Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct f lower color

The genus Rhododendron(Ericaceae),with more than 1000 species highly diverse in f lower color,is providing distinct ornamental values and a model system for f lower color studies.Here,we investigated the divergence between two parental species with different f lower color widely used for azalea breeding.Gapless genome assembly was generated for the yellow-f lowered azalea,Rhododendron molle.Comparative genomics found recent proliferation of long terminal repeat retrotransposons(LTR-RTs),especially Gypsy,has resulted in a 125 Mb(19%)genome size increase in species-specific regions,and a significant amount of dispersed gene duplicates(13402)and pseudogenes(17437).Metabolomic assessment revealed that yellow f lower coloration is attributed to the dynamic changes of carotenoids/f lavonols biosynthesis and chlorophyll degradation.Time-ordered gene co-expression networks(TO-GCNs)and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct f lower pigmentation.B3 and ERF TFs were found dominating the gene regulation of carotenoids/f lavonols characterized pigmentation in R.molle,while WRKY,ERF,WD40,C2H2,and NAC TFs collectively regulated the anthocyanins characterized pigmentation in the red-f lowered R simsii.This study employed a multi-omics strategy in disentangling the complex divergence between two important azaleas and provided references for further functional genetics and molecular breeding.

Neuroprotective effect of interleukin-6 regulation of voltage-gated Na^+ channels of cortical neurons is time-and dose-dependent

Interleukin-6 has been shown to be involved in nerve injury and nerve regeneration, but the effects of long-term administration of high concentrations of interleukin-6 on neurons in the central nervous system is poorly understood. This study investigated the effects of 24 hour expo-sure of interleukin-6 on cortical neurons at various concentrations （0.1, 1, 5 and 10 ng/mL） and the effects of 10 ng/mL interleukin-6 exposure to cortical neurons for various durations （2, 4, 8, 24 and 48 hours） by studying voltage-gated Na＋ channels using a patch-clamp technique. Volt-age-clamp recording results demonstrated that interleukin-6 suppressed Na＋ currents through its receptor in a time- and dose-dependent manner, but did not alter voltage-dependent activation and inactivation. Current-clamp recording results were consistent with voltage-clamp recording results. Interleukin-6 reduced the action potential amplitude of cortical neurons, but did not change the action potential threshold. The regulation of voltage-gated Na＋channels in rat corti-cal neurons by interleukin-6 is time- and dose-dependent.

Haplotype-resolved genome assembly and allele- specific gene expression in cultivated ginger

Ginger(Zingiber officinale)is one of the most valued spice plants worldwide;it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance.Here,we present a haplotype-resolved,chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb.Remarkable structural variation was identified between haplotypes,and two inversions larger than 15Mb on chromosome 4 may be associated with ginger infertility.We performed a comprehensive,spatiotemporal,genome-wide analysis of allelic expression patterns,revealing that most alleles are coordinately expressed.The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements,greater coding sequence divergence,more relaxed selection pressure,and more transcription factor binding site differences.We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis.Our allele-aware assembly provides a powerful platform for future functional genomics,molecular breeding,and genome editing in ginger.

Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome

Polyploidization plays a key role in plant evolution,but the forces driving the fate of homoeologs in polyploid genomes,i.e.,paralogs resulting from a whole-genome duplication(WGD)event,remain to be elucidated.Here,we present a chromosome-scale genome assembly of tetraploid scarlet sage(Salvia splendens),one of the most diverse ornamental plants.We found evidence for three WGD events following an older WGD event shared by most eudicots(theγevent).A comprehensive,spatiotemporal,genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries,which could be associated with genomic rearrangements,transposable element proximity discrepancies,coding sequence variation,selection pressure,and transcription factor binding site differences.The observed differences between homoeologs may reflect the first step toward sub-and/or neofunctionalization.This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.

Genomic clines across the species boundary between a hybrid pine and its progenitor in the eastern Tibetan Plateau

Most species have clearly defined distribution ranges and ecological niches.The genetic and ecological causes of species differentiation and the mechanisms that maintain species boundaries between newly evolved taxa and their progenitors are,however,less clearly defined.This study investigated the genetic structure and clines in Pinus densata,a pine of hybrid origin on the southeastern Tibetan Plateau,to gain an understanding of the contemporary dynamics of species barriers.We analyzed genetic diversity in a range-wide collection of P.densata and representative populations of its progenitors,Pinus tabuliformis and Pinus yunnanensis,using exome capture sequencing.We detected four distinct genetic groups within P.densata that reflect its migration history and major gene-flow barriers across the landscape.The demographies of these genetic groups in the Pleistocene were associated with regional glaciation histories.Interestingly,population sizes rebounded rapidly during interglacial periods,suggesting persistence and resilience of the species during the Quaternary ice age.In the contact zone between P.densata and P.yunnanensis,3.36%of the analyzed loci(57849)showed exceptional patterns of introgression,suggesting their potential roles in either adaptive introgression or reproductive isolation.These outliers showed strong clines along critical climate gradients and enrichment in a number of biological processes relevant to high-altitude adaptation.This indicates that ecological selection played an important role in generating genomic heterogeneity and a genetic barrier across a zone of species transition.Our study highlights the forces that operate to maintain species boundaries and promote speciation in the Qinghai-Tibetan Plateau and other mountain systems.