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

作　　者：黄秋岚 田程飘 刘功德 毛立彦 邓小红 龙凌云 HUANG Qiu-lan;TIAN Cheng-piao;LIU Gong-de;MAO Li-yan;DENG Xiao-hong;LONG Ling-yun(Guangxi Subtropical Crops Research Institute,Nanning,Guangxi 530001,China;Guangxi Key Laboratory of Quality and Safety Control for Subtropical Fruits,Nanning,Guangxi 530001,China)

机构地区：[1]广西亚热带作物研究所,广西南宁530001 [2]广西亚热带特色水果质量安全控制重点实验室,广西南宁530001

出　　处：《南方农业学报》2025年第2期583-591,共9页Journal of Southern Agriculture

基　　金：广西重点研发计划项目(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);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)。

摘　　要：【目的】分析脆蜜金柑果肉转录组中简单重复序列(SSR)的分布情况及序列特征,为金柑属的遗传多样性分析、SSR分子标记开发及分子辅助育种等提供参考依据。【方法】以脆蜜金柑为试验材料,通过DNBSEQ-G99高通量测序平台对其果肉组织进行转录组测序,高质量测序数据经严格过滤、拼接及组装后,使用MISA对转录组测序得到的Unigenes进行SSR位点检索,并分析其分布情况及序列特征。【结果】脆蜜金柑果肉转录组测序数据经质控及组装后共获得32257条Unigenes,Unigenes总长度为63342722 bp;经MISA搜索,鉴定出22447个SSR位点,分布在11119条Unigenes上,SSR发生频率为34.47%,平均分布距离为2.82 kb。在22447个SSR位点中,以单核苷酸重复类型数量最多(14002个),占62.38%;其次是二核苷酸重复类型(3949个)和三核苷酸重复类型(3980个),分别占17.59%和17.73%。从22447个SSR位点共搜索出116种重复基元种类,且以A/T、AG/CT和AT/AT这3种重复基元的数量占绝对优势(合计占73.99%);A/T是单核苷酸重复基元中的绝对优势基元,占59.41%;AG/CT是二核苷酸重复基元中的优势基元,占8.87%;AAT/ATT是三核苷酸重复基元中的优势基元,占4.55%。SSR重复基元出现频次从5次到44次均有分布,以出现频次大于10次的SSR重复基元数量最多(10395个,占46.31%),其次是出现频次为10次的SSR重复基元(4997个,占22.26%)。脆蜜金柑果肉转录组SSR位点的平均基序长度为29.63 bp,以基序长度在12~20 bp的SSR位点数量最多(12692个,占56.54%),呈中度多态性。采用Primer3设计SSR引物,共有17118个SSR位点可设计出引物,成功率为76.26%。【结论】脆蜜金柑果肉转录组SSR位点数量庞大,基元类型丰富,呈中度以上多态性,可用于开发SSR分子标记,为金柑及其他柑橘属植物的遗传图谱绘制、病害抗病分析及种质资源鉴定等研究提供技术支撑。【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 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 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 obtained,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 i

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 

分 类 号：S666.9[农业科学—果树学]