A high-quality Bougainvillea genome provides new insights into evolutionary history and pigment biosynthetic pathways in the Caryophyllales.

Bougainvillea is a perennial ornamental shrub that is highly regarded in ornamental horticulture around the world. However, the absence of genome data limits our understanding of the pathways involved in bract coloration and breeding. Here, we report a chromosome-level assembly of the giga-genome of Bougainvillea × buttiana 'Mrs Butt', a cultivar thought to be the origin of many other Bougainvillea cultivars. The assembled genome is ~5 Gb with a scaffold N50 of 151 756 278 bp and contains 86 572 genes which have undergone recent whole-genome duplication. We confirmed that multiple rounds of whole-genome multiplication have occurred in the evolutionary history of the Caryophyllales, reconstructed the relationship in the Caryophyllales at whole genome level, and found discordance between species and gene trees as the result of complex introgression events. We investigated betalain and anthocyanin biosynthetic pathways and found instances of independent evolutionary innovations in the nine different Caryophyllales species. To explore the potential formation mechanism of diverse bract colors in Bougainvillea, we analyzed the genes involved in betalain and anthocyanin biosynthesis and found extremely low expression of ANS and DFR genes in all cultivars, which may limit anthocyanin biosynthesis. Our findings indicate that the expression pattern of the betalain biosynthetic pathway did not directly correlate with bract color, and a higher expression level in the betalain biosynthetic pathway is required for colored bracts. This improved understanding of the correlation between gene expression and bract color allows plant breeding outcomes to be predicted with greater certainty.

TMT proteomics analysis of a pseudocereal crop, quinoa (Chenopodium quinoa Willd.), during seed maturation.

Quinoa (Chenopodium quinoa Willd.), an Andean native crop, is increasingly popular around the world due to its high nutritional content and stress tolerance. The production and the popularity of this strategic global food are greatly restricted by many limiting factors, such as seed pre-harvest sprouting, bitter saponin, etc. To solve these problems, the underlying mechanism of seed maturation in quinoa needs to be investigated. In this study, based on the investigation of morphological characteristics, a quantitative analysis of its global proteome was conducted using the combinational proteomics of tandem mass tag (TMT) labeling and parallel reaction monitoring (PRM). The proteome changes related to quinoa seed maturation conversion were monitored to aid its genetic improvement. Typical changes of morphological characteristics were discovered during seed maturation, including mean grain diameter, mean grain thickness, mean hundred-grain weight, palea, episperm color, etc. With TMT proteomics analysis, 581 differentially accumulated proteins (DAPs) were identified. Functional classification analysis and Gene Ontology enrichment analysis showed that most DAPs involved in photosynthesis were downregulated, indicating low levels of photosynthesis. DAPs that participated in glycolysis, such as glyceraldehyde-3-phosphate dehydrogenase, pyruvate decarboxylase, and alcohol dehydrogenase, were upregulated to fulfill the increasing requirement of energy consumption during maturation conversion. The storage proteins, such as globulins, legumins, vicilins, and oleosin, were also increased significantly during maturation conversion. Protein-protein interaction analysis and function annotation revealed that the upregulation of oleosin, oil body-associated proteins, and acyl-coenzyme A oxidase 2 resulted in the accumulation of oil in quinoa seeds. The downregulation of ß-amyrin 28-oxidase was observed, indicating the decreasing saponin content, during maturation, which makes the quinoa "sweet". By the PRM and qRT-PCR analysis, the expression patterns of most selected DAPs were consistent with the result of TMT proteomics. Our study enhanced the understanding of the maturation conversion in quinoa. This might be the first and most important step toward the genetic improvement of quinoa.

Transcriptome comparison reveals candidate genes responsible for the betalain-/anthocyanidin-production in bougainvilleas.

