) | + | | Algae, Vascular plants (''Lactuca'', ''Sisymbrium'' etc.) |
+ | |- | ||
+ | | 18S rRNA gene | ||
+ | | Forward | ||
+ | | 18S1560 | ||
+ | | <tt>GCGTTGATTA CGT</tt> | ||
+ | | [[Nakahara_Tsubota_Handa_Watanabe_Deguchi_2004|Nakahara et al. (2004b)]] | ||
+ | | Algae | ||
|- | |- | ||
| ITS | | ITS | ||
116行目: | 151行目: | ||
| 18S1659B | | 18S1659B | ||
| <tt>CGTCGCTCCT ACCGATTG</tt> | | <tt>CGTCGCTCCT ACCGATTG</tt> | ||
− | | Oguri et al. (2003) | + | | [[Oguri_Yamaguchi_Tsubota_Deguchi_2003|Oguri et al. (2003)]] |
− | | Bryophytes (''Leucobryum'' etc.), Vascular plants (''Halophila'', ''Lactuca'' etc.) | + | | Bryophytes (''Leucobryum'' etc.), Vascular plants (''Halophila'', ''Lactuca'', ''Sisymbrium'' etc.) |
|- | |- | ||
| ITS | | ITS | ||
123行目: | 158行目: | ||
| 18S1764B | | 18S1764B | ||
| <tt>AGAGGAAGGA GAAGTCGTAA C</tt> | | <tt>AGAGGAAGGA GAAGTCGTAA C</tt> | ||
− | | Oguri et al. (2003) | + | | [[Oguri_Yamaguchi_Tsubota_Deguchi_2003|Oguri et al. (2003)]] |
− | | Bryophytes (''Leucobryum'' etc.), Vascular plants (''Halophila'', ''Lactuca'' etc.) | + | | Bryophytes (''Leucobryum'' etc.), Vascular plants (''Halophila'', ''Lactuca'', ''Sisymbrium'' etc.) |
|- | |- | ||
| ITS | | ITS | ||
130行目: | 165行目: | ||
| 18SrDNAHTF1 | | 18SrDNAHTF1 | ||
| <tt>AAGGTTTCCG TAGGTGAACC TGC</tt> | | <tt>AAGGTTTCCG TAGGTGAACC TGC</tt> | ||
− | | Tsubota et al. (2012) | + | | [[Tsubota_Kubo_Takeuchi_Nakahara-Tsubota_Inoue_Uchida_Mukai_2012|Tsubota et al. (2012)]] |
− | | Vascular plants (''Lactuca'' etc.) | + | | Vascular plants (''Lactuca'', ''Sisymbrium'' etc.) |
|- | |- | ||
| ITS | | ITS | ||
137行目: | 172行目: | ||
| 18srRNA | | 18srRNA | ||
| <tt>TCCGTAGGTG AACCTGCGG</tt> | | <tt>TCCGTAGGTG AACCTGCGG</tt> | ||
− | | Oguri et al. (2003) | + | | [[Oguri_Yamaguchi_Tsubota_Deguchi_2003|Oguri et al. (2003)]] |
− | | Bryophytes (''Leucobryum'' etc.), Vascular plants (''Halophila'' etc.) | + | | Bryophytes (''Leucobryum'' etc.), Vascular plants (''Halophila'', ''Sisymbrium'' etc.) |
|- | |- | ||
| ITS | | ITS | ||
144行目: | 179行目: | ||
| 5.8S10B | | 5.8S10B | ||
| <tt>CTCAGCAACG GATATCTTGG</tt> | | <tt>CTCAGCAACG GATATCTTGG</tt> | ||
− | | Oguri et al. (2003) | + | | [[Oguri_Yamaguchi_Tsubota_Deguchi_2003|Oguri et al. (2003)]] |
| Bryophytes (''Leucobryum'' etc.), Vascular plants (''Halophila'' etc.) | | Bryophytes (''Leucobryum'' etc.), Vascular plants (''Halophila'' etc.) | ||
|- | |- | ||
151行目: | 186行目: | ||
| 5srRNA | | 5srRNA | ||
| <tt>ACGATGAAGA ACGCAGCG</tt> | | <tt>ACGATGAAGA ACGCAGCG</tt> | ||
− | | Oguri et al. (2003) | + | | [[Oguri_Yamaguchi_Tsubota_Deguchi_2003|Oguri et al. (2003)]] |
| Bryophytes (''Leucobryum'' etc.), Vascular plants (''Halophila'' etc.) | | Bryophytes (''Leucobryum'' etc.), Vascular plants (''Halophila'' etc.) | ||
|- | |- | ||
