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1.
Nat Commun ; 11(1): 5346, 2020 10 22.
Artigo em Inglês | MEDLINE | ID: mdl-33093471

RESUMO

The mechanism that creates vitreous endosperm in the mature maize kernel is poorly understood. We identified Vitreous endosperm 1 (Ven1) as a major QTL influencing this process. Ven1 encodes ß-carotene hydroxylase 3, an enzyme that modulates carotenoid composition in the amyloplast envelope. The A619 inbred contains a nonfunctional Ven1 allele, leading to a decrease in polar and an increase in non-polar carotenoids in the amyloplast. Coincidently, the stability of amyloplast membranes is increased during kernel desiccation. The lipid composition in endosperm cells in A619 is altered, giving rise to a persistent amyloplast envelope. These changes impede the gathering of protein bodies and prevent them from interacting with starch grains, creating air spaces that cause an opaque kernel phenotype. Genetic modifiers were identified that alter the effect of Ven1A619, while maintaining a high ß-carotene level. These studies provide insight for breeding vitreous kernel varieties and high vitamin A content in maize.


Assuntos
Carotenoides/metabolismo , Zea mays/metabolismo , Alelos , Mapeamento Cromossômico , Cruzamentos Genéticos , Endosperma/genética , Endosperma/metabolismo , Endosperma/ultraestrutura , Genes de Plantas , Microscopia Eletrônica de Varredura , Microscopia Eletrônica de Transmissão , Oxigenases de Função Mista/genética , Oxigenases de Função Mista/metabolismo , Fenótipo , Melhoramento Vegetal , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Plastídeos/genética , Plastídeos/metabolismo , Plastídeos/ultraestrutura , Locos de Características Quantitativas , Sementes/genética , Sementes/metabolismo , Sementes/ultraestrutura , Zea mays/genética , Zea mays/ultraestrutura
2.
Proc Natl Acad Sci U S A ; 117(28): 16448-16455, 2020 07 14.
Artigo em Inglês | MEDLINE | ID: mdl-32601224

RESUMO

Mitochondrial and plastid genomes in land plants exhibit some of the slowest rates of sequence evolution observed in any eukaryotic genome, suggesting an exceptional ability to prevent or correct mutations. However, the mechanisms responsible for this extreme fidelity remain unclear. We tested seven candidate genes involved in cytoplasmic DNA replication, recombination, and repair (POLIA, POLIB, MSH1, RECA3, UNG, FPG, and OGG1) for effects on mutation rates in the model angiosperm Arabidopsis thaliana by applying a highly accurate DNA sequencing technique (duplex sequencing) that can detect newly arisen mitochondrial and plastid mutations even at low heteroplasmic frequencies. We find that disrupting MSH1 (but not the other candidate genes) leads to massive increases in the frequency of point mutations and small indels and changes to the mutation spectrum in mitochondrial and plastid DNA. We also used droplet digital PCR to show transmission of de novo heteroplasmies across generations in msh1 mutants, confirming a contribution to heritable mutation rates. This dual-targeted gene is part of an enigmatic lineage within the mutS mismatch repair family that we find is also present outside of green plants in multiple eukaryotic groups (stramenopiles, alveolates, haptophytes, and cryptomonads), as well as certain bacteria and viruses. MSH1 has previously been shown to limit ectopic recombination in plant cytoplasmic genomes. Our results point to a broader role in recognition and correction of errors in plant mitochondrial and plastid DNA sequence, leading to greatly suppressed mutation rates perhaps via initiation of double-stranded breaks and repair pathways based on faithful homologous recombination.


Assuntos
Proteínas de Arabidopsis/metabolismo , Arabidopsis/genética , Arabidopsis/metabolismo , Mitocôndrias/genética , Proteína MutS de Ligação de DNA com Erro de Pareamento/metabolismo , Plastídeos/genética , Proteínas de Arabidopsis/genética , Regulação da Expressão Gênica de Plantas , Genoma Mitocondrial , Genoma de Planta , Genomas de Plastídeos , Mitocôndrias/metabolismo , Proteína MutS de Ligação de DNA com Erro de Pareamento/genética , Mutação , Taxa de Mutação , Plastídeos/metabolismo
3.
Nat Commun ; 11(1): 3051, 2020 06 19.
Artigo em Inglês | MEDLINE | ID: mdl-32561724

RESUMO

The phylum Cnidaria represents a close outgroup to Bilateria and includes familiar animals including sea anemones, corals, hydroids, and jellyfish. Here we report genome sequencing and assembly for true jellyfish Sanderia malayensis and Rhopilema esculentum. The homeobox gene clusters are characterised by interdigitation of Hox, NK, and Hox-like genes revealing an alternate pathway of ANTP class gene dispersal and an intact three gene ParaHox cluster. The mitochondrial genomes are linear but, unlike in Hydra, we do not detect nuclear copies, suggesting that linear plastid genomes are not necessarily prone to integration. Genes for sesquiterpenoid hormone production, typical for arthropods, are also now found in cnidarians. Somatic and germline cells both express piwi-interacting RNAs in jellyfish revealing a conserved cnidarian feature, and evidence for tissue-specific microRNA arm switching as found in Bilateria is detected. Jellyfish genomes reveal a mosaic of conserved and divergent genomic characters evolved from a shared ancestral genetic architecture.


