Members Of Clade Research Articles

Complete Coding Genome Sequence of an Influenza A/H3N8 Equine Virus Isolated in Kazakhstan in 2007.

ABSTRACTHere, we reported the complete coding sequence of the influenza A/equine/Otar/3/2007 (H3N8) equine virus, first isolated in Kazakhstan in 2007. The hemagglutinin (HA) sequences of the Kazakhstan isolates appeared to be closely related to viruses isolated in early 2000 in Asia. Phylogenetic analysis characterized the Kazakhstan isolates as a member of the Florida sublineage clade 2 by the HA protein sequence.

Genome-wide identification of wheat ABC1K gene family and functional dissection of TaABC1K3 and TaABC1K6 involved in drought tolerance.

Activity of BC1 complex kinase (ABC1K) serves as an atypical kinase family involved in plant stress resistance. This study identified 44 ABC1K genes in the wheat genome, which contained three clades (I–III). TaABC1K genes generally had similar structural features, but differences were present in motif and exon compositions from different clade members. More type II functional divergence sites were detected between clade I and clade III and no positive selection site were found in TaABC1K family. The three-dimensional structure prediction by Alphafold2 showed that TaABC1K proteins had more α-helixes with a relatively even distribution, and different clade members had differences in the content of secondary structures. The cis-acting element analysis showed that TaABC1K genes contained abundant cis-acting elements related to plant hormones and environmental stress response in the promoter region, and generally displayed a significantly upregulated expression under drought stress. In particular, both TaABC1K3 and TaABC1K6 genes from clade I was highly induced by drought stress, and their overexpression in yeast and Arabidopsis enhanced drought tolerance by suppressing active oxygen burst and reducing photosynthesis impairment. Meanwhile, TaABC1K3 and TaABC1K6 could, respectively, complement the function of Arabidopsis abc1k3 and abc1k6 mutants and reduce photosynthesis damage caused by drought stress.

YTH Domain Proteins Play an Essential Role in Rice Growth and Stress Response

As the most prevalent epi-transcriptional modification, m6A modifications play essential roles in regulating RNA fate. The molecular functions of YTH521-B homology (YTH) domain proteins, the most known READER proteins of m6A modifications, have been well-studied in animals. Although plants contain more YTH domain proteins than other eukaryotes, little is known about their biological importance. In dicot species Arabidopsis thaliana, the YTHDFA clade members ECT2/3/4 and CPSF30-L are well-studied and important for cell proliferation, plant organogenesis, and nitrate transport. More emphasis is needed on the biological functions of plant YTH proteins, especially monocot YTHs. Here we presented a detailed phylogenetic relationship of eukaryotic YTH proteins and clustered plant YTHDFC clade into three subclades. To determine the importance of monocot YTH proteins, YTH knockout mutants and RNAi-induced knockdown plants were constructed and used for phenotyping, transcriptomic analysis, and stress treatments. Knocking out or knocking down OsYTHs led to the downregulation of multicellular organismal regulation genes and resulted in growth defects. In addition, loss-of-function ythdfa mutants led to better salinity tolerance whereas ythdfc mutants were more sensitive to abiotic stress. Overall, our study establishes the functional relevance of rice YTH genes in plant growth regulation and stress response.

Genome-Wide Analysis of the WOX Transcription Factor Genes in Dendrobium catenatum Lindl.

The WUSCHEL-related homeobox (WOX) proteins are a class of transcription factors exclusive to plants. They can promote cell division or inhibit stem cell differentiation to regulate plant growth and development. However, the WOX transcription factor genes in the monocotyledon Dendrobium catenatum Lindl. remain relatively uncharacterized. Specifically, the effects of phytohormones on their expression levels are unclear. In this study, we identified and analyzed 10 candidate DcaWOX transcription factor genes in D. catenatum. The DcaWOX family was divided into the modern/WUS, intermediate, and ancient clades. The subcellular localization analysis detected DcaWOX-GFP fusion proteins in the tobacco epidermal leaf cell nucleus. In DcaWOX, members of the WUS clade with the WUS-box motif can significantly activate the expression of TPL in vivo, while members of the intermediate and ancient clades cannot. The expression of the DcaWOX genes varied among the examined tissues. Moreover, the DcaWOX expression patterns were differentially affected by the phytohormone treatments, with differences detected even between homologs of the same gene. Furthermore, the gene expression patterns were consistent with the predicted cis-acting elements in the promoters. The above results suggest that DcaWOX may have an important role in its growth and development and resistance to stress. The results of this comprehensive investigation of the DcaWOX gene family provide the basis for future studies on the roles of WOX genes in D. catenatum.