158行目: | 193行目: | ||
| 5.8S43H | | 5.8S43H | ||
| <tt>GAAGAACGTA GCGAAATGCG A</tt> | | <tt>GAAGAACGTA GCGAAATGCG A</tt> | ||
− | | Tsubota et al. (2009) | + | | [[Tsubota_Kubo_Mukai_2009|Tsubota et al. (2009)]] |
− | | Vascular plants (''Halophila'', ''Lactuca'' etc.) | + | | Vascular plants (''Halophila'', ''Lactuca'', ''Sisymbrium'' etc.) |
|- | |- | ||
| ITS | | ITS | ||
165行目: | 200行目: | ||
| 5.8S51HV | | 5.8S51HV | ||
| <tt>TAGCGAAATG CGATACTTGG</tt> | | <tt>TAGCGAAATG CGATACTTGG</tt> | ||
− | | Tsubota et al. (2013) | + | | [[坪田・久保・大野・井上・中原-坪田・武内・松井・内田・向井_2013|Tsubota et al. (2013)]] |
| Vascular plants (''Sisymbrium'' etc.) | | Vascular plants (''Sisymbrium'' etc.) | ||
|- | |- | ||
172行目: | 207行目: | ||
| 5.8S114HV | | 5.8S114HV | ||
| <tt>AGTTGCGCCC GAAGC</tt> | | <tt>AGTTGCGCCC GAAGC</tt> | ||
− | | Tsubota et al. (2013) | + | | [[坪田・久保・大野・井上・中原-坪田・武内・松井・内田・向井_2013|Tsubota et al. (2013)]] |
| Vascular plants (''Sisymbrium'' etc.) | | Vascular plants (''Sisymbrium'' etc.) | ||
|- | |- | ||
186行目: | 221行目: | ||
| 26S166BR | | 26S166BR | ||
| <tt>GAGGACGCTT CTCCAGACTA C</tt> | | <tt>GAGGACGCTT CTCCAGACTA C</tt> | ||
− | | Oguri et al. (2003) | + | | [[Oguri_Yamaguchi_Tsubota_Deguchi_2003|Oguri et al. (2003)]] |
− | | Bryophytes (''Leucobryum'' etc.), Vascular plants (''Halophila'', ''Lactuca'' etc.) | + | | Bryophytes (''Leucobryum'' etc.), Vascular plants (''Halophila'', ''Lactuca'', ''Sisymbrium'' etc.) |
|- | |- | ||
| ITS | | ITS | ||
193行目: | 228行目: | ||
| 26S102BR | | 26S102BR | ||
| <tt>CCGGTTCGCT CGCCG</tt> | | <tt>CCGGTTCGCT CGCCG</tt> | ||
− | | Oguri et al. (2003) | + | | [[Oguri_Yamaguchi_Tsubota_Deguchi_2003|Oguri et al. (2003)]] |
− | | Bryophytes (''Leucobryum'' etc.), Vascular plants (''Halophila'', ''Lactuca'' etc.) | + | | Bryophytes (''Leucobryum'' etc.), Vascular plants (''Halophila'', ''Lactuca'', ''Sisymbrium'' etc.) |
|- | |- | ||
| ITS | | ITS | ||
| Reverse | | Reverse | ||
− | | | + | | 26SrDNAHTR1 |
− | | <tt> | + | | <tt>AAGGGAATCC TTGTAAGTTT CT</tt> |
− | | | + | | [[Tsubota_Kubo_Takeuchi_Nakahara-Tsubota_Inoue_Uchida_Mukai_2012|Tsubota et al. (2012)]] |
− | | | + | | Vascular plants (''Lactuca'', ''Sisymbrium'' etc.) |
|- | |- | ||
| ITS | | ITS | ||
| Reverse | | Reverse | ||
− | | | + | | 26SrDNAHTR2 |
− | | <tt></tt> | + | | <tt>AAGTTTCTTT TCCTCCGCTT A</tt> |
− | | Tsubota et al. (2012) | + | | [[Tsubota_Kubo_Takeuchi_Nakahara-Tsubota_Inoue_Uchida_Mukai_2012|Tsubota et al. (2012)]] |
− | | Vascular plants (''Lactuca'' etc.) | + | | Vascular plants (''Lactuca'', ''Sisymbrium'' etc.) |
|- | |- | ||
| ITS | | ITS | ||
| Reverse | | Reverse | ||
− | | | + | | 25srRNA |
− | | <tt> | + | | <tt>TCCTCCGCTT AGTGATATGC</tt> |
− | | | + | | [[Oguri_Yamaguchi_Tsubota_Deguchi_2003|Oguri et al. (2003)]] |
