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1.
Blood Adv ; 4(11): 2489-2500, 2020 Jun 09.
Artigo em Inglês | MEDLINE | ID: mdl-32502269

RESUMO

Mycosis fungoides (MF) is a slowly progressive cutaneous T-cell lymphoma (CTCL) for which there is no cure. In the early plaque stage, the disease is indolent, but development of tumors heralds an increased risk of metastasis and death. Previous research into the genomic landscape of CTCL revealed a complex pattern of >50 driver mutations implicated in more than a dozen signaling pathways. However, the genomic mechanisms governing disease progression and treatment resistance remain unknown. Building on our previous discovery of the clonotypic heterogeneity of MF, we hypothesized that this lymphoma does not progress in a linear fashion as currently thought but comprises heterogeneous mutational subclones. We sequenced exomes of 49 cases of MF and identified 28 previously unreported putative driver genes. MF exhibited extensive intratumoral heterogeneity (ITH) of a median of 6 subclones showing a branched phylogenetic relationship pattern. Stage progression was correlated with an increase in ITH and redistribution of mutations from stem to clades. The pattern of clonal driver mutations was highly variable, with no consistent mutations among patients. Similar intratumoral heterogeneity was detected in leukemic CTCL (Sézary syndrome). Based on these findings, we propose a model of MF pathogenesis comprising divergent evolution of cancer subclones and discuss how ITH affects the efficacy of targeted drug therapies and immunotherapies for CTCL.

2.
Nat Ecol Evol ; 2020 Jun 22.
Artigo em Inglês | MEDLINE | ID: mdl-32572216

RESUMO

Genome analysis of the pico-eukaryotic marine green alga Prasinoderma coloniale CCMP 1413 unveils the existence of a novel phylum within green plants (Viridiplantae), the Prasinodermophyta, which diverged before the split of Chlorophyta and Streptophyta. Structural features of the genome and gene family comparisons revealed an intermediate position of the P. coloniale genome (25.3 Mb) between the extremely compact, small genomes of picoplanktonic Mamiellophyceae (Chlorophyta) and the larger, more complex genomes of early-diverging streptophyte algae. Reconstruction of the minimal core genome of Viridiplantae allowed identification of an ancestral toolkit of transcription factors and flagellar proteins. Adaptations of P. coloniale to its deep-water, oligotrophic environment involved expansion of light-harvesting proteins, reduction of early light-induced proteins, evolution of a distinct type of C4 photosynthesis and carbon-concentrating mechanism, synthesis of the metal-complexing metabolite picolinic acid, and vitamin B1, B7 and B12 auxotrophy. The P. coloniale genome provides first insights into the dawn of green plant evolution.

3.
Nat Plants ; 6(2): 95-106, 2020 02.
Artigo em Inglês | MEDLINE | ID: mdl-31844283

RESUMO

Mounting evidence suggests that terrestrialization of plants started in streptophyte green algae, favoured by their dual existence in freshwater and subaerial/terrestrial environments. Here, we present the genomes of Mesostigma viride and Chlorokybus atmophyticus, two sister taxa in the earliest-diverging clade of streptophyte algae dwelling in freshwater and subaerial/terrestrial environments, respectively. We provide evidence that the common ancestor of M. viride and C. atmophyticus (and thus of streptophytes) had already developed traits associated with a subaerial/terrestrial environment, such as embryophyte-type photorespiration, canonical plant phytochrome, several phytohormones and transcription factors involved in responses to environmental stresses, and evolution of cellulose synthase and cellulose synthase-like genes characteristic of embryophytes. Both genomes differed markedly in genome size and structure, and in gene family composition, revealing their dynamic nature, presumably in response to adaptations to their contrasting environments. The ancestor of M. viride possibly lost several genomic traits associated with a subaerial/terrestrial environment following transition to a freshwater habitat.

