Elucidation of genomic organizations of transgenic soybean plants through de novo genome assembly with short paired-end reads.

ABSTRACT: Elucidation of the genomic organizations of transgene insertion sites is essential for the genetic studies of transgenic plants. Herein, we establish an analysis pipeline that identifies the transgene insertion sites as well as the presence of vector backbones, through de novo genome assembly with high-throughput sequencing data in two transgenic soybean lines, AtYUCCA6-#5 and 35S-UGT72E3/2-#7. Sequencing data of approximately 28× and 29× genome coverages for each line generated by high-throughput sequencing were de novo assembled. The databases generated from the de novo assembled sequences were used to search contigs that contained putative insertion sites and their flanking sequences (integration sites) of transgene fragments using transgenic vector sequences as queries. The predicted i

SUBMITTER: Kim MS 

PROVIDER: S-EPMC10231564 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature