Marques et al. describe the establishment of a Portuguese coalition for biodiversity genomics. Encompassing a part of continental Europe that have a high heterogeneity with regard to natural geography (coast, forests, mountains, large rivers, wetter and drier areas, etc.), and the far-flung Atlantic archipelagos Madeira and Azores (and Selvagens), and of course the corresponding marine environments, Portugal has a high and varied biodiversity. As elsewhere, the Portuguese biodiversity is under strain. The authors use well recognised references to build a case for this situation, including the IUCN Red List. The arguments follow what can be called classic reasoning in biodiversity conservation. The manuscript describes how Portuguese groups focusing on biodiversity genomics and other relevant topics have gone together to form the Portuguese branch of the European Reference Genome Atlas (ERGA) and their participation in the ERGA Pilot phase. Through a national inclusive process, they selected six species to be included in the pilot sequencing. The six species are described, including the reasons for inclusion in the pilot sequencing, and the rough outlines of the processes of sampling, sequencing and assembling the genomes.

In this reviewer's opinion, the efforts described here and those of the collected ERGA, Biodiversity Genomics Europe, Earth Biogenome Project, Darwin Tree of Life and other initiatives are highly justified considering the biodiversity situation. It is a good thing for the possibility of influencing practical national political decisions that papers describing national initiatives become available, especially from less resourceful countries (as Portugal is an EU "widening country"). There are plenty of examples of international agreements that are used as "political garnish", but are minimally put into practical political decisions at the national or local levels. I hope that the present paper can become a nudge in that direction for the Portuguese environment.

The manuscript is well written. It is easy to follow the arguments and explanations. For each of the six Portuguese pilot species, it is shortly mentioned how or what the genome assemblies can contribute to with regard to biological or evolutionary knowledge about the species, and/or its protection. Naturally, this kind of descriptive policy/perspective paper cannot go into all kinds of details, and I am looking forward to reading the species-related genome papers that will arise from these efforts. Hopefully, some years into the future, this and other ERGA efforts will also give rise to some papers that describe the practical consequences for conservation and protection of the sequenced species.

The article Building a Portuguese Coalition for Biodiversity Genomics by Marques et al. aims at describing the engagement of researchers from Portuguese institutions in the use of genomics to inventory and characterize biodiversity to inform conservation policies and management and restoration practices. The diverse territories ofPortugal's land and sea, from continental Europe to the Atlantic islands, makes Portugal an important reservoirof biodiversity. The participation of these researchers in the European Reference Genome Atlas (ERGA) initiative has strengthened the creation of the Biogenome Portugal.
The article outlines Portugal's contribution to ERGA's pilot project (https://www.erga-biodiversity.eu/pilot-project), which will produce high-quality reference genomes of more than 98 species. It details the current state of six endemic, iconic, and/or endangered species from Portugal, including plants, insects, and vertebrates (fish, birds, and mammals) from either the mainland of Portugal or the Azores islands. For each species, there is a thorough explanation of sample collection and processing as well as the current state of sequencing and assembly, however none of the species' data analysis are mentioned.
The article then goes on to detail the development of Biogenome Portugal, a national Portuguese network for biodiversity genomics. This network will link the nation's genomics research community, and aims to promote Portugal’s active participation in global biodiversity genomics initiatives, facilitate the exchange of knowledge and infrastructure, organise advanced training programmes, and support knowledge dissemination and outreach initiatives. Members of the network will have a variety of specialties, including those in genomics, ecology, taxonomy, evolution, and other areas, and they will come from different taxonomic groups.

I only have two major comments:
1-    The article doesn't make any reference of the Earth Biogenome project (EBP). The EBP, set up as aninternational confederated network of networks with numerous linked global or taxon-specific projects, intends to sequence, catalogue, and characterise the genome of all of Earth's eukaryotic species. Launched in 2018, it is one of the most important efforts taking place in biology right now. In fact, ERGA is an outstanding initiative and one of the most important EBP affiliated projects. Thus, the EBP must be mentioned and referred in the manuscript.
2-    If possible, a brief statement on what has been discovered about at least one species should be included to give the reader a taste of science. I understand that the genome of the two first species described has already been assembled and, ideally, annotated. Even though further papers with scientific material will presumably follow with this one, perhaps the authors can briefly indicate if anything interesting or novel has already been discovered from the sequence.

Minor issue: It could be great to list or show the locations where the samples were taken from in Figure 2.