Lineage-Specific CYP80 Expansion and Benzylisoquinoline Alkaloid Diversity in Early-Diverging Eudicots.

Menispermaceae species, as early-diverging eudicots, can synthesize valuable benzylisoquinoline alkaloids (BIAs) like bisbenzylisoquinoline alkaloids (bisBIAs) and sinomenines with a wide range of structural diversity. However, the evolutionary mechanisms responsible for their chemo-diversity are not well understood. Here, a chromosome-level genome assembly of Menispermum dauricum is presented and demonstrated the occurrence of two whole genome duplication (WGD) events that are shared by Ranunculales and specific to Menispermum, providing a model for understanding chromosomal evolution in early-diverging eudicots. The biosynthetic pathway for diverse BIAs in M. dauricum is reconstructed by analyzing the transcriptome and metabolome. Additionally, five catalytic enzymes - one norcoclaurine synthase (NCS) and four cytochrome P450 monooxygenases (CYP450s) - from M. dauricum are responsible for the formation of the skeleton, hydroxylated modification, and C-O/C-C phenol coupling of BIAs. Notably, a novel leaf-specific MdCYP80G10 enzyme that catalyzes C2'-C4a phenol coupling of (S)-reticuline into sinoacutine, the enantiomer of morphinan compounds, with predictable stereospecificity is discovered. Moreover, it is found that Menispermum-specific CYP80 gene expansion, as well as tissue-specific expression, has driven BIA diversity in Menispermaceae as compared to other Ranunculales species. This study sheds light on WGD occurrences in early-diverging eudicots and the evolution of diverse BIA biosynthesis.

A Phylogenetic and Morphological Evolution Study of Ribes L. in China Using RAD-Seq.

Ribes L. belongs to the Grossulariaceae family and has important edible, medicinal, ornamental, and landscaping values. Taxonomic classification within this genus is difficult due to its large variety of species, wide distribution, large morphological variations, and presence of two complex taxonomic groups with bisexual or unisexual flowers. Our study aims to clarify the phylogenetic relationships of Ribes L. taxa in China, and further, to provide a reference for a revised global classification of it. The phylogenetic analysis of 52 Ribes L. samples from 30 species was constructed based on restriction site-associated DNA sequencing and single nucleotide polymorphisms. Afterward, two important taxonomic characters were selected for ancestral state reconstruction over the molecular phylogeny. The results showed that the 52 samples could be divided into six branches, i.e., six subgenera, which caused some controversy regarding the morphological classification of Ribes L. in China. The molecular phylogeny supported the separation of subg. Coreosma from subg. Ribesia and subg. Hemibotrya from subg. Berisia and validated the rationale for recognizing subg. Grossularia as an independent subgenus, the rationality of which was further verified by the reconstruction of ancestor traits. Gene flow among Ribes L. was identified and further confirmed our results.

The ncRNAs Involved in the Regulation of Abiotic Stress-Induced Anthocyanin Biosynthesis in Plants.

Plants have evolved complicated defense and adaptive systems to grow in various abiotic stress environments such as drought, cold, and salinity. Anthocyanins belong to the secondary metabolites of flavonoids with strong antioxidant activity in response to various abiotic stress and enhance stress tolerance. Anthocyanin accumulation often accompanies the resistance to abiotic stress in plants to scavenge reactive oxygen species (ROS). Recent research evidence showed that many regulatory pathways such as osmoregulation, antioxidant response, plant hormone response, photosynthesis, and respiration regulation are involved in plant adaption to stress. However, the molecular regulatory mechanisms involved in controlling anthocyanin biosynthesis in relation to abiotic stress response have remained obscure. Here, we summarize the current research progress of specific regulators including small RNAs, and lncRNAs involved in the molecular regulation of abiotic stress-induced anthocyanin biosynthesis. In addition, an integrated regulatory network of anthocyanin biosynthesis controlled by microRNAs (miRNAs), long non-coding RNAs (lncRNAs), transcription factors, and stress response factors is also discussed. Understanding molecular mechanisms of anthocyanin biosynthesis for ROS scavenging in various abiotic stress responses will benefit us for resistance breeding in crop plants.

Comparative Analysis of Chloroplast Genome and New Insights Into Phylogenetic Relationships of Polygonatum and Tribe Polygonateae.

