Genome-wide comprehensive analysis of transcriptomes and small RNAs offers insights into the molecular mechanism of alkaline stress tolerance in a citrus rootstock

Alkaline stress has serious-negative effects on citrus production.Ziyang xiangcheng(Citrus junos Sieb.ex Tanaka)(Cj)is a rootstock that is tolerant to alkaline stress and iron deficiency.Trifoliate orange(Poncirus trifoliata(L.)Raf.)(Pt),the most widely used rootstock in China,is sensitive to alkaline stress.To investigate the molecular mechanism underlying the tolerance of Cj to alkaline stress,next-generation sequencing was employed to profile the root transcriptomes and small RNAs of Cj and Pt seedlings that were cultured in nutrient solutions along a three pH gradient.This two-level regulation data set provides a system-level view of molecular events with a precise resolution.The data suggest that the auxin pathway may play a central role in the inhibitory effect of alkaline stress on root growth and that the regulation of auxin homeostasis under alkaline stress is important for the adaptation of citrus to alkaline stress.Moreover,the jasmonate(JA)pathway exhibits the opposite response to alkaline stress in Cj and Pt and may contribute to the differences in the alkaline stress tolerance and iron acquisition between Cj and Pt.The dataset provides a wealth of genomic resources and new clues to further study the mechanisms underlying alkaline stress resistance in Cj.

Genomic and transcriptomic analyses of Citrus sinensis varieties provide insights into Valencia orange fruit mastication trait formation

Valencia orange(Citrus sinensis Osbeck)(VO)is a type of late-ripening sweet orange whose ripening occurs 4 to 5 months later than that of the mid-ripening common sweet orange(CO).Notably,the mastication trait of VO fruit is inferior to that of CO fruit.To date,how inferior pulp mastication trait forms in VO has not been determined.In this study,13 VO varieties and 12 CO varieties were subjected to whole-genome resequencing.A total of 2.98 million SNPs were identified from 25 varieties,and a SNP molecular marker was developed to distinguish VO and CO.Moreover,144 and 141 genes identified by selective sweep analysis were selected during VO and CO evolution,respectively.Based on gene functional enrichment analysis,most of the selected VO genes were related to the stress response and lignin biosynthesis.Simultaneously,we comparatively analyzed the transcriptome profiles of peel and pulp tissues among three VO varieties and three CO varieties,and the results demonstrated differences in lignin biosynthesis between VO and CO fruits.Furthermore,coexpression network analysis was performed to identify hub genes of lignin-related and variety-specific networks,which included CsERF74,CsNAC25,CsHSFB3,CsSPL4/13,etc.Overall,this study provides important insights into the mastication trait formation of Valencia orange fruit.