Uneven DNA barcode representation among tree communities and regions in tropical South America

DNA barcode has become an important tool for identifying species, accelerating biodiversity assessments. However, most species still lack barcode data, especially in tropical biomes. We used a comprehensive DNA barcode library for South American tree species and identified geographic and phylogenetic gaps in DNA sequences. We compiled distribution data for 11 525 tree species across 3283 sites in four ecoregions: Amazônia, Caatinga, Cerrado, and Mata Atlântica, and searched GenBank for the main plant DNA barcodes: ITS2, matk, rbcL, and trnH-psbA. To assess phylogenetic diversity gaps, we used a dated molecular phylogeny of 1100 angiosperm genera found in tropical South America. Only around 25% of species have sequences available in GenBank for the selected DNA markers. Most species lacking sequences occur in the Mata Atlântica and Amazônia ecoregions. Moreover, missing species on GenBank are not randomly distributed across the angiosperm phylogeny, leading to large phylogenetic gaps. By calculating phylogenetic endemism, we identified new priority sites for future fieldwork, highlighting the importance of biodiversity metrics beyond species richness. This work revealed major geographic and phylogenetic gaps in DNA barcode data for tropical tree species in South America, helping to guide targeted sampling and improve conservation planning based on biodiversity and evolutionary analyses.