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1.
Molecules ; 25(18)2020 Sep 04.
Artigo em Inglês | MEDLINE | ID: mdl-32899754

RESUMO

The emergence of the Coronavirus Disease 2019 (COVID-19) caused by the SARS-CoV-2 virus has led to an unprecedented pandemic, which demands urgent development of antiviral drugs and antibodies; as well as prophylactic approaches, namely vaccines. Algae biotechnology has much to offer in this scenario given the diversity of such organisms, which are a valuable source of antiviral and anti-inflammatory compounds that can also be used to produce vaccines and antibodies. Antivirals with possible activity against SARS-CoV-2 are summarized, based on previously reported activity against Coronaviruses or other enveloped or respiratory viruses. Moreover, the potential of algae-derived anti-inflammatory compounds to treat severe cases of COVID-19 is contemplated. The scenario of producing biopharmaceuticals in recombinant algae is presented and the cases of algae-made vaccines targeting viral diseases is highlighted as valuable references for the development of anti-SARS-CoV-2 vaccines. Successful cases in the production of functional antibodies are described. Perspectives on how specific algae species and genetic engineering techniques can be applied for the production of anti-viral compounds antibodies and vaccines against SARS-CoV-2 are provided.


Assuntos
Antivirais/farmacologia , Produtos Biológicos/farmacologia , Chlamydomonas reinhardtii/genética , Infecções por Coronavirus/tratamento farmacológico , Lectinas/farmacologia , Pneumonia Viral/tratamento farmacológico , Polifenóis/farmacologia , Polissacarídeos/farmacologia , Antivirais/química , Antivirais/isolamento & purificação , Betacoronavirus/efeitos dos fármacos , Betacoronavirus/patogenicidade , Produtos Biológicos/química , Produtos Biológicos/isolamento & purificação , Núcleo Celular/química , Núcleo Celular/genética , Núcleo Celular/metabolismo , Chlamydomonas reinhardtii/química , Chlamydomonas reinhardtii/metabolismo , Cloroplastos/química , Cloroplastos/genética , Cloroplastos/metabolismo , Infecções por Coronavirus/prevenção & controle , Engenharia Genética/métodos , Humanos , Lectinas/química , Lectinas/isolamento & purificação , Coronavírus da Síndrome Respiratória do Oriente Médio/efeitos dos fármacos , Coronavírus da Síndrome Respiratória do Oriente Médio/patogenicidade , Pandemias , Polifenóis/química , Polifenóis/isolamento & purificação , Polissacarídeos/química , Polissacarídeos/isolamento & purificação , Vírus da SARS/efeitos dos fármacos , Vírus da SARS/patogenicidade , Síndrome Respiratória Aguda Grave/tratamento farmacológico , Vacinas Virais/biossíntese , Vacinas Virais/farmacologia
2.
BMC Evol Biol ; 20(1): 96, 2020 07 31.
Artigo em Inglês | MEDLINE | ID: mdl-32736519

RESUMO

BACKGROUND: Chloroplast genome sequence data is very useful in studying/addressing the phylogeny of plants at various taxonomic ranks. However, there are no empirical observations on the patterns, directions, and mutation rates, which are the key topics in chloroplast genome evolution. In this study, we used Calycanthaceae as a model to investigate the evolutionary patterns, directions and rates of both nucleotide substitutions and structural mutations at different taxonomic ranks. RESULTS: There were 2861 polymorphic nucleotide sites on the five chloroplast genomes, and 98% of polymorphic sites were biallelic. There was a single-nucleotide substitution bias in chloroplast genomes. A â†’ T or T â†’ A (2.84%) and G â†’ C or C â†’ G (3.65%) were found to occur significantly less frequently than the other four transversion mutation types. Synonymous mutations kept balanced pace with nonsynonymous mutations, whereas biased directions appeared between transition and transversion mutations and among transversion mutations. Of the structural mutations, indels and repeats had obvious directions, but microsatellites and inversions were non-directional. Structural mutations increased the single nucleotide mutations rates. The mutation rates per site per year were estimated to be 0.14-0.34 × 10- 9 for nucleotide substitution at different taxonomic ranks, 0.64 × 10- 11 for indels and 1.0 × 10- 11 for repeats. CONCLUSIONS: Our direct counts of chloroplast genome evolution events provide raw data for correctly modeling the evolution of sequence data for phylogenetic inferences.


