A chromosome-scale genome of Rhus chinensis Mill. provides new insights into plant-insect interaction and gallotannins biosynthesis.

Rhus chinensis Mill., an economically valuable Anacardiaceae species, is parasitized by the galling aphid Schlechtendalia chinensis, resulting in the formation of the Chinese gallnut (CG). Here, we report a chromosomal-level genome assembly of R. chinensis, with a total size of 389.40 Mb and scaffold N50 of 23.02 Mb. Comparative genomic and transcriptome analysis revealed that the enhanced structure of CG and nutritional metabolism contribute to improving the adaptability of R. chinensis to S. chinensis by supporting CG and galling aphid growth. CG was observed to be abundant in hydrolysable tannins (HT), particularly gallotannin and its isomers. Tandem repeat clusters of dehydroquinate dehydratase/shikimate dehydrogenase (DQD/SDH) and serine carboxypeptidase-like (SCPL) and their homologs involved in HT production were determined as specific to HT-rich species. The functional differentiation of DQD/SDH tandem duplicate genes and the significant contraction in the phenylalanine ammonia-lyase (PAL) gene family contributed to the accumulation of gallic acid and HT while minimizing the production of shikimic acid, flavonoids, and condensed tannins in CG. Furthermore, we identified one UDP glucosyltransferase (UGT84A), three carboxylesterase (CXE), and six SCPL genes from conserved tandem repeat clusters that are involved in gallotannin biosynthesis and hydrolysis in CG. We then constructed a regulatory network of these genes based on co-expression and transcription factor motif analysis. Our findings provide a genomic resource for the exploration of the underlying mechanisms of plant-galling insect interaction and highlight the importance of the functional divergence of tandem duplicate genes in the accumulation of secondary metabolites.

Catalytic Asymmetric Synthesis of 3,3'-Bisindoles Bearing Single Axial Chirality.

A catalytic asymmetric synthesis of 3,3'-bisindoles bearing single axial chirality has been established via chiral phosphoric acid (CPA)-catalyzed enantioselective addition reaction of 3,3'-bisindoles with ninhydrin-derived 3-indolylmethanols. The selection of ninhydrin-derived 3-indolylmethanols as suitable electrophiles is based on the consideration that the symmetric and bulky moiety of ninhydrin would increase the steric congestion around the axis to generate stable axial chirality and avoid the generation of central chirality. By this approach, a series of 3,3'-bisindoles bearing single axial chirality were synthesized via the dynamic kinetic resolution (DKR) process in generally acceptable yields and considerable enantioselectivities. In addition, an in-depth investigation on the property (stability and rotation barrier) of the synthesized axially chiral 3,3'-bisindoles was carried out, thus providing useful information on this class of axially chiral frameworks. This approach makes use of the strategy of dynamic kinetic resolution of 3,3'-bisindoles, therefore expanding the generality and applicability of this strategy for catalytic asymmetric synthesis of 3,3'-bisindoles bearing single axial chirality.

Genome size is not correlated with effective population size in the Oryza species.

Genome sizes vary widely across the tree of life and the evolutionary mechanism underlined remains largely unknown. Lynch and Conery (2003) proposed that evolution of genome complexity was driven mainly by nonadaptive stochastic forces and presented the observation that genome size was negatively correlated with effective population size (N(e)) as a strong support for their hypothesis. Here, we analyzed the relation between N(e) and genome size for 10 diploid Oryza species that showed about fourfold genome size variation. Using sequences of more than 20 nuclear genes, we estimated N(e) for each species after correction for the effects of demography and heterogeneity of mutation rates among loci and species. Pairwise comparisons and correlation analyses did not detect a negative relationship between N(e) and genome size despite about 6.5-fold interspecies N(e) variation. By calculating phylogenetically independent contrasts (PICs) for N(e), we repeated correlation analysis and did not find any correlation between N(e) and genome size. These observations suggest that the genome size variation in the Oryza species cannot be explained simply by the effect of effective population size.

Microsatellite markers for Dayaoshania cotinifolia (Gesneriaceae), a critically endangered perennial herb.

PREMISE OF THE STUDY: Microsatellite primers were developed for the critically endangered species Dayaoshania cotinifolia (Gesneriaceae) to evaluate population genetic diversity and detect population history. • METHODS AND RESULTS: In our study, 15 primer sets were developed using an enriched genomic library. These are the first microsatellite loci developed for this genus. Genetic diversity was measured using 40 individuals. The number of alleles per locus ranged from one to six, and the incidence of observed heterozygosities was 0.365 and 0.410 in two populations. • CONCLUSIONS: The described markers will be useful in future population genetics studies of this critically endangered species.

Isolation and characterization of 50 nuclear microsatellite markers for Cathaya argyrophylla, a Chinese endemic conifer.

PREMISE OF THE STUDY: Microsatellite primers were developed for the endangered Cathaya argyrophylla (Pinaceae) to investigate its genetic diversity and population genetic structure, as well as its evolutionary history. • METHODS AND RESULTS: Fifty dinucleotide microsatellite loci were identified in two populations. The number of alleles per locus ranged from 1 to 6, with a mean of 2.84. The observed and expected heterozygosities ranged from 0 to 0.889 and from 0 to 0.779, respectively. • CONCLUSIONS: These markers will facilitate further studies on the population genetics and evolutionary history of Cathaya argyrophylla.

Development and characterization of microsatellite loci in Taihangia rupestris (Rosaceae), a rare cliff herb.

PREMISE OF THE STUDY: Microsatellite primers were developed for the rare Taihangia rupestris (Rosaceae) to evaluate genetic diversity, population genetic structure, mating system, and demographic events of this species. • METHODS AND RESULTS: Ten primer sets were developed using an enriched genomic library and were successfully amplified in T. rupestris var. ciliata and T. rupestris var. rupestris. The number of alleles per locus ranged from 2 to 21; the observed and expected heterozygosities ranged from 0.300 to 0.950 and from 0.328 to 0.956, respectively, in the two varieties. • CONCLUSIONS: The markers described here will be useful for studies of genetic variation, genetic structure, and mating systems of T. rupestris, which are important for the future conservation of this rare species.