Members of Polygonatum are perennial herbs that have been widely used in traditional Chinese medicine to invigorate Qi, moisten the lung, and benefit the kidney and spleen among patients. However, the phylogenetic relationships and intrageneric taxonomy within Polygonatum have long been controversial because of the complexity of their morphological variations and lack of high-resolution molecular markers. The chloroplast (cp) genome is an optimal model for deciphering phylogenetic relationships in related families. In the present study, the complete cp genome of 26 species of Trib. Polygonateae were de novo assembled and characterized; all species exhibited a conserved quadripartite structure, that is, two inverted repeats (IR) containing most of the ribosomal RNA genes, and two unique regions, large single sequence (LSC) and small single sequence (SSC). A total of 8 highly variable regions (rps16-trnQ-UUG, trnS-GCU-trnG-UCC, rpl32-trnL-UAG, matK-rps16, petA-psbJ, trnT-UGU-trnL-UAA, accD-psaI, and trnC-GCA-petN) that might be useful as potential molecular markers for identifying Polygonatum species were identified. The molecular clock analysis results showed that the divergence time of Polygonatum might occur at ∼14.71 Ma, and the verticillate leaf might be the ancestral state of this genus. Moreover, phylogenetic analysis based on 88 cp genomes strongly supported the monophyly of Polygonatum. The phylogenetic analysis also suggested that Heteropolygonatum may be the sister group of the Polygonatum, but the Disporopsis, Maianthemum, and Disporum may have diverged earlier. This study provides valuable information for further species identification, evolution, and phylogenetic research of Polygonatum.

A high-quality genome sequence of alkaligrass provides insights into halophyte stress tolerance.

Alkaligrass (Puccinellia tenuiflora) is a monocotyledonous halophytic forage grass widely distributed in Northern China. It belongs to the Gramineae family and shares a close phylogenetic relationship with the cereal crops, wheat and barley. Here, we present a high-quality chromosome-level genome sequence of alkaligrass assembled from Illumina, PacBio and 10× Genomics reads combined with genome-wide chromosome conformation capture (Hi-C) data. The ∼1.50 Gb assembled alkaligrass genome encodes 38,387 protein-coding genes, and 54.9% of the assembly are transposable elements, with long terminal repeats being the most abundant. Comparative genomic analysis coupled with stress-treated transcriptome profiling uncovers a set of unique saline- and alkaline-responsive genes in alkaligrass. The high-quality genome assembly and the identified stress related genes in alkaligrass provide an important resource for evolutionary genomic studies in Gramineae and facilitate further understanding of molecular mechanisms underlying stress tolerance in monocotyledonous halophytes. The alkaligrass genome data is freely available at http://xhhuanglab.cn/data/alkaligrass.html .

Thladiantha Dubia Mosaic Virus: A Novel Potyvirus Infecting Manchurian Tubergourd (Thladiantha dubia) in Northeast China.

A new virus with flexuous, filamentous particles approximately 650 nm long was discovered in Manchurian tubergourd (Thladiantha dubia Bunge) leaves exhibiting severe mosaic symptoms. The whole genome sequence of the virus was determined by reverse transcription-polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE). The entire genome consisted of 10,112 nucleotides (nt) excluding the poly (A) tail, which shared the highest nucleotide sequence identity (73.8%) with that of papaya leaf distortion mosaic virus Hainan-DF isolate (PLDMV-Hainan-DF). A phylogenetic analysis showed that this virus clustered with PLDMV isolates in a subbranch within the potyviral clade. Of the 23 species of indicator plants tested, only potato and its original host were systemically infected by the virus tested upon mechanical inoculation. A field survey showed that the virus was widely distributed on T. dubia and potatoes in Northeast China. Moreover, this virus displayed a high degree of genetic variation as evaluated by the sequences of the coat protein (CP) gene. Based on these results, the name Thladiantha dubia mosaic virus (ThDMV) is proposed for this new potyvirus.

Complete chloroplast genome sequence of an endangered tree species, Magnolia sieboldii (Magnoliaceae).

The characteristic of complete chloroplast (cp) genome of Magnolia sieboldii, an endangered species in China, was first sequenced in this study. It showed a typical quadripartite structure with a length of 160,177 bp. It composed of a large single copy (LSC) region of 88,238 bp, a small single copy (SSC) region of 18,763 bp, and a pair of inverted repeat (IR) regions of 26,588 bp. Further maximum parsimony phylogenetic analysis was performed based on 38 complete plastomes from 30 magnoliids and basal angiosperm species. The result supported a close relationship among M. grandiflora, M. officinals, M. sieboldii, and M. tripetala.

Studies on the regioselective nucleophilic aromatic substitution (S(N)Ar) reaction of 2-substituted 3,5-dichloropyrazines.

Differences in regioselectivity were observed during the S(N)Ar reaction of amines with unsymmetrical 3,5-dichloropyrazines. This study revealed that when the 2-position of the pyrazine was occupied with an electron-withdrawing group (EWG), nucleophilic attack occurred preferentially at the 5-position. When the 2-position was substituted with an electron-donating group (EDG), nucleophilic attack occurred preferentially at the 3-position. These results are reported along with a computational rationale for the experimental observations based on the Fukui index at the reacting centers.