Assuntos
Calycanthaceae/genética , Evolução Molecular , Genoma de Cloroplastos , Mutação/genética , Nucleotídeos/genética , Polimorfismo de Nucleotídeo Único/genética , Alelos , Sequência de Bases , Cloroplastos/genética , Inversão Cromossômica/genética , Loci Gênicos , Mutação INDEL/genética , Repetições de Microssatélites/genética , Taxa de Mutação , Filogenia , Especificidade da Espécie
3.
PLoS One ; 15(7): e0235354, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32609773

RESUMO

The Chinese chestnut (Castanea mollissima Bl.) was introduced into Japan about 100 years ago. Since then, a number of Chinese chestnut cultivars and Japanese-Chinese hybrid cultivars have been selected by farmers and plant breeders, but little information has been available about their origins and genetic relationships. A classification based on simple sequence repeat markers was conducted using 230 cultivars including Japanese chestnut (Castanea crenata Sieb. et Zucc.) cultivars originated in Japan, Japanese-Chinese hybrid cultivars, and Chinese chestnut cultivars originated in both Japan and China. First, a search for synonyms (cultivars with identical genotypes) revealed 23 synonym groups among the Chinese chestnut cultivars, and all but one cultivar from each synonym group was omitted from further analyses. Second, genetic structure analysis showed a clear division between Japanese and Chinese chestnut, and most of the Japanese and Chinese cultivars had a simple genetic structure corresponding to the expected species. On the other hand, most Japanese-Chinese hybrid cultivars had admixed genetic structure. Through a combination of parentage and chloroplast haplotype analyses, 16 of the 18 hybrid cultivars in this study were inferred to have parent-offspring relationships with other cultivars originated in Japan. Finally, Bayesian clustering and chloroplast haplotype analysis showed that the 116 Chinese chestnut cultivars could be divided into two groups: one originated in the Hebei region of China and the other originated in the Jiangsu and Anhui regions of China. The Chinese chestnut cultivars selected in Japan showed various patterns of genetic structure including Hebei origin, Jiangsu or Anhui origin, and admixed. The chestnut cultivar genetic classifications obtained in this study will be useful for both Japanese and Chinese chestnut breeding programs.


Assuntos
Cloroplastos/genética , Fagaceae/classificação , Fagaceae/genética , Repetições de Microssatélites/genética , China , Deriva Genética , Genótipo , Japão , Filogenia , Melhoramento Vegetal
4.
PLoS One ; 15(7): e0235622, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32614898

RESUMO

Volvox sect. Volvox is an interesting group of green algae; it comprises mostly monoicous species, but evidence suggests an evolution towards dioicy. Based on cultured strains originating from Thailand, we describe Volvox longispiniferus, a novel species in Volvox sect. Volvox. This species is distinguished from others in the section by the large number of sperm packets in its monoicous sexual spheroids and by the long spines on its zygote wall. Phylogenetic analyses indicate that V. longispiniferus is distinct from the other species of two monophyletic groups within Volvox sect. Volvox. In addition, the novel species produces more zygotes when different cultures are combined compared with a single culture, suggesting a preference for outcrossing.


Assuntos
Volvox/classificação , Cloroplastos/genética , DNA Ribossômico/classificação , DNA Ribossômico/genética , Complexo de Proteína do Fotossistema II/genética , Filogenia , Ribulose-Bifosfato Carboxilase/classificação , Ribulose-Bifosfato Carboxilase/genética , Tailândia , Volvox/genética
5.
PLoS One ; 15(6): e0227525, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32555586

RESUMO

The fossil record provides an invaluable insight into the temporal origins of extant lineages of organisms. However, establishing the relationships between fossils and extant lineages can be difficult in groups with low rates of morphological change over time. Molecular dating can potentially circumvent this issue by allowing distant fossils to act as calibration points, but rate variation across large evolutionary scales can bias such analyses. In this study, we apply multiple dating methods to genome-wide datasets to infer the origin of extant species of Isoetes, a group of mostly aquatic and semi-aquatic isoetalean lycopsids, which closely resemble fossil forms dating back to the Triassic. Rate variation observed in chloroplast genomes hampers accurate dating, but genome-wide nuclear markers place the origin of extant diversity within this group in the mid-Paleogene, 45-60 million years ago. Our genomic analyses coupled with a careful evaluation of the fossil record indicate that despite resembling forms from the Triassic, extant Isoetes species do not represent the remnants of an ancient and widespread group, but instead have spread around the globe in the relatively recent past.


Assuntos
Variação Genética , Genômica , Filogenia , Traqueófitas/genética , Evolução Biológica , Cloroplastos/genética , Fósseis , Perfilação da Expressão Gênica , Software
6.
Plant Mol Biol ; 104(1-2): 39-53, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32564178

