No abstract

Lauraceae includes the genus Phoebe, and the family is linked to the evolution of magnoliids. We sequenced the genome of Phoebe bournei Nanmu. The assembled genome size was 989.19 Mb, with a contig N50 value of 2.05 Mb. A total of 28,198 protein-coding genes were annotated in P. bournei. Whole-genome duplication (WGD) analysis showed that Lauraceae has experienced two WGD events; the older WGD event occurred just before the divergence of Lauraceae and Magnoliales, and the more recent WGD was shared by all lineages of Lauraceae. The phylogenetic tree showed that magnoliids form a sister clade to monocots and eudicots. We also identified 63 MADS-box genes, including AGL12-like genes that may be related to the regulation of P. bournei roots and FIN219-like genes encoding GH3 proteins, which are involved in photomorphogenesis. SAUR50-like genes involved in light signal-mediated pedicel or stem development were also identified. Four ATMYB46-and three PtrEPSP-homologous genes related to lignin biosynthesis were identified. These genes may be associated with the formation of straight trunks in P. bournei. Overall, the P. bournei reference genome provides insight into the origin, evolution, and diversification of Phoebe and other magnoliids.

Plant anthocyanin biosynthesis is well understood, but the regulatory mechanism in purple foliage tea remains unclear. Using isobaric tag for relative and absolute quantification (iTRAQ), 815 differential proteins were identified in the leaves of Zijuan tea, among which 20 were associated with the regulation of anthocyanin metabolism. We found that the abundances of anthocyanin synthesis-related enzymes such as chalcone synthase, chalcone isomerase, dihydroflavonol 4-reductase and anthocyanin synthetase, as well as anthocyanin accumulation-related UDP-glucosyl transferase and ATP-binding cassette (ABC) transporters in the purple leaves were all significantly higher than those in the green leaves. The abundances of the transcription factors bHLH and HY5, regulating anthocyanin biosynthesis at transcriptional level were also obviously higher in purple leaves than those in green leaves. In addition, bifunctional 3-dehydroquinate dehydratase and chorismate mutase in purple leaves were distinctly higher in abundance compared to green leaves, which provided sufficient phenylalanine substrate for anthocyanin synthesis. Furthermore, lignin synthesis was found to be reduced due to the lower abundances of cinnamoyl-CoA reductase 1, peroxidase 15 and laccase-6, which resulted in increase of intermediates flow into anthocyanin synthesis pathway. The physiological data were consistent with proteomic results. These four aspects of biosynthetic regulation contribute to anthocyanin accumulation in purple leaves of Zijuan tea.

To improve our understanding of the origin and evolution of mycoheterotrophic plants, we here present the chromosome-scale genome assemblies of two sibling orchid species: partially mycoheterotrophic Platanthera zijinensis and holomycoheterotrophic Platanthera guangdongensis. Comparative analysis shows that mycoheterotrophy is associated with increased substitution rates and gene loss, and the deletion of most photoreceptor genes and auxin transporter genes might be linked to the unique phenotypes of fully mycoheterotrophic orchids. Conversely, trehalase genes that catalyse the conversion of trehalose into glucose have expanded in most sequenced orchids, in line with the fact that the germination of orchid non-endosperm seeds needs carbohydrates from fungi during the protocorm stage. We further show that the mature plant of P. guangdongensis, different from photosynthetic orchids, keeps expressing trehalase genes to hijack trehalose from fungi. Therefore, we propose that mycoheterotrophy in mature orchids is a continuation of the protocorm stage by sustaining the expression of trehalase genes. Our results shed light on the molecular mechanism underlying initial, partial and full mycoheterotrophy.

The marvelously diverse Orchidaceae constitutes the largest family of angiosperms. The genus Cymbidium in Orchidaceae is well known for its unique vegetation, floral morphology, and flower scent traits. Here, a chromosome-scale assembly of the genome of Cymbidium ensifolium (Jianlan) is presented. Comparative genomic analysis showed that C. ensifolium has experienced two whole-genome duplication (WGD) events, the most recent of which was shared by all orchids, while the older event was the τ event shared by most monocots. The results of MADS-box genes analysis provided support for establishing a unique gene model of orchid flower development regulation, and flower shape mutations in C. ensifolium were shown to be associated with the abnormal expression of MADS-box genes. The most abundant floral scent components identified included methyl jasmonate, acacia alcohol and linalool, and the genes involved in the floral scent component network of C. ensifolium were determined. Furthermore, the decreased expression of photosynthesis-antennae and photosynthesis metabolic pathway genes in leaves was shown to result in colorful striped leaves, while the increased expression of MADS-box genes in leaves led to perianth-like leaves. Our results provide fundamental insights into orchid evolution and diversification.

To elucidate chloroplast genome evolution within neotropical-paleotropical bamboos, we fully characterized the chloroplast genome of the woody bamboo Guadua angustifolia. This genome is 135,331 bp long and comprises of an 82,839-bp large single-copy (LSC) region, a 12,898-bp small single-copy (SSC) region, and a pair of 19,797-bp inverted repeats (IRs). Comparative analyses revealed marked conservation of gene content and sequence evolutionary rates between neotropical and paleotropical woody bamboos. The neotropical herbaceous bamboo Cryptochloa strictiflora differs from woody bamboos in IR/SSC boundaries in that it exhibits slightly contracted IRs and a faster substitution rate. The G. angustifolia chloroplast genome is similar in size to that of neotropical herbaceous bamboos but is ~3 kb smaller than that of paleotropical woody bamboos. Dissimilarities in genome size are correlated with differences in the lengths of intergenic spacers, which are caused by large-fragment insertion and deletion. Phylogenomic analyses of 62 taxa yielded a tree topology identical to that found in preceding studies. Divergence time estimation suggested that most bamboo genera diverged after the Miocene and that speciation events of extant species occurred during or after the Pliocene.

BackgroundCamellia species are ancient oilseed plants with a history of cultivation over two thousand years. Prior to oil extraction, natural seed drying is often practiced, a process affecting fatty acid quality and quantity. MicroRNAs (miRNA) of lipid metabolism associated with camellia seed natural drying are unexplored. To obtain insight into the function of miRNAs in lipid metabolism during natural drying, Illumina sequencing of C. oleifera and C. meiocarpa small-RNA was conducted.ResultsA total of 274 candidate miRNAs were identified and 3733 target unigenes were annotated by performing a BLASTX. Through integrated GO and KEGG function annotation, 23 miRNA regulating 131 target genes were identified as lipid metabolism, regulating fatty acid biosynthesis, accumulation and catabolism. We observed one, two, and four miRNAs of lipid metabolism which were specially expressed in C. Meiocarpa, C. oleifera, and the two species collectively, respectively. At 30% moisture contents, C. meiocarpa and C. oleifer produced nine and eight significant differentially expressed miRNAs, respectively, with high fatty acid synthesis and accumulation activities. Across the two species, 12 significant differentially expressed miRNAs were identified at the 50% moisture content.ConclusionsSequencing of small-RNA revealed the presence of 23 miRNAs regulating lipid metabolism in camellia seed during natural drying and permitted comparative miRNA profiles between C. Meiocarpa and C. oleifera. Furthermore, this study successfully identified the best drying environment at which the quantity and quality of lipid in camellia seed are at its maximum.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3923-z) contains supplementary material, which is available to authorized users.

No abstract