− | | Vascular plants ('' | + | | Bryophytes (''Leucobryum'' etc.), Vascular plants (''Halophila'', ''Sisymbrium'' etc.) |
|- | |- | ||
| ITS | | ITS | ||
221行目: | 256行目: | ||
| 5.8S124HR | | 5.8S124HR | ||
| <tt>CGGGCGCAAC TTGCGTTCA</tt> | | <tt>CGGGCGCAAC TTGCGTTCA</tt> | ||
− | | | + | | [[Tsubota_Kubo_Mukai_2009|Tsubota et al. (2009)]] |
− | | Vascular plants (''Halophila'', ''Lactuca'' etc.) | + | | Vascular plants (''Halophila'', ''Lactuca'', ''Sisymbrium'' etc.) |
|- | |- | ||
| ITS | | ITS | ||
228行目: | 263行目: | ||
| 5.8S102BR | | 5.8S102BR | ||
| <tt>ACTCGATGAT TCGCGGA</tt> | | <tt>ACTCGATGAT TCGCGGA</tt> | ||
− | | Oguri et al. (2003) | + | | [[Oguri_Yamaguchi_Tsubota_Deguchi_2003|Oguri et al. (2003)]] |
| Bryophytes (''Leucobryum'' etc.), Vascular plants (''Halophila'' etc.) | | Bryophytes (''Leucobryum'' etc.), Vascular plants (''Halophila'' etc.) | ||
|- | |- | ||
− | | | + | | 18S rRNA gene |
+ | | Reverse | ||
+ | | 5.8SR–2 | ||
+ | | <tt>ACTACGTATC GCATTTCGCT</tt> | ||
+ | | [[Nakahara_Tsubota_Handa_Watanabe_Deguchi_2004|Nakahara et al. (2004b)]] | ||
+ | | Algae | ||
+ | |- | ||
+ | | 18S rRNA gene | ||
| Reverse | | Reverse | ||
− | | | + | | 5.8SR–3 |
− | | <tt> | + | | <tt>CATTTCGCTG CGTTCTTCAT</tt> |
− | | | + | | [[Nakahara_Tsubota_Handa_Watanabe_Deguchi_2004|Nakahara et al. (2004b)]] |
− | | Algae | + | | Algae |
|- | |- | ||
| 18S rRNA gene & ITS | | 18S rRNA gene & ITS | ||
| Reverse | | Reverse | ||
| 5.8SR-1 | | 5.8SR-1 | ||
− | | <tt></tt> | + | | <tt>GTATCGCATT TCGCTGCGTT CTTCATCG</tt> |
− | | Handa et al. (2003) | + | | [[Handa_Nakahara_Tsubota_Deguchi_Nakano_2003|Handa et al. (2003)]] |
| Algae (''Stichococcus'' etc.) | | Algae (''Stichococcus'' etc.) | ||
|- | |- | ||
249行目: | 291行目: | ||
| 5srRNAR | | 5srRNAR | ||
| <tt>CGCTGCGTTC TTCATCGT</tt> | | <tt>CGCTGCGTTC TTCATCGT</tt> | ||
− | | Handa et al. (2003) | + | | [[Handa_Nakahara_Tsubota_Deguchi_Nakano_2003|Handa et al. (2003)]]; [[Oguri_Yamaguchi_Tsubota_Deguchi_2003|Oguri et al. (2003)]] |
− | | Algae (''Stichococcus'' etc.) | + | | Algae (''Stichococcus'' etc.), Bryophytes (''Leucobryum'' etc.), Vascular plants (''Halophila'', ''Sisymbrium'' etc.) |
|- | |- | ||
| 18S rRNA gene | | 18S rRNA gene | ||
256行目: | 298行目: | ||
| 18Sprimer B | | 18Sprimer B | ||
| <tt>CCCGGGATCC AAGCTTGATC CTTCTGCAGG TTCACCTAC</tt> | | <tt>CCCGGGATCC AAGCTTGATC CTTCTGCAGG TTCACCTAC</tt> | ||
− | | Medlin et al. (1988) | + | | [[Medlin_Elwood_Stickel_Sogin_1988|Medlin et al. (1988)]] |
| Algae (''Stichococcus'' etc.) | | Algae (''Stichococcus'' etc.) | ||
|- | |- | ||
263行目: | 305行目: | ||
| 18S3Rh | | 18S3Rh | ||
| <tt>TGATCCTTCT GCAGGTTC</tt> | | <tt>TGATCCTTCT GCAGGTTC</tt> | ||
− | | Nakahara et al. ( | + | |[[Nakahara_Handa_Watanabe_Deguchi_2004|Nakahara et al. (2004a)]] |