Molecular phylogeny of Japanese marine Tanytarsini chironomids (Chironomidae: Chironominae).

Tanytarsini is a large tribe of Chironomidae with at least 11 recorded marine species grouped in three genera. In this study, we performed a phylogenic analysis using molecular data from 13 Tanytarsini genera, including all Japanese marine species in a large tribe of Chironominae, to estimate their phylogenetic positions and evolutionary history. The phylogenetic reconstruction grouped the marine species in two clades. One clade was composed of five marine Tanytarsus and two marine Pontomyia species within a larger clade of Tanytarsus. Pontomyia is considered to have morphologically specialized and adapted to marine environments by rapid evolution, although it formed a clade with Tanytarsus. The only one species of Tanytarsus, T. pelagicus, clustered as a member of the second clade, which was mainly composed by species of the genus Paratanytarsus. Thus, weredescribe T. pelagicus as Paratanytarsus pelagicus.

Digging deeper into the taxonomy of Cylindrospermum and description of Johanseniella tripurensis gen. et sp. nov. from India.

The wet soil-inhabiting cyanobacterium URH-6-PS was collected from the state of Tripura, India, and characterized using a polyphasic approach. Initial microscopic analysis indicated the strain to be a member of the genus Cylindrospermum, however, the 16S rRNA gene phylogenetic analysis showed some interesting results. The strain URH-6-PS clustered in the Clade I, which positioned itself outside the Cylindrospermum sensu stricto clade with strong probability/bootstrap support, indicating that the strain may not belong to the genus Cylindrospermum. Further, analysis of the 16S-23S ITS region using the folded secondary structures of the D1-D1', Box-B, and V3 helices and the 16S-23S ITS percentage dissimilarity values clearly indicated the distinctiveness of strain URH-6-PS from other members of the Clade I. The detailed investigations conducted in this study provided sufficient evidence that the taxonomic status of the members of Clade I need to be revised. Interestingly, all members of the clade I originated from tropical and subtropical habitats while members of the Cylindrospermum sensu stricto clade have been reported from temperate conditions. Previous studies had also indicated the possibility of the formation of tropical and subtropical Cylindrospermum-like genera, and thus this comes across as a much-awaited study to resolve the taxonomic complexities around the genus Cylindrospermum. Based on the results obtained in this study and the trends observed in the earlier studies, we describe a novel Cylindrospermum-like genus Johanseniella gen. nov., with the type species Johanseniellatripurensis sp. nov. in accordance with the International Code of Nomenclature for algae, fungi, and plants.

Diversity and Composition of Methanotroph Communities in Caves.

ABSTRACTMethane oxidizing microorganisms (methanotrophs) are ubiquitous in the environment and represent a major sink for the greenhouse gas methane (CH4). Recent studies have demonstrated methanotrophs are abundant and contribute to CH4 dynamics in caves. However, very little is known about what controls the distribution and abundance of methanotrophs in subterranean ecosystems. Here, we report a survey of soils collected from > 20 caves in North America to elucidate the factors shaping cave methanotroph communities. Using 16S rRNA sequencing, we recovered methanotrophs from nearly all (98%) of the samples, including cave sites where CH4 concentrations were at or below detection limits (≤0.3 ppmv). We identified a core methanotroph community among caves comprised of high-affinity methanotrophs. Although associated with local-scale mineralogy, methanotroph composition did not systematically vary between the entrances and interior of caves, where CH4 concentrations varied. We also observed methanotrophs are able to disperse readily between cave systems showing these organisms have low barriers to dispersal. Lastly, the relative abundance of methanotrophs was positively correlated with cave-air CH4 concentrations, suggesting these microorganisms contribute to CH4 flux in subterranean ecosystems.IMPORTANCE Recent observations have shown the atmospheric greenhouse gas methane (CH4) is consumed by microorganisms (methanotrophs) in caves at rates comparable to CH4 oxidation in surface soils. Caves are abundant in karst landscapes that comprise 14% of Earth’s land surface area, and therefore may represent a potentially important, but overlooked, CH4 sink. We sampled cave soils to gain a better understand the community composition and structure of cave methanotrophs. Our results show the members of the USC-γ clade are dominant in cave communities and can easily disperse through the environment, methanotroph relative abundance was correlated with local scale mineralogy of soils, and the relative abundance of methanotrophs was positively correlated with CH4 concentrations in cave air.

