No abstract

Vascular plants appeared ~410 million years ago then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes (1). We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first non-seed vascular plant genome reported. By comparing gene content in evolutionary diverse taxa, we found that the transition from a gametophyte- to sporophyte-dominated life cycle required far fewer new genes than the transition from a non-seed vascular to a flowering plant, while secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in post-transcriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the tasiRNA pathway and extensive RNA editing of organellar genes.

Long-term climate change and periodic environmental extremes threaten food and fuel security1 and global crop productivity2–4. Although molecular and adaptive breeding strategies can buffer the effects of climatic stress and improve crop resilience5, these approaches require sufficient knowledge of the genes that underlie productivity and adaptation6—knowledge that has been limited to a small number of well-studied model systems. Here we present the assembly and annotation of the large and complex genome of the polyploid bioenergy crop switchgrass (Panicum virgatum). Analysis of biomass and survival among 732 resequenced genotypes, which were grown across 10 common gardens that span 1,800 km of latitude, jointly revealed extensive genomic evidence of climate adaptation. Climate–gene–biomass associations were abundant but varied considerably among deeply diverged gene pools. Furthermore, we found that gene flow accelerated climate adaptation during the postglacial colonization of northern habitats through introgression of alleles from a pre-adapted northern gene pool. The polyploid nature of switchgrass also enhanced adaptive potential through the fractionation of gene function, as there was an increased level of heritable genetic diversity on the nondominant subgenome. In addition to investigating patterns of climate adaptation, the genome resources and gene–trait associations developed here provide breeders with the necessary tools to increase switchgrass yield for the sustainable production of bioenergy.

POT1 is a single-copy gene in yeast and humans that encodes a single-strand telomere binding protein required for chromosome end protection and telomere length regulation. In contrast, Arabidopsis harbors multiple, divergent POT-like genes that bear signature N-terminal OB-fold motifs, but otherwise share limited sequence similarity. Here, we report that plants null for AtPOT1 show no telomere deprotection phenotype, but rather exhibit progressive loss of telomeric DNA. Genetic analysis indicates that AtPOT1 acts in the same pathway as telomerase. In vitro levels of telomerase activity in pot1 mutants are significantly reduced and are more variable than wild-type. Consistent with this observation, AtPOT1 physically associates with active telomerase particles. Although low levels of AtPOT1 can be detected at telomeres in unsynchronized cells and in cells arrested in G2, AtPOT1 binding is significantly enhanced during S-phase, when telomerase is thought to act at telomeres. Our findings indicate that AtPOT1 is a novel accessory factor for telomerase required for positive telomere length regulation, and they underscore the coordinate and extraordinarily rapid evolution of telomere proteins and the telomerase enzyme.

Pot1 (protection of telomeres 1) is a single-stranded telomere binding protein that is essential for chromosome end protection and telomere length homeostasis. Arabidopsis encodes two Pot1-like proteins, dubbed AtPot1 and AtPot2. Here we show that telomeres in transgenic plants expressing a truncated AtPot1 allele lacking the N-terminal oligonucleotide/oligosaccharide binding fold (P1⌬N) are 1 to 1.5 kb shorter than in the wild type, suggesting that AtPot1 contributes to the positive regulation of telomere length control. In contrast, telomere length is unperturbed in plants expressing the analogous region of AtPot2. A strikingly different phenotype is observed in plants overexpressing the AtPot2 N terminus (P2⌬C) but not the corresponding region in AtPot1. Although bulk telomeres in P2⌬C mutants are 1 to 2 kb shorter than in the wild type, these plants resemble late-generation telomerase-deficient mutants with severe growth defects, sterility, and massive genome instability, including bridged chromosomes and aneuploidy. The genome instability associated with P2⌬C mutants implies that AtPot2 contributes to chromosome end protection. Thus, Arabidopsis has evolved two Pot genes that function differently in telomere biology. These findings provide unanticipated information about the evolution of single-stranded telomere binding proteins.Telomeres are the essential protein-DNA structures at the ends of linear eukaryotic chromosomes whose primary functions are to facilitate complete replication of the chromosome terminus and to sequester it from DNA repair machinery and exonucleolytic attack (5, 7, 11). In most organisms, the DNA component of telomeres consists of tandem repeats of simple G-rich sequences that terminate in a single-stranded 3Ј extension. The telomere can fold back on itself to form a t-loop, where the 3Ј G-overhang invades the duplex region of the telomere to create a displaced loop consisting of singlestranded G-rich repeats (18). During S phase, the t-loop is thought to unfold, allowing telomerase access to the G-overhang for telomere length maintenance (50). The G-overhang associates with single-stranded specific proteins (42, 50). The first G-strand binding protein identified, telomere end binding protein (TEBP), was found in the hypotrichous ciliate Oxytricha nova. TEBP is a heterodimer of ␣ and ␤ subunits that binds tenaciously to the 3Ј terminus of the G-overhang (35) via four oligonucleotide/oligosaccharide binding folds (OB folds) (21). The OB fold is a structurally conserved feature also associated with single-stranded telomere binding proteins in fungi and vertebrates (45). The Saccharomyces cerevisiae protein, Cdc13p, is the best characterized of this class of proteins (12,42,50). A multifunctional protein, Cdc13p binds the single-stranded G-overhang and provides telomere end protection, facilitates telomerase recruitment and repression, and coordinates telomeric G-and C-strand synthesis through interactions with lagging-strand replication machinery (50).A distant relative of TEBP called ...