− | | Algae, Vascular plants (''Lactuca'' etc.) | + | | Algae, Vascular plants (''Lactuca'', ''Sisymbrium'' etc.) |
|- | |- | ||
| 18S rRNA gene | | 18S rRNA gene | ||
270行目: | 312行目: | ||
| 18S4Rh | | 18S4Rh | ||
| <tt>CTGCAGGTTC ACCTACGGA</tt> | | <tt>CTGCAGGTTC ACCTACGGA</tt> | ||
− | | Nakahara et al. ( | + | |[[Nakahara_Handa_Watanabe_Deguchi_2004|Nakahara et al. (2004a)]] |
+ | | Algae | ||
+ | |- | ||
+ | | 18S rRNA gene | ||
+ | | Reverse | ||
+ | | 18S1747R | ||
+ | | <tt>CTCCTTCCTC TAGGTGGGA</tt> | ||
+ | | [[Nakahara_Tsubota_Handa_Watanabe_Deguchi_2004|Nakahara et al. (2004b)]] | ||
| Algae | | Algae | ||
|- | |- | ||
277行目: | 326行目: | ||
| 18S1617R | | 18S1617R | ||
| <tt>CAGGGACGTA ATCAACGC</tt> | | <tt>CAGGGACGTA ATCAACGC</tt> | ||
− | | Handa et al. (2003) | + | | [[Handa_Nakahara_Tsubota_Deguchi_Nakano_2003|Handa et al. (2003)]] |
| Algae (''Stichococcus'' etc.), Vascular plants (''Lactuca'' etc.) | | Algae (''Stichococcus'' etc.), Vascular plants (''Lactuca'' etc.) | ||
|- | |- | ||
284行目: | 333行目: | ||
| 18S1442R | | 18S1442R | ||
| <tt>TCTAAGGGCA TCACAGAC</tt> | | <tt>TCTAAGGGCA TCACAGAC</tt> | ||
− | | Handa et al. (2003) | + | | [[Handa_Nakahara_Tsubota_Deguchi_Nakano_2003|Handa et al. (2003)]] |
− | | Algae (''Stichococcus'' etc.), Vascular plants (''Lactuca'' etc.) | + | | Algae (''Stichococcus'' etc.), Vascular plants (''Lactuca'', ''Sisymbrium'' etc.) |
+ | |- | ||
+ | | 18S rRNA gene | ||
+ | | Reverse | ||
+ | | 18S1317R | ||
+ | | <tt>TTACCGGAAT CAACCTGACA AGGCAAC</tt> | ||
+ | | [[Nakahara_Tsubota_Handa_Watanabe_Deguchi_2004|Nakahara et al. (2004b)]] | ||
+ | | Algae | ||
|- | |- | ||
| 18S rRNA gene | | 18S rRNA gene | ||
291行目: | 347行目: | ||
| 18S1125R | | 18S1125R | ||
| <tt>CAGCCTTGCG ACCATACTCC</tt> | | <tt>CAGCCTTGCG ACCATACTCC</tt> | ||
− | | Handa et al. (2003) | + | | [[Handa_Nakahara_Tsubota_Deguchi_Nakano_2003|Handa et al. (2003)]] |
| Algae (''Stichococcus'' etc.) | | Algae (''Stichococcus'' etc.) | ||
|- | |- | ||
298行目: | 354行目: | ||
| 18S909R | | 18S909R | ||
| <tt>CCAAGAATTT CACCTCTGAC</tt> | | <tt>CCAAGAATTT CACCTCTGAC</tt> | ||
− | | Handa et al. (2003) | + | | [[Handa_Nakahara_Tsubota_Deguchi_Nakano_2003|Handa et al. (2003)]] |
− | | Algae (''Stichococcus'' etc.), Vascular plants (''Lactuca'' etc.) | + | | Algae (''Stichococcus'' etc.), Vascular plants (''Lactuca'', ''Sisymbrium'' etc.) |
|- | |- | ||
| 18S rRNA gene | | 18S rRNA gene | ||
305行目: | 361行目: | ||
| 18SNS2 | | 18SNS2 | ||
| <tt>GGCTGCTGGC ACCAGACTTG C</tt> | | <tt>GGCTGCTGGC ACCAGACTTG C</tt> | ||
− | | White et al. (1990); Kocher & White (1992) | + | | [[White_et_al_1990|White et al. (1990)]]; [[Kocher_White_1992|Kocher & White (1992)]] |
− | | Fungi, Algae (''Stichococcus'' etc.), Vascular plants (''Lactuca'' etc.) | + | | Fungi, Algae (''Stichococcus'' etc.), Vascular plants (''Lactuca'', ''Sisymbrium'' etc.) |
