Coming of age for COI metabarcoding of whole organism community DNA: towards bioinformatic harmonisation

Abstract

Metabarcoding of DNA extracted from community samples of whole organisms\n(whole organism community DNA, wocDNA) is increasingly being applied to\nterrestrial, marine and freshwater metazoan communities to provide\nrapid, accurate and high resolution data for novel molecular ecology\nresearch. The growth of this field has been accompanied by considerable\ndevelopment that builds on microbial metabarcoding methods to develop\nappropriate and efficient sampling and laboratory protocols for whole\norganism metazoan communities. However, considerably less attention has\nfocused on ensuring bioinformatic methods are adapted and applied\ncomprehensively in wocDNA metabarcoding. In this study we examined over\n600 papers and identified 111 studies that performed COI metabarcoding\nof wocDNA. We then systematically reviewed the bioinformatic methods\nemployed by these papers to identify the state-of-the-art. Our results\nshow that the increasing use of wocDNA COI metabarcoding for metazoan\ndiversity is characterised by a clear absence of bioinformatic\nharmonisation, and the temporal trends show little change in this\nsituation. The reviewed literature showed (i) high heterogeneity across\npipelines, tasks and tools used, (ii) limited or no adaptation of\nbioinformatic procedures to the nature of the COI fragment, and (iii) a\nworrying underreporting of tasks, software and parameters. Based upon\nthese findings we propose a set of recommendations that we think the\nwocDNA metabarcoding community should consider to ensure that\nbioinformatic methods are appropriate, comprehensive and comparable. We\nbelieve that adhering to these recommendations will improve the\nlong-term integrative potential of wocDNA COI metabarcoding for\nbiodiversity science.