RESUMO

Plants are exposed to various environmental cues that lead to reactive oxygen species (ROS) accumulation. ROS production and detoxification are tightly regulated to maintain balance. Although studies of glucose (Glc) are always accompanied by ROS in animals, the role of Glc in respect of ROS in plants is unclear. We isolated gsm2 (Glc-hypersensitive mutant 2), a mutant with a notably chlorotic-cotyledon phenotype. The chloroplast-localized GSM2 was characterized as a transaldolase in the pentose phosphate pathway. With 3% Glc treatment, fewer or no thylakoids were observed in gsm2 cotyledon chloroplasts than in wild-type cotyledon chloroplasts, suggesting that GSM2 is required for chloroplast protection under stress. gsm2 also showed evaluated accumulation of ROS with 3% Glc treatment and was more sensitive to exogenous H2O2 than the wild type. Gene expression analysis of the antioxidant enzymes in gsm2 revealed that chloroplast damage to gsm2 cotyledons results from the accumulation of excessive ROS in response to Glc. Moreover, the addition of diphenyleneiodonium chloride or phenylalanine can rescue Glc-induced chlorosis in gsm2 cotyledons. This work suggests that GSM2 functions to maintain ROS balance in response to Glc during early seedling growth and sheds light on the relationship between Glc, the pentose phosphate pathway and ROS.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/metabolismo , Homeostase , RNA Helicases/metabolismo , Espécies Reativas de Oxigênio/metabolismo , Transaldolase/metabolismo , Ácido Abscísico/metabolismo , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Clorofila/metabolismo , Cloroplastos/genética , Cloroplastos/metabolismo , Cotilédone/metabolismo , Regulação da Expressão Gênica de Plantas , Germinação , Glucuronidase/metabolismo , Peróxido de Hidrogênio/metabolismo , Via de Pentose Fosfato/genética , Via de Pentose Fosfato/fisiologia , Fenótipo , RNA Helicases/genética , RNA de Plantas/genética , RNA de Plantas/isolamento & purificação , Plântula/genética , Plântula/metabolismo , Transaldolase/genética
7.
PLoS One ; 15(4): e0232295, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32353023

RESUMO

In Rubiaceae phylogenetics, the number of markers often proved a limitation with authors failing to provide well-supported trees at tribal and generic levels. A robust phylogeny is a prerequisite to study the evolutionary patterns of traits at different taxonomic levels. Advances in next-generation sequencing technologies have revolutionized biology by providing, at reduced cost, huge amounts of data for an increased number of species. Due to their highly conserved structure, generally recombination-free, and mostly uniparental inheritance, chloroplast DNA sequences have long been used as choice markers for plant phylogeny reconstruction. The main objectives of this study are: 1) to gain insight in chloroplast genome evolution in the Rubiaceae (Ixoroideae) through efficient methodology for de novo assembly of plastid genomes; and, 2) to test the efficiency of mining SNPs in the nuclear genome of Ixoroideae based on the use of a coffee reference genome to produce well-supported nuclear trees. We assembled whole chloroplast genome sequences for 27 species of the Rubiaceae subfamily Ixoroideae using next-generation sequences. Analysis of the plastid genome structure reveals a relatively good conservation of gene content and order. Generally, low variation was observed between taxa in the boundary regions with the exception of the inverted repeat at both the large and short single copy junctions for some taxa. An average of 79% of the SNP determined in the Coffea genus are transferable to Ixoroideae, with variation ranging from 35% to 96%. In general, the plastid and the nuclear genome phylogenies are congruent with each other. They are well-resolved with well-supported branches. Generally, the tribes form well-identified clades but the tribe Sherbournieae is shown to be polyphyletic. The results are discussed relative to the methodology used and the chloroplast genome features in Rubiaceae and compared to previous Rubiaceae phylogenies.


Assuntos
Cloroplastos/genética , DNA de Cloroplastos/genética , Genoma de Cloroplastos/genética , Genoma de Planta/genética , Rubiaceae/genética , Coffea/genética , Evolução Molecular , Genômica/métodos , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Filogenia , Polimorfismo de Nucleotídeo Único/genética , Análise de Sequência de DNA/métodos
8.
Proc Natl Acad Sci U S A ; 117(22): 12452-12463, 2020 06 02.
Artigo em Inglês | MEDLINE | ID: mdl-32404426

RESUMO

Plastid isoprenoid-derived carotenoids serve essential roles in chloroplast development and photosynthesis. Although nearly all enzymes that participate in the biosynthesis of carotenoids in plants have been identified, the complement of auxiliary proteins that regulate synthesis, transport, sequestration, and degradation of these molecules and their isoprenoid precursors have not been fully described. To identify such proteins that are necessary for the optimal functioning of oxygenic photosynthesis, we screened a large collection of nonphotosynthetic (acetate-requiring) DNA insertional mutants of Chlamydomonas reinhardtii and isolated cpsfl1 The cpsfl1 mutant is extremely light-sensitive and susceptible to photoinhibition and photobleaching. The CPSFL1 gene encodes a CRAL-TRIO hydrophobic ligand-binding (Sec14) domain protein. Proteins containing this domain are limited to eukaryotes, but some may have been retargeted to function in organelles of endosymbiotic origin. The cpsfl1 mutant showed decreased accumulation of plastidial isoprenoid-derived pigments, especially carotenoids, and whole-cell focused ion-beam scanning-electron microscopy revealed a deficiency of carotenoid-rich chloroplast structures (e.g., eyespot and plastoglobules). The low carotenoid content resulted from impaired biosynthesis at a step prior to phytoene, the committed precursor to carotenoids. The CPSFL1 protein bound phytoene and ß-carotene when expressed in Escherichia coli and phosphatidic acid in vitro. We suggest that CPSFL1 is involved in the regulation of phytoene synthesis and carotenoid transport and thereby modulates carotenoid accumulation in the chloroplast.