|- | |- | ||
| 18S rRNA gene | | 18S rRNA gene | ||
| Reverse | | Reverse | ||
− | | 18S325R++ | + | | 18S325R++<ref name="chu1">[[Tsubota_Kubo_Takeuchi_Nakahara-Tsubota_Inoue_Uchida_Mukai_2012|坪田ほか(2012)]]では表中で初出となっているが,実際には[[Nakahara_Tsubota_Handa_Watanabe_Deguchi_2004|Nakahara et al.(2004b)]]が初出.</ref><ref name="chu2">The first appearance of this primer was not in Table 1 of [[Tsubota_Kubo_Takeuchi_Nakahara-Tsubota_Inoue_Uchida_Mukai_2012|Tsubota et al. (2012)]] but in Table 2 of [[Nakahara_Tsubota_Handa_Watanabe_Deguchi_2004|Nakahara et al. (2004b)]].</ref> |
| <tt>CGAAAGTTGA TAGGGCAG</tt> | | <tt>CGAAAGTTGA TAGGGCAG</tt> | ||
− | | Tsubota et al. (2012) | + | | [[Nakahara_Tsubota_Handa_Watanabe_Deguchi_2004|Nakahara et al. (2004b)]]; [[Tsubota_Kubo_Takeuchi_Nakahara-Tsubota_Inoue_Uchida_Mukai_2012|Tsubota et al. (2012)]] |
| Algae, Vascular plants (''Lactuca'' etc.) | | Algae, Vascular plants (''Lactuca'' etc.) | ||
|} | |} | ||
− | == | + | == 脚注 == |
− | + | {{Reflist|1}} | |
− | + | ||
− | + | =[[テンプレート:PCR_primers_References|References]]= | |
+ | {{PCR_primers_References}} | ||
+ | ==[[テンプレート:primers|関連ページ]]== | ||
+ | {{primers}} | ||
---- | ---- | ||
− | [ | + | [https://www.digital-museum.hiroshima-u.ac.jp/~museum/ デジタル自然史博物館] / [https://www.hiroshima-u.ac.jp 広島大学] / [https://www.digital-museum.hiroshima-u.ac.jp/~museum/plant/ 植物] / [[コケ|コケ植物(蘚苔類)]] / [[コケ/情報|情報]] にもどる |
[[Category:広島大学デジタル自然史博物館]] | [[Category:広島大学デジタル自然史博物館]] | ||
330行目: | 389行目: | ||
[[Category:実験]] | [[Category:実験]] | ||
[[Category:PCR]] | [[Category:PCR]] | ||
+ | [[Category:primer]] | ||
[[Category:研究]] | [[Category:研究]] | ||
[[Category:系統]] | [[Category:系統]] | ||
[[Category:生物]] | [[Category:生物]] |
2022年9月20日 (火) 21:54時点における版
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
PCR primers
nuclear
18S rRNA gene and ITS region
Analyzed region | Forward / Reverse | Primer name | Sequence (5'–3') | References | For |
18S rRNA gene | Forward | 18SPrimer A | CCGAATTCGT CGACAACCTG GTTGATCCTG CCAGT | Medlin et al. (1988) | Algae (Stichococcus etc.) |
18S rRNA gene | Forward | 18S1Fh | AACCTGGTTG ATCCTGCC | Nakahara et al. (2004a) | Algae, Vascular plants (Lactuca, Sisymbrium etc.) |
18S rRNA gene | Forward | 18S2Fh | GTTGATCCTG CCAGTAGTCA | Nakahara et al. (2004a) | Algae |
18S rRNA gene | Forward | 18SNS1 | GTAGTCATAT GCTTGTCTC | White et al. (1990); Kocher & White (1992) | Fungi, Algae (Stichococcus etc.), Vascular plants (Lactuca etc.) |
18S rRNA gene | Forward | 18S156 | TCTAGAGCTA ATACGTGCG | Nakahara et al. (2004b) | Algae |
18S rRNA gene | Forward | 18S325R | CTGCCCTATC AACTTTCG | Nakahara et al. (2004b) | Algae (Chlorella etc.) |
18S rRNA gene | Forward | 18S323 | CGATGGTAGG ATAGAGG | Handa et al. (2003) | Algae (Stichococcus etc.) |
