Comparative Transcriptomic Analysis of Two Tomato Cultivars with Different Shelf-Life Traits

Tomato(Solanum lycopersicum)is a perishable fruit because of its fast water loss and susceptibility to pathogens in the post-harvest stage,which leads to huge economic losses every year.In this study,firstly from 19 tomato cultivars,we screened out two cultivars,Riogrand and SalarF1,having long and short shelf-life spans,respectively.Secondly,shelf-life analysis was carried out for both cultivars at room temperature.Results exhibited that Riogrand showed higher firmness and less weight loss than SalarF1.The ethylene production was higher in SalarF1,compared with Riogrand during post-harvest storages.We performed transcriptomic analysis of both cultivars in different storage stages.We discovered 2913,2188,and 11,119 differentially expressed genes(DEGs)for three post-harvest stages(0,20,and 40 Days Post-Harvest(DPH)),respectively.These genes are enriched in ethylene biosynthesis and response,as well as cell wall-related genes.Ethylene response factor(ERF)ERF2 and ERF4 were highly expressed in SalarF1 with a short shelf life in 40 DPH,and the ethylene biosynthetic genes ACO1,ACO4,ACS6,and ACS2 were significantly upregulated in SalarF1.Regarding cell wall loosening and cell wall-related genes XTH3,XTH7,XTH23,1,3;1,4-β-D-Gluc-like,pGlcT1,Cellulase,PGH1,PL5,PL-like 1,PL-like 2 exhibited the highest levels of significance,being notably upregulated in the last stage of SalarF1.The quantitative real-time polymerase chain reaction(qRT-PCR)analysis validated these gene expressions,which is in line with the transcriptome analysis.The findings suggested that the extension of tomato fruit shelf life is mostly dependent on ethylene biosynthesis,signaling pathway genes,cell wall loosening,and cell wall-associated genes.

Telomere-to-telomere and gap-free reference genome assembly of the kiwifruit Actinidia chinensis

Kiwifruit is an economically and nutritionally important fruit crop with extremely high contents of vitamin C.However,the previously released versions of kiwifruit genomes all have a mass of unanchored or missing regions.Here,we report a highly continuous and completely gap-free reference genome of Actinidia chinensis cv.‘Hongyang’,named Hongyang v4.0,which is the first to achieve two de novo haploid-resolved haplotypes,HY4P and HY4A.HY4P and HY4A have a total length of 606.1 and 599.6 Mb,respectively,with almost the entire telomeres and centromeres assembled in each haplotype.In comparison with Hongyang v3.0,the integrity and contiguity of Hongyang v4.0 is markedly improved by filling all unclosed gaps and correcting some misoriented regions,resulting in∼38.6–39.5 Mb extra sequences,which might affect 4263 and 4244 protein-coding genes in HY4P and HY4A,respectively.Furthermore,our gap-free genome assembly provides the first clue for inspecting the structure and function of centromeres.Globally,centromeric regions are characterized by higher-order repeats that mainly consist of a 153-bp conserved centromere-specific monomer(Ach-CEN153)with different copy numbers among chromosomes.Functional enrichment analysis of the genes located within centromeric regions demonstrates that chromosome centromeres may not only play physical roles for linking a pair of sister chromatids,but also have genetic features for participation in the regulation of cell division.The availability of the telomere-to-telomere and gap-free Hongyang v4.0 reference genome lays a solid foundation not only for illustrating genome structure and functional genomics studies but also for facilitating kiwifruit breeding and improvement.

Tomato SlAN11 regulates flavonoid biosynthesis and seed dormancy by interaction with bHLH proteins but not with MYB proteins

The flavonoid compounds are important secondary metabolites with versatile human nutritive benefits and fulfill a multitude of functions during plant growth and development.The abundance of different flavonoid compounds are finely tuned with species-specific pattern by a ternary MBW complex,which consists of a MYB,a bHLH,and a WD40 protein,but the essential role of SlAN11,which is a WD40 protein,is not fully understood in tomato until now.In this study,a tomato WD40 protein named as SlAN11 was characterized as an effective transcription regulator to promote plant anthocyanin and seed proanthocyanidin(PA)contents,with late flavonoid biosynthetic genes activated in 35S::SlAN11 transgenic lines,while the dihydroflavonol flow to the accumulation of flavonols or their glycosylated derivatives was reduced by repressing the expression of SlFLS in this SlAN11-overexpressed lines.The above changes were reversed in 35S::SlAN11-RNAi transgenic lines except remained levels of flavonol compounds and SlFLS expression.Interestingly,our data revealed that SlAN11 gene could affect seed dormancy by regulating the expressions of abscisic acid(ABA)signaling-related genes SlABI3 and SlABI5,and the sensitivity to ABA treatment in seed germination is conversely changed by SlAN11-overexpressed or-downregulated lines.Yeast two-hybrid assays demonstrated that SlAN11 interacted with bHLH but not with MYB proteins in the ternary MBW complex,whereas bHLH interacted with MYB in tomato.Our results indicated that low level of anthocyanins in tomato fruits,with low expression of bHLH(SlTT8)and MYB(SlANT1 and SlAN2)genes,remain unchanged upon modification of SlAN11 gene alone in the transgenic lines.These results suggest that the tomato WD40 protein SlAN11,coordinating with bHLH and MYB proteins,plays a crucial role in the fine adjustment of the flavonoid biosynthesis and seed dormancy in tomato.

Searching for exoplanets with HEPS:I.detection probability of Earth-like planets in multiple systems

The astrometry method has great advantages in searching for exoplanets in the habitable zone around solar-like stars. However, the presence of multiple planets may cause a problem with degeneracy when trying to compute accurate planet parameters from observation data and reduce detectability. The degeneracy problem is extremely critical, especially in a space mission which has limited observation time and cadence. In this series of papers, we study the detectability of habitable Earth-mass planets in different types of multi-planet systems, aiming to find the most favorable targets for the potential space mission–Habitable ExoPlanet Survey(HEPS). In the first paper, we present an algorithm to find planets in the habitable zone around solar-like stars using astrometry. We find the detectability can be well described by planets' signal-to-noise ratio(SNR) and a defined parameter S = M2/(T1-T2)2, where M2 and T2are the mass and period of the second planet, respectively. T1 is the period of the planet in the habitable zone. The parameter S represents the influence of planetary architectures. We fit the detectability as a function of both the SNR of the planet in the habitable zone and the parameter S. An Earth-like planet in a habitable zone is harder to detect(with detectability PHP< 80%) in a system with a hot Jupiter or warm Jupiter(within2 AU), in which the parameter S is large. These results can be used in target selections and to determine the priority of target stars for HEPS, especially when we select and rank nearby planet hosts with a single planet.