Multi-omics analysis reveals the evolutionary origin of diterpenoid alkaloid biosynthesis pathways in Aconitum

Diterpenoid alkaloids(DAs) have been often utilized in clinical practice due to their analgesic and anti-infammatory properties. Natural DAs are prevalent in the family Ranunculaceae, notably in the Aconitum genus. Nevertheless, the evolutionary origin of the biosynthesis pathway responsible for DA production remains unknown.In this study, we successfully assembled a highquality, pseudochromosome-level genome of the DA-rich species Aconitum vilmorinianum(A.vilmorinianum)(5.76 Gb). An A. vilmorinianumspecific whole-genome duplication event was discovered using comparative genomic analysis,which may aid in the evolution of the DA biosynthesis pathway. We identified several genes involved in DA biosynthesis via integrated genomic, transcriptomic, and metabolomic analyses. These genes included enzymes encoding target ent-kaurene oxidases and aminotransferases, which facilitated the activation of diterpenes and insertion of nitrogen atoms into diterpene skeletons, thereby mediating the transformation of diterpenes into DAs. The divergence periods of these genes in A. vilmorinianum were further assessed, and it was shown that two major types of genes were involved in the establishment of the DA biosynthesis pathway. Our integrated analysis offers fresh insights into the evolutionary origin of DAs in A.vilmorinianum as well as suggestions for engineering the biosynthetic pathways to obtain desired DAs.

What are the evolutionary origins of stomatal responses to abscisic acid in land plants?

The evolution of active stomatal closure in response to leaf water deficit, mediated by the hormone abscisic acid （ABA）, has been the subject of recent debate. Two different models for the timing of the evolution of this response recur in the literature. A single-step model for stomatal control suggests that stomata evolved active, ABA- mediated control of stomatal aperture, when these structures first appeared, prior bryophyte and vascular plant gradualistic model for stomatal to the divergence of neages. In contrast, a control proposes that the most basal vascular plant stomata responded passively to changes in leaf water status. This model suggests that active ABA-driven mechanisms for stomatal responses to water status instead evolved after the divergence of seed plants, culminating in the complex, ABA-mediated responses observed in modern angiosperms. Here we review the findings that form the basis for these two models, including recent work that provides critical molecular insights into resolving this intriguing debate, and find strong evidence to support a gradualistic model for stomatal evolution.

A Mesozoic Pompeii: History of the Jehol Biota's Rise and Fall

The Jehol fauna was initially represented by a bony fish, concostracan and an insect, as a Lycoptera davidi-Eosestheria-Ephemeropsis trisetalis association,but since the researches of recent decades, the Jehol Biota is now completely different from the past low-diversity, and encompasses a native terrestrial biota that includes many well-preserved vertebrates, invertebrates and plants. There are more than 20 important biological categories, thousands of taphonomically unusual fossils, especially noted for the wide variety of biological tissues. The Jehol Biota has caused a sensation in the world with its wide distribution, large quantity, great variety, fine preservation and detailed information, which records the rise and fall of the numerous taxa, and provides significant evidence for three origins： of birds, eutherian mammals, and angiosperms. The Jehol Biota is a highlight of basic scientific research in China, and we honor it as a world-class fossil treasury and ＂a Mesozoic Pompeii＂.

Cloning and Sequence Analysis of lef-3 Gene from Pieris rapae Granulovirus

To better understand the origination and evolution of lef-3 gene from baculovirus genome and determine the relationships between various viruses at molecular level, late expression factor 3 gene （lef-3） fragments of Pieris rapae granulovirus were obtained through conventional PCR method and sequenced after cloned into T-vector. Then, bioinformatics analysis on lef-3 gene and its encoding sequences were conducted by using bid-softs. Four mutations were appeared in the ORF of cloned lef-3 gene, which did not alter the characteristics of amino acids. It was inferred that PiraGV LEF-3 protein contained 399 amino acids, the molecular weight of which was 3.99 kD. Prediction of the LEF-3 advanced structure and homology comparison between other LEF-3 from various baculoviruses showed that the lef-3 gene might encode the single-stranded DNA-binding protein. The result of BLAST revealed that the lef-3 gene only existed in Lepidoptera host for the baculovirus genome, and the evolution analysis illustrated that lef-3 gene could be divided into 3 groups including one granulovirus （GV） group and 2 nucleopolyhedrovirus （NPV） groups. The selection pressure analysis of GV lef-3 gene coding region showed that the majority of lef-3 genes performed negative selection, while the Ka/Ks differed from different lef-3 gene, to some extent, which also performed positive selection. The origination analysis revealed that lef-3 gene of baculovirus might derive from bacteria. The lef-3 gene of PiraGV was cloned successfully and the possible patterns of origination and evolution were speculated through bioinformatics analysis.