4.
Annu Rev Plant Biol ; 71: 741-765, 2020 Apr 29.
Artigo em Inglês | MEDLINE | ID: mdl-31851546

RESUMO

The 1,000 Plants (1KP) initiative was the first large-scale effort to collect next-generation sequencing (NGS) data across a phylogenetically representative sampling of species for a major clade of life, in this case theViridiplantae, or green plants. As an international multidisciplinary consortium, we focused on plant evolution and its practical implications. Among the major outcomes were the inference of a reference species tree for green plants by phylotranscriptomic analysis of low-copy genes, a survey of paleopolyploidy (whole-genome duplications) across the Viridiplantae, the inferred evolutionary histories for many gene families and biological processes, the discovery of novel light-sensitive proteins for optogenetic studies in mammalian neuroscience, and elucidation of the genetic network for a complex trait (C4 photosynthesis). Altogether, 1KP demonstrated how value can be extracted from a phylodiverse sequencing data set, providing a template for future projects that aim to generate even more data, including complete de novo genomes, across the tree of life.

5.
Cell ; 179(5): 1057-1067.e14, 2019 11 14.
Artigo em Inglês | MEDLINE | ID: mdl-31730849

RESUMO

The transition to a terrestrial environment, termed terrestrialization, is generally regarded as a pivotal event in the evolution and diversification of the land plant flora that changed the surface of our planet. Through phylogenomic studies, a group of streptophyte algae, the Zygnematophyceae, have recently been recognized as the likely sister group to land plants (embryophytes). Here, we report genome sequences and analyses of two early diverging Zygnematophyceae (Spirogloea muscicola gen. nov. and Mesotaenium endlicherianum) that share the same subaerial/terrestrial habitat with the earliest-diverging embryophytes, the bryophytes. We provide evidence that genes (i.e., GRAS and PYR/PYL/RCAR) that increase resistance to biotic and abiotic stresses in land plants, in particular desiccation, originated or expanded in the common ancestor of Zygnematophyceae and embryophytes, and were gained by horizontal gene transfer (HGT) from soil bacteria. These two Zygnematophyceae genomes represent a cornerstone for future studies to understand the underlying molecular mechanism and process of plant terrestrialization.

6.
Gigascience ; 8(10)2019 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-31644802

RESUMO

BACKGROUND: The 1000 Plant transcriptomes initiative (1KP) explored genetic diversity by sequencing RNA from 1,342 samples representing 1,173 species of green plants (Viridiplantae). FINDINGS: This data release accompanies the initiative's final/capstone publication on a set of 3 analyses inferring species trees, whole genome duplications, and gene family expansions. These and previous analyses are based on de novo transcriptome assemblies and related gene predictions. Here, we assess their data and assembly qualities and explain how we detected potential contaminations. CONCLUSIONS: These data will be useful to plant and/or evolutionary scientists with interests in particular gene families, either across the green plant tree of life or in more focused lineages.


Assuntos
Genes de Plantas , Viridiplantae/genética , Proteínas de Plantas/genética , Análise de Sequência de RNA , Transcriptoma
7.
Blood ; 134(18): 1517-1527, 2019 10 31.
Artigo em Inglês | MEDLINE | ID: mdl-31515249

RESUMO

Mycosis fungoides (MF) is a mature T-cell lymphoma currently thought to develop primarily in the skin by a clonal expansion of a transformed, resident memory T cell. However, this concept does not explain the key characteristics of MF, such as the debut with multiple, widespread skin lesions or inability of skin-directed therapies to provide cure. The testable inference of the mature T-cell theory is the clonality of MF with respect to all rearranged T-cell receptor (TCR) genes. Here, we used a whole-exome sequencing approach to detect and quantify TCR-α, ß, and γ clonotypes in tumor cell clusters microdissected from MF lesions. This method allowed us to calculate the tumor cell fraction of the sample and therefore an unequivocal identification of the TCR clonotypes as neoplastic. Analysis of TCR sequences from 29 patients with MF stage I to IV proved the existence of multiple T-cell clones within the tumor cell fraction, with a considerable variation between patients and between lesions from the same patient (median, 11 clones; range, 2-80 clones/sample). We have also detected multiple neoplastic clones in the peripheral blood in all examined patients. Based on these findings, we propose that circulating neoplastic T-cell clones continuously replenish the lesions of MF, thus increasing their heterogeneity by a mechanism analogous to the consecutive tumor seeding. We hypothesize that circulating neoplastic clones might be a promising target for therapy and could be exploited as a potential biomarker in MF.


