Scutellaria baicalensis Georgi is important in Chinese traditional medicine where preparations of dried roots, ''Huang Qin,'' are used for liver and lung complaints and as complementary cancer treatments. We report a high-quality reference genome sequence for S. baicalensis where 93% of the 408.14-Mb genome has been assembled into nine pseudochromosomes with a super-N50 of 33.2 Mb. Comparison of this sequence with those of closely related species in the order Lamiales, Sesamum indicum and Salvia splendens, revealed that a specialized metabolic pathway for the synthesis of 4 0 -deoxyflavone bioactives evolved in the genus Scutellaria. We found that the gene encoding a specific cinnamate coenzyme A ligase likely obtained its new function following recent mutations, and that four genes encoding enzymes in the 4 0 -deoxyflavone pathway are present as tandem repeats in the genome of S. baicalensis. Further analyses revealed that gene duplications, segmental duplication, gene amplification, and point mutations coupled to gene neo-and subfunctionalizations were involved in the evolution of 4 0 -deoxyflavone synthesis in the genus Scutellaria. Our study not only provides significant insight into the evolution of specific flavone biosynthetic pathways in the mint family, Lamiaceae, but also will facilitate the development of tools for enhancing bioactive productivity by metabolic engineering in microbes or by molecular breeding in plants. The reference genome of S. baicalensis is also useful for improving the genome assemblies for other members of the mint family and offers an important foundation for decoding the synthetic pathways of bioactive compounds in medicinal plants.

Aim Many subtropical organisms exhibit an East Asian‐Tethyan disjunction, a distribution split between East Asia and the Mediterranean. The underlying mechanisms and timing have remained unclear to date. The evolutionary history of Quercus section Ilex Loudon, a representative East Asian‐Tethyan disjunct lineage with a rich and widespread fossil record, was investigated to understand the key drivers of this disjunction. Location Eurasia. Methods The phylogeny of Quercus section Ilex was reconstructed using RAD‐seq. Divergence times were estimated based on three fossil calibrations. Ancestral range and niche were reconstructed on the calibrated tree to infer the timing of transitions in geographic distributions and niche. Convergence in ecological space was estimated by fitting alternative multiple‐regime Ornstein‐Uhlenbeck models. Leaf shape affinities among extant and fossil taxa of section Ilex were assessed using geometric morphometric approaches. Results Six clades were well resolved in section Ilex. Ancestral range reconstruction and divergence time dating suggest a wide distribution along the East Tethys seaway, with initial divergence at the mid‐Eocene, and all six clades originating before the Miocene. The section dispersed from East Asia to the Mediterranean at the Eocene‐Oligocene boundary. A shift toward higher elevations was detected in the Himalayan clade during the middle or late Miocene. European fossil lineages during the early Miocene differ in leaf morphology from later lineages, which we infer to be a consequence of adaptive differentiation or species turnover. Main conclusions Quercus section Ilex was widespread along the East Tethys seaway from the middle Eocene onward. The European holly oaks originated from an East Asian ancestral lineage that dispersed to Europe via the Tibet‐Himalaya corridor in the Oligocene. Lowlands along the margins of the Himalayas and through an Oligocene Tibetan valley served as the dispersal route(s) for these species. Changing climates drove Miocene extinction and local adaptation of European lineages.

Many important crops (e.g., tuber, root, and tree crops) are cross-pollinating. For these crops, no inbred lines are available for genetic study and breeding because they are self-incompatible, clonally propagated, or have a long generation time, making the identification of agronomically important genes difficult, particularly in crops with a complex autopolyploid genome. In this study, we developed a method, OutcrossSeq, for mapping agronomically important loci in outcrossing crops based on whole-genome low-coverage resequencing of a large genetic population, and designed three computation algorithms in OutcrossSeq for different types of outcrossing populations. We applied OutcrossSeq to a tuberous root crop (sweet potato, autopolyploid), a tree crop (walnut tree, highly heterozygous diploid), and hybrid crops (double-cross populations) to generate high-density genotype maps for the outcrossing populations, which enable precise identification of genomic loci underlying important agronomic traits. Candidate causative genes at these loci were detected based on functional clues. Taken together, our results indicate that OutcrossSeq is a robust and powerful method for identifying agronomically important genes in heterozygous species, including polyploids, in a cost-efficient way. The OutcrossSeq software and its instruction manual are available for downloading at www.xhhuanglab.cn/tool/OutcrossSeq.html.

