Biodiv Sci ›› 2011, Vol. 19 ›› Issue (3): 284-294. DOI: 10.3724/SP.J.1003.2011.11250
Special Issue: 物种形成与系统进化
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Nancai Pei1,3,*(), Jinlong Zhang2,3, Xiangcheng Mi2, Xuejun Ge1
Received:
2010-10-14
Accepted:
2011-03-08
Online:
2011-05-20
Published:
2013-12-10
Contact:
Nancai Pei
Nancai Pei, Jinlong Zhang, Xiangcheng Mi, Xuejun Ge. Plant DNA barcodes promote the development of phylogenetic commu- nity ecology[J]. Biodiv Sci, 2011, 19(3): 284-294.
Fig. 1 Illustration of supermatrix approach in sequence alignment for phylogenetic analysis (adopted from Kress et al., 2009). The first column represents species name, while others represent sequence alignments of rbcL, matK, and trnH-psbA. In trnH-psbA, each order consists of a dataset.
Fig. 2 A graphic representation of phylogenetic trees of ten species using Phylomatic (A) and Barcode (B, C) approaches. Sp 1-10 means species 1-10. (A) Phylogenetic relationships of Sp 2-10 are not well-resolved, i.e., there are polytomies among these taxa when using an online query tool Phylomatic; (B) Phylogenetic relationships of Sp 3-5, and Sp 6-8 are not well-resolved using a two-locus DNA barcode (rbcL+matK); (C) Phylogenetic relationships of Sp 1-10 are well-resolved using a supermatrix of three DNA barcodes (rbcL+matK+trnH-psbA).
标记 Marker | 引物 Primer | 序列 Sequence (5′- 3′) | 长度 Size (bp) | 参考文献 Reference |
---|---|---|---|---|
rbcL | SI_F | ATGTCACCACAAACAGAGACTAAAGC | 554 | |
SI_R | GTYAAATCAAGTCCACCYCG | |||
matK | KIM_3F | CGTACAGTACTTTTGTGTTTACGAG | Average 850 | Kim KJ, unpublished primers |
KIM_1R | ACCCAGTCCATCTGGAAATCTTGGTTC | |||
KIM_1F | AATATCCAAATACCAAATCC | Average 850 | Kim KJ, unpublished primers | |
KIM_1R | ACCCAGTCCATCTGGAAATCTTGGTTC | |||
2.1a-f | ATCCATCTGGAAATCTTAGTTC | Average 890 | www.kew.org/barcoding/protocols.html | |
5r | GTTCTAGCACAAGAAAGTCG | |||
trnH-psbA | psbA | GTTATGCATGAACGTAATGCTC | 280-750, average 470 | Sang et al., 1997 |
trnH | CGCGCATGGTGGATTCACAATCC | Tate & Simpson (2003) |
Appendix 1 Primer pairs for barcode loci rbcL, matK, and trnH-psbA
标记 Marker | 引物 Primer | 序列 Sequence (5′- 3′) | 长度 Size (bp) | 参考文献 Reference |
---|---|---|---|---|
rbcL | SI_F | ATGTCACCACAAACAGAGACTAAAGC | 554 | |
SI_R | GTYAAATCAAGTCCACCYCG | |||
matK | KIM_3F | CGTACAGTACTTTTGTGTTTACGAG | Average 850 | Kim KJ, unpublished primers |
KIM_1R | ACCCAGTCCATCTGGAAATCTTGGTTC | |||
KIM_1F | AATATCCAAATACCAAATCC | Average 850 | Kim KJ, unpublished primers | |
KIM_1R | ACCCAGTCCATCTGGAAATCTTGGTTC | |||
2.1a-f | ATCCATCTGGAAATCTTAGTTC | Average 890 | www.kew.org/barcoding/protocols.html | |
5r | GTTCTAGCACAAGAAAGTCG | |||
trnH-psbA | psbA | GTTATGCATGAACGTAATGCTC | 280-750, average 470 | Sang et al., 1997 |
trnH | CGCGCATGGTGGATTCACAATCC | Tate & Simpson (2003) |
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