Genomic sequencing using 454 pyrosequencing and development of an SSR primer database for 'Lagerstroemia indica' L

• Published in: Plant omics Vol. 8; no. 1
• Main Authors: Jing Wang, Xiaogang Dai, Yingnan Chen, Yanling Yang, Xinye Zhang, Shuxian Li, Tongming Yin
• Format: Journal Article
• Published: 01.01.2015
• Subjects: Crape myrtle, Common; Genomes; Lagerstroemia; Microsatellites (Genetics)
• ISSN: 1836-0661; 1836-3644

Crape myrtles ('Lagerstroemia' spp.) represent a large group of woody flowing piants. Despite their high ornamental value and popularity, few genomic sequences and marker resources are available for them. 'Lagerstroemia indica' is one of the most widely cultivated crape myrtle species. In this study, we partially sequenced the genome of 'L. indica' using newly updated 454 sequencing technology. Over 1.2 million high-quality reads in a total length of 837.4 Mb were generated. The average read length was 679 bp. Of the reads, 779,744 (63.2%) were assembled into 65,129 contigs covering a physical length of 93.6 Mb and with N50 contig size of 1,648 bp. The contigs were used to recover microsatellites with repeat motifs of 1-6 bp. A total of 33,026 microsatellites were detected. An SSR primer database was established based on the flanking sequences of the detected microsatellites. A PCR survey of subset of these SSR primers revealed that 89.5% amplified successfully, and 66.7% of the loci were polymorphic. The polymorphic information contents of the polymorphic SSRs ranged from 0.08 to 0.79, with an average value of 0.44. This study provided valuable genomic sequences and marker resources for future genetic studies on 'Lagerstroemia' species.