南方农业学报2025，Vol.56Issue(2)：583-591,9.DOI:10.3969/j.issn.2095-1191.2025.02.022
脆蜜金柑果肉转录组SSR分布及其序列特征分析
Distribution of SSR and sequence characteristics in transcrip-tome of Fortunella crassifolia Swingle cv.Cuimi pulp
摘要
Abstract
[Objective]To analyze the distribution and sequence characteristics of simple repeat sequence(SSR)in the transcriptome of the fruit pulp of Fortunella crassifolia Swingle cv.Cuimi,which could provide reference basis for ge-netic 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 se-quencing platform was used to sequence the transcriptome of the fruit pulp tissue,and the high-quality sequences data ob-tained were filtered,spliced and assembled.Then,the unigenes obtained from transcriptome sequencing were searched for SSR loci using MISA,and then analyzed for their distribution and sequence features.[Result]After quality control and 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%.[Con-clusion]The number of SSR loci in transcriptome of the fruit pulp of F.crassifolia Swingle cv.Cuimi is large,with abun-dant 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 di-sease resistance and the identification of germplasm resources.关键词
脆蜜金柑/转录组/简单重复序列(SSR)/序列特征/重复基元Key words
Fortunella crassifiolia Swingle cv.Cuimi/transcriptome/simple sequence repeat(SSR)/sequence characteristics/repeat motif分类
农业科技引用本文复制引用
黄秋岚,田程飘,刘功德,毛立彦,邓小红,龙凌云..脆蜜金柑果肉转录组SSR分布及其序列特征分析[J].南方农业学报,2025,56(2):583-591,9.基金项目
广西重点研发计划项目(桂科AB19245035) （桂科AB19245035）
国家现代农业产业技术体系广西创新团队建设专项(nycytxgxcxtd-2021-05-03) （nycytxgxcxtd-2021-05-03）
广西农业科学院基本科研业务专项项目(桂农科2022YM16,桂农科2021YT143) Guangxi Key Research and Development Plan Project(Guike AB19245035) （桂农科2022YM16,桂农科2021YT143）
Construction Pro-ject of Guangxi Innovation Team of China Agriculture Research System(nycytxgxcxtd-2021-05-03) （nycytxgxcxtd-2021-05-03）
Basic Research Pro-ject of Guangxi Academy of Agricultural Sciences(Guinongke 2022YM16,Guinongke 2021YT143) （Guinongke 2022YM16,Guinongke 2021YT143）