A new species of Paranecepsia (Euphorbiaceae-Acalyphoideae) from Madagascar and its relationships among the ‘alchorneoids clade’

The formerly monotypic genus Paranecepsia Radcl.-Sm. is expanded with the description and illustration of a second species, Paranecepsia andrafiabensis Barberá & O.Lachenaud sp. nov. Molecular phylogenetic analyses of plastid rbcL and trnL-F data confirm a sister relationship between the new species and P. alchorneifolia Radcl.-Sm., as members of the alchorneoids clade. Paranecepsia andrafiabensis sp. nov. is notable for expanding the character states for the genus (now including both 2- and 3-locular ovary species) and broadening the geographic range of the genus from continental Africa to Madagascar. The new species adds to the diverse karst limestone endemics of northwestern Madagascar, where it has a very restricted distribution at the base of the western wall of the Ankarana tsingy. An amended generic description of Paranecepsia and a key to the species are also presented. Paranecepsia andrafiabensis sp. nov. is provisionally assessed as VU D1 based on the IUCN Red List criteria.

The chloroplast genome of Farsetia hamiltonii Royle, phylogenetic analysis, and comparative study with other members of Clade C of Brassicaceae

BackgroundFarsetia hamiltonii Royle is a medicinally important annual plant from the Cholistan desert that belongs to the tribe Anastaticeae and clade C of the Brassicaceae family. We provide the entire chloroplast sequence of F.hamiltonii, obtained using the Illumina HiSeq2500 and paired-end sequencing. We compared F. hamiltonii to nine other clade C species, including Farsetia occidentalis, Lobularia libyca, Notoceras bicorne, Parolinia ornata, Morettia canescens, Cochlearia borzaeana, Megacarpaea polyandra, Biscutella laevigata, and Iberis amara. We conducted phylogenetic research on the 22 Brassicaceae species, which included members from 17 tribes and six clades.ResultsThe chloroplast genome sequence of F.hamiltonii of 154,802 bp sizes with 36.30% GC content and have a typical structure comprised of a Large Single Copy (LSC) of 83,906 bp, a Small Single Copy (SSC) of 17,988 bp, and two copies of Inverted Repeats (IRs) of 26,454 bp. The genomes of F. hamiltonii and F. occidentalis show shared amino acid frequencies and codon use, RNA editing sites, simple sequence repeats, and oligonucleotide repeats. The maximum likelihood tree revealed Farsetia as a monophyletic genus, closely linked to Morettia, with a bootstrap score of 100. The rate of transversion substitutions (Tv) was higher than the rate of transition substitutions (Ts), resulting in Ts/Tv less than one in all comparisons with F. hamiltonii, indicating that the species are closely related. The rate of synonymous substitutions (Ks) was greater than non-synonymous substitutions (Ka) in all comparisons with F. hamiltonii, with a Ka/Ks ratio smaller than one, indicating that genes underwent purifying selection. Low nucleotide diversity values range from 0.00085 to 0.08516, and IR regions comprise comparable genes on junctions with minimal change, supporting the conserved status of the selected chloroplast genomes of the clade C of the Brassicaceae family. We identified ten polymorphic regions, including rps8-rpl14, rps15-ycf1, ndhG-ndhI, psbK-psbI, ccsA-ndhD, rpl36-rps8, petA-psbJ, ndhF-rpl32, psaJ-rpl3, and ycf1 that might be exploited to construct genuine and inexpensive to solve taxonomic discrepancy and understand phylogenetic relationship amongst Brassicaceae species.ConclusionThe entire chloroplast sequencing of F. hamiltonii sheds light on the divergence of genic chloroplast sequences among members of the clade C. When other Farsetia species are sequenced in the future, the full F. hamiltonii chloroplast will be used as a source for comprehensive taxonomical investigations of the genus. The comparison of F. hamiltonii and other clade C species adds new information to the phylogenetic data and evolutionary processes of the clade. The results of this study will also provide further molecular uses of clade C chloroplasts for possible plant genetic modifications and will help recognise more Brassicaceae family species.

