A likely paleo-autotetraploidization event shaped the high conservation of Nyssaceae genome

Scientific knowledge about the ancestral genome of core eudicot plant kingdom can potentially have profound impacts on both basic and applied research,including evolution,genetics,genomics,ecology,agriculture,forestry,and global climate.To investigate which plant conserves best the core eudicots common ancestor genome,we compared Arcto-Tertiary relict Nyssaceae and 30 other eudicot plant families.The genomes of Davidia involucrata(a known living fossil),Camptotheca acuminata and Nyssa sinensis,one per existent genus of Nyssaceae,were performed comparative genomic analysis.We found that Nyssaceae originated from a single Nyssaceae common tetraploidization event(NCT)-autotetraploidization 28-31 Mya after the core eudicot common hexaploidization(ECH).We identified Nyssaceae orthologous and paralogous genes,determined its chromosomal evolutionary trajectory,and reconstructed the Nyssaceae most recent ancestor genome.D.involucrata genome contained the entire seven paleochromosomes and 17 ECH-generated eudicot common ancestor chromosomes and was the slowest in mutation among the analyzed 42 species of 31 plant families.Combing both its high retention of paleochromosomes and its low mutation rate,D.involucrata provides the best case in conservation of the core eudicot paleogenome.

Interaction between insulin-like growth factor binding protein-related protein 1 and transforming growth factor beta 1 in primary hepatic stellate cells

BACKGROUND: We previously showed that insulin-like growth factor binding protein-related protein 1 (IGFBPrP1) is a novel mediator in liver fibrosis. Transforming growth factor beta 1 (TGF beta 1) is known as the strongest effector of liver fibrosis. Therefore, we aimed to investigate the detailed interaction between IGFBPrP1 and TGF beta 1 in primary hepatic stellate cells (HSCs). METHODS: We overexpressed TGF beta 1 or IGFBPrP1 and inhibited TGF beta 1 expression in primary HSCs for 6, 12, 24, 48, 72, and 96 hours to investigate their interaction and observe the accompanying expressions of a-smooth muscle actin (alpha-SMA), collagen I, fibronectin, and phosphorylated-mothers against decapentaplegic homolog 2/3 (p-Smad2/3). RESULTS: We found that the adenovirus vector encoding the TGF beta 1 gene (AdTGF beta 1) induced IGFBPrP1 expression while that of alpha-SMA, collagen I, fibronectin, and TGF beta 1 increased gradually. Concomitantly, AdIGFBPrP1 upregulated TGF beta 1, alpha-SMA, collagen I, fibronectin, and p-Smad2/3 in a time-dependent manner while IGFBPrP1 expression was decreased at 96 hours. Inhibition of TGF beta 1 expression reduced the IGFBPrP1-stimulated expression of alpha-SMA, collagen I, fibronectin, and p-Smad2/3. CONCLUSIONS: These findings for the first time suggest the existence of a possible mutually regulation between IGFBPrP1 and TGF beta 1, which likely accelerates liver fibrosis progression. Furthermore, IGFBPrP1 likely participates in liver fibrosis in a TGF beta 1-depedent manner, and may act as an upstream regulatory factor of TGF beta 1 in the Smad pathway.

Coriander Genomics Database:a genomic,transcriptomic,and metabolic database for coriander

Coriander(Coriandrum sativum L.),also known as cilantro,is a globally important vegetable and spice crop.Its genome and that of carrot are models for studying the evolution of the Apiaceae family.Here,we developed the Coriander Genomics Database(CGDB,http://cgdb.bio2db.com/)to collect,store,and integrate the genomic,transcriptomic,metabolic,functional annotation,and repeat sequence data of coriander and carrot to serve as a central online platform for Apiaceae and other related plants.Using these data sets in the CGDB,we intriguingly found that seven transcription factor(TF)families showed significantly greater numbers of members in the coriander genome than in the carrot genome.The highest ratio of the numbers of MADS TFs between coriander and carrot reached 3.15,followed by those for tubby protein(TUB)and heat shock factors.As a demonstration of CGDB applications,we identified 17 TUB family genes and conducted systematic comparative and evolutionary analyses.RNA-seq data deposited in the CGDB also suggest dose compensation effects of gene expression in coriander.CGDB allows bulk downloading,significance searches,genome browser analyses,and BLAST searches for comparisons between coriander and other plants regarding genomics,gene families,gene collinearity,gene expression,and the metabolome.A detailed user manual and contact information are also available to provide support to the scientific research community and address scientific questions.CGDB will be continuously updated,and new data will be integrated for comparative and functional genomic analysis in Apiaceae and other related plants.