The hexaploid sweet potato is one of the most important root crops worldwide. However, its genetic origins, especially that of its tetraploid progenitor, are unclear. In this study, we conceived a pipeline consisting of a genome-wide variation-based phylogeny and a novel haplotype-based phylogenetic analysis (HPA) to determine that the tetraploid accession CIP695141 of Ipomoea batatas 4x from Peru is the tetraploid progenitor of sweet potato. We detected biased gene exchanges between subgenomes. The B1 to B2 subgenome conversions were almost 3-fold higher than the B2 to B1 subgenome conversions. Our analyses revealed that the genes involved in storage root formation, sugar transport, stress resistance, and maintenance of genome stability have been selected during the speciation and domestication of sweet potato. This study sheds lights on the evolution of sweet potato and paves a way for the improvement of sweet potato.

The East Asian subtropics mostly occupied by evergreen broad-leaved forests (EBLFs), is one of the global diversity centers for evergreen oaks. Evergreen oaks are keystone canopy trees in EBLFs with important ecosystem function and crucial significance for regional biodiversity conservation. However, the species composition and diversity of Asian evergreen oaks are poorly understood. Here, we test whether the four chloroplast markers atpI-atpH, matK, psbA-trnH, and ycf1, can discriminate the two evergreen oak sections in Asia – Cyclobalanopsis and Ilex. Two hundred and seventy-two individuals representing 57 species were scanned and 17 species from other oaks sections were included for phylogenetic reconstruction. The genetic diversity of the Quercus sections was also compared. Overall, we found that universal chloroplast DNA (cpDNA) barcoding markers could resolve two clades in Quercus, i.e., subgenus Cerris (Old World Clade) and subgenus Quercus (New World Clade). The chloroplast markers distinguished the main sections, with few exceptions. Each cpDNA region showed no barcoding gap and none of them provided good resolution at the species level. The best species resolution (27.78%) was obtained when three or four markers were combined and analyzed using BLAST. The high conservation of the cpDNA and complicated evolutionary patterns, due to incomplete lineage sorting, interspecific hybridization and introgressions may hinder the ability of cpDNA markers to discriminate different species. When comparing diversification pattern across Quercus sections (Cyclobalanopsis, Ilex, Cerris, Quercus, and Protobalanus), we found that section Ilex was the most genetically diverse, and section Cyclobalanopsis was lower genetically diverse. This diversification pattern may have resulted from the interplay of the Eurasia Cenozoic tectonic movements, climate changes and different niches of their ancestral lineages.

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Scutellaria baicalensis, is one of the most traditional medicinal plants in the Lamiaceae family, and has been widely used to treat liver and lung complaints and as a complementary cancer treatment in traditional Chinese medicine. The preparation from its roots, called “Huang Qin,” is rich in specialized flavones such as baicalein, wogonin, and their glycosides which lack a 4′-hydroxyl group on the B ring (4′-deoxyflavones), with anti-tumor, antioxidant, and antiviral activities. Baicalein has recently been reported to inhibit the replication of the COVID-19 virus. These 4′-deoxyflavones are found only in the order Lamiales and were discovered in the genus Scutellaria, suggesting that a new metabolic pathway synthesizing 4′-deoxyflavones evolved recently in this genus. In this review, we focus on the class of 4′-deoxyflavones in S. baicalensis and their pharmacological properties. We also describe the apparent evolutionary route taken by the genes encoding enzymes involved in the novel, root-specific, biosynthetic pathway for baicalein and wogonin, which provides insights into the evolution of specific flavone biosynthetic pathways in the mint family.