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.

OsNRAMP2 facilitates Cd efflux from vacuoles and contributes to the difference in grain Cd accumulation between japonica and indica rice

Cadmium(Cd)accumulation in rice grain is of health concern.Identifying genes involved in grain Cd accumulation and performing molecular breeding may reduce it.In this study,knockout of OsNRAMP2,a member of the NRAMP family,reduced grain Cd concentrations by more than 38%,and overexpressing OsNRAMP2 increased grain Cd concentrations by more than 50%.Physiological experiments showed that OsNRAMP2 facilitated Cd translocation from root to shoot by positively regulating Cd efflux from the vacuoles.At filling stage,OsNRAMP2 was highly expressed in all tissues except for husk,suggesting its role in Cd remobilization.Changes in OsNRAMP2 expression affected the concentrations of Fe,Mn,Zn,and Cu in grain and also affected rice growth.Phylogenetic analysis showed that the distribution of OsNRAMP2 haplotypes between japonica and indica was different.Among the four haplotypes of OsNRAMP2,Hap 1,with a 6-bp nucleotide insertion in exon 1,had grain Cd concentration at least 45.3%lower than any of the other three haplotypes.Almost all(99.3%)japonica accessions but rare indica accessions(4.44%)from the 3K sequenced rice genomes carry Hap 1 of OsNRAMP2.Our study sheds light on the molecular mechanism of grain Cd accumulation and provides a promising target for low-Cd rice breeding.

Physiological and genome-wide gene expression analyses of cold-induced leaf rolling at the seedling stage in rice(Oryza sativa L.)

Leaf rolling and discoloration are two chilling-injury symptoms that are widely used as indicators for the evaluation of cold tolerance at the seedling stage in rice. However, the difference in cold-response mechanisms underlying these two traits remains unknown. In the present study, a cold-tolerant rice cultivar, Lijiangxintuanheigu, and a cold-sensitive cultivar, Sanhuangzhan-2, were subjected to low-temperature treatments and physiolog-ical and genome-wide gene expression analyses were conducted. Leaf rolling occurred at temperatures lower than 11℃, whereas discoloration appeared at moderately low temperatures such as 13℃. Chlorophyll contents in both cultivars were significantly decreased at 13℃, but not altered at 11℃. In contrast, the relative water content and relative electrolyte leakage of both cultivars decreased significantly at 11℃, but did not change at 13℃. Expression of genes associated with calcium signaling and abscisic acid (ABA) degradation was significantly altered at 11℃ in comparison with 25℃ and 13℃. Numerous genes in the DREB, MYB, bZIP, NAC, Zinc finger, bHLH, and WRKY gene families were differentially expressed. Many aquaporin genes and the key genes in trehalose and starch synthesis were down regulated at 11℃ in comparison with 25℃ and 13℃. These results suggest that the two chilling injury symptoms are temperature-specific and are controlled by different mechanisms. Cold-induced leaf rolling is associated with calcium and ABA signaling pathways and is regulated by multiple transcriptional regulators. The suppression of aquaporin genes and reduced accumulation of soluble sugars under cold stress results in a reduction in cellular water potential and consequently leaf rolling.

应对越南南海政策的措施

面对日益严峻的南海局势,我国曾经提出了“主权归我、搁置争议、共同开发”的解决原则,但在巨大的现实利益面前,此原则没有得到南海声索国的广泛认同,甚至招致部分声索国的反对,其中态度最为激烈的是越南。本文将从越南的地缘环境、历史进程、国家实力三个方面分析越南的南海主张,以及中国应对越南南海政策相应措施。

Comparative physiological and transcriptomic analyses illuminate common mechanisms by which silicon alleviates cadmium and arsenic toxicity in rice seedlings

The inessential heavy metal/loids cadmium(Cd)and arsenic(As),which often co-occur in polluted paddy soils,are toxic to rice.Silicon(Si)treatment is known to reduce Cd and As toxicity in rice plants.To better understand the shared mechanisms by which Si alleviates Cd and As stress,rice seedlings were hydroponically exposed to Cd or As,then treated with Si.The addition of Si significantly ameliorated the inhibitory effects of Cd and As on rice seedling growth.Si supplementation decreased Cd and As translocation from roots to shoots,and significantly reduced Cd-and As-induced reactive oxygen species generation in rice seedlings.Transcriptomics analyses were conducted to elucidate molecular mechanisms underlying the Si-mediated response to Cd or As stress in rice.The expression patterns of the differentially expressed genes in Cd-or As-stressed rice roots with and without Si application were compared.The transcriptomes of the Cd-and As-stressed rice roots were similarly and profoundly reshaped by Si application,suggesting that Si may play a fundamental,active role in plant defense against heavy metal/loid stresses by modulating whole genome expression.We also identified two novel genes,0s01g0524500 and 0s06g0514800,encoding a myeloblastosis(MYB)transcription factor and a thionin,respectively,which may be candidate targets for Si to alleviate Cd and As stress in rice,as well as for the generation of Cd-and/or As-resistant plants.This study provides valuable resources for further clarification of the shared molecular mechanisms underlying the Si-mediated alleviation of Cd and As toxicity in rice.

Comparative transcriptomics provide new insights into the mechanisms by which foliar silicon alleviates the effects of cadmium exposure in rice

Silicon(Si)has been shown to alleviate Cd stress in rice.Here,we investigated the beneficial effects of foliar Si in an indica rice Huanghuazhan(HHZ).Our results showed that foliar Si in-creases the dry weight and decreases Cd translocation in Cd-exposed rice at the grain-filling stage only,implying that the filling stage is critical for foliar Si to reduce Cd accumulation.We also investigated the transcriptomics in flag leaves(FLs),spikelets(SPs),and node Is(NIs)of Cd-exposed HHZ after foliar Si application at the filling stage.Importantly,the gene expression profiles associated with the Si-mediated alleviation of Cd stress were tissue spe-cific,while shared pathways were mediated by Si in Cd-exposed rice tissues.Furthermore,after the Si treatment of Cd-exposed rice,the ATP-binding cassette(ABC)-transporters were mostly upregulated in FL and SP,while the bivalent cation transporters were mostly down-regulated in FL and NI,possibly helping to reduce Cd accumulation.The genes associated with essential nutrient transporters,carbohydrate and secondary metabolite biosynthesis,and cytochrome oxidase activity were mostly upregulated in Cd-exposed FL and SP,which may help to alleviate oxidative stress and improve plant growth under Cd exposure.Inter-estingly,genes responsible for signal transduction were negatively regulated in FL,but pos-itively regulated in SP,by foliar Si.Our results provide transcriptomic evidence that foliar Si plays an active role in alleviating the effects of Cd exposure in rice.In particular,foliar Si may alter the expression pattern of genes associated with transport,biosynthesis and metabolism,and oxidation reduction.