Preferential gene retention increases the robustness of cold regulation in Brassicaceae and other plants after polyploidization

Cold stress profoundly affects plant growth and development and is a key factor affecting the geographic distribution and evolution of plants.Plants have evolved adaptive mechanisms to cope with cold stress.Here,through the genomic analysis of Arabidopsis,three Brassica species and 17 other representative species,we found that both cold-related genes(CRGs)and their collinearity were preferentially retained after polyploidization followed by genome instability,while genome-wide gene sets exhibited a variety of other expansion mechanisms.The coldrelated regulatory network was increased in Brassicaceae genomes,which were recursively affected by polyploidization.By combining our findings regarding the selective retention of CRGs from this ecological genomics study with the available knowledge of cold-induced chromosome doubling,we hypothesize that cold stress may have contributed to the success of polyploid plants through both increasing polyploidization and selectively maintaining CRGs during evolution.This hypothesis requires further biological and ecological exploration to obtain solid supporting evidence,which will potentially contribute to understanding the generation of polyploids and to the field of ecological genomics.

Heat-stress-induced sprouting and differential gene expression in growing potato tubers: Comparative transcriptomics with that induced by postharvest sprouting

Crops face increased risk from heat stress due to climate change.Potato(Solanum tuberosum L.)tubers grown in hot summers often have defects including pre-harvest sprouting(“heat sprouts”).We have used 18 potato cultivars to investigate whether heat stress(HS)conditions alone could cause heat sprouting and dormancy changes in tubers.We also examined transcriptomic responses of potato to HS and whether these responses are like those induced by postharvest sprouting.We demonstrated that HS alone caused heat sprouts and shortened postharvest dormancy period,heat-sprouted tubers became dormant after harvest,and cultivars varied substantially for producing heat spouts but there was no clear association with cultivar maturity earliness.Cultivar Innovator did not show any heat sprouts and still had long dormancy.Dormancy-associated genes(DOG1 and SLP)were downregulated in HS tubers like in postharvest sprouting tubers.We have identified 1201 differentially expressed genes,14 enriched GO terms and 12 enriched KEGG pathways in response to HS in growing tubers of‘Russet Burbank’.Transcriptomic response of‘Russet Burbank’to HS showed significant similarities to that of postharvest non-HS sprouted tubers.Gibberellin biosynthesis pathway was enriched in heat-stressed tubers and was likely involved in heat sprouting and dormancy release.Heat sprouting and postharvest sprouting shared common candidate genes and had significant similarity in gene expression.Our study has significance for selecting potato cultivars for farming,planning storage and utilization of heat-stressed tubers,identifying sprouting-related genes,understanding heat-stress biology,and breeding heat-tolerant potato cultivars,especially for sustainable potato production under climate change.

Paleo-polyploidization in Lycophytes

Lycophytes and seed plants constitute the typical vascular plants.Lycophytes have been thought to have no paleo-polyploidization although the event is known to be critical for the fast expansion of seed plants.Here,genomic analyses including the homologous gene dot plot analysis detected multiple paleo-polyploidization events,with one occurring approximately 13–15 million years ago(MYA)and another about 125–142 MYA,during the evolution of the genome of Selaginella moellendorffii,a model lycophyte.In addition,comparative analysis of reconstructed ancestral genomes of lycophytes and angiosperms suggested that lycophytes were affected by more paleopolyploidization events than seed plants.Results from the present genomic analyses indicate that paleo-polyploidization has contributed to the successful establishment of both lineages—lycophytes and seed plants—of vascular plants.