Assuntos
Genes Homeobox , Família Multigênica , RNA/genética , Cifozoários/genética , Cifozoários/fisiologia , Animais , Biologia do Desenvolvimento , Genoma , Genoma Mitocondrial , Hormônios/genética , MicroRNAs/genética , Mitocôndrias/genética , Filogenia , Plastídeos/genética , RNA Interferente Pequeno/genética , Análise de Sequência de DNA , Especificidade da Espécie , Transcriptoma
4.
Food Chem ; 326: 126986, 2020 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-32407998

RESUMO

In the present work, a barcode-DNA analysis method is described for the detection of plant oil adulteration in milk and dairy products. The method relies on the fact that plant DNA should not be present in readily detectable amounts in a dairy product unless it contains undeclared plant material. Thus, a universal plant barcode is chosen as the target to be amplified from dairy samples. Accordingly, barcode PCR-CE (PCR-capillary electrophoresis) assays are described, which do not require preliminary information on the species source of the adulterant oil type. Two PCR-CE assays, one operating on the plastid trnL (UAA) intron and the other targeting its inner P6 loop in nested format, were shown to detect corn, soybean, rapeseed and sunflower oils in clarified butter, milk and yogurt. Both barcodes are robustly amplified with extremely conserved primers. While the intron provides the species discrimination ability, the P6 loop provides superior detection sensitivity.


Assuntos
DNA de Plantas/análise , Laticínios/análise , Eletroforese Capilar/métodos , Leite/química , Óleos Vegetais/química , Animais , Código de Barras de DNA Taxonômico , DNA de Plantas/genética , DNA de Plantas/metabolismo , Óleos Vegetais/metabolismo , Plastídeos/genética , Reação em Cadeia da Polimerase , Soja/genética , Iogurte/análise , Zea mays/genética
5.
PLoS One ; 15(5): e0232602, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32379799

RESUMO

Scutellaria, or skullcaps, are medicinally important herbs in China, India, Japan, and elsewhere. Though Scutellaria is the second largest and one of the more taxonomically challenging genera within Lamiaceae, few molecular systematic studies have been undertaken within the genus; in part due to a paucity of available informative markers. The lack of informative molecular markers for Scutellaria hinders our ability to accurately and robustly reconstruct phylogenetic relationships, which hampers our understanding of the diversity, phylogeny, and evolutionary history of this cosmopolitan genus. Comparative analyses of 15 plastomes, representing 14 species of subfamily Scutellarioideae, indicate that plastomes within Scutellarioideae contain about 151,000 nucleotides, and possess a typical quadripartite structure. In total, 590 simple sequence repeats, 489 longer repeats, and 16 hyper-variable regions were identified from the 15 plastomes. Phylogenetic relationships among the 14 species representing four of the five genera of Scutellarioideae were resolved with high support values, but the current infrageneric classification of Scutellaria was not supported in all analyses. Complete plastome sequences provide better resolution at an interspecific level than using few to several plastid markers in phylogenetic reconstruction. The data presented here will serve as a foundation to facilitate DNA barcoding, species identification, and systematic research within Scutellaria, which is an important medicinal plant resource worldwide.


Assuntos
Genomas de Plastídeos/genética , Plastídeos/genética , Scutellaria/classificação , Evolução Molecular , Filogenia
6.
Mol Phylogenet Evol ; 150: 106854, 2020 09.
Artigo em Inglês | MEDLINE | ID: mdl-32439485

RESUMO

Paleo-environmental data show that the distribution of African rain forests was affected by Quaternary climate changes. In particular, the Dahomey Gap (DG) - a 200 km wide savanna corridor currently separating the West African and Central African rain forest blocks and containing relict rain forest fragments - was forested during the mid-Holocene and possibly during previous interglacial periods, whereas it was dominated by open vegetation (savanna) during glacial periods. Genetic signatures of past population fragmentation and demographic changes have been found in some African forest plant species using nuclear markers, but such events appear not to have been synchronous or shared across species. To better understand the colonization history of the DG by rain forest trees through seed dispersal, the plastid genomes of two widespread African forest legume trees, Anthonotha macrophylla and Distemonanthus benthamianus, were sequenced in 47 individuals for each species, providing unprecedented phylogenetic resolution of their maternal lineages (857 and