Rodríguez Rodríguez, GonzaloMartínez Ballesteros, HugoSánchez Llamas, EduardoBande Ramudo, RobertoFernández Otero, Rosa2023-02-232023-02-232022Rodríguez-Rodríguez G, Ballesteros HM, Sánchez-Llamas E, Bande R and Otero RF (2022) The state of the art in cost-benefit of HTS methods for stock assessment: An overview. Front. Mar. Sci. 9:1005534. doi: 10.3389/fmars.2022.10055342296-7745http://hdl.handle.net/10347/30200Over the past two decades, enormous progresses have been made in high-throughput sequencing (HTS) method development. This fact unveiled the potential usefulness of HTS methods in a wide range of fields such as fishery assessment and management, for which their application has been extensively discussed. As a consequence of the rapid development, sequencing costs have continuously declined, leading to a general claim that HTS methods are cost-efficient compared with traditional ones. Within this context, the underlying research objective is to assess the cost-effectiveness of genomic techniques through a review of the state of the art (SoA) on three HTS methods: i) environmental DNA (eDNA); ii) epigenetics method for age determination through DNA methylation (DNAm), and; iii) close-kin mark-recapture (CKMR) applied on marine ecosystems and fisheries and for stock assessment purposes. The SoA review of the literature on HTS methods was performed through the snow-balling systematic reviewing approach. The analysis has considered the set of processes and variables necessary to perform the stock assessment and compared the capacity of current and HTS methods for providing the required data. Research reveals that HTS methods constitute a promising tool for fishery research and, particularly, for improving scientific advice. Nevertheless, up to now, only one research, on a non-commercial species, has been conducted on the application of HTS methods for stock assessment purposes. Although some partial data are present in the literature, no systematic analysis on costs has been found. This paper suggests that the future research agenda should attempt to straddle both the scenarios for the transition process, considering complementary implementation and substitution possibilities and their cost-efficiency. Clarifying these questions is likely to pave the way for the effective and step-wise implementation of these methods in fishery management; thus, further research is recommended to encompass the transition processeng© 2022 Rodríguez-Rodríguez, Ballesteros, Sánchez-Llamas, Bande and Otero. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these termsAtribución 4.0 Internacionalhttp://creativecommons.org/licenses/by/4.0/FisheriesStock assessmentHTS methodsClose-kin mark-recaptureeDNADNAmjournal article10.3389/fmars.2022.1005534open access