Assuntos
Micose Fungoide/patologia , Células Neoplásicas Circulantes/patologia , Neoplasias Cutâneas/patologia , Células Clonais/patologia , Humanos
8.
Elife ; 82019 08 02.
Artigo em Inglês | MEDLINE | ID: mdl-31373555

RESUMO

Although geographic isolation is a leading driver of speciation, the tempo and pattern of divergence at the genomic level remain unclear. We examine genome-wide divergence of putatively single-copy orthologous genes (POGs) in 20 allopatric species/variety pairs from diverse angiosperm clades, with 16 pairs reflecting the classic eastern Asia-eastern North America floristic disjunction. In each pair, >90% of POGs are under purifying selection, and <10% are under positive selection. A set of POGs are under strong positive selection, 14 of which are shared by 10-15 pairs, and one shared by all pairs; 15 POGs are annotated to biological processes responding to various stimuli. The relative abundance of POGs under different selective forces exhibits a repeated pattern among pairs despite an ~10 million-year difference in divergence time. Species divergence times are positively correlated with abundance of POGs under moderate purifying selection, but negatively correlated with abundance of POGs under strong purifying selection.


Assuntos
Evolução Molecular , Genes de Plantas , Variação Genética , Plantas/genética , Seleção Genética , Extremo Oriente , Especiação Genética , América do Norte , Folhas de Planta/genética , Plantas/classificação
9.
Sci Rep ; 9(1): 10482, 2019 07 19.
Artigo em Inglês | MEDLINE | ID: mdl-31324835

RESUMO

Hidden Markov models representing 167 protein sequence families were used to infer the presence or absence of homologs within the transcriptomes of 183 algal species/strains. Statistical analyses of the distribution of HMM hits across major clades of algae, or at branch points on the phylogenetic tree of 98 chlorophytes, confirmed and extended known cases of metabolic loss and gain, most notably the loss of the mevalonate pathway for terpenoid synthesis in green algae but not, as we show here, in the streptophyte algae. Evidence for novel events was found as well, most remarkably in the recurrent and coordinated gain or loss of enzymes for the glyoxylate shunt. We find, as well, a curious pattern of retention (or re-gain) of HMG-CoA synthase in chlorophytes that have otherwise lost the mevalonate pathway, suggesting a novel, co-opted function for this enzyme in select lineages. Finally, we find striking, phylogenetically linked distributions of coding sequences for three pathways that synthesize the major membrane lipid phosphatidylcholine, and a complementary phylogenetic distribution pattern for the non-phospholipid DGTS (diacyl-glyceryl-trimethylhomoserine). Mass spectrometric analysis of lipids from 25 species was used to validate the inference of DGTS synthesis from sequence data.

