Distribution of SSR and sequence characteristics in transcriptome of Fortunella crassifolia Swingle cv. Cuimi pulp

【Objective】 To analyze the distribution and sequence characteristics of simple repeat sequence（SSR） inthe transcriptome of the fruit pulp of Fortunella crassifolia Swingle cv. Cuimi, which could provide reference basis for genetic diversity analysis, SSR molecular marker development and molecular assisted breeding in the genus Fortunella.【Method】F. crassifolia Swingle cv. Cuimi was used as the experimental material. The DNBSEQ-G99 high-throughput sequencing platform was used to sequence the transcriptome of the fruit pulp tissue, and the high-quality sequences data obtained were filtered, spliced and assembled. Then, the unigenes obtained from transcriptome sequencing were searchedfor SSR loci using MISA, and then analyzed for their distribution and sequence features. 【Result】 After quality controland assembly of F. crassifolia Swingle cv. Cuimi pulp transcriptome sequencing data, a total of 32257 unigenes were ob-tained, with a total unigenes length of 63342722 bp; 22447 SSR loci were identified by MISA searching, distributed on 11119 unigenes,with a frequency of SSR occurrence of 34.47%,and an average distribution distance of 2.82 kb.Among the 22447 SSR loci,the repeat type number of mononucleotide（14002） was the largest,accounted for 62.38%,followed by dinucleotide（3949） and trinucleotide（3980）,accounting for 17.59% and 17.73% respectively.A total of 116 repeat motif types were searched from 22447 SSR loci,and the number of A/T,AG/CT and AT/AT repeat motifs was absolutely dominant （73.99%）;A/T was the absolute dominant motif among the mononucleotide motifs,accounting for 59.41%;AG/CT was the dominant motif among the dinucleotide motifs,accounting for 8.87%;AAT/ATT was the dominant motif among the trinucleotide motifs,accounting for 4.55%.The types of SSR repeat unit was distributed from 5 to 44 times,with the largest number of SSR repeat motif occurring more than 10 times（10395,accounted for 46.31%）,followed by SSR repeat motifs with a frequency of 10 times（4997,accounted for 22.26%）.The average motif length of SSR loci in the transcriptome of F.crassifolia Swingle cv.Cuimi pulp was 29.63 bp,with the highest number of SSR loci with motif lengths ranging from 12 to 20 bp（12692,accounted for 56.54%）,which showed moderate polymorphism.Primer3 was used to design SSR primers,and a total of 17118 SSR loci could be designed primers with a success rate of 76.26%. 【Conclusion】 The number of SSR loci in transcriptome of the fruit pulp of F.crassifolia Swingle cv.Cuimi is large,with abundant motif types and presented as moderate polymorphism and above,can be used to develop SSR molecular markers.The results can provide technical support for the genetic mapping of kumquat and other Citrus plants,the analysis of disease resistance and the identification of germplasm resources.