Microsatellite And Nucleotide Variation Characters In Juglans Regia L.Genome By High Throughput Sequencing Technology

Walnut(Juglans regia L.) is an economically important woody plant in Juglandaceae family. In this study, genome sequencing of J.regia was performed with Roche 454 GS-FLX sequencer. A total of 541,176 high-quality reads were produced with an average read length of 359 bp. We obtained 31,362 contigs(≥100bp) after assembling with the Roche Newbler de novo Assembler(Version 2.8); the total length of the assembly was 15.1 Mb. Then we found the microsatellites(SSRs) and nucleotide variations(SNPs and InDels) from the assembled sequence, the following results are obtained:1. There were 9,787 microsatellites in the assembled genome sequence, among them, the hexanucleotide repeats were the most abundant(5,883), accounting for 60.11% of all microsatellites, following by the mononucleotide(1,289) and tetranucleotide repeats(889) are the second and third abundant, which accounted for 13.17% and 9.07%. The number of dinucleotide(768), trinucleotide(549) and pentanucleotide(409) repeats were found to accounted for 7.85% %, 5.61 and 4.18%, respectively.2. For different types of repeat, the main motifs of mono-, di- and trinucleotide were A/T, AT/TA and AG/CT and AAT/ATT, while AAAT, AAAAT and AAAAAT were the dominant repeat motifs in tetra-, penta- and hexanucleotide repeats respectively. There was a bias of A/T nucleotide in microsatellites of walnut genome.3. The length of microsatellite in J. regia genome was mainly less than 20 bp. It can be found that the variation of microsatellites was negatively correlated with the lengths of repeat motifs,which suggested that the microsatellites with shorter repeat motifs would change faster than those longer with repeat motifs.4. Totally, 49,202 nucleotide variations were detected including 48,165 single nucleotide polymorphisms(SNPs) and 1,037 insertions / deletions(InDels). Among the detected SNPs, the number of transitions(35,480) was much more than that of transversions(12,685), with a ratio of 2.79:1. Within transitions, C/T transitions were slightly more abundant than that of G/A. Among transversions, A/T transversions were much more common than the other three types of transversions. As for the detected InDels, single nucleotide changes accounted for 52.65% of all InDels. Additionally, the InDels’ number was negatively correlated with its length.