Targeted suppression of human IBD-associated gut microbiota commensals by phage consortia for treatment of intestinal inflammation

Human gut commensals are increasingly suggested to impact non-communicable diseases, such as inflammatory bowel diseases (IBD), yet their targeted suppression remains a daunting unmet challenge. In four geographically distinct IBD cohorts (n= 537), we identify a clade of Klebsiella pneumoniae (Kp) strains, featuring a unique antibiotics resistance and mobilome signature, to be strongly associated with disease exacerbation and severity. Transfer of clinical IBD-associated Kp strains into colitis-prone, germ-free, and colonized mice enhances intestinal inflammation. Stepwise generation of a lytic five-phage combination, targeting sensitive and resistant IBD-associated Kp clade members through distinct mechanisms, enables effective Kp suppression in colitis-prone mice, driving an attenuated inflammation and disease severity. Proof-of-concept assessment of Kp-targeting phages in an artificial human gut and in healthy volunteers demonstrates gastric acid-dependent phage resilience, safety, and viability in the lower gut. Collectively, we demonstrate the feasibility of orally administered combination phage therapy in avoiding resistance, while effectively inhibiting non-communicable disease-contributing pathobionts.

A new species of stream toad of the genus Ansonia Stoliczka, 1870 (Anura: Bufonidae) from Nakhon Si Thammarat Range in southern Thailand.

An integrative taxonomic analysis confirmed the new species status of a recently discovered upland population of Ansonia from Thongsong, Thongsong District, Nakhon Si Thammarat Province, Thailand from the sky island archipelago south of the Isthmus of Kra. Ansonia infernalis sp. nov. is a member of the Thai-Burmese clade within the more inclusive Thai-Malaya Peninsula clade of western and southern Thailand. It is separated from all other species of Ansonia by a unique combination of morphometric and discrete morphological and color pattern characteristics and is the sister species of a clade of eight other species found north of the Isthmus of Kra. Ansonia infernalis sp. nov. is the newest member of a long list of range-restricted endemics from the sky island archipelago of the Thai-Malay Peninsula and continues to underscore the unexplored nature of this region and its need for conservation.

Marine Microbial Communities of North and South Shelves of Iceland

The North Atlantic Ocean surrounds Iceland, influencing its climate and hosting a rich ecosystem that provides the Icelandic nation with economically valuable marine species. The basis of the Icelandic marine ecosystem consists of communities of diverse microorganisms including bacteria, archaea, and unicellular eukaryotes. While the primary production of Icelandic waters has been monitored since the 50s, there is limited knowledge of the taxonomic and metabolic diversity of the marine microorganisms in Icelandic waters based on molecular techniques. In this study, we conducted annual sampling at four hydrographic stations over several years to characterize marine microbial communities and their metabolic potential. Using 16S ribosomal RNA gene amplicon sequencing and metagenomics, we resolved the microbial community composition on the North and South Shelves of Iceland, analyzed its evolution from 2011 to 2018, identified frequently occurring taxa, and predicted their potential metabolism. The results showed correlations between the marine microbial community profiles and the water masses in spring, between the North and South Shelves of Iceland. The differences in marine microbial diversity appear to be linked to the average seawater temperature in the mixed surface layer at each sampling station which also constrains the relative abundance of photosynthetic microorganisms. This study set a baseline for the marine microbial diversity in Icelandic marine waters and identified three photosynthetic microorganisms – the cyanobacteria Synechococcus and two members of the Chlorophyta clade – as valuable indicator species for future monitoring, as well as for application in ecosystem modeling in context with research on climate change.