Assuntos
Carotenoides/metabolismo , Chlamydomonas reinhardtii/crescimento & desenvolvimento , Cloroplastos/metabolismo , Proteínas de Plantas/metabolismo , Chlamydomonas reinhardtii/classificação , Chlamydomonas reinhardtii/genética , Chlamydomonas reinhardtii/metabolismo , Cloroplastos/química , Cloroplastos/genética , Fotossíntese , Filogenia , Proteínas de Plantas/química , Proteínas de Plantas/genética , Domínios Proteicos
9.
BMC Evol Biol ; 20(1): 51, 2020 05 06.
Artigo em Inglês | MEDLINE | ID: mdl-32375634

RESUMO

BACKGROUND: Raw second-generation (2G) lignocellulosic biomass materials have the potential for development into a sustainable and renewable source of energy. Poplar is regarded as a promising 2G material (P. davidiana Dode×P. bolleana Lauch, P. bolleana, P. davidiana, P. euphratica, et al). However, their large-scale commercialization still faces many obstacles. For example, drought prevents sufficient irrigation or rainfall, which can reduce soil moisture and eventually destroy the chloroplast, the plant photosynthetic organelle. Heterosis is widely used in the production of drought-tolerant materials, such as the superior clone "Shanxinyang" selected from the offspring of Populus davidiana Dode×Populus bolleana Lauch. Because it produces good wood and is easily genetically transformed, "Shanxinyang" has become a promising material for use in tree genetics. It is also one of the most abundant biofuel plants in northern China. Understanding the genetic features of chloroplasts, the cp transcriptome and physiology is crucial to elucidating the chloroplast drought-response model. RESULTS: In this study, the whole genome of "Shanxinyang" was sequenced. The chloroplast genome was assembled, and chloroplast structure was analysed and compared with that of other popular plants. Chloroplast transcriptome analysis was performed under drought conditions. The total length of the "Shanxinyang" chloroplast genome was 156,190 bp, the GC content was 36.75%, and the genome was composed of four typical areas (LSC, IRa, IRb, and SSC). A total of 114 simple repeats were detected in the chloroplast genome of "Shanxinyang". In cp transcriptome analysis, we found 161 up-regulated and 157 down-regulated genes under drought, and 9 cpDEGs was randomly selected to conduct reverse transcription (RT)-qPCR., in which the Log2 (fold change) was significantly consistent with the qPCR results. The analysis of chloroplast transcription under drought provided clues for understanding chloroplast function under drought. The phylogenetic position of "Shanxinyang" within Populus was analysed by using the chloroplast genome sequences of 23 Populus plants, showing that "Shanxinyang" belongs to Sect. Populus and is sister to Populus davidiana. Further, mVISTA analysis showed that the variation in non-coding (regulatory) regions was greater than that in coding regions, which suggests that further attention should be paid to the chloroplast in order to obtain new evolutionary or functional insights related to aspects of plant biology. CONCLUSIONS: Our findings indicate that complex prokaryotic genome regulation occurs when processing transcripts under drought stress. The results not only offer clues for understanding the chloroplast genome and transcription features in woody plants but also serve as a basis for future molecular studies on poplar species.


Assuntos
Cloroplastos/genética , Secas , Filogenia , Populus/classificação , Populus/genética , Transcriptoma/genética , Composição de Bases/genética , Sequência de Bases , Éxons/genética , Regulação da Expressão Gênica de Plantas , Genoma de Cloroplastos , Íntrons/genética , Sequências Repetidas Invertidas/genética , Anotação de Sequência Molecular
10.
Mol Genet Genomics ; 295(4): 981-999, 2020 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-32306107

RESUMO

Leaf color is an important characteristic of normal chloroplast development. Variegated plants have green- and white-sectored leaves, which can be used to identify important pathways and molecular mechanisms of chloroplast development. We studied two Brassica napus variegation mutants from same one variegated ancestor, designated ZY-4 and ZY-8, which have different degrees of variegation. When grown in identical conditions, the ratio of white sectors in ZY-4 leaves is higher than in ZY-8. In both mutants, the cells in green sectors contain normal chloroplasts; while, the cells in white sectors contain abnormal plastids. Seedling chloroplasts ultrastructure of both mutants showed that the biogenesis of chloroplasts was blocked in early stages; delayed development and structual damage in ZY-4 were more serious than in ZY-8. Employing bulked segregant analysis(BSA), two bulks (BY142 and BY137) from BC2F1 lines derived from ZY-4 and ZS11, and one bulk (BY56) from BC2F1 lines derived from ZY-8 and ZS11, and screening by Brassica 60K SNP BeadChip Array, showed the candidate regions localized in chromosome A08 (BY142), C04 (BY137), and A08 (BY56), respectively. Transcriptome analysis of five seedling development stages of ZY-4, ZY-8, and ZS11 showed that photosynthesis, energy metabolism-related pathways and translation-related pathways were important for chloroplast biogenesis. The number of down- or up-regulated genes related to immune system process in ZY-4 was more than in ZY-8. The retrograde signaling pathway was mis-regulated in both mutants. DEG analysis indicated that both mutants showed photooxidative damages. By coupling transcriptome and BSA CHIP analyses, some candidate genes were identified. The gene expression pattern of carotene biosynthesis pathway was disrupted in both mutants. However, histochemical analysis of ROS revealed that there was no excessive accumulation of ROS in ZY-4 and ZY-8. Taken together, our data indicate that the disruption of carotene biosynthetic pathways leads to the variegation phenotypes of ZY-4 and ZY-8 and there are some functions that can compensate for the disruption of carotene biosynthesis in ZY-4 and ZY-8 to reduce ROS and prevent seedling mortality.


