"Results and DiscussionIn the present study we examined, available non-redundant RAD bottle gourd genomicsequence for the distribution of perfect microsatellites. Repeats were first examined on a wholegenome basis using genomic DNA sequence of bottle gourd and microsatellite content in DNAsequences. Further SSR frequencies were studied and compared with cucumber and Arabidopsis.Distribution of SSR types in genomic sequencesFirst, a total of 171,019 SSR markers with perfect repeats were detected in the bottlegourd then after removing redundant SSR markers, we finally found 45,066 perfect SSRs. Thecontent of perfect microsatellites primers in genomic sequences of bottle gourd is summarized inTable 1. An overall density across the genome is 134.60 SSRs/Mbp (i.e., one SSR every 0.4 MBof sequence, excluding mononucleotide and compound SSRs). Expectedly, bottle gourd showedlowest microsatellite density among the species compared with that of cucumber (536.60SSR/Mbp) and Arabidopsis (364.10 SSR/Mbp) (Table 2), this was due to lack of complete wholegenome sequence data. Tetranucleotides were the most common SSR type in bottle gourd genomic sequencerepresenting nearly 34% of all SSRs, followed by tri- (30.73%) and dinucleotides (21%) (Table2). Penta and hexanucleotides were the least frequent repeat types, together representing lessthan 15% of the total SSRs. The distribution of SSR types in bottle gourd was most similar tothat of cucumber, which had comparable relative and absolute frequencies for almost each SSRtype, then Arabidopsis. In bottle gourd tetranucleotides were predominated as in cucumberwhereas Arabidopsis has trinucleotides as abundant one. The distribution of bottle gourd microsatellites with respect to the number of repeat units is shown in Fig. 1. For all SSR types, microsatellite frequency declined as seen increased innumber of repeat units. However, the frequency of this variation was more gradual in allnucleotides from di- to tetranucleotides than in longer repeat types, from penta- tohexanucleotides showing the most dramatic reduction in frequency as they increased repeat units(Table 2). As a concern, the mean number of repeat units in dinucleotides are 9.0, which weretwice as that of the number of repeat units in tetranucleotides (4.5) (Table 2), showing thepresence of more varied motifs in dinucleotide irrespective of that it contain a less number ofSSRs than tetranucleotides. Although tetra, penta and hexa having almost the same mean repeatnumber like 4.5, 4 and 4 respectively, showing equal contribution to the genome portion that isoccupied by SSRs nucleotides. Trinucleotides repeat motif occurred more frequently than tetra,penta and hexanuclotide in the RAD genome data with a mean of 6.5.Distribution of microsatellite motifsStudied related calculations used for cucumber and Arabidopsis, which is presented assupplemental data [Additional file 1, Supplement Table S1 (for bottle gourd), Supplement TableS2 (for both cucumber and Arabidopsis)] available with the online version of this paper. Therelative frequency (%) of SSR types with different number of repeats, present in the bottle gourdgenome represent in Fig. 2. The main results of this analysis were outlined via different motifwise separately.Dinucleotide motifs: In bottle gourd genomic sequences, analysis of the di nucleotidesequence shows AT motif was intensely present (Additional file 1, Table S1) and CG repeatswere the least frequent dinucleotides in bottle gourd. In addition, relate to other both species, the existence of AT also being the amplest single motif, regardless of repeat type. Whereas, GCshowed the least frequent repeat in both cucumber and Arabidopsis, in all across the genomicdata sets examined. Comprehensive frequencies of individual dinucleotide motifs are mentionedin Additional file 1, Table S2.Trinucleotide motifs: In bottle gourd, trinucleotide repeats were second most abundant ingenomic sequences available. Investigating frequencies of diverse trinucleotides revealed thatrepeats of AAT were more common in bottle gourd genomic data along with cucumber. But thispattern is not similar to that of Arabidopsis, as in Arabidopsis AAG is predominant one.Conversely, CGT were the rarest trinucleotides in genomic DNA of bottle gourd whereas CCGshows the least abundant in both cucumber and Arabidopsis, irrespective with that of bottlegourd. Tetranucleotide motifs: Tetranucleotide repeats were far more frequent in genomicsequences of bottle gourd (Table 2). The AT-rich motifs AAAT, TTTA, ATTT, TTAT andAATA were, the most abundant tetranucleotides in bottle gourd genomic data, togetherrepresenting ~62% of all tetramer repeats. Whereas GC-rich repeats like ACGC, AGGC, CCCG,GCAG, GCCT, GCGG etc. were the least, with relative frequencies of >0.1% (Additional file 1,Table S1). A comparable distribution was perceived in the other dicots also, showing a clearprevalence of these similar AT-rich motifs in study. Pentanucleotide motifs: Bottle gourd genomic sequences had the least frequency ofpentanucleotide repeats. Among them AT rich penta repeats were the predominant oneaccounting a total of ~51% penta repeats most common motifs among them are AAAAT,ATTTT, TTTTA, TAAAA, TTTAT etc. followed by AAAAG (see Additional file 1, Table S1).In general, these motifs also predominated in both other species, like cucumber had the highest density of AAAAG followed by AAAAT repeats in genomic sequences, whereas Arabidopsishad the highest frequency of AAAAT motif followed by AAAAC, AAAAG. Analysis ofpentanucleotide frequencies in genomic DNA from all three species revealed that, in both bottlegourd and Arabidopsis, AAAAT was the most abundant repeat, with the next most frequentrepeats, AAAAG or AAAAC, but with cucumber AAAAG is more dominant motif than theAAAAT. Hexanucleotide motifs: In bottle gourd genomic sequence least frequent SSRs are thehexanucleotide accounting only 4.3% among all SSRs. AT-rich hexanucleotide motifs such asAAAAAT, ATTTTT, TATTTT, AAAATA, TTATTT etc. together contribute to 43.38% inbottle gourd genomic data. In all motifs AAAAAT is the most frequent repeat present followedby AAAAAG, TAAAAA, contributing 43.38% of total hexanucleotide. Similarly Arabidopsisalso has AAAAAT has the predominant one and in cucumber AAAAAG followed by AAAAATare frequently present. "