Cloning,Sequencing of F and HN Genes and Molecular Characteristics of Goose Paramyxovirus BZ02 Isolate

[ Objective] The aim of this study was to clone and sequence F and HN genes of the isolated goose paramyxovirus and thus further investigate on its pathogenesis and evolutionary origins. [ Method] According to the published F and HN gene sequences of Avian Paramyxovirus Typelat home and abroad, two pairs of primers （ FF, FR; HNF, HNR） were designed by DNAstar software, and Fand HNgenes were also amplified by PCR. The PCR products were recovered and ligated to T vector, while the positive clones were identified by ampicillin plate screening and PCR. After bacteria shaking, the plasmid was extracted and sent to Shanghai Sangon for sequencing. The sequences were compared with the sequences in GenBank, and the phylogenetic tree was drawn by DNAstar software. Meanwhile, the phylogenetic analysis of amino acid residues was also studied. [Result] The ORF of Fgene was 1 662 bp encoding 553 amino acids, and its cleavage site was 112R-R-Q-K-R-F117, which was consistent with the characteristics of virulent strains. 101-bit and 121-bit amino acid residues were K （Lys） and D （Asp）. The ORF of HN gene was 1 716 bp encoding 571 amino acids. The homology of HN sequence in 29 strains of goose paramyxovirus to YG97 was the highest, accounting for 99.6%. Analysis of glycosylation sites revealed that glycosylation site of BZ02 strain at 538 -540aa disappeared. The phylogenetic tree drawn by HN genes was highly consistent with that drawn by Fgenes. Compared with the homology of F and HN nucleotide sequence of the published typelgoose paramyxovirus in China, BZ02, JG97, HG97 and YG97 were divided into the same sub-group, and the nucleotide and amino acid sequences homologies were highest between BZ02 and YG97 strain. E Condusionl BZ02, JG97, HG97 and YG97 have the same evolutionary origin or all originate from YG97.

Evidence for a mouse origin of the SARS-CoV-2 Omicron variant

The rapid accumulation of mutations in the SARS-CoV-2 Omicron variant that enabled its outbreak raises questions as to whether its proximal origin occurred in humans or another mammalian host. Here, we identified 45 point mutations that Omicron acquired since divergence from the B.1.1 lineage. We found that the Omicron spike protein sequence was subjected to stronger positive selection than that of any reported SARS-CoV-2 variants known to evolve persistently in human hosts, suggesting a possibility of hostjumping. The molecular spectrum of mutations(i.e., the relative frequency of the 12 types of base substitutions) acquired by the progenitor of Omicron was significantly different from the spectrum for viruses that evolved in human patients but resembled the spectra associated with virus evolution in a mouse cellular environment. Furthermore, mutations in the Omicron spike protein significantly overlapped with SARS-CoV-2 mutations known to promote adaptation to mouse hosts, particularly through enhanced spike protein binding affinity for the mouse cell entry receptor. Collectively, our results suggest that the progenitor of Omicron jumped from humans to mice, rapidly accumulated mutations conducive to infecting that host,then jumped back into humans, indicating an inter-species evolutionary trajectory for the Omicron outbreak.

Host-specific asymmetric accumulation of mutation types reveals that the origin of SARS-CoV-2 is consistent with a natural process

The capacity of RNA viruses to adapt to new hosts and rapidly escape the host immune system is largely attributable to de novo genetic diversity that emerges through mutations in RNA.Although the molecular spectrum of de novo mutations—the relative rates at which various base substitutions occur—are widely recognized as informative toward understanding the evolution of a viral genome,little attention has been paid to the possibility of using molecular spectra to infer the host origins of a virus.Here,we characterize the molecular spectrum of de novo mutations for SARS-CoV-2 from transcriptomic data obtained from virus-infected cell lines,enabled by the use of sporadic junctions formed during discontinuous transcription as molecular barcodes.We find that de novo mutations are generated in a replication-independent manner,typically on the genomic strand,and highly dependent on mutagenic mechanisms specific to the host cellular environment.De novo mutations will then strongly influence the types of base substitutions accumulated during SARS-CoV-2 evolution,in an asymmetric manner favoring specific mutation types.Consequently,similarities between the mutation spectra of SARS-CoV-2 and the bat coronavirus RaTG13,which have accumulated since their divergence strongly suggest that SARS-CoV-2 evolved in a host cellular environment highly similar to that of bats before its zoonotic transfer into humans.Collectively,our findings provide data-driven support for the natural origin of SARS-CoV-2.