Assuntos
Brassica napus/genética , Carotenoides/metabolismo , Plastídeos/genética , Transcriptoma/genética , Arabidopsis/genética , Brassica napus/crescimento & desenvolvimento , Brassica napus/metabolismo , Cloroplastos/genética , Regulação da Expressão Gênica de Plantas/genética , Mutação/genética , Fotossíntese/genética , Desenvolvimento Vegetal/genética , Folhas de Planta/genética , Folhas de Planta/crescimento & desenvolvimento , Folhas de Planta/metabolismo , Plastídeos/metabolismo
11.
BMC Bioinformatics ; 21(Suppl 2): 83, 2020 Mar 11.
Artigo em Inglês | MEDLINE | ID: mdl-32164552

RESUMO

BACKGROUND: Previously, a seven-cluster pattern claiming to be a universal one in bacterial genomes has been reported. Keeping in mind the most popular theory of chloroplast origin, we checked whether a similar pattern is observed in chloroplast genomes. RESULTS: Surprisingly, eight cluster structure has been found, for chloroplasts. The pattern observed for chloroplasts differs rather significantly, from bacterial one, and from that latter observed for cyanobacteria. The structure is provided by clustering of the fragments of equal length isolated within a genome so that each fragment is converted in triplet frequency dictionary with non-overlapping triplets with no gaps in frame tiling. The points in 63-dimensional space were clustered due to elastic map technique. The eight cluster found in chloroplasts comprises the fragments of a genome bearing tRNA genes and exhibiting excessively high GC-content, in comparison to the entire genome. CONCLUSION: Chloroplasts exhibit very specific symmetry type in distribution of coding and non-coding fragments of a genome in the space of triplet frequencies: this is mirror symmetry. Cyanobacteria may have both mirror symmetry, and the rotational symmetry typical for other bacteria.


Assuntos
Cloroplastos/genética , Genoma de Cloroplastos , Composição de Bases , Análise por Conglomerados , Cianobactérias/genética , RNA de Transferência/genética
12.
Cytogenet Genome Res ; 160(2): 100-109, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32146470

RESUMO

Chloroplasts and mitochondria are semi-autonomous organelles and have their own genomes (cytoplasmic genomes). Physical radiations (e.g., γ-rays) have been widely used in artificial mutation induction for plant germplasm enhancement and for breeding new cultivars. However, little is known at the genomic level about which kind of cytoplasmic mutations and/or characteristics could be induced in plants. The present study aimed to investigate the type, number, and distribution of inheritable cytoplasmic mutations induced by γ-rays in rice (Oryza sativa L.). Six plants were selected from the 2nd generation (M2) populations after γ-ray (137Cs) irradiation of the rice cultivar Nipponbare, 2 each for the 3 irradiation doses (150, 250, and 350 Gy), and their genomes were sequenced on an Illumina platform. Together with the whole-genome sequencing data of 3 external Nipponbare control plants, single-base substitutions (SBSs) and insertions/deletions (InDels) in chloroplast (cp) and mitochondrial (mt) genomes were identified and analyzed in-depth using bioinformatic tools. The majority of SBSs and InDels identified were background mutations in the 6 M2 plants, and the number of induced mutations varied greatly among the plants. Most induced mutations were present in a heterogeneous state, reflecting the fact that multiple cp and mt copies existed in the progenitor cells. The induced mutations were distributed in different genomic regions in the 6 M2 plants, including exonic regions, but none of them was predicted to cause nonsynonymous mutations or frameshifts. Our study thus revealed, at the genomic level, characteristics of cytoplasmic mutations induced by γ-rays in rice.