Phylogenetically Distant BABY BOOM Genes From Setaria italica Induce Parthenogenesis in Rice.

The combination of apomixis and hybrid production is hailed as the holy grail of agriculture for the ability of apomixis to fix heterosis of F1 hybrids in succeeding generations, thereby eliminating the need for repeated crosses to produce F1 hybrids. Apomixis, asexual reproduction through seed, achieves this feat by circumventing two processes that are fundamental to sexual reproduction (meiosis and fertilization) and replacing them with apomeiosis and parthenogenesis, resulting in seeds that are clonal to the maternal parent. Parthenogenesis, embryo development without fertilization, has been genetically engineered in rice, maize, and pearl millet using PsASGR-BABY BOOM-like (PsASGR-BBML) transgenes and in rice using the OsBABY BOOM1 (OsBBM1) cDNA sequence when expressed under the control of egg cell-specific promoters. A phylogenetic analysis revealed that BABY BOOM (BBM)/BBML genes from monocots cluster within three different clades. The BBM/BBML genes shown to induce parthenogenesis cluster within clade 1 (the ASGR-BBML clade) along with orthologs from other monocot species, such as Setaria italica. For this study, we tested the parthenogenetic potential of three BBM transgenes from S. italica, each a member of a different phylogenetic BBM clade. All transgenes were genomic constructs under the control of the AtDD45 egg cell-specific promoter. All SiBBM transgenes induced various levels of parthenogenetic embryo development, resulting in viable haploid T1 seedlings. Poor seed set and lower haploid seed production were characteristics of multiple transgenic lines. The results presented in this study illustrate that further functional characterization of BBMs in zygote/embryo development is warranted.

Two distinct evolutionary conserved neural degeneration pathways characterized in a colonial chordate

Colonial tunicates are marine organisms that possess multiple brains simultaneously during their colonial phase. While the cyclical processes of neurogenesis and neurodegeneration characterizing their life cycle have been documented previously, the cellular and molecular changes associated with such processes and their relationship with variation in brain morphology and individual (zooid) behavior throughout adult life remains unknown. Here, we introduce Botryllus schlosseri as an invertebrate model for neurogenesis, neural degeneration, and evolutionary neuroscience. Our analysis reveals that during the weekly colony budding (i.e., asexual reproduction), prior to programmed cell death and removal by phagocytes, decreases in the number of neurons in the adult brain are associated with reduced behavioral response and significant change in the expression of 73 mammalian homologous genes associated with neurodegenerative disease. Similarly, when comparing young colonies (1 to 2 y of age) to those reared in a laboratory for ∼20 y, we found that older colonies contained significantly fewer neurons and exhibited reduced behavioral response alongside changes in the expression of 148 such genes (35 of which were differentially expressed across both timescales). The existence of two distinct yet apparently related neurodegenerative pathways represents a novel platform to study the gene products governing the relationship between aging, neural regeneration and degeneration, and loss of nervous system function. Indeed, as a member of an evolutionary clade considered to be a sister group of vertebrates, this organism may be a fundamental resource in understanding how evolution has shaped these processes across phylogeny and obtaining mechanistic insight.

Late middle Miocene Metatheria (Mammalia: Didelphimorphia and Paucituberculata) from Juan Guerra, San Martín Department, Peruvian Amazonia

