Gap-free genome assembly and comparative analysis reveal the evolution and anthocyanin accumulation mechanism of Rhodomyrtus tomentosa

Rhodomyrtus tomentosa is an important f leshy-fruited tree and a well-known medicinal plant of the Myrtaceae family that is widely cultivated in tropical and subtropical areas of the world.However,studies on the evolution and genomic breeding of R.tomentosa were hindered by the lack of a reference genome.Here,we presented a chromosome-level gap-free T2T genome assembly of R.tomentosa using PacBio and ONT long read sequencing.We assembled the genome with size of 470.35 Mb and contig N50 of∼43.80 Mb with 11 pseudochromosomes.A total of 33382 genes and 239.31 Mb of repetitive sequences were annotated in this genome.Phylogenetic analysis elucidated the independent evolution of R.tomentosa starting from 14.37MYA and shared a recent WGD event with other Myrtaceae species.We identified four major compounds of anthocyanins and their synthetic pathways in R.tomentosa.Comparative genomic and gene expression analysis suggested the coloring and high anthocyanin accumulation in R.tomentosa tends to be determined by the activation of anthocyanin synthesis pathway.The positive selection and up-regulation of MYB transcription factors were the implicit factors in this process.The copy number increase of downstream anthocyanin transport-related OMT and GST gene were also detected in R.tomentosa.Expression analysis and pathway identification enriched the importance of starch degradation,response to stimuli,effect of hormones,and cell wall metabolism during the f leshy fruit development in Myrtaceae.Our genome assembly provided a foundation for investigating the origins and differentiation of Myrtaceae species and accelerated the genetic improvement of R.tomentosa.

A high-quality genome assembly of Morinda officinalis,a famous native southern herb in the Lingnan region of southern China

Morinda officinalis is a well-known medicinal and edible plant that is widely cultivated in the Lingnan region of southern China.Its dried roots(called bajitian in traditional Chinese medicine)are broadly used to treat various diseases,such as impotence and rheumatism.Here,we report a high-quality chromosome-scale genome assembly of M.officinalis using Nanopore single-molecule sequencing and Hi-C technology.The assembled genome size was 484.85Mb with a scaffold N50 of 40.97 Mb,and 90.77%of the assembled sequences were anchored on eleven pseudochromosomes.The genome includes 27,698 protein-coding genes,and most of the assemblies are repetitive sequences.Genome evolution analysis revealed that M.officinalis underwent core eudicotγgenome triplication events but no recent whole-genome duplication(WGD).Likewise,comparative genomic analysis showed no large-scale structural variation after species divergence between M.officinalis and Coffea canephora.Moreover,gene family analysis indicated that gene families associated with plant–pathogen interactions and sugar metabolism were significantly expanded in M.officinalis.Furthermore,we identified many candidate genes involved in the biosynthesis of major active components such as anthraquinones,iridoids and polysaccharides.In addition,we also found that the DHQS,GGPPS,TPS-Clin,TPS04,sacA,and UGDH gene families—which include the critical genes for active component biosynthesis—were expanded in M.officinalis.This study provides a valuable resource for understanding M.officinalis genome evolution and active component biosynthesis.This work will facilitate genetic improvement and molecular breeding of this commercially important plant.

Hysteresis of Dam Slope Safety Factor under Water Level Fluctuations Based on the LEM Coupled with FEM Method

Water level variations have caused numerous dam slope collapse disasters around the world,illustrating the large influence of water level fluctuations on dam slopes.The required indoor tests were conducted and a numerical model of an actual earth-filled dam was constructed to investigate the influences of the water level fluctuation rate and the hysteresis of the soil-water characteristic curve(SWCC)on the stability of the upstream dam slope.The results revealed that the free surface in the dam body for the desorption SWCC during water level fluctuations was higher than that for the adsorption SWCC,which would be more evident at higher water levels.The safety factor of the upstream dam slope initially decreased and then increased for the most dangerous water level as the water level rose and fell.The water level fluctuation rate mainly influenced the initial section of the safety factor variation curve,while the SWCC hysteresis mainly affected the minimum safety factor of the water level fluctuations.The desorption SWCC is suggested for engineering design.Furthermore,a quick prediction method is proposed to estimate the safety factor of upstream dam slopes with identical structures.

ALS-linked C9orf72 dipeptide repeats inhibit starvation-induced autophagy through modulating BCL2–BECN1 interaction

Growing evidences indicate that dysfunction of autophagy contributes to the disease pathogenesis of amyotrophic lateral sclerosis(ALS)and frontotemporal dementia(FTD),two neurodegenerative disorders.The GGGGCC·GGCCCC repeat RNA expansion in chromosome 9 open reading frame 72(C9orf72)is the most genetic cause of both ALS and FTD.According to the previous studies,GGGGCC·GGCCCC repeat undergoes the unconventional repeat-associated non-ATG translation,which produces dipeptide repeat(DPR)proteins.Although there is a growing understanding that C9orf72 DPRs have a strong ability to harm neurons and induce C9orf72-linked ALS/FTD,whether these DPRs can affect autophagy remains unclear.In the present study,we find that poly-GR and poly-PR,two arginine-containing DPRs which display the most cytotoxic properties according to the previous studies,strongly inhibit starvation-induced autophagy.Moreover,our data indicate that arginine-rich DPRs enhance the interaction between BCL2 and BECN1/Beclin 1 by inhibiting BCL2 phosphorylation,therefore they can impair autophagic clearance of neurodegenerative disease-associated protein aggregates under starvation condition in cells.Importantly,our study not only highlights the role of C9orf72 DPR in autophagy dysfunction,but also provides novel insight that pharmacological intervention of autophagy using SW063058,a small molecule compound that can disrupt the interaction between BECN1 and BCL2,may reduce C9orf72 DPR-induced neurotoxicity.