Assuntos
Raios gama/efeitos adversos , Mutação , Oryza/efeitos da radiação , Sequenciamento Completo do Genoma/métodos , Cloroplastos/genética , Cloroplastos/efeitos da radiação , Genoma de Planta/efeitos da radiação , Sequenciamento de Nucleotídeos em Larga Escala , Mitocôndrias/genética , Mitocôndrias/efeitos da radiação , Oryza/genética , Proteínas de Plantas/genética , Proteínas de Plantas/efeitos da radiação , Sementes/genética , Sementes/efeitos da radiação
13.
Mol Phylogenet Evol ; 147: 106784, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32135308

RESUMO

The Amelanchier-Malacomeles-Peraphyllum (AMP) clade consists of ca. 26 species distributed in North and Central America, Europe, Asia, and northwestern Africa. While molecular and morphological data strongly support this clade, relationships of its genera are uncertain. Support for the monophyly of Amelanchier and for the phylogenetic positions of Malacomeles and Peraphyllum has varied between studies. Our goals were to reconstruct a robust phylogeny of the AMP clade in the framework of Maleae and clarify the phylogenetic placements of Malacomeles and Peraphyllum. This study employs sequences of the whole plastome and nuclear ribosomal DNA (nrDNA) repeats assembled using genome skimming with 131 samples representing 115 species in 31 genera of Rosaceae, especially Maleae. Maximum likelihood (ML) and Bayesian analysis (BI) of whole plastome datasets strongly supported Amelanchier as not monophyletic, with Peraphyllum sister to eastern North American Amelanchier and Malacomeles sister to the western North American-Eurasian Amelanchier. In contrast, nrDNA recovered the monophyly of Amelanchier, with Peraphyllum sister to Amelanchier and Malacomeles sister to the Amelanchier-Peraphyllum clade. The strong topological conflicts between plastome and nrDNA phylogenies of Peraphyllum and of Malacomeles are best explained by ancient chloroplast capture that occurred in SW North America.


Assuntos
Núcleo Celular/genética , Cloroplastos/genética , DNA Ribossômico/genética , Genoma de Cloroplastos , Genômica/métodos , Filogenia , Rosaceae/classificação , Rosaceae/genética , Teorema de Bayes , Mapeamento Cromossômico , Evolução Molecular , Geografia , Rosaceae/anatomia & histologia , Análise de Sequência de DNA
14.
Nat Commun ; 11(1): 1417, 2020 03 17.
Artigo em Inglês | MEDLINE | ID: mdl-32184398

RESUMO

Holliday junctions (HJs) are key DNA intermediates in genetic recombination and are eliminated by nuclease, termed resolvase, to ensure genome stability. HJ resolvases have been identified across all kingdoms of life, members of which exhibit sequence-dependent HJ resolution. However, the molecular basis of sequence selectivity remains largely unknown. Here, we present the chloroplast resolvase MOC1, which cleaves HJ in a cytosine-dependent manner. We determine the crystal structure of MOC1 with and without HJs. MOC1 exhibits an RNase H fold, belonging to the retroviral integrase family. MOC1 functions as a dimer, and the HJ is embedded into the basic cleft of the dimeric enzyme. We characterize a base recognition loop (BR loop) that protrudes into and opens the junction. Residues from the BR loop intercalate into the bases, disrupt the C-G base pairing at the crossover and recognize the cytosine, providing the molecular basis for sequence-dependent HJ resolution by a resolvase.


Assuntos
Arabidopsis/enzimologia , Cloroplastos/enzimologia , DNA Cruciforme/metabolismo , Oryza/enzimologia , Proteínas de Plantas/química , Proteínas de Plantas/metabolismo , Recombinases/química , Recombinases/metabolismo , Soja/enzimologia , Arabidopsis/química , Arabidopsis/genética , Arabidopsis/metabolismo , Sequência de Bases , Cloroplastos/química , Cloroplastos/genética , DNA Cruciforme/química , DNA Cruciforme/genética , DNA de Plantas/química , DNA de Plantas/genética , DNA de Plantas/metabolismo , Oryza/química , Oryza/genética , Oryza/metabolismo , Recombinases/genética , Soja/química , Soja/genética , Soja/metabolismo
15.
PLoS One ; 15(2): e0229408, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32092117

RESUMO

The chloroplast is a central part of plant cells, as this is the organelle where the photosynthesis, fixation of inorganic carbon, and other key functions related to fatty acid synthesis and amino acid synthesis occur. Since this organelle should be an integral part of any genome-scale metabolic model for a microalgae or a higher plant, it is of great interest to generate a detailed and standardized chloroplast model. Additionally, we see the need for a novel type of sub-model template, or organelle model, which could be incorporated into a larger, less specific genome-scale metabolic model, while allowing for minor differences between chloroplast-containing organisms. The result of this work is the very first standardized chloroplast model, iGR774, consisting of 788 reactions, 764 metabolites, and 774 genes. The model is currently able to run in three different modes, mimicking the chloroplast metabolism of three photosynthetic microalgae-Nannochloropsis gaditana, Chlamydomonas reinhardtii and Phaeodactylum tricornutum. In addition to developing the chloroplast metabolic network reconstruction, we have developed multiple software tools for working with this novel type of sub-model in the COBRA Toolbox for MATLAB, including tools for connecting the chloroplast model to a genome-scale metabolic reconstruction in need of a chloroplast, for switching the model between running in different organism modes, and for expanding it by introducing more reactions either related to one of the current organisms included in the model, or to a new organism.


