Phylogenetic relationships among the five groups of extant seed plants are presently quite unclear. For example, morphological studies consistently identify the Gnetales as the extant sister group to angiosperms (the so-called ''anthophyte'' hypothesis), whereas a number of molecular studies recover gymnosperm monophyly, and few agree with the morphology-based placement of Gnetales. To better resolve these and other unsettled issues, we have generated a new molecular data set of mitochondrial small subunit rRNA sequences, and have analyzed these data together with comparable data sets for the nuclear small subunit rRNA gene and the chloroplast rbcL gene. All nuclear analyses strongly ally Gnetales with a monophyletic conifers, whereas all mitochondrial analyses and those chloroplast analyses that take into account saturation of third-codon position transitions actually place Gnetales within conifers, as the sister group to the Pinaceae. Combined analyses of all three genes strongly support this latter relationship, which to our knowledge has never been suggested before. The combined analyses also strongly support monophyly of extant gymnosperms, with cycads identified as the basal-most group of gymnosperms, Ginkgo as the next basal, and all conifers except for Pinaceae as sister to the Gnetales ؉ Pinaceae clade. According to these findings, the Gnetales may be viewed as extremely divergent conifers, and the many morphological similarities between angiosperms and Gnetales (e.g., double fertilization and flower-like reproductive structures) arose independently. E xtant seed plants (angiosperms and four groups of gymnosperms: cycads, conifers, Ginkgo, and Gnetales) differ from all other living land plants by several characters, the most notable, of course, being reproduction via seeds. Each of the five groups of seed plants is generally thought to be monophyletic; however, relationships among the groups are controversial. A common theme of most morphological studies of seed plant phylogeny is that extant gymnosperms are not monophyletic, with the Gnetales (Ephedra, Gnetum, and Welwitschia) being the sister group of angiosperms (1-7). Some studies have even concluded that angiosperms arose from within the Gnetales (8, 9). The anthophyte hypothesis, that angiosperms and Gnetales (plus the extinct Bennettitales and Pentoxylon) form a monophyletic group, is a major basis for understanding character evolution leading to flowering plants. For example, this hypothesis fits nicely with Friedman's studies (10,11) showing that Gnetales, like angiosperms, undergo a kind of double fertilization (but without formation of triploid endosperm). Relationships among the three remaining gymnosperm groups vary depending on which morphological characters are used and the sampling of fossil taxa (1-9, 12); the most consistent result is that cycads tend to be the basal-most seed plants.Molecular studies have generated an even more diverse set of phylogenetic hypotheses for seed plants, especially with respect to the position of the Gneta...

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PrimerZ (http://genepipe.ngc.sinica.edu.tw/primerz/) is a web application dedicated primarily to primer design for genes and human SNPs. PrimerZ accepts genes by gene name or Ensembl accession code, and SNPs by dbSNP rs or AFFY_Probe IDs. The promoter and exon sequence information of all gene transcripts fetched from the Ensembl database (http://www.ensembl.org) are processed before being passed on to Primer3 (http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi) for individual primer design. All results returned from Primer 3 are organized and integrated in a specially designed web page for easy browsing. Besides the web page presentation, csv text file export is also provided for enhanced user convenience.PrimerZ automates highly standard but tedious gene primer design to improve the success rate of PCR experiments. More than 2000 primers have been designed with PrimerZ at our institute since 2004 and the success rate is over 70%. The addition of several new features has made PrimerZ even more useful to the research community in facilitating primer design for promoters, exons and SNPs.

VarioWatch (http://genepipe.ncgm.sinica.edu.tw/variowatch/) has been vastly improved since its former publication GenoWatch in the 2008 Web Server Issue. It is now at least 10 000-times faster in annotating a variant. Drastic speed increase, through complete re-design of its working mechanism, makes VarioWatch capable of annotating millions of human genomic variants generated from next generation sequencing in minutes, if not seconds. While using MegaQuery of VarioWatch to quickly annotate variants, users can apply various filters to retrieve a subgroup of variants according to the risk levels, interested regions, etc. that satisfy users’ requirements. In addition to performance leap, many new features have also been added, such as annotation on novel variants, functional analyses on splice sites and in/dels, detailed variant information in tabulated form, plus a risk level decision tree regarding the analyzed variant. Up to 1000 target variants can be visualized with our carefully designed Genome View, Gene View, Transcript View and Variation View. Two commonly used reference versions, NCBI build 36.3 and NCBI build 37.2, are supported. VarioWatch is unique in its ability to annotate comprehensively and efficiently millions of variants online, immediately delivering the results in real time, plus visualizes up to 1000 annotated variants.