Highlights d A database combining genomic information and chromatin profiles for Marchantia d Correlations between chromatin marks and transcription are conserved in land plants d A significant portion of constitutive heterochromatin is marked by H3K27me3 d Insights into the evolution of TAD organization in plants

Environmental stress is a major driver of ecological community dynamics and agricultural productivity. This is especially true for soil water availability, because drought is the greatest abiotic inhibitor of worldwide crop yields. Here, we test the genetic basis of drought responses in the genetic model for C4 perennial grasses, Panicum hallii, through population genomics, field-scale gene-expression (eQTL) analysis, and comparison of two complete genomes. While gene expression networks are dominated by local cis-regulatory elements, we observe three genomic hotspots of unlinked trans-regulatory loci. These regulatory hubs are four times more drought responsive than the genome-wide average. Additionally, cis- and trans-regulatory networks are more likely to have opposing effects than expected under neutral evolution, supporting a strong influence of compensatory evolution and stabilizing selection. These results implicate trans-regulatory evolution as a driver of drought responses and demonstrate the potential for crop improvement in drought-prone regions through modification of gene regulatory networks.

Little is known about the protein composition of plant telomeres. We queried the Arabidopsis thaliana genome data base in search of genes with similarity to the human telomere proteins hTRF1 and hTRF2. hTRF1/ hTRF2 are distinguished by the presence of a single Myb-like domain in their C terminus that is required for telomeric DNA binding in vitro. Twelve Arabidopsis genes fitting this criterion, dubbed TRF-like (TRFL), fell into two distinct gene families. Notably, TRFL family 1 possessed a highly conserved region C-terminal to the Myb domain called Myb-extension (Myb-ext) that is absent in TRFL family 2 and hTRF1/hTRF2. Immunoprecipitation experiments revealed that recombinant proteins from TRFL family 1, but not those from family 2, formed homodimers and heterodimers in vitro. DNA binding studies with isolated C-terminal fragments from TRFL family 1 proteins, but not family 2, showed specific binding to double-stranded plant telomeric DNA in vitro. Removal of the Myb-ext domain from TRFL1, a family 1 member, abolished DNA binding. However, when the Myb-ext domain was introduced into the corresponding region in TRFL3, a family 2 member, telomeric DNA binding was observed. Thus, Myb-ext is required for binding plant telomeric DNA and defines a novel class of proteins in Arabidopsis.Telomeres are the specialized nucleoprotein structures that comprise the natural ends of linear eukaryotic chromosomes and ensure their complete replication and stability (1, 2). In most eukaryotes, telomeric DNA is composed of tandem arrays of simple G-rich repeat sequences terminating in a singlestrand 3Ј-overhang, which is maintained through the action of the telomerase reverse transcriptase (1). Both the double and single-strand regions of the telomere are coated with nonhistone proteins that provide protection for telomeric DNA and regulate telomerase access to the chromosome terminus. Proteins that bind double-strand telomeric DNA are typified in vertebrates by TRF1 and TRF2 and in budding and fission yeast by Rap1 and Taz1,.Human TRF1 (hTRF1) 1 behaves as a negative regulator of telomere length; overexpression results in telomere shortening, whereas a dominant negative allele induces telomere elongation (9, 10). hTRF1 mediates telomere length control through interactions with other telomere-associated factors including tankyrase (11), TIN2 (12), PinX1 (13), and Pot1 (14). Although hTRF2 contributes to telomere length regulation (10), its major function is to conceal telomere ends from detection as doublestrand breaks (15, 16). Inhibition of hTRF2 in cultured human cells results in the loss of the 3Ј-overhang and the formation of covalently fused telomeres (15). In addition, compromised hTRF2 function culminates in cell cycle arrest and ATM/p53-mediated apoptosis (16).The functional domains of vertebrate TRF1 and TRF2 have been studied in some detail (17). The two proteins have similar molecular masses (50 -60 kDa), and resemble each other in domain structure. Although the N terminus is highly acidic in hTRF1 and highly basic in...