Assuntos
Cloroplastos/genética , Biologia Computacional/métodos , Redes e Vias Metabólicas/genética , Microalgas/genética , Modelos Biológicos , Software , Chlamydomonas reinhardtii/genética , Chlamydomonas reinhardtii/metabolismo , Cloroplastos/metabolismo , Diatomáceas/genética , Diatomáceas/metabolismo , Genoma/fisiologia , Microalgas/ultraestrutura , Fotossíntese/genética
16.
Nucleic Acids Res ; 48(6): 3195-3210, 2020 04 06.
Artigo em Inglês | MEDLINE | ID: mdl-32095829

RESUMO

Methylation of nucleotides in ribosomal RNAs (rRNAs) is a ubiquitous feature that occurs in all living organisms. The formation of methylated nucleotides is performed by a variety of RNA-methyltransferases. Chloroplasts of plant cells result from an endosymbiotic event and possess their own genome and ribosomes. However, enzymes responsible for rRNA methylation and the function of modified nucleotides in chloroplasts remain to be determined. Here, we identified an rRNA methyltransferase, CMAL (Chloroplast MraW-Like), in the Arabidopsis chloroplast and investigated its function. CMAL is the Arabidopsis ortholog of bacterial MraW/ RsmH proteins and accounts to the N4-methylation of C1352 in chloroplast 16S rRNA, indicating that CMAL orthologs and this methyl-modification nucleotide is conserved between bacteria and the endosymbiont-derived eukaryotic organelle. The knockout of CMAL in Arabidopsis impairs the chloroplast ribosome accumulation and accordingly reduced the efficiency of mRNA translation. Interestingly, the loss of CMAL leads not only to defects in chloroplast function, but also to abnormal leaf and root development and overall plant morphology. Further investigation showed that CMAL is involved in the plant development probably by modulating auxin derived signaling pathways. This study uncovered the important role of 16S rRNA methylation mediated by CMAL in chloroplast ribosome biogenesis and plant development.


Assuntos
Metiltransferases/genética , Desenvolvimento Vegetal/genética , RNA Ribossômico 16S/genética , Ribossomos/genética , Arabidopsis/genética , Arabidopsis/crescimento & desenvolvimento , Cloroplastos/genética , Regulação da Expressão Gênica de Plantas/genética , Metilação , Folhas de Planta/genética , Folhas de Planta/crescimento & desenvolvimento , Plastídeos/genética , RNA Mensageiro/genética , RNA de Plantas/genética
17.
Gene ; 736: 144410, 2020 Apr 30.
Artigo em Inglês | MEDLINE | ID: mdl-32007581

RESUMO

Magnoliaceae is a primitive taxon in the angiosperms, comprising approximately 240 species in 2-17 genera. Many of them have been widely cultivated due to their horticultural and medicinal value. However, there are uncertainties and controversies about the delimitation of the genera except Liriodendron L. in this family. The Yulania taxa is also the focus of dispute at the genus and section levels. In this study, we compared ten Yulania plastomes, including the newly sequenced M. polytepala. The plastome-wide comparative analysis demonstrated that 1) Yulania cp genomes were highly conserved, and the majority differences existed in IR regions with the loss/retention of trnV-GAC or ycf15 gene, 2) mutational hotspots with high levels of nucleotide diversity (Pi > 0.02) existed in both coding (rpoA, and ycf1) and no-coding (ccsA-ndhD, ndhE-ndhG, ndhF-rpl32, petA-psbJ, rpl32-trnL, rps3-rps19, and trnH-psbA) regions among the genus Yulania. Combined with other data from Magnoliaceae plastomes, our reconstructed molecular phylogenetic tree revealed that Yulania is monophyletic, separated from the genus Magnolia L. (=Magnolia subg. Magnolia L.), but seems a sister of Michelia L. Moreover, M. polytepala which belongs to the genus Yulania is most closely related to M. liliiflora. All these results indicated that plastome data may contribute to investigating taxonomy, population genetics and phylogeny of Yulania.


Assuntos
Cloroplastos/genética , Genoma de Cloroplastos/genética , Genoma de Planta/genética , Magnolia/genética , Magnoliaceae/genética , Genética Populacional/métodos , Genômica/métodos , Magnoliopsida/genética , Filogenia
18.
BMC Genomics ; 21(1): 114, 2020 Jan 31.
Artigo em Inglês | MEDLINE | ID: mdl-32005143

