1. Molecular Phylogeny and Biogeography

1.1 Phylogenetics and phylogenomics of the Bambusoideae (Gramineae).

The bamboo subfamily (Bambusoideae), the rice subfamily (the Erhartoideae) and the Pooideae (to which wheat belongs) are closely related and compose the BEP clade in the grass family. The Bambusoideae includes three major tribes, the woody Bambuseae from the pantropics, the herbaceous Olyreae mainly from the neotropics and the temperate Arundinarieae mainly from the Old World. There are about 392 species of 23 genera in Arundinarieae in China, and 142 species of 11 genera in Bambuseae in the Old World tropics of China. Molecular phylogenetic studies were performed on woody bamboos to address the relationships among genera and the two widely subtribes (Arundinariinae and Shibataeinae) in Arundinarieae based on chloroplast sequences and nuclear GBSSI and ITS data. We studied the phylogenetic relationships among the paleotropic woody bamboos (the Bambusinae + Dinochloa clade and the Melocanninae clade) based on ITS, GBSSI and plastid trnL-F, and those among the lineages of Arundinarieae based on eight non-coding plastid regions (atpI/H, psaA-ORF170, rpl32-trnL, rpoB-trnC, rps16-trnQ, trnD/T, trnS/G, and trnT/L) and two nuclear genes, i.e., GBSSI and Leafy. Several papers were published in Molecular Phylogenetics and Evolution, Taxon, Botanical Journal of the Linnean Society, and PLoS ONE in last few years (Zhang and Li, 2010; Zeng et al., 2010; Yang et al., 2010; Zhang et al., 2012; Yang et al., 2013). The publications bridged some important gaps of our knowledge of bamboo phylogeny. Eleven major lineages were identified within Arundinarieae based on eight non-coding plastid regions using a large sampling strategy. However, the relationships among the major lineages within Arundinarieae were not well resolved (Zeng et al., 2010; Yang et al., 2013). The nuclear phylogeny was incongruent with the plastid results which indicated that hybridization, introgression, or lineage sorting may occurred in Arundinarieae (Zhang et al., 2012; Yang et al., 2013).

To evaluate the potential of chloroplast phylogenomics in resolving phylogenetic relationships of Arundinarieae, six complete woody bamboos chloroplast genomes were determined using Illumina sequencing. A total of 24 complete chloroplast genomes from Poaceae were analyzed, providing a strong support for the sister relationship between Bambusoideae and Pooideae within the BEP clade. The relationships within Arundinarieae were also well resolved and chloroplast phylogenomics could be used to resolve major relationships within Arundinarieae (Zhang et al., 2011). Currently more chloroplast genomes sampled from all the lineages of Arundinarieae are under analyses.

1.2 Molecular Phylogeny of Urticaceae

Urticaceae is one of the large Angiosperm families, but relationships within it remain poorly known. This study presents the first densely sampled molecular phylogeny of Urticaceae. Two nuclear (ITS and 18S), four chloroplast (matK, rbcL, rpll4–rps8–infA–rpl36, trnL–trnF) and one mitochondrial (matR) loci of 169 accessions representing 122 species, representing 47 of the 54 recognized genera within Urticaceae, including four of the six sometimes separated as Cecropiaceae were sampled. Major results were received: (1) Urticaceae including Cecropiaceae was monophyletic, Cecropiaceae was biphyletic, with both lineages nested within Urticaceae; (2) Urticaceae can be divided into four well-supported clades; (4) previously erected tribes or subfamilies were broadly supported, with some additions and alterations; (5) the monophyly of many genera was supported, whereas Boehmeria, Pellionia, Pouzolzia and Urera were clearly polyphyletic, while Urtica and Pilea each had a small genus nested within them; (6) relationships between genera were clarified, mostly with substantial support. These results clarify that some morphological characters have been overstated and others understated in previous classifications of the family, and provide a strong foundation for future studies on biogeography, character evolution, and circumscription of difficult genera (Wu et al., 2013). 

1.3 Phylogenetics and Biogeography of Adiantum (Pteridaceae)

Adiantum consists of about 150 –200 species mostly with a pantropical distribution, yet the classifications of Adiantum have been based primarily on regional studies. Five plastid markers (atpA, atpB, rbcL, trnL-F and rps4-trnS) were employed to construct the molecular phylogeny of Chinese Adiantum. The monophyly of Adiantum was supported. Six main clades are supported within Chinese Adiantum, which are only partially consistent with Lin’s classification of the genus. The phylogeny suggests that convergent evolution in frond architecture has occurred in Adiantum (Lu et al., 2012). The Adiantum pedatum complex has a distribution of eastern Asian-North American disjunction. The biogeography and diversification history of the complex have been studied with DIVA, LAGRANGE, and BEAST. An eastern Asian origin of the A. pedatum complex was proposed. The age of the crown A. pedatum complex is dated to be at 4.27 (2.24-6.57) million years ago. The eastern Asian -North American disjunction in the complex was inferred to be the result of two intercontinental migrations, one from eastern Asia into North America in the late Tertiary and the other from North America back to eastern Asia in the Pleistocene (Lu et al., 2011).  

2. Plant DNA barcoding in China 

To evaluate the universality and effectiveness of the four candidate barcodes (i.e. rbcL, matK, trnH-psbA and ITS), a coordinated effort has been made to further evaluate the markers, as a response to the call of the Third International Barcoding of Life Conference in 2009. A large data set, involving 6,286 individuals representing 1,757 species in 141 genera of 75 families of seed plants, was pooled by the China Plant BOL Group. Comprehensive analysis of the dataset was made to assess the universality, sequence quality and discriminatory power of the markers. The results indicated that the three chloroplast markers showed higher level of universality, while ITS performed moderately well in angiosperms, but not so in gymnosperms. As to the discriminatory power, ITS provided the highest among the four markers, and a combination of ITS with any chloroplast DNA marker could improve species discrimination significantly. Based on a comprehensive evaluation, ITS should be incorporated into the core barcode for seed plants (China Plant BOL Group, 2011). 

In addition, some DNA barcoding studies have been carried out in Adiantum (Pteridaceae), Cyrtomium (Dryopteridaceae), Cyatheaceae, and the temperate woody bamboos (Bambusoideae) (Cai et al. 2012), and Gentianopsis paludosa (Gentianaceae) (Xue and Li, 2011). In 2012, the next-generation Flora, iFlora was proposed to be a major effort to catalogue plants of China by integrating traditional floristic elements, DNA barcodes and geo-referenced collections (Li et al., 2012).

3. Plant diversity and germplasm conservation 

China is home to four of the 34 global biodiversity hotspots, with 31,000 species of vascular plants, including many ‘living fossils’ that survived the climate changes of the Miocene and the Pleistocene glaciations, and the origin of many cultivated, medicinal and ornamental plants. Prof. Li has been coordinating the construction of the Germplasm Bank of Wild Species (GBOWS) of the Kunming Institute of Botany, Chinese Academy of Sciences since 2004. As of December 2010, totals for the seed bank at GBOWS include 44,549 seed accessions of 5,732 species, accounting for 20% of native species of seed plants in China. He was invited to write a review, “The science and economics of ex situ plant conservation" together with Hugh Pritchard of the Millennium Seed Bank of the Royal Botanic Gardens Kew, UK. In this paper, the important roles of the Germplasm Bank in achieving the Global Strategy for Plant Conservation and significance in global food security were presented. Developing ex situ conservation approaches for plants, cryo-preservation, a relaunched Target 8 of the GSPC (2011 -2020) were highlighted (Li and Pritchard 2009).