Genome-wide genetic variation identification and fruit-associated trait comparisons between kumquat (Fortunella japonica) and Clementine mandarin
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. Overall design: The materials from Clementine mandarin and Kumquat were collected in the experiment fields of the National Citrus Breeding Center at Huazhong Agricultural University (30°28' N, 114°21' E, 30). Healthy leaves without insect damage of Clementine mandarin and Kumquat were used as materials for re-sequencing. The five developmental stages of Clementine mandarin fruit were collected at 15, 30, 45, 100 and 180 days after flowering (DAF), respectively. Meanwhile, the five developmental stages of Kumquat fruit were also collected at 15, 30, 45, 80 and 120 DAF, respectively. And fruit growth including length, width, and fresh weight during fruit developmental stage can be seen in Figure 5A. To prepare a representative sample of total RNA from Clementine mandarin and kumquat tissues for RNA-sequencing (RNA-Seq), different developmental stages of fruit from roughly equal numbers of Clementine mandarin and kumquat were pooled for each sample. All plant tissues were sampled according to the demands of each experiment, immediately frozen in liquid nitrogen, and stored at -80? until used. All materials were collected from three individual plants for RNA and DNA extraction.