18S rRNA gene | Forward | 18S410 | CCACATCCAA GGAAGGCAGC | Handa et al. (2003) | Algae (Stichococcus etc.), Vascular plants (Lactuca, Sisymbrium etc.) |
18S rRNA gene | Forward | 18S575 | CGGTAATTCC AGCTCCA | Handa et al. (2003) | Algae (Stichococcus etc.), Vascular plants (Lactuca etc.) |
18S rRNA gene | Forward | 18S578 | CCAGCTCCAA TAGCGTATAT TT | Nakahara et al. (2004b) | Algae |
18S rRNA gene | Forward | 18S705 | GGCTCCTGGG CTTCACTG | Handa et al. (2003) | Algae (Stichococcus etc.) |
18S rRNA gene | Forward | 18S791 | AGCATGGGAT AACACGATAG GA | Nakahara et al. (2004b) | Algae |
18S rRNA gene | Forward | 18S921 | GAAAGACGAA CTACTGCGA | Handa et al. (2003) | Algae (Stichococcus etc.), Vascular plants (Lactuca, Sisymbrium etc.) |
18S rRNA gene | Forward | 18S1171 | GCTTAATTTG ACTCAACAC | Tsubota et al. (2012) | Algae, Vascular plants (Lactuca etc.) |
18S rRNA gene | Forward | 18S1208 | TACCAGGTCC AGACATAGTG AGG | Handa et al. (2003) | Algae (Stichococcus etc.) |
18S rRNA gene | Forward | 18S1288 | TGGGTTGCCT TGTCA | Nakahara et al. (2004a) | Algae |
18S rRNA gene | Forward | 18S1307 | ACGAGACCTC AGCCTGCT | Nakahara et al. (2004a) | Algae |
18S rRNA gene | Forward | 18S1421 | CAGGTCTGTG ATGCCCTTAG A | Nakahara et al. (2004a) | Algae, Vascular plants (Lactuca, Sisymbrium etc.) |
18S rRNA gene | Forward | 18S1560 | GCGTTGATTA CGT | Nakahara et al. (2004b) | Algae |
ITS | Forward | 18S1659B | CGTCGCTCCT ACCGATTG | Oguri et al. (2003) | Bryophytes (Leucobryum etc.), Vascular plants (Halophila, Lactuca, Sisymbrium etc.) |
ITS | Forward | 18S1764B | AGAGGAAGGA GAAGTCGTAA C | Oguri et al. (2003) | Bryophytes (Leucobryum etc.), Vascular plants (Halophila, Lactuca, Sisymbrium etc.) |
ITS | Forward | 18SrDNAHTF1 | AAGGTTTCCG TAGGTGAACC TGC | Tsubota et al. (2012) | Vascular plants (Lactuca, Sisymbrium etc.) |
ITS | Forward | 18srRNA | TCCGTAGGTG AACCTGCGG | Oguri et al. (2003) | Bryophytes (Leucobryum etc.), Vascular plants (Halophila, Sisymbrium etc.) |
ITS | Forward | 5.8S10B | CTCAGCAACG GATATCTTGG | Oguri et al. (2003) | Bryophytes (Leucobryum etc.), Vascular plants (Halophila etc.) |
ITS | Forward | 5srRNA | ACGATGAAGA ACGCAGCG | Oguri et al. (2003) | Bryophytes (Leucobryum etc.), Vascular plants (Halophila etc.) |
ITS | Forward | 5.8S43H | GAAGAACGTA GCGAAATGCG A | Tsubota et al. (2009) | Vascular plants (Halophila, Lactuca, Sisymbrium etc.) |
ITS | Forward | 5.8S51HV | TAGCGAAATG CGATACTTGG | Tsubota et al. (2013) | Vascular plants (Sisymbrium etc.) |
ITS | Forward | 5.8S114HV | AGTTGCGCCC GAAGC | Tsubota et al. (2013) | Vascular plants (Sisymbrium etc.) |
ITS | Reverse | 26S166BR | GAGGACGCTT CTCCAGACTA C | Oguri et al. (2003) | Bryophytes (Leucobryum etc.), Vascular plants (Halophila, Lactuca, Sisymbrium etc.) |
