Tropical Plant Biology

, Volume 9, Issue 3, pp 117–135 | Cite as

Genome-Wide Comparative Analysis of Microsatellites in Pineapple

  • Jingping Fang
  • Chenyong Miao
  • Rukai Chen
  • Ray MingEmail author


Pineapple (Ananas comosus (L.) Merrill) is the second most important tropical fruit in term of international trade. The availability of whole genomic sequences and expressed sequence tags (ESTs) offers an opportunity to identify and characterize microsatellite or simple sequence repeat (SSR) markers in pineapple. A total of 278,245 SSRs and 41,962 SSRs with an overall density of 728.57 SSRs/Mb and 619.37 SSRs/Mb were mined from genomic and ESTs sequences, respectively. 5′-untranslated regions (5′-UTRs) had the greatest amount of SSRs, 3.6–5.2 fold higher SSR density than other regions. For repeat length, 12 bp was the predominant repeat length in both assembled genome and ESTs. Class I SSRs were underrepresented compared with class II SSRs. For motif length, dinucleotide repeats were the most abundant in genomic sequences, whereas trinucleotides were the most common motif in ESTs. Tri- and hexanucleotides of total SSRs were more prevalent in ESTs than in the whole genome. The SSR frequency decreased dramatically as repeat times increased. AT was the most frequent single motif across the entire genome while AG was the most abundant motif in ESTs. Across six examined plant species, the pineapple genome displayed the highest density, substantially more than the second-place cucumber. Annotation and expression analyses were also conducted for genes containing SSRs. This thorough analysis of SSR markers in pineapple provided valuable information on the frequency and distribution of SSRs in the pineapple genome. This genomic resource will expedite genomic research and pineapple improvement.


Ananas comosus (L.) Merrill Expressed sequence tag (EST) Expression patterns Motif Repeat Simple sequence repeats (SSRs) 



amplified fragment length polymorphism


Base pair


Crassulacean Acid Metabolism


Coding sequences


Expressed sequence tag


Number of fragments per kilobase of exon per million fragments mapped


Gene Ontology


Kyoto Encyclopedia of Genes and Genomes


Kilo base pairs


Marker-assisted selection


Mega base pairs


Randomly amplified polymorphic DNA


Restriction fragment length polymorphism


Simple sequence repeat


Short tandem repeat


Untranslated regions



This work was supported startup fund from Fujian Agriculture and Forestry University to R.M.

Supplementary material

12042_2016_9163_MOESM1_ESM.docx (85 kb)
ESM 1 (DOCX 85 kb)


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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Jingping Fang
    • 1
    • 2
  • Chenyong Miao
    • 2
  • Rukai Chen
    • 1
  • Ray Ming
    • 2
    • 3
    Email author
  1. 1.Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
  2. 2.FAFU and UIUC-SIB Joint Center for Genomics and BiotechnologyFujian Agriculture and Forestry UniversityFuzhouChina
  3. 3.Department of Plant BiologyUniversity of Illinois at Urbana-ChampaignUrbanaUSA

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