10.
BMC Genomics ; 20(1): 604, 2019 Jul 23.
Artigo em Inglês | MEDLINE | ID: mdl-31337347

RESUMO

BACKGROUND: RNA-Seq data is inherently nonuniform for different transcripts because of differences in gene expression. This makes it challenging to decide how much data should be generated from each sample. How much should one spend to recover the less expressed transcripts? The sequencing technology used is another consideration, as there are inevitably always biases against certain sequences. To investigate these effects, we first looked at high-depth libraries from a set of well-annotated organisms to ascertain the impact of sequencing depth on de novo assembly. We then looked at libraries sequenced from the Universal Human Reference RNA (UHRR) to compare the performance of Illumina HiSeq and MGI DNBseq™ technologies. RESULTS: On the issue of sequencing depth, the amount of exomic sequence assembled plateaued using data sets of approximately 2 to 8 Gbp. However, the amount of genomic sequence assembled did not plateau for many of the analyzed organisms. Most of the unannotated genomic sequences are single-exon transcripts whose biological significance will be questionable for some users. On the issue of sequencing technology, both of the analyzed platforms recovered a similar number of full-length transcripts. The missing "gap" regions in the HiSeq assemblies were often attributed to higher GC contents, but this may be an artefact of library preparation and not of sequencing technology. CONCLUSIONS: Increasing sequencing depth beyond modest data sets of less than 10 Gbp recovers a plethora of single-exon transcripts undocumented in genome annotations. DNBseq™ is a viable alternative to HiSeq for de novo RNA-Seq assembly.


Assuntos
RNA-Seq/métodos , Animais , Arabidopsis , Éxons , Biblioteca Gênica , Humanos , Anotação de Sequência Molecular , Fases de Leitura Aberta , Oryza
11.
Blood Adv ; 3(7): 1175-1184, 2019 04 09.
Artigo em Inglês | MEDLINE | ID: mdl-30967393

RESUMO

Mycosis fungoides (MF), the most common type of cutaneous T-cell lymphoma, is believed to represent a clonal expansion of a transformed skin-resident memory T cell. T-cell receptor (TCR) clonality (ie, identical sequences of rearranged TCRα, TCRß, and TCRγ), the key premise of this hypothesis, has been difficult to document conclusively because malignant cells are not readily distinguishable from the tumor-infiltrating reactive lymphocytes that contribute to the TCR clonotypic repertoire of MF. Here, we have successfully adopted targeted whole-exome sequencing (WES) to identify the repertoire of rearranged TCR genes in tumor-enriched samples from patients with MF. Although some of the investigated MF biopsies had the expected frequency of monoclonal rearrangements of TCRγ corresponding to that of tumor cells, the majority of the samples presented multiple TCRγ, TCRα, and TCRß clonotypes by WES. Our findings are compatible with the model in which the initial malignant transformation in MF does not occur in mature memory T cells but rather at the level of T-lymphocyte progenitors before TCRß or TCRα rearrangements. We have also shown that WES can be combined with whole-transcriptome sequencing in the same sample, which enables comprehensive characterization of the TCR repertoire in relation to tumor content. WES/whole-transcriptome sequencing might be applicable to other types of T-cell lymphomas to determine clonal dominance and clonotypic heterogeneity in these malignancies.

12.
J Infect Dis ; 220(8): 1377-1387, 2019 09 13.
Artigo em Inglês | MEDLINE | ID: mdl-30799482

RESUMO

Zika virus (ZIKV) is an emerging pathogen that can cause microcephaly and other neurological defects in developing fetuses. The cellular response to ZIKV in the fetal brain is not well understood. Here, we show that ZIKV infection of human fetal astrocytes (HFAs), the most abundant cell type in the brain, results in elevated expression and secretion of fibroblast growth factor 2 (FGF2). This cytokine was shown to enhance replication and spread of ZIKV in HFAs and human fetal brain explants. The proviral effect of FGF2 is likely mediated in part by suppression of the interferon response, which would represent a novel mechanism by which viruses antagonize host antiviral defenses. We posit that FGF2-enhanced virus replication in the fetal brain contributes to the neurodevelopmental disorders associated with in utero ZIKV infection. As such, targeting FGF2-dependent signaling should be explored further as a strategy to limit replication of ZIKV.