ITS | Reverse | 26S102BR | CCGGTTCGCT CGCCG | Oguri et al. (2003) | Bryophytes (Leucobryum etc.), Vascular plants (Halophila, Lactuca, Sisymbrium etc.) |
ITS | Reverse | 26SrDNAHTR1 | AAGGGAATCC TTGTAAGTTT CT | Tsubota et al. (2012) | Vascular plants (Lactuca, Sisymbrium etc.) |
ITS | Reverse | 26SrDNAHTR2 | AAGTTTCTTT TCCTCCGCTT A | Tsubota et al. (2012) | Vascular plants (Lactuca, Sisymbrium etc.) |
ITS | Reverse | 25srRNA | TCCTCCGCTT AGTGATATGC | Oguri et al. (2003) | Bryophytes (Leucobryum etc.), Vascular plants (Halophila, Sisymbrium etc.) |
ITS | Reverse | 5.8S124HR | CGGGCGCAAC TTGCGTTCA | Tsubota et al. (2009) | Vascular plants (Halophila, Lactuca, Sisymbrium etc.) |
ITS | Reverse | 5.8S102BR | ACTCGATGAT TCGCGGA | Oguri et al. (2003) | Bryophytes (Leucobryum etc.), Vascular plants (Halophila etc.) |
18S rRNA gene | Reverse | 5.8SR–2 | ACTACGTATC GCATTTCGCT | Nakahara et al. (2004b) | Algae |
18S rRNA gene | Reverse | 5.8SR–3 | CATTTCGCTG CGTTCTTCAT | Nakahara et al. (2004b) | Algae |
18S rRNA gene & ITS | Reverse | 5.8SR-1 | GTATCGCATT TCGCTGCGTT CTTCATCG | Handa et al. (2003) | Algae (Stichococcus etc.) |
18S rRNA gene & ITS | Reverse | 5srRNAR | CGCTGCGTTC TTCATCGT | Handa et al. (2003); Oguri et al. (2003) | Algae (Stichococcus etc.), Bryophytes (Leucobryum etc.), Vascular plants (Halophila, Sisymbrium etc.) |
18S rRNA gene | Reverse | 18Sprimer B | CCCGGGATCC AAGCTTGATC CTTCTGCAGG TTCACCTAC | Medlin et al. (1988) | Algae (Stichococcus etc.) |
18S rRNA gene | Reverse | 18S3Rh | TGATCCTTCT GCAGGTTC | Nakahara et al. (2004a) | Algae, Vascular plants (Lactuca, Sisymbrium etc.) |
18S rRNA gene | Reverse | 18S4Rh | CTGCAGGTTC ACCTACGGA | Nakahara et al. (2004a) | Algae |
18S rRNA gene | Reverse | 18S1747R | CTCCTTCCTC TAGGTGGGA | Nakahara et al. (2004b) | Algae |
18S rRNA gene | Reverse | 18S1617R | CAGGGACGTA ATCAACGC | Handa et al. (2003) | Algae (Stichococcus etc.), Vascular plants (Lactuca etc.) |
18S rRNA gene | Reverse | 18S1442R | TCTAAGGGCA TCACAGAC | Handa et al. (2003) | Algae (Stichococcus etc.), Vascular plants (Lactuca, Sisymbrium etc.) |
18S rRNA gene | Reverse | 18S1317R | TTACCGGAAT CAACCTGACA AGGCAAC | Nakahara et al. (2004b) | Algae |
18S rRNA gene | Reverse | 18S1125R | CAGCCTTGCG ACCATACTCC | Handa et al. (2003) | Algae (Stichococcus etc.) |
18S rRNA gene | Reverse | 18S909R | CCAAGAATTT CACCTCTGAC | Handa et al. (2003) | Algae (Stichococcus etc.), Vascular plants (Lactuca, Sisymbrium etc.) |
18S rRNA gene | Reverse | 18SNS2 | GGCTGCTGGC ACCAGACTTG C | White et al. (1990); Kocher & White (1992) | Fungi, Algae (Stichococcus etc.), Vascular plants (Lactuca, Sisymbrium etc.) |
18S rRNA gene | Reverse | 18S325R++[1][2] | CGAAAGTTGA TAGGGCAG | Nakahara et al. (2004b); Tsubota et al. (2012) | Algae, Vascular plants (Lactuca etc.) |
脚注
- ↑ 坪田ほか(2012)では表中で初出となっているが,実際にはNakahara et al.(2004b)が初出.
