Original title: LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons
Some DNA elements in plant genomes can copy themselves and insert elsewhere. Many search programs look for a familiar pattern at the ends of these elements, but they can also produce many false finds. LTR_retriever searches genome sequences for these elements and builds libraries of them, while also finding some with unusual end patterns. The abstract reports high accuracy in model plants and says the program can work with long sequencing reads.
Imagine sorting a pile of mail by looking for a familiar mark on each envelope. Some real letters have a different mark, while some envelopes that match the usual mark are not letters at all. In this paper, the mail is plant DNA, and the sorter finds both familiar and unusual copying elements while aiming to avoid false finds.
Plant researchers need accurate maps of these DNA elements to annotate genes well. Finding unusual elements too matters because the abstract reports that many non-standard Copia elements lie near or within genes, where they may affect gene evolution and could serve as mutagenesis tools.
The abstract reports results in model plants and a test using long reads from Arabidopsis, but does not give performance figures for every plant genome or sequencing setup. It does not describe how the program compares with specific alternatives, or establish that the reported gene locations cause changes in gene evolution. The proposed use as a mutagenesis tool is potential, not a demonstrated outcome in the abstract.
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LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons — Shujun Ou, Ning Jiang — PLANT PHYSIOLOGY — doi:10.1104/pp.17.01310
Abstract licence: CC BY
Explanation generated by Synthesis from the abstract — it is not the original paper.