Project description:Kumquat (Fortunella classifolia Swingle) was thought as a close relative to citrus according to fruit morphology taxonomic, but kumquat fruit as well as its flowering characteristic are distinct from other citrus species, the trees usually blooms on the medium of June, obviously later than other citrus species, moreover many kumquat accessions could be blossom more than one times during one growth season, as this reason, the kumquat fruits could be consecutively ripen over several months, which made the study of globe genes expression profile for different development stage fruit easy. Kumquat is non-climacteric fruit, however the kumquat fruit ripening process, especially genes expression change in young and ripe kumquat fruits are less known, so studying on the global genes expression profiles of kumquat fruits in young and ripe stage are especially helpful to identify ripening-related genes and unravel the mechanism of ripening process.
Project description:We performed whole genome re-sequencing to reveal the comprehensive genetic variation of the fruit development between kumquat (Fortunella japonica) and Clementine mandarin. Total 5,865,235 single-nucleotide polymorphisms (SNPs) and 414,447 insertion/deletion (InDels) were identified in the two citrus species. Meanwhile, a total of 640,801 SNPs and 20,733 InDels were identified based on integrative analysis of genome and transcriptome of fruit. The variation feature, genomic distribution, functional effect and other characteristics of these genetic variation were explored. Total 1,090 differentially expressed genes (DEGs) were found during fruit development process of kumquat and Clementine mandarin by RNA-sequencing. Gene Ontology revealed that these genes were involved in various molecular functional and biological processes. Meanwhile, the genetic variation of 939 DEGs and 74 multiple fruit development pathway genes from previous reported were also identified. In addition, a global survey of genes splicing events identified 24,237 specific alternative splicing (AS) events in the two citrus species and showed that intron retention is the most prevalent pattern of alternative splicing.