13.
Syst Biol ; 68(4): 594-606, 2019 07 01.
Artigo em Inglês | MEDLINE | ID: mdl-30535394

RESUMO

Sequencing of target-enriched libraries is an efficient and cost-effective method for obtaining DNA sequence data from hundreds of nuclear loci for phylogeny reconstruction. Much of the cost of developing targeted sequencing approaches is associated with the generation of preliminary data needed for the identification of orthologous loci for probe design. In plants, identifying orthologous loci has proven difficult due to a large number of whole-genome duplication events, especially in the angiosperms (flowering plants). We used multiple sequence alignments from over 600 angiosperms for 353 putatively single-copy protein-coding genes identified by the One Thousand Plant Transcriptomes Initiative to design a set of targeted sequencing probes for phylogenetic studies of any angiosperm group. To maximize the phylogenetic potential of the probes, while minimizing the cost of production, we introduce a k-medoids clustering approach to identify the minimum number of sequences necessary to represent each coding sequence in the final probe set. Using this method, 5-15 representative sequences were selected per orthologous locus, representing the sequence diversity of angiosperms more efficiently than if probes were designed using available sequenced genomes alone. To test our approximately 80,000 probes, we hybridized libraries from 42 species spanning all higher-order groups of angiosperms, with a focus on taxa not present in the sequence alignments used to design the probes. Out of a possible 353 coding sequences, we recovered an average of 283 per species and at least 100 in all species. Differences among taxa in sequence recovery could not be explained by relatedness to the representative taxa selected for probe design, suggesting that there is no phylogenetic bias in the probe set. Our probe set, which targeted 260 kbp of coding sequence, achieved a median recovery of 137 kbp per taxon in coding regions, a maximum recovery of 250 kbp, and an additional median of 212 kbp per taxon in flanking non-coding regions across all species. These results suggest that the Angiosperms353 probe set described here is effective for any group of flowering plants and would be useful for phylogenetic studies from the species level to higher-order groups, including the entire angiosperm clade itself.


Assuntos
Sondas de DNA , Magnoliopsida/genética , Análise de Sequência de DNA/métodos , Análise por Conglomerados
14.
Plant Physiol ; 179(2): 382-390, 2019 02.
Artigo em Inglês | MEDLINE | ID: mdl-30538166

RESUMO

Red algae (Rhodophyta) and land plants belong to the monophyletic clade Archaeplastida, and taxa of both groups are rich producers of terpene secondary metabolites. The terpene carbon skeletons of land plants are made by two types of terpene synthases: typical plant terpene synthases and microbial-type terpene synthases (MTPSLs); however, terpene biosynthesis in red algae is poorly understood. By systematic sequence analysis of seven genomes and 34 transcriptomes of red algae, MTPSL homologs were identified within one genome and two transcriptomes, whereas no homolog of typical plant terpene synthase genes was found. Phylogenetic analysis showed that red algae MTPSLs group with bacterial terpene synthases. Analysis of the genome assembly and characterization of neighboring genes demonstrated red algal MTPSLs to be bona fide red algal genes and not microbial contaminants. MTPSL genes from Porphyridium purpureum and Erythrolobus australicus were characterized via heterologous expression in Escherichia coli and demonstrated to have sesquiterpene synthase activities. We detected a number of volatile sesquiterpenes in the headspace of P. purpureum and E. australicus cultures, most identical to the in vitro products of the respective MTPSLs. Expression of the MTPSL gene in P. purpureum was found to be induced by methyl jasmonate, suggesting a role for this gene in host defense. In summary, this study indicates that the formation of terpene carbon skeletons in red algae is carried out by MTPSLs that are phylogenetically unrelated to typical plant terpene synthases and most likely originated in Rhodophyta via horizontal gene transfer from bacteria.


