New sequencing technologies facilitate the generation of large-scale molecular data sets for constructing the plant tree of life. We describe a new probe set for target enrichment sequencing to generate nuclear sequence data to build phylogenetic trees with any flagellate land plants, including hornworts, liverworts, mosses, lycophytes, ferns, and all gymnosperms. METHODS: We leveraged existing transcriptome and genome sequence data to design the GoFlag 451 probes, a set of 56,989 probes for target enrichment sequencing of 451 exons that are found in 248 single-copy or low-copy nuclear genes across flagellate plant lineages. RESULTS: Our results indicate that target enrichment using the GoFlag451 probe set can provide large nuclear data sets that can be used to resolve relationships among both distantly and closely related taxa across the flagellate land plants. We also describe the GoFlag 408 probes, an optimized probe set covering 408 of the 451 exons from the GoFlag 451 probe set that is commercialized by RAPiD Genomics. CONCLUSIONS: A target enrichment approach using the new probe set provides a relatively low-cost solution to obtain large-scale nuclear sequence data for inferring phylogenetic relationships across flagellate land plants.

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The plastomes of are the smallest reported for a fern so far. The loss of the gene suite is associated with the reduction of the small single copy, instead of the inverted repeat as noted for other groups of plants. Putative C-to-U and U-to-C transitions were observed in several instances in the three plastomes, suggesting that posttranscriptional modification of RNA is likely a common phenomenon in this clade as well.

36Premise of the study: New sequencing technologies enable the possibility of generating large-37 scale molecular datasets for constructing the plant tree of life. We describe a new probe set for 38 target enrichment sequencing to generate nuclear sequence data to build phylogenetic trees with 39 any flagellate plants, comprising hornworts, liverworts, mosses, lycophytes, ferns, and 40 gymnosperms. 41 Methods and Results: We leveraged existing transcriptome and genome sequence data to design 42 a set of 56,989 probes for target enrichment sequencing of 451 nuclear exons and non-coding 43 flanking regions across flagellate plant lineages. We describe the performance of target 44 enrichment using the probe set across flagellate plants and demonstrate the potential of the data 45 to resolve relationships among both ancient and closely related taxa. 46 Conclusions: A target enrichment approach using the new probe set provides a relatively low-47 cost solution to obtain large-scale nuclear sequence data for inferring phylogenetic relationships 48 across flagellate plants. 49 50

Isolated monoliths of granitic and/or gneissic rock rising abruptly from the surrounding landscape are known as inselbergs. Dome-shaped inselbergs are common throughout the Atlantic Forest in south-eastern Brazil, a region known as Sugarloaf Land (SLL). This study aimed to create the first checklist of vascular plant species occurring on lowland inselbergs in SLL, with a focus on vegetation islands. We used information from online databases, our own field sampling and data from previously-published studies. We found 548 vascular plant species (505 angiosperms; 43 ferns and lycophytes) belonging to 69 families and 212 genera. Of all identified species, 536 are native and 12 are naturalised. We updated the information currently available in Flora do Brasil 2020, as 59% of the angiosperms and 63% of the ferns and lycophytes on our checklist were not previously characterised as occurring on rock outcrops. As a first step towards generating a Virtual Herbarium of lowland inselberg vascular plants, we added barcode vouchers with images available online for 75% of the total number of vascular species. In the official lists of endangered species, 115 angiosperms and five ferns and lycophytes are mentioned. However, the conservation status of many species have not yet been evaluated (77% angiosperms; 88% ferns and lycophytes), thus this list is an important step towards their conservation. The information provided herein is essential for management programmes related to rock outcrops in Brazil as they are facing serious threats to conservation.

Epiphytes are hyper‐diverse and one of the frequently undervalued life forms in plant surveys and biodiversity inventories. Epiphytes of the Atlantic Forest, one of the most endangered ecosystems in the world, have high endemism and radiated recently in the Pliocene. We aimed to (1) compile an extensive Atlantic Forest data set on vascular, non‐vascular plants (including hemiepiphytes), and lichen epiphyte species occurrence and abundance; (2) describe the epiphyte distribution in the Atlantic Forest, in order to indicate future sampling efforts. Our work presents the first epiphyte data set with information on abundance and occurrence of epiphyte phorophyte species. All data compiled here come from three main sources provided by the authors: published sources (comprising peer‐reviewed articles, books, and theses), unpublished data, and herbarium data. We compiled a data set composed of 2,095 species, from 89,270 holo/hemiepiphyte records, in the Atlantic Forest of Brazil, Argentina, Paraguay, and Uruguay, recorded from 1824 to early 2018. Most of the records were from qualitative data (occurrence only, 88%), well distributed throughout the Atlantic Forest. For quantitative records, the most common sampling method was individual trees (71%), followed by plot sampling (19%), and transect sampling (10%). Angiosperms (81%) were the most frequently registered group, and Bromeliaceae and Orchidaceae were the families with the greatest number of records (27,272 and 21,945, respectively). Ferns and Lycophytes presented fewer records than Angiosperms, and Polypodiaceae were the most recorded family, and more concentrated in the Southern and Southeastern regions. Data on non‐vascular plants and lichens were scarce, with a few disjunct records concentrated in the Northeastern region of the Atlantic Forest. For all non‐vascular plant records, Lejeuneaceae, a family of liverworts, was the most recorded family. We hope that our effort to organize scattered epiphyte data help advance the knowledge of epiphyte ecology, as well as our understanding of macroecological and biogeographical patterns in the Atlantic Forest. No copyright restrictions are associated with the data set. Please cite this Ecology Data Paper if the data are used in publication and teaching events.

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A new genus of grammitid ferns, Leucotrichum, is described. Segregated from Lellingeria on the basis of molecular analyses and morphological characters, it comprises five species distributed in the Antilles, Central America, and Southeastern Brazil. We present a phylogeny based on two cpDNA genes, atpB and rbcL, showing the relationships between Leucotrichum and other genera of grammitid ferns. Both Bayesian and Maximum Parsimony analyses support the monophyly of Leucotrichum, with bootstrap value of 100% and posterior probability value of 1.0, and its sister-group relationship to the Terpsichore lanigera group. Leucotrichum is characterized by seven morphological characters: arching fronds, clathrate rhizome scales, blackish rhizome scale cell walls, laterally marginate petioles, laminar apices subconform to the lateral pinnae, pinna costae without blackish sclerenchyma, and hairs bearing acicular branch cells. We also provide a key, descriptions, complete synonymy, discussions, specimens examined, and illustrations for all the species.