「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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<span style="font-size:10">[http://www.hiroshima-u.ac.jp/index-j.html 広島大学] > [http://www.digital-museum.hiroshima-u.ac.jp/~museum/ デジタル自然史博物館] > [http://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>
+
<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]] =
== chloroplast ==
 
* [[PCR_primers_cp_rbcL|rbcL]]
 
* [[PCR_primers_cp_rps4|rps4]]
 
* [[PCR_primers_cp_matK|matK]]
 
* [[PCR_primers_cp_trnL-F|trnL-F]]
 
 
 
== nuclear ==
 
== nuclear ==
* [[PCR_primers_18SrRNA_ITSs|18S rRNA gene and ITS region]]
+
=== 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
26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.)
 
|-
 
|-
33行目: 25行目:
 
| 18S1Fh
 
| 18S1Fh
 
| <tt>AACCTGGTTG ATCCTGCC</tt>
 
| <tt>AACCTGGTTG ATCCTGCC</tt>
| Nakahara et al. (2004)
+
| [[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
40行目: 32行目:
 
| 18S2Fh
 
| 18S2Fh
 
| <tt>GTTGATCCTG CCAGTAGTCA</tt>
 
| <tt>GTTGATCCTG CCAGTAGTCA</tt>
| Nakahara et al. (2004)
+
| [[Nakahara_Handa_Watanabe_Deguchi_2004|Nakahara et al. (2004a)]]
 
| Algae
 
| Algae
 
|-
 
|-
47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
54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.)
 
|-
 
|-
61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
68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
75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
82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
89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.)
 
|-
 
|-
96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.)
 
|-
 
|-
103行目: 123行目:
 
| 18S1288
 
| 18S1288
 
| <tt>TGGGTTGCCT TGTCA</tt>
 
| <tt>TGGGTTGCCT TGTCA</tt>
| Nakahara et al. (2004)
+
| [[Nakahara_Handa_Watanabe_Deguchi_2004|Nakahara et al. (2004a)]]
 
| Algae
 
| Algae
 
|-
 
|-
110行目: 130行目:
 
| 18S1307
 
| 18S1307
 
| <tt>ACGAGACCTC AGCCTGCT</tt>
 
| <tt>ACGAGACCTC AGCCTGCT</tt>
| Nakahara et al. (2004)
+
| [[Nakahara_Handa_Watanabe_Deguchi_2004|Nakahara et al. (2004a)]]
 
| Algae
 
| Algae
 
|-
 
|-
117行目: 137行目:
 
| 18S1421
 
| 18S1421
 
| <tt>CAGGTCTGTG ATGCCCTTAG A</tt>
 
| <tt>CAGGTCTGTG ATGCCCTTAG A</tt>
| Nakahara et al. (2004)
+
| [[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
124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
131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
138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
145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
152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.)
 
|-
 
|-
159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.)
 
|-
 
|-
166行目: 193行目:
 
| 5.8S43H
 
| 5.8S43H
 
| <tt>GAAGAACGTA GCGAAATGCG A</tt>
 
| <tt>GAAGAACGTA GCGAAATGCG A</tt>
| Tsubota et al. (2009) Halophila Hikobia
+
| [[Tsubota_Kubo_Mukai_2009|Tsubota et al. (2009)]]
| Vascular plants (''Halophila'', ''Lactuca'' etc.)
+
| Vascular plants (''Halophila'', ''Lactuca'', ''Sisymbrium'' etc.)
 
|-
 
|-
 
| ITS
 
| ITS
 
| Forward
 
| Forward
 
| 5.8S51HV
 
| 5.8S51HV
| <tt></tt>
+
| <tt>TAGCGAAATG CGATACTTGG</tt>
|  
+
| [[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.)
 
|-
 
|-
 
| ITS
 
| ITS
 
| Forward
 
| Forward
 
| 5.8S114HV
 
| 5.8S114HV
| <tt></tt>
+
| <tt>AGTTGCGCCC GAAGC</tt>
|  
+
| [[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.)
 
