Abstract
Papaya (Carica papaya L.) is one of the most economically, medicinally and nutritionally important tropical fruit crops. Expressed sequence tags (ESTs) derived simple sequence repeat (SSR) markers are more valuable as they are derived from conserved genic portion. Development of EST-SSRs markers through in silico approach is cheaper, less time consuming and labour-intensive. In this study, we aimed to mine SSRs and developed EST-SSR primers from papaya floral ESTs. A total of 75,846 papaya floral ESTs were downloaded from public database National Centre for Biotechnology Information (NCBI). A total of 26,039 floral unigenes (7961 contigs and 18,078 singletons) were generated after assembly of these ESTs. From these floral unigenes, 433,782 perfect SSRs, 204,968 compound SSRs and 6061 imperfect SSRs were mined, respectively. In perfect SSRs, mononucleotide repeats were most abundant (94.7%) followed by tri- (3.1%) and di-nucleotide repeats (1.7%). The frequencies of tetra-, hexa- and penta-nucleotide repeats accounted for only (0.17%), (0.04%) and (0.03%), respectively. In mononucleotide repeats, the most abundant motif was A/T (69.3%) and in di- and tri-nucleotide repeats were AG/CT (61%) and AAG/CTT (31%), respectively. In imperfect SSRs, mononucleotide repeats (56.5%) were most abundant. 176 different types of motifs were identified. A total of 3807 primer pairs for floral papaya ESTs were successfully designed. These developed EST-SSR primers are being used for the genetic improvement of papaya such as study of cross-transferability across genera/species, evaluation of genetic diversity, and identification of sex-specific markers. These EST derived SSRs can also be used in filling gaps in existing linkage maps in papaya.
Highlights
Papaya (Carica papaya L.) is an edible fruit crop of the family Caricaceae, originally native to Central and South America and distributed in tropical and subtropical regions worldwide
A total of 75,846 papaya floral Expressed sequence tags (ESTs) were downloaded from National Centre for Biotechnology Information (NCBI) in FASTA format
A total of 26,039 floral unigenes (7960 contigs and 18,079 singletons), were generated after assembly of papaya floral EST sequences (Table 1). These assembled floral unigenes were further utilized for mining of simple sequence repeat (SSR)
Summary
Papaya (Carica papaya L.) is an edible fruit crop of the family Caricaceae, originally native to Central and South America and distributed in tropical and subtropical regions worldwide It is diploid species (2n = 18) and dicotyledonous plant. According to the percentage of US recommended daily allowances, papaya fruit ranked first among 35 most commonly used fruits It is highly nutritious and contains antioxidant vitamins (A, C and E), thiamine, folate, riboflavin, niacin, potassium, iron, calcium and fibre. A proteolytic enzyme, papain (EC: 3.4.22.2) is extracted from the latex of unripe fruit which is commonly used in food processing such as in tenderization of meat, to clarify beer and juice and in industry for making soap, shampoo, lotions, skin care products and toothpastes [6] It can be used in several medical applications such as for digestion improvement and in treatment of fever, ulcers, muscular dystrophy and osteoporosis [7]
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