RESUMO

BACKGROUND: Chloroplast (cp) genome information would facilitate the development and utilization of Taxodium resources. However, cp genome characteristics of Taxodium were poorly understood. RESULTS: We determined the complete cp genome sequences of T. distichum, T. mucronatum, and T. ascendens. The cp genomes are 131,947 bp to 132,613 bp in length, encode 120 genes with the same order, and lack typical inverted repeat (IR) regions. The longest small IR, a 282 bp trnQ-containing IR, were involved in the formation of isomers. Comparative analysis of the 3 cp genomes showed that 91.57% of the indels resulted in the periodic variation of tandem repeat (TR) motifs and 72.46% single nucleotide polymorphisms (SNPs) located closely to TRs, suggesting a relationship between TRs and mutational dynamics. Eleven hypervariable regions were identified as candidates for DNA barcode development. Hypothetical cp open reading frame 1(Ycf1) was the only one gene that has an indel in coding DNA sequence, and the indel is composed of a long TR. When extended to cupressophytes, ycf1 genes have undergone a universal insertion of TRs accompanied by extreme length expansion. Meanwhile, ycf1 also located in rearrangement endpoints of cupressophyte cp genomes. All these characteristics highlight the important role of repeats in the evolution of cp genomes. CONCLUSIONS: This study added new evidence for the role of repeats in the dynamics mechanism of cp genome mutation and rearrangement. Moreover, the information of TRs and hypervariable regions would provide reliable molecular resources for future research focusing on the infrageneric taxa identification, phylogenetic resolution, population structure and biodiversity for the genus Taxodium and Cupressophytes.


Assuntos
Cloroplastos/genética , Análise de Sequência de DNA/métodos , Taxodium/classificação , Evolução Molecular , Variação Genética , Tamanho do Genoma , Genoma de Cloroplastos , Sequenciamento de Nucleotídeos em Larga Escala , Filogenia , Taxodium/genética
19.
PLoS One ; 15(1): e0227625, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31914145

RESUMO

Natural hybridization plays important roles in plant evolution and speciation. In this study, we sequenced ribosomal internal transcribed spacer (nrITS), four low-copy nuclear genes (Dbr1, SOS4a, SOS4b and PCRF1) and the chloroplast intergenic spacer trnV-trnM to test the hypothesis of hybridization between two species of Phyllagathis and Sporoxeia (Sonerileae/Dissochaeteae, Melastomataceae). Our results provided compelling evidence for the hybridization hypothesis. All hybrid individuals sampled were first-generation hybrids. The failure of flower production in the F1 hybrid individuals may work as the barrier preventing later-generation hybridization or backcross. Analysis of the chloroplast trnV-trnM sequences showed that the hybridization is bidirectional with S. petelotii as the major maternal parent. Several factors, such as sympatry, similar habitat preference, overlapping flowering season and shared pollinators, might have contributed to this hybridization event. The "intergeneric" hybridization reported in this study suggests close relationship between P. longicalcarata and S. petelotii.


Assuntos
Quimera , Melastomataceae/genética , Proteínas de Plantas/genética , China , Cloroplastos/genética , DNA Espaçador Ribossômico/genética , Flores/genética , Melastomataceae/anatomia & histologia , Melastomataceae/fisiologia
20.
Plant Mol Biol ; 102(6): 659-676, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-31997112

RESUMO

KEY MESSAGE: Seven divergence hotspots as plastid markers for DNA barcoding was selected, and the phylogeny of 13 Lagerstroemia species based on the cp genome data was reconstructed within Myrtales. The Lagerstroemia species used in this study originated in China and have high economic and ecological value. The shared interspecific morphological characteristics and intraspecific morphological variation resulting from hybridization among Lagerstroemia taxa have made resolving their classification problems and phylogenetic relationships difficult. Systematic comparative genomic analysis has been shown to resolve phylogenetic relationships. We sequenced and annotated 6 Lagerstroemia cp genomes (Lagerstroemia excelsa, Lagerstroemia limii, Lagerstroemia siamica, Lagerstroemia tomentosa, Lagerstroemia venusta, and Lagerstroemia calyculata) for the first time and combined them with previously published genomes for Lagerstroemia species. Bioinformatics was used to analyse the 13 cp genomes in terms of gene structure and organization, codon usage, contraction and expansion of inverted repeat regions, repeat structure, divergence hotspots, species pairwise Ka/Ks ratios and phylogenetic relationships. The length varied between 152,049 bp in Lagerstroemia subcostata and 152,521 bp in L. venusta. We selected seven divergence hotspots in the cp genomes that had the potential to act as plastid markers to distinguish Lagerstroemia species. The phylogenetic relationships within Myrtales inferred from the cp genomes of 13 Lagerstroemia species and 27 other Myrtales species were highly supported, which illustrated several novel relationships within Myrtales. Taken together, our results provide comprehensive chloroplast genomic resources, which can be used further for species identification and molecular breeding of Lagerstroemia species.


Assuntos
Cloroplastos/genética , Genoma de Cloroplastos/genética , Lagerstroemia/classificação , Lagerstroemia/genética , Filogenia , Sequência de Bases , Bases de Dados de Ácidos Nucleicos , Evolução Molecular , Anotação de Sequência Molecular , Proteínas de Plantas/genética , Plastídeos , Análise de Sequência de DNA
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