Assuntos
Proteínas de Algas/metabolismo , Alquil e Aril Transferases/metabolismo , Proteínas de Bactérias/metabolismo , Rodófitas/genética , Terpenos/metabolismo , Acetatos/farmacologia , Proteínas de Algas/genética , Alquil e Aril Transferases/genética , Proteínas de Bactérias/genética , Ciclopentanos/farmacologia , Evolução Molecular , Regulação Enzimológica da Expressão Gênica/efeitos dos fármacos , Oxilipinas/farmacologia , Filogenia , Porphyridium/efeitos dos fármacos , Porphyridium/genética , Porphyridium/metabolismo , Rodófitas/citologia , Rodófitas/metabolismo , Sesquiterpenos/análise , Sesquiterpenos/metabolismo , Técnicas de Cultura de Tecidos , Compostos Orgânicos Voláteis/análise , Compostos Orgânicos Voláteis/metabolismo
15.
Nat Commun ; 9(1): 2343, 2018 06 14.
Artigo em Inglês | MEDLINE | ID: mdl-29904055

RESUMO

Metastasis is the most lethal aspect of cancer, yet current therapeutic strategies do not target its key rate-limiting steps. We have previously shown that the entry of cancer cells into the blood stream, or intravasation, is highly dependent upon in vivo cancer cell motility, making it an attractive therapeutic target. To systemically identify genes required for tumor cell motility in an in vivo tumor microenvironment, we established a novel quantitative in vivo screening platform based on intravital imaging of human cancer metastasis in ex ovo avian embryos. Utilizing this platform to screen a genome-wide shRNA library, we identified a panel of novel genes whose function is required for productive cancer cell motility in vivo, and whose expression is closely associated with metastatic risk in human cancers. The RNAi-mediated inhibition of these gene targets resulted in a nearly total (>99.5%) block of spontaneous cancer metastasis in vivo.


Assuntos
Regulação Neoplásica da Expressão Gênica , Transplante de Neoplasias , Interferência de RNA , Animais , Linhagem Celular Tumoral , Movimento Celular , Embrião de Galinha , Colágeno/química , Feminino , Perfilação da Expressão Gênica , Humanos , Masculino , Camundongos , Camundongos Nus , Camundongos SCID , Invasividade Neoplásica , Metástase Neoplásica , Fenótipo , Neoplasias da Próstata/patologia , RNA Interferente Pequeno/metabolismo
16.
Science ; 361(6398)2018 07 13.
Artigo em Inglês | MEDLINE | ID: mdl-29794220

RESUMO

The root nodule symbiosis of plants with nitrogen-fixing bacteria affects global nitrogen cycles and food production but is restricted to a subset of genera within a single clade of flowering plants. To explore the genetic basis for this scattered occurrence, we sequenced the genomes of 10 plant species covering the diversity of nodule morphotypes, bacterial symbionts, and infection strategies. In a genome-wide comparative analysis of a total of 37 plant species, we discovered signatures of multiple independent loss-of-function events in the indispensable symbiotic regulator NODULE INCEPTION in 10 of 13 genomes of nonnodulating species within this clade. The discovery that multiple independent losses shaped the present-day distribution of nitrogen-fixing root nodule symbiosis in plants reveals a phylogenetically wider distribution in evolutionary history and a so-far-underestimated selection pressure against this symbiosis.


Assuntos
Fenômenos Fisiológicos Bacterianos , Fabaceae , Fixação de Nitrogênio , Nitrogênio/metabolismo , Nódulos Radiculares de Plantas/microbiologia , Simbiose , Evolução Molecular , Fabaceae/classificação , Fabaceae/genética , Fabaceae/microbiologia , Genoma de Planta , Genômica , Filogenia
17.
Gigascience ; 7(3): 1-9, 2018 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-29618049

RESUMO

Understanding plant evolution and diversity in a phylogenomic context is an enormous challenge due, in part, to limited availability of genome-scale data across phylodiverse species. The 10KP (10,000 Plants) Genome Sequencing Project will sequence and characterize representative genomes from every major clade of embryophytes, green algae, and protists (excluding fungi) within the next 5 years. By implementing and continuously improving leading-edge sequencing technologies and bioinformatics tools, 10KP will catalogue the genome content of plant and protist diversity and make these data freely available as an enduring foundation for future scientific discoveries and applications. 10KP is structured as an international consortium, open to the global community, including botanical gardens, plant research institutes, universities, and private industry. Our immediate goal is to establish a policy framework for this endeavor, the principles of which are outlined here.


