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De-Zhu Li,
Lian-Ming Gao,
Hong-Tao Li,
Hong Wang,
Xue-Jun Ge,
Jian-Quan Liu,
Zhi-Duan Chen,
Shi-Liang Zhou,
Shi-Lin Chen,
Jun-Bo Yang,
Cheng-Xin Fu, Chun-Xia Zeng,
Hai-Fei Yan,
Ying-Jie Zhu,
Yong-Shuai Sun,
Si-Yun Chen,
Lei Zhao,
Kun Wang,
Tuo Yang,
Guang-Wen Duan
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ABSTRACT: The monophyly of tribe Arundinarieae (the temperate woody bamboos) has been unequivocally recovered in previous molecular phylogenetic studies. In a recent phylogenetic study, 10 major lineages in Arundinarieae were resolved based on eight non-coding plastid regions, which conflicted significantly with morphological classifications both at the subtribal and generic levels. Nevertheless, relationships among and within the 10 lineages remain unclear. In order to further unravel the evolutionary history of Arundinarieae, we used the nuclear GBSSI gene sequences along with those of eight plastid regions for phylogenetic reconstruction, with an emphasis on Chinese species. The results of the plastid analyses agreed with previous studies, whereas 13 primary clades revealed in the GBSSI phylogeny were better resolved at the generic level than the plastid phylogeny. Our analyses also revealed many inconsistencies between the plastid DNA and the nuclear GBSSI trees. These results implied that the nuclear genome and the plastid genome had different evolutionary trajectories. The patterns of incongruence suggested that lack of informative characters, incomplete lineage sorting, and/or hybridization (introgression) could be the causes. Seven putative hybrid species were hypothesized, four of which are discussed in detail on the basis of topological incongruence, chromosome numbers, morphology, and distribution patterns, and those taxa probably resulted from homoploid hybrid speciation. Overall, our study indicates that the tribe Arundinarieae has undergone a complex evolution.
Molecular Phylogenetics and Evolution 03/2012; 63(3):777-97. · 3.61 Impact Factor
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ABSTRACT: Microsatellite primers were developed in the Chinese endangered and endemic orchid, Cymbidium tortisepalum, to investigate its genetic diversity and population genetic structure, and to identify its varieties.
Using the Fast Isolation by AFLP of Sequences Containing repeats (FIASCO) protocol, 15 primer sets were identified in two wild populations. The number of alleles per locus ranged from two to six, with a mean of 3.5. The observed and expected heterozygosities varied from 0.250 to 0.917 and from 0.228 to 0.841, respectively. All of these primers successfully amplified in the congener C. goeringii, and 12 were found useful in C. faberi and C. sinense.
These markers will facilitate further studies on the population genetics and molecular identification of C. tortisepalum, its varieties, and other congener species.
American Journal of Botany 12/2011; 99(1):e11-3. · 2.66 Impact Factor
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De-Zhu Li,
Lian-Ming Gao,
Hong-Tao Li,
Hong Wang,
Xue-Jun Ge,
Jian-Quan Liu,
Zhi-Duan Chen,
Shi-Liang Zhou,
Shi-Lin Chen,
Jun-Bo Yang,
Cheng-Xin Fu, Chun-Xia Zeng,
Hai-Fei Yan,
Ying-Jie Zhu,
Yong-Shuai Sun,
Si-Yun Chen,
Lei Zhao,
Kun Wang,
Tuo Yang,
Guang-Wen Duan
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ABSTRACT: A two-marker combination of plastid rbcL and matK has previously been recommended as the core plant barcode, to be supplemented with additional markers such as plastid trnH-psbA and nuclear ribosomal internal transcribed spacer (ITS). To assess the effectiveness and universality of these barcode markers in seed plants, we sampled 6,286 individuals representing 1,757 species in 141 genera of 75 families (42 orders) by using four different methods of data analysis. These analyses indicate that (i) the three plastid markers showed high levels of universality (87.1-92.7%), whereas ITS performed relatively well (79%) in angiosperms but not so well in gymnosperms; (ii) in taxonomic groups for which direct sequencing of the marker is possible, ITS showed the highest discriminatory power of the four markers, and a combination of ITS and any plastid DNA marker was able to discriminate 69.9-79.1% of species, compared with only 49.7% with rbcL + matK; and (iii) where multiple individuals of a single species were tested, ascriptions based on ITS and plastid DNA barcodes were incongruent in some samples for 45.2% of the sampled genera (for genera with more than one species sampled). This finding highlights the importance of both sampling multiple individuals and using markers with different modes of inheritance. In cases where it is difficult to amplify and directly sequence ITS in its entirety, just using ITS2 is a useful backup because it is easier to amplify and sequence this subset of the marker. We therefore propose that ITS/ITS2 should be incorporated into the core barcode for seed plants.
