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Genome-Wide Comparative Analysis of Microsatellites in Pineapple

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Abstract

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.

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Abbreviations

AFLP:

amplified fragment length polymorphism

bp:

Base pair

CAM:

Crassulacean Acid Metabolism

CDS:

Coding sequences

EST:

Expressed sequence tag

FPKM:

Number of fragments per kilobase of exon per million fragments mapped

GO:

Gene Ontology

KEGG:

Kyoto Encyclopedia of Genes and Genomes

kb:

Kilo base pairs

MAS:

Marker-assisted selection

Mb:

Mega base pairs

RAPD:

Randomly amplified polymorphic DNA

RFLP:

Restriction fragment length polymorphism

SSR:

Simple sequence repeat

STR:

Short tandem repeat

UTR:

Untranslated regions

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Acknowledgments

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

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Authors and Affiliations

  1. Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China

    Jingping Fang & Rukai Chen

  2. FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China

    Jingping Fang, Chenyong Miao & Ray Ming

  3. Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA

    Ray Ming

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  1. Jingping Fang
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  2. Chenyong Miao
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Correspondence to Ray Ming.

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Communicated by: Paulo Arruda

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Fang, J., Miao, C., Chen, R. et al. Genome-Wide Comparative Analysis of Microsatellites in Pineapple. Tropical Plant Biol. 9, 117–135 (2016). https://doi.org/10.1007/s12042-016-9163-6

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