The occurrence of betalains and anthocyanins is mutually exclusive, which is a curious phenomenon in the plant kingdom, and the biochemical mechanisms for this restriction are unknown. In the present study, we performed transcriptome analysis of two betalain-producing species, red Bougainvillea glabra Choisy. 'Sanderiana' (R) and white B. glabra 'Alba' (W) by transcriptome sequencing. In total, we obtained 69692 (Red) and 60727 (White) genes with an average length of 665 and 728bp respectively. Out of 3106 significantly differentially-expressed genes (71%), 1003 were R-specific (32%), and 1605 were W-specific (52%). To validate betalain-/anthocyanidin-biosynthesis genes detected (cytochrome P 450 76AD1 (CYP76AD1), dihydroxy-phenylalanine (DOPA)-4,5-dioxygenase (DODA), cyclo DOPA-5-O-glycosyltransferase (cyclo-DOPA-5-GT) dihydroflavonol 4-reductase (DFR), leucoanthocyanidin dioxygenase (LDOX)), real-time PCR was performed in leaves and three development stages of flowers in four Bougainvilleas, red R, white W, orange Bougainvillea×buttiana 'Salmoea' (O) and purple B. glabra 'Formosa' (P). Contents of betalains were also measured. The results showed that betalains accumulation was consistent with the expression level of DODA in O. A correlation between expression of CYP76AD1 and cyclo-DOPA-5GT and betalains was not discovered. This suggests that production of betacyanins was under the regulation of more complex factors. Both DFR and LDOX responsible for anthocyanidin production were first validated in floral organs and leaves in betalain-producing plants by real-time PCR. These findings suggest a fully functioning anthocyanin pathway, at least, to the stage of LDOX in bougainvilleas.

Chemoselective synthesis of substituted pyrazoles through AgOTf-catalyzed cascade propargylic substitution-cyclization-aromatization.

A cascade AgOTf-catalyzed chemoselective approach to 3,5/1,3-disubstitued pyrazoles from propargylic alcohols and para-tolylsulfonohydrazide has been developed. Good chemoselectivity is observed depending on the different substituents in the alkyne moiety of the propargylic alcohols, generating two different kinds of products through different aromatization mechanisms. The pyrazolo[5,1-a]isoquinoline skeleton can also be effectively constructed by this method through a cascade bicyclization process.

The use of SSRs for predicting the hybrid yield and yield heterosis in 15 key inbred lines of Chinese maize.

A challenge to maize breeders is to predict and identify inbred lines that can produce highly heterotic hybrids precisely. In the present study we surveyed the genetic diversity among 15 elite inbred lines of maize in China with SSR markers and assessed the relationship between SSR marker and hybrid yield/yield heterosis in a diallel set of 105 crosses. Forty-three SSR primers selected from all sixty-three primers gave stable profiles amplified in the sample of 15 inbred lines, which could clearly resolve on 4% metaphor agarose gel. The average number of alleles per SSR locus was 4.44 with a range from 2 to 9. The polymorphism information content (PIC) for the SSR loci varied from 0.28 to 0.81 with a mean of 0.6281. Genetic similarity (GS) among 15 lines was estimated with 191 alleles identified as raw data, the Nei's coefficient of GS ranged from 0.492 for 478 vs HZ4 up to 0.745 for E28 to ZH64 with a mean of 0.619. The cluster diagram based upon the SSR data grouped the 15 lines into families consistent with the yield heterotic response of these. Genetic distance (GD) based on SSR data was significantly correlated with hybrid yield/yield heterosis, the correlation coefficient (r) being 0.5432 and 0.4271 in 1999 and 0.4305 and 0.3614 in 1998 field test, respectively, whereas the determination coefficient (r2) was lower. The correlation between GD based on SSR data and hybrid yield/yield heterosis changed alone with the difference of number and pedigree relationship among parents that were used in this study. SSR makers showed high polymorphism and could be used to assess the relationship between inbred lines of maize, but it was difficult to predict the yield heterosis of maize.