Genome-Wide Comparative Analyses of Microsatellites in Papaya

Abstract

Microsatellites, or simple sequence repeats (SSRs), are highly polymorphic and universally distributed in eukaryotes. SSRs have been used extensively as sequence tagged markers in genetic studies. Recently, the functional and evolutionary importance of SSRs has received considerable attention. Here we report the mining and characterization of the SSRs in papaya genome. We analyzed SSRs from 277.4 Mb of whole genome shotgun (WGS) sequences, 51.2 Mb bacterial artificial chromosome (BAC) end sequences (BES), and 13.4 Mb expressed sequence tag (EST) sequences. The papaya SSR density was one SSR per 0.7 kb of DNA sequence in the WGS, which was higher than that in BES and EST sequences. SSR abundance was dramatically reduced as the repeat length increased. According to SSR motif length, dinucleotide repeats were the most common motif in class I, whereas hexanucleotides were the most copious in class II SSRs. The tri-and hexanucleotide repeats of both classes were greater in EST sequences compared to genomic sequences. In class I SSR, AT and AAT were the most frequent motifs in BES and WGS sequences. By contrast, AG and AAG were the most abundant in EST sequences. For SSR marker development, 9,860 primer pairs were surveyed for amplification and polymorphism. Successful amplification and polymorphic rates were 66.6% and 17.6%, respectively. The highest polymorphic rates were achieved by AT, AG, and ATG motifs. The genome wide analysis of microsatellites revealed their frequency and distribution in papaya genome, which varies among plant genomes. This complete set of SSRs markers throughout the genome will assist diverse genetic studies in papaya and related species.

Cloning of the Papaya Chromoplast-Specific Lycopene β-Cyclase, CpCYC-b, Controlling Fruit Flesh Color Reveals Conserved Microsynteny and a Recombination Hot Spot

“…S5). Analysis with the papaya repeat database revealed one Ty1/Copia-type retroelement and less than 2% lowcomplexity DNA (Nagarajan et al, 2008;Wang et al, 2008). The BAC sequences were searched against the papaya whole genome shotgun sequence and aligned to supercontig_195 of the C. papaya Core Annotation database.…”

Genetic characterization of papaya plants (Carica papaya L.) derived from the first backcross generation

“…In plant breeding, as well as genetic analysis, this marker has had a variety of applications due to its multi-allelic nature, reproducibility, high information content, codominant inheritance, high abundance, and extensive coverage of the genome (Gupta and Varshney, 2000) but distributed in a non-random way (Wang et al, 2008). In the papaya genome, microsatellites are the more abundant type of tandem repetition, with a density of one every 0.7 kb; however, it represents only 0.19% of the entire genome of this species (Moore and Ming, 2008;Wang et al, 2008).…”

Analysis of Simple Sequence Repeats Information from Floral Expressed Sequence Tags Resources of Papaya (<i>Carica papaya</i> L.)

“…All three types namely perfect, imperfect and compound SSRs were identified using the higher as compared to the earlier report of papaya in which 10,688 SSRs were identified [39]. In the present study, the average frequency or density of perfect, imperfect and compound SSR were identified as 3610.84 SSR/Mb, 50.45 SSR/Mb and 5118.52 SSR/Mb respectively which is higher than the previous studies of papaya in which density of perfect SSRs reported were 1340 SSR/Mb [39], 746 SSR/Mb [44] and 656 SSR/Mb [45]. Such variations in the density of identified microsatellites are usual among different reports, mainly due to differences in the algorithms, parameter settings, minimal repeat length, the SSR search crite-…”

“…Only few studies of microsatellite analysis from genomic sequences [39] and from ESTs [40] have been performed in papaya. Moreover, only limited genic or EST-SSR markers, which emerge from transcribed portion of the genome, therefore becomes more important, are available in C. papaya.…”