RESUMO
The world's herbaria collectively house millions of diverse plant specimens, including endangered or extinct species and type specimens. Unlocking genetic data from the typically highly degraded DNA obtained from herbarium specimens was difficult until the arrival of high-throughput sequencing approaches, which can be applied to low quantities of severely fragmented DNA. Target enrichment involves using short molecular probes that hybridise and capture genomic regions of interest for high-throughput sequencing. In this study on herbariomics, we used this targeted sequencing approach and the Angiosperms353 universal probe set to recover up to 351 nuclear genes from 435 herbarium specimens that are up to 204 years old and span the breadth of angiosperm diversity. We show that on average 207 genes were successfully retrieved from herbarium specimens, although the mean number of genes retrieved and target enrichment efficiency is significantly higher for silica gel-dried specimens. Forty-seven target nuclear genes were recovered from a herbarium specimen of the critically endangered St Helena boxwood, Mellissia begoniifolia, collected in 1815. Herbarium specimens yield significantly less high-molecular-weight DNA than silica gel-dried specimens, and genomic DNA quality declines with sample age, which is negatively correlated with target enrichment efficiency. Climate, taxon-specific traits, and collection strategies additionally impact target sequence recovery. We also detected taxonomic bias in targeted sequencing outcomes for the 10 most numerous angiosperm families that were investigated in depth. We recommend that (1) for species distributed in wet tropical climates, silica gel-dried specimens should be used preferentially; (2) for species distributed in seasonally dry tropical climates, herbarium and silica gel-dried specimens yield similar results, and either collection can be used; (3) taxon-specific traits should be explored and established for effective optimisation of taxon-specific studies using herbarium specimens; (4) all herbarium sheets should, in future, be annotated with details of the preservation method used; (5) long-term storage of herbarium specimens should be in stable, low-humidity, and low-temperature environments; and (6) targeted sequencing with universal probes, such as Angiosperms353, should be investigated closely as a new approach for DNA barcoding that will ensure better exploitation of herbarium specimens than traditional Sanger sequencing approaches.
RESUMO
Os resultados do primeiro inventário botânico detalhado da região do Parque Estadual Cristalino, Mato Grosso, Brasil, são apresentados, incluindo uma lista de espécies. Um total de 1366 espécies de plantas vasculares distribuídas em 626 gêneros e 151 famílias foram registradas. As famílias com maior número de espécies foram Leguminosae, Rubiaceae, Melastomataceae, Malvaceae sensu lato e Moraceae. A flora inclui pelo menos sete novas espécies e diversos endemismos da região da Serra do Cachimbo, assim como muitos registros novos para o estado e alguns novos para o Brasil. Mais estudos provavelmente irão incrementar o número de espécies de forma significativa. Apesar da região apresentar uma diversidade alfa relativamente baixa em comparação a outras regiões já estudadas na Amazônia, a sua grande heterogeneidade de fitofisionomias é refletida numa elevada diversidade beta. Levando em conta esta riqueza biológica, situação importante mas ainda pouco estudada da margem ecotonal da Amazônia meridional, e sua posição estratégica com relação ao avanço sul-norte do deflorestamento, a região do Cristalino ocupa alta prioridade em termos de conservação.
The results of the first detailed botanical inventory in the region of the Cristalino State Park, Mato Grosso, Brazil, are presented, including an annotated checklist. A total of 1366 species of vascular plants, representing 626 genera and 151 families, were recorded. The most species-diverse families included Leguminosae, Rubiaceae, Melastomataceae, Malvaceae (sens. lat.) and Moraceae. The flora includes at least seven new species and several endemics from the Serra do Cachimbo, as well as many new records for the State of Mato Grosso and several for Brazil. Further studies are likely to increase the number of species significantly. The region does not show high alpha-diversity by Amazonian standards but is ecologically diverse, resulting in high levels of beta-diversity. Considering this biological richness, its situation within the important yet relatively poorly studied ecotone of the Amazonian margin, and its strategic position at the advancing frontier of deforestation pushing northwards into the basin, Cristalino is a high priority for conservation.