Currently, marsupials (modern members of the Metatheria clade) are widely distributed in tropical and subtropical areas of South America, but poorly represented in the fossil record of these regions. Except for the species-rich fossiliferous localities of La Venta in Colombia, additional Miocene metatherians from tropical, equatorial South America are sparsely reported in Bolivia, Brazil, Peru, and Venezuela. Here, we introduce new metatherian remains recovered from the late middle Miocene locality of TAR-31, San Martín Department, Peru, which has been assigned to the Laventan South American Land Mammal Age (∼13 Ma) by mammalian biostratigraphy. Three metatherian taxa are recognized at TAR-31: the didelphid didelphimorph ‘Thylamys’ cf. ‘T.’ colombianus, and the paucituberculatans aff. Palaeothentes and Pitheculites ipururensis sp. nov. This assemblage and the presence of a cebid primate at TAR-31 suggests predominantly humid and warm tropical conditions, with the occurrence of both forests and drier habitats in the surroundings. Comparisons with other Miocene metatherian assemblages at low and mid latitudes of South America clearly confirm close relationships between TAR-31 and La Venta (agreeing with observations based on monkeys and rodents), as well as, to a lesser extent, with Acre River local faunas and Madre de Dios (MD-67) in Brazil and Peru, respectively. The current results support the hypothesis that Western Amazonia was a single and consistent biogeographical region for land mammals over middle Miocene times, at the western edge of the Pebas Mega-Wetland System, and highlight the role of the Amazonian region concerning marsupial Neogene radiation. U–Pb analysis made on detrital zircon grains from TAR-31 gave a maximum depositional age of 17.4 ± 0.12 Ma (i.e., 4 Ma older than the biostratigraphical age), with a mixed detrital source likely comprising Precambrian (Western Amazon Craton), Neoproterozoic (Neoproterozoic mobile belts), and Phanerozoic rocks (Andes).

TGA factors promote plant root growth by modulating redox homeostasis or response.

To identify novel regulators of stem cell renewal, we mined an existing but little explored cell type-specific transcriptome dataset for the Arabidopsis root. A member of the TGA family of transcription factors, TGA8, was found to be specifically expressed in the quiescent center (QC). Mutation in TGA8 caused a subtle root growth phenotype, suggesting functional redundancy with other TGA members. Using a promoter::HGFP transgenic approach, we showed that all TGA factors were expressed in the root, albeit at different levels and with distinct spatial patterns. Mutant analyses revealed that all TGA factors examined contribute to root growth by promoting stem cell renewal, meristem activity, and cell elongation. Combining transcriptome analyses, histochemical assays, and physiological tests, we demonstrated that functional redundancy exists among members of clades II and V or those in clades I and III. These two groups of TGA factors act differently, however, as their mutants responded to oxidative stress differently and quantitative reverse transcription polymerase chain reaction assays showed they regulate different sets of genes that are involved in redox homeostasis. Our study has thus uncovered a previously unrecognized broad role and a mechanistic explanation for TGA factors in root growth and development.

Differential Trafficking and Expression of PIR Proteins in Acute and Chronic Plasmodium Infections.

Plasmodium multigene families are thought to play important roles in the pathogenesis of malaria. Plasmodium interspersed repeat (pir) genes comprise the largest multigene family in many Plasmodium species. However, their expression pattern and localisation remain to be elucidated. Understanding protein subcellular localisation is fundamental to reveal the functional importance and cell-cell interactions of the PIR proteins. Here, we use the rodent malaria parasite, Plasmodium chabaudi chabaudi, as a model to investigate the localisation pattern of this gene family. We found that most PIR proteins are co-expressed in clusters during acute and chronic infection; members of the S7 clade are predominantly expressed during the acute-phase, whereas members of the L1 clade dominate the chronic-phase of infection. Using peptide antisera specific for S7 or L1 PIRS, we show that these PIRs have different localisations within the infected red blood cells. S7 PIRs are exported into the infected red blood cell cytoplasm where they are co-localised with parasite-induced host cell modifications termed Maurer’s clefts, whereas L1 PIRs are localised on or close to the parasitophorous vacuolar membrane. This localisation pattern changes following mosquito transmission and during progression from acute- to chronic-phase of infection. The presence of PIRs in Maurer’s clefts, as seen for Plasmodium falciparum RIFIN and STEVOR proteins, might suggest trafficking of the PIRs on the surface of the infected erythrocytes. However, neither S7 nor L1 PIR proteins detected by the peptide antisera are localised on the surface of infected red blood cells, suggesting that they are unlikely to be targets of surface variant-specific antibodies or to be directly involved in adhesion of infected red blood cells to host cells, as described for Plasmodium falciparum VAR proteins. The differences in subcellular localisation of the two major clades of Plasmodium chabaudi PIRs across the blood cycle, and the apparent lack of expression on the red cell surface strongly suggest that the function(s) of this gene family may differ from those of other multigene families of Plasmodium, such as the var genes of Plasmodium falciparum.