Assuntos
Clorófitas/genética , Variação Genética , Filogenia , Embriófitas/genética , Fungos/genética , Genoma Fúngico/genética , Genoma de Planta/genética , Anotação de Sequência Molecular
18.
Elife ; 72018 03 27.
Artigo em Inglês | MEDLINE | ID: mdl-29580381

RESUMO

The small signaling molecule auxin controls numerous developmental processes in land plants, acting mostly by regulating gene expression. Auxin response proteins are represented by large families of diverse functions, but neither their origin nor their evolution is understood. Here, we use a deep phylogenomics approach to reconstruct both the origin and the evolutionary trajectory of all nuclear auxin response protein families. We found that, while all subdomains are ancient, a complete auxin response mechanism is limited to land plants. Functional phylogenomics predicts defined steps in the evolution of response system properties, and comparative transcriptomics across six ancient lineages revealed how these innovations shaped a sophisticated response mechanism. Genetic analysis in a basal land plant revealed unexpected contributions of ancient non-canonical proteins in auxin response as well as auxin-unrelated function of core transcription factors. Our study provides a functional evolutionary framework for understanding diverse functions of the auxin signal.


Assuntos
Embriófitas/crescimento & desenvolvimento , Ácidos Indolacéticos/metabolismo , Proteínas Nucleares/metabolismo , Reguladores de Crescimento de Planta/metabolismo , Proteínas de Plantas/metabolismo , Embriófitas/genética , Evolução Molecular , Proteínas Nucleares/genética , Proteínas de Plantas/genética , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
19.
New Phytol ; 218(3): 1049-1060, 2018 05.
Artigo em Inglês | MEDLINE | ID: mdl-29460505

RESUMO

Insights into the evolution of plant cell walls have important implications for comprehending these diverse and abundant biological structures. In order to understand the evolving structure-function relationships of the plant cell wall, it is imperative to trace the origin of its different components. The present study is focused on plant 1,4-ß-xylan, tracing its evolutionary origin by genome and transcriptome mining followed by phylogenetic analysis, utilizing a large selection of plants and algae. It substantiates the findings by heterologous expression and biochemical characterization of a charophyte alga xylan synthase. Of the 12 known gene classes involved in 1,4-ß-xylan formation, XYS1/IRX10 in plants, IRX7, IRX8, IRX9, IRX14 and GUX occurred for the first time in charophyte algae. An XYS1/IRX10 ortholog from Klebsormidium flaccidum, designated K. flaccidumXYLAN SYNTHASE-1 (KfXYS1), possesses 1,4-ß-xylan synthase activity, and 1,4-ß-xylan occurs in the K. flaccidum cell wall. These data suggest that plant 1,4-ß-xylan originated in charophytes and shed light on the origin of one of the key cell wall innovations to occur in charophyte algae, facilitating terrestrialization and emergence of polysaccharide-based plant cell walls.


Assuntos
Parede Celular/metabolismo , Carofíceas/enzimologia , Pentosiltransferases/metabolismo , Células Vegetais/metabolismo , Motivos de Aminoácidos , Vias Biossintéticas , Carofíceas/genética , Evolução Molecular , Células HEK293 , Humanos , Pentosiltransferases/química , Filogenia
20.
Plant J ; 93(3): 515-533, 2018 02.
Artigo em Inglês | MEDLINE | ID: mdl-29237241

RESUMO

The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene- and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant-specific cell growth and tissue organization. The P. patens genome lacks the TE-rich pericentromeric and gene-rich distal regions typical for most flowering plant genomes. More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.


Assuntos
Evolução Biológica , Bryopsida/genética , Cromossomos de Plantas , Genoma de Planta , Centrômero , Cromatina/genética , Metilação de DNA , Elementos de DNA Transponíveis , Variação Genética , Polimorfismo de Nucleotídeo Único , Recombinação Genética , Sintenia
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