|-
 
|-
 
|
 
|
194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
201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
| 25srRNA
+
| 26SrDNAHTR1
| <tt>TCCTCCGCTT AGTGATATGC</tt>
+
| <tt>AAGGGAATCC TTGTAAGTTT CT</tt>
| Oguri et al. (2003)
+
| [[Tsubota_Kubo_Takeuchi_Nakahara-Tsubota_Inoue_Uchida_Mukai_2012|Tsubota et al. (2012)]]
| Bryophytes (''Leucobryum'' etc.), Vascular plants (''Halophila'' etc.)
+
| Vascular plants (''Lactuca'', ''Sisymbrium'' etc.)
 
|-
 
|-
 
| ITS
 
| ITS
 
| Reverse
 
| Reverse
| 26SrDNAHTR1
+
| 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
| 26SrDNAHTR2
+
| 25srRNA
| <tt>AAGTTTCTTT TCCTCCGCTT A</tt>
+
| <tt>TCCTCCGCTT AGTGATATGC</tt>
| Tsubota et al. (2012)
+
| [[Oguri_Yamaguchi_Tsubota_Deguchi_2003|Oguri et al. (2003)]]
| Vascular plants (''Lactuca'' etc.)
+
| Bryophytes (''Leucobryum'' etc.), Vascular plants (''Halophila'', ''Sisymbrium'' etc.)
 
|-
 
|-
 
| ITS
 
| ITS
229行目: 256行目:
 
| 5.8S124HR
 
| 5.8S124HR
 
| <tt>CGGGCGCAAC TTGCGTTCA</tt>
 
| <tt>CGGGCGCAAC TTGCGTTCA</tt>
| Tsuota et al. (2009)
+
| [[Tsubota_Kubo_Mukai_2009|Tsubota et al. (2009)]]
| Vascular plants (''Halophila'', ''Lactuca'' etc.)
+
| Vascular plants (''Halophila'', ''Lactuca'', ''Sisymbrium'' etc.)
 
|-
 
|-
 
| ITS
 
| ITS
236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.)
 
|-
 
|-
| ITS
+
| 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
| 5srRNAR
+
| 5.8SR–3
| <tt>CGCTGCGTTC TTCATCGT</tt>
+
| <tt>CATTTCGCTG CGTTCTTCAT</tt>
| Handa et al. (2003); Oguri et al. (2003)
+
| [[Nakahara_Tsubota_Handa_Watanabe_Deguchi_2004|Nakahara et al. (2004b)]]
| Algae (''Stichococcus'' etc.), Bryophytes (''Leucobryum'' etc.), Vascular plants (''Halophila'' etc.)
+
| 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.)
 
|-
 
|-
257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
264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.)
 
|-
 
|-
271行目: 305行目:
 
| 18S3Rh
 
| 18S3Rh
 
| <tt>TGATCCTTCT GCAGGTTC</tt>
 
| <tt>TGATCCTTCT GCAGGTTC</tt>
| Nakahara et al. (2004)
+
|[[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
278行目: 312行目:
 
| 18S4Rh
 
| 18S4Rh
 
| <tt>CTGCAGGTTC ACCTACGGA</tt>
 
| <tt>CTGCAGGTTC ACCTACGGA</tt>
| Nakahara et al. (2004)
+
|[[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
 
|-
 
|-
285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.)
 
|-
 
|-
292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
299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.)
 
|-
 
|-
306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
313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.)
 
|}
 
|}
  
== References ==
+
== 脚注 ==
* 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.
+
{{Reflist|1}}
* 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.
+
 
* 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.]
+
=[[テンプレート:PCR_primers_References|References]]=
* 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.]
+
{{PCR_primers_References}}
  
 +
==[[テンプレート:primers|関連ページ]]==
 +
{{primers}}
 
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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

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 Chlorella vulgaris (X13688) and the 5.8S rRNA gene of Chlamydomonas tetragama (AB004866).
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

  1. 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.
  2. 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

関連ページ


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