Mobility of the syntaxin PEN1 in Arabidopsis reflects functional specialization of the conserved SYP12 clade

ABSTRACT Plant innate immunity toward cell-wall penetrating filamentous pathogens relies on the conserved SYP12 clade of secretory syntaxins. In Arabidopsis, the two closely related SYP12 clade members, PEN1 and SYP122, play an overlapping role in this general immunity, which can be complemented by two SYP12 clade members from Marchantia (MpSYP12A and MpSYP12B). However, in addition to the conserved SYP12 clade function, PEN1 alone mediates pre-invasive immunity toward powdery mildew fungi, which likely reflects a specialization of its functionality. Here, we show that the PEN1-specific specialization in immunity correlates with a continuous BFA-sensitive recycling and the ability to accumulate strongly at the growing cell plate. This contrasts with the behavior of SYP122, MpSYP12A, and MpSYP12B, all being more stable at the plasma membrane. We suggest that the highly mobile SYP12 specialization observed for PEN1 is required for a fast pre-invasive immune response to resist attack from powdery mildew fungi.

Genome sequence for the blue-flowered Andean shrub Iochroma cyaneum reveals extensive discordance across the berry clade of Solanaceae.

The tomato (Solanum lycopersicum L.) family, Solanaceae, is a model clade for a wide range of applied and basic research questions. Currently, reference-quality genomes are available for over 30 species from seven genera, and these include numerous crops as well as wild species [e.g., Jaltomata sinuosa (Miers) Mione and Nicotiana attenuata Torr. ex S. Watson]. Here we present the genome of the showy-flowered Andean shrub Iochroma cyaneum (Lindl.) M. L. Green, a woody lineage from the tomatillo (Physalis philadelphica Lam.) subfamily Physalideae. The assembled size of the genome (2.7 Gb) is more similar in size to pepper (Capsicum annuum L.) (2.6 Gb) than to other sequenced diploid members of the berry clade of Solanaceae [e.g., potato (Solanum tuberosum L.), tomato, and Jaltomata]. Our assembly recovers 92% of the conserved orthologous set, suggesting a nearly complete genome for this species. Most of the genomic content is repetitive (69%), with Gypsy elements alone accounting for 52% of the genome. Despite the large amount of repetitive content, most of the 12 I. cyaneum chromosomes are highly syntenic with tomato. Bayesian concordance analysis provides strong support for the berry clade, including I. cyaneum, but reveals extensive discordance along the backbone, with placement of chili pepper and Jaltomata being highly variable across gene trees. The I. cyaneum genome contributes to a growing wealth of genomic resources in Solanaceae and underscores the need for expanded sampling of diverse berry genomes to dissect major morphological transitions.

The first fossil record of a giant horsetail (Equisetum, Equisetaceae) is from the Miocene of Patagonia, Argentina

A Miocene macroflora recovered from Ñirihuau Formation sediments exposed at Quebrada Vera site in northwesterern Patagonia, Argentina, is recorded and described for the first time. The assemblage is composed exclusively of free-sporing plants, mainly by Equisetum remains with subordinate occurrences of four fern morphotypes (represented by bi-, tri- and pinnate fronds). Equisetum imprints and molds include distinctive jointed stems with whorls of linear and basally fused leaves, numerous scars of lateral branches arranged in a radially symmetrical pattern situated at the nodes, and nodal diaphragms of up to 4 cm in diameter. The large size and regular branching of the stems link the fossils to the South American giant members of the genus and they probably represent a new fossil species. This is the first conclusive fossil record of a giant Equisetum worldwide, and consequently, it is biogeographically and evolutionarily relevant. The new findings attest that members of the giant horsetail clade were components of the Patagonian vegetation in the Miocene, implying that the age of the clade must predate that estimated from morphological and/or molecular data. The plant fossil assemblage represents part of a wetland community probably growing close to a riverside or lakeshore in coincidence with previous sedimentological estimates.