Efficient precision genome editing requires a quick, quantitative, and inexpensive assay of editing outcomes. Here we present ICE (Inference of CRISPR Edits), which enables robust batch analysis of CRISPR edits using Sanger data. ICE proposes potential editing outcomes for single guide, multiplex editing, base editing, and homology-directed repair experiments and then determines which are supported by the data via regression. Additionally, we develop a score called ICE-D (Discordance) that can provide information on large or unexpected edits. We empirically confirm through over 1,800 edits that the ICE algorithm is robust, reproducible, and can analyze CRISPR experiments within days after transfection. We also confirm that ICE strongly correlates with NGS analysis (Amp-Seq). ICE is an improvement over current analysis tools in that it provides batch analysis, is free to use, and can detect a wider variety of edits. It provides investigators with a reliable editing tool that can significantly expedite CRISPR editing workflows. Our ICE tool is available online at ice.synthego.com and the source code is at github.com/synthego-open/ice

Tree ferns recently were identified as the closest sister group to the hyperdiverse clade of ferns, the polypods. Although most of the 600 species of tree ferns are arborescent, the group encompasses a wide range of morphological variability, from diminutive members to the giant scaly tree ferns, Cyatheaceae. This well-known family comprises most of the tree fern diversity (∼500 species) and is widespread in tropical, subtropical, and south temperate regions of the world. Here we investigate the phylogenetic relationships of scaly tree ferns based on DNA sequence data from five plastid regions (rbcL, rbcL-accD IGS, rbcL-atpB IGS, trnG-trnR, and trnL-trnF). A basal dichotomy resolves Sphaeropteris as sister to all other taxa and scale features support these two clades: Sphaeropteris has conform scales, whereas all other taxa have marginate scales. The marginate-scaled clade consists of a basal trichotomy, with the three groups here termed (1) Cyathea (including Cnemidaria, Hymenophyllopsis, Trichipteris), (2) Alsophila sensu stricto, and (3) Gymnosphaera (previously recognized as a section within Alsophila) + A. capensis. Scaly tree ferns display a wide range of indusial structures, and although indusium shape is homoplastic it does contain useful phylogenetic information that supports some of the larger clades recognised.

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An annotated list of the pteridophytes of Brazilian Amazonia is presented, with the geographic occurrence of the species by States and Territories. The flora includes 12 families, 58 genera and 279 species, with only four species possibly endemic. Two new combinations are Arachnoides macrostegia (Hook.) Tryon & Conant and Thelypteris juruensis (C. Chr.) Tryon & Conant. Some general comments on the geography of Amazonian ferns are included as well as ecological studies presenting data on the local environmental preferences of six species.

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The chloroplast genome of most land plants is highly conserved. In contrast, physical and gene mapping studies have revealed a highly rearranged chloroplast genome in species representing four families of ferns. In all four, there has been a rare duplication of the psbA gene and the order of the psbA, 16S, and 23S rRNA genes has been inverted. Our analysis shows that the described rearrangement results from a minimum of two inversions within the inverted repeat. This chloroplast DNA structure provides unambiguous evidence that phylogenetically links families of ferns once thought to belong to different major evolutionary lineages.The chloroplast DNA (cpDNA) of most land plants is a circular molecule 120-160 kilobases (kb), which codes for 120 genes and typically contains an inverted repeat (IR). These repeated sequences range in size from 9.4 to 76 kb, code for several genes including those for 16S and 23S rRNA, and are separated by small single copy (SSC) and large single copy (LSC) regions (1-3). Gene order is remarkably similar in the cpDNAs of the fern Osmunda, the gymnosperm Ginkgo, and many angiosperms and differs from that in the bryophyte Marchantia primarily by a 30-kb inversion (4-6). This 30-kb inversion places the psbA gene close to the IR in Osmunda and in most gymnosperms and angiosperms (3, 4). The rRNA genes are part of an operon typically oriented with the 16S gene nearer to the LSC region and the 23S gene closer to the SSC region (Fig. 1A). Structural changes (such as gene duplications, gene losses, and inversions) are relatively rare and have been documented mainly in angiosperms (refs. 7-10, but see ref. 11).In this report, we describe the chloroplast genome shared by several ferns and show that it differs considerably from the typical structure detailed above. These differences provide molecular evidence about the evolutionary relationships of these ferns, which have been in dispute, and demonstrate that the chloroplast genomes of groups other than angiosperms have been markedly changed during evolution. Evidence concerning relationships at higher taxonomic levels is especially needed in ferns in which different phylogenies based on morphological characters are not concordant (12-15). Reasons for these discrepancies include (i) the use of narrative methods of phylogenetic analysis where the line of reasoning and the characters used are not made explicit, (ii) difficulties in identifying homologous parts in structurally simple organisms, and (iii) problems in determining the primitive or advanced states ofcharacters. The latter situation arises from the paucity of evidence from the fossil record (15-17) and the difficulty in choosing appropriate outgroups for many extant taxa due to the antiquity of ferns and the loss of many potential outgroups through extinction. MATERIALS AND METHODSLeaves of Polystichum acrostichoides (Michx.) Schott were collected in western Massachusetts and a voucher specimen (Sprague in 1986) was deposited at the Dean Herbarium of Indiana University. Leaves ...

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