Early detection of invasive species in marine ecosystems using high-throughput sequencing: technical challenges and possible solutions

Introduction and spread of invasive non-indigenous species (NIS) has been clearly recognized as a growing global problem in marine and coastal ecosystems. Early detection of NIS has been recognized as one of the first priorities and effective ways in management programs. However, the detection of an array of rare NIS based on traditional morphological methods represents enormous technical challenges in the marine realm, as numerous poorly studied organisms may be small and/or have insufficient morphological distinctive features. The use of DNA-based approaches has largely increased the detection accuracy and efficiency. Owing to many obvious advantages such as the high capacity to detect extremely low-abundance species and low cost per sequence, high-throughput sequencing (HTS)-based methods have been popularly proposed for early detection of marine NIS. Although HTS-based approaches have been approved robust for the census of NIS in aquatic ecosystems, especially for those present at extremely low abundance, many factors in experimental design and data collection can cause errors including both false negatives and false positives. Here we identify factors responsible for both error types, discuss causes and consequences, and propose possible solutions when utilizing HTS for early detection of NIS in marine and coastal ecosystems.