- ↑ The first appearance of this primer was not in Table 1 of Tsubota et al. (2012) but in Table 2 of Nakahara et al. (2004b).
References
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- Bruni, I., Galimberti, A., Caridi, L., Scaccabarozzi, D., De Mattia, F., Casiraghi, M. & Labra, M. 2015. A DNA barcoding approach to identify plant species in multiflower honey. Food Chem. 170: 308-315.
- Buck, W. R., Goffinet, B. & Shaw, A. J. 2000. Testing morphological concepts of orders of pleurocarpous mosses (Bryophyta) using phylogenetic reconstructions based on trnL-trnF and rps4 sequences. Mol. Phylogenet. Evol. 16: 180-198.
- Demesure, B., Sodzi, N. & Petit, R. J. 1995. A set of universal primers for amplification of polymorphic non-coding regions of mitochondrial and chloroplast DNA in plants. Mol. Ecol. 4: 129-131.
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- Hamilton, M. B. 1999. Four primer pairs for the amplification of chloroplast intergenic regions with intraspecific variation. Mol. Ecol. 8: 521–523.
- Handa, S., Nakahara, M., Tsubota, H., Deguchi, H. & Nakano, T. 2003. A new aerial alga, Stichococcus ampulliformis sp. nov. (Trebouxiophyceae, Chlorophyta) from Japan. Phycol. Res. 51: 203-210.
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- Kocher, T. D. & White, T. J. 1992. Evolutionary analysis via PCR. In Erlich, H. A. (ed.), PCR Technology: Principles and Applications for DNA Amplification, pp. 137–147. Oxford University Press, New York.
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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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- Nadot, S., Bajon, R. & Lejeune, B. 1994. The chloroplast gene rps4 as a tool for the study of Poaceae phylogeny. Pl. Syst. Evol. 191: 27–38.
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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.
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- 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.]
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- 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.
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- 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.
- Tsubota, H., Kubo, H. & Mukai, S. 2009. A new finding of seagrass Halophila nipponica J.Kuo (Hydrocharitaceae) from Miyajima Island in Hiroshima Prefecture, SW Japan. Hikobia 15: 339-347 (in Japanese with English Abstract and Tables). [坪田博美・久保晴盛・向井誠二. 2009. 広島県宮島近海で見つかったヤマトウミヒルモHalophila nipponica J.Kuoについて. Hikobia 15: 339-347.]
- Tsubota, H., Kubo, H., Takeuchi, K., Nakahara-Tsubota, M., Inoue, Y., Uchida, S. & Mukai, S. 2012. Notes on naturalized plants in Hiroshima Prefecture: 3. New locality and nrITS variation of Lactuca serriola L. (Asteraceae). Hikobia 16: 197-202 (in Japanese with English Abstract and Tables). [坪田博美・久保晴盛・武内一恵・中原-坪田美保・井上侑哉・内田慎治・向井誠二. 2012. 広島の帰化植物3.トゲヂシャとマルバトゲヂシャ. Hikobia 16: 197-202.]
- Tsubota, H., Kubo, H., Ohno, A., Inoue, Y., Nakahara-Tsubota, M., Takeuchi, K., Matsui, K., Uchida, S. & Mukai, S. 2013. Notes on naturalized plants in Hiroshima Prefecture: 4. New locality and phylogeny of Sisymbrium orientale L. (Brassicaceae) and its related species. Hikobia 16: 321-334. [坪田博美・久保晴盛・大野彰洋・井上侑哉・中原-坪田美保・武内一恵・松井健一・内田慎治・向井誠二. 2013. 広島の帰化植物4.イヌカキネガラシおよびその近縁種. Hikobia 16: 321-334.]
- Tsubota, H., Era, Y., Ikeda, S., Kubo, H., Takeuchi, K., Nakahara-Tsubota, M., Uchida, S. & Mukai, S. 2015a. Notes on naturalized plants in Hiroshima Prefecture, SW Japan: 6. New locality of Cotula australis (Sieber ex Spreng.) Hook.f. (Asteraceae). Hikobia 17(1): 73-79. [坪田博美・惠良友三郎・池田誠慈・久保晴盛・武内一恵・中原-坪田美保・内田慎治・向井誠二. 2015a. 広島の帰化植物6.マメカミツレ. Hikobia 17(1): 73-79.]
- 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
デジタル自然史博物館 / 広島大学 / 植物 / コケ植物(蘚苔類) / 情報 にもどる