TITLE:
Analysis of Simple Sequence Repeats Information from Floral Expressed Sequence Tags Resources of Papaya (Carica papaya L.)
AUTHORS:
Priyanka Priyanka, Dileep Kumar, Anurag Yadav, Kusum Yadav, U. N. Dwivedi
KEYWORDS:
Papaya (Carica papaya L.), In Silico, Simple Sequence Repeats, Expressed Sequence Tags (ESTs), SSR Mining, EST-SSR, SSR Motifs, Primer Pairs
JOURNAL NAME:
American Journal of Plant Sciences,
Vol.8 No.9,
August
24,
2017
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.