Proceedings of the National Academy of Sciences 11/2011; 108(49):19641-6. · 9.68 Impact Factor
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ABSTRACT: Currently, all monoterpenoid indole alkaloids (MIAs) have been derived from strictosidine, which originates from the condensation of tryptophan with secologanin in a 1:1 ratio. However, our phytochemical research on Alstonia rostrata revealed a potential new precursor for these compounds. We isolated the alstrostines A and B, and it was determined that they were derived from tryptophan and secologanin in a 1:2 ratio, which supported the presence of a new type of MIA precursor.
Organic Letters 06/2011; 13(14):3568-71. · 5.86 Impact Factor
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ABSTRACT: Microsatellite primers were developed for the important and popular ornamental spring orchid, Cymbidium goeringii, to investigate its genetic diversity and population genetic structure.
Using the Fast Isolation by AFLP of Sequences Containing (FIASCO) repeats protocol, 15 primer sets were identified in two wild populations. The number of alleles per locus ranged from 2 to 5, with a mean of 3.3. The observed and expected heterozygosities varied from 0.167 to 0.917 and from 0.159 to 0.822, respectively. All these primers successfully amplified in the congener C. tortisepalum, and 12 primers were found useful in C. faberi and C. sinense.
These markers will facilitate further studies on the population genetics of Cymbidium goeringii and other congeneric species.
American Journal of Botany 04/2011; 98(4):e76-7. · 2.66 Impact Factor
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Helvetica Chimica Acta 10/2010; 93(10):2037 - 2044. · 1.48 Impact Factor
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ABSTRACT: The temperate bamboos (tribe Arundinarieae) are notorious for being taxonomically extremely difficult. China contains some of the world's greatest diversity of the tribe Arundinarieae, with most genera and species endemic. Previous investigation into phylogenetic relationships of the temperate bamboos revealed several major clades, but emphasis on the species-level relationships among taxa in North America and Japan. To further elucidate relationships among the temperate bamboos, a very broad sampling of Chinese representatives was examined. We produced 9463 bp of sequences from eight non-coding chloroplast regions for 146 species in 26 genera and 5 outgroups. The loci sequenced were atpI/H, psaA-ORF170, rpl32-trnL, rpoB-trnC, rps16-trnQ, trnD/T, trnS/G, and trnT/L. Phylogenetic analyses using maximum parsimony and Bayesian inference supported the monophyly of Arundinarieae. The two major subtribes, Arundinariinae and Shibataeinae, defined on the basis of different synflorescence types, were indicated to be polyphyletic. Most genera in this tribe were confirmed to be paraphyletic or polyphyletic. The cladograms suggest that Arundinarieae is divided into ten major lineages. In addition to six lineages suggested in a previous molecular study (Bergbamboes, the African alpine bamboos, Chimonocalamus, the Shibataea clade, the Phyllostachys clade, and the Arundinaria clade), four additional lineages were recovered in our results, each represented by a single species: Gaoligongshania megalothyrsa, Indocalamus sinicus, Indocalamus wilsonii, Thamnocalamus spathiflorus. Our analyses also indicate that (1) even more than 9000 bp of fast-evolving plastid sequence data cannot resolve the inter- and infra-relationships among and within the ten lineages of the tribe Arundinarieae; (2) an extensive sampling is indispensable for phylogeny reconstruction in this tribe, especially given that many genera appear to be paraphyletic or polyphyletic. Perhaps the ideal way to further illuminate relationships among the temperate bamboos is to sample multiple nuclear loci or whole chloroplast sequences in order to obtain sufficient variation.
Molecular Phylogenetics and Evolution 04/2010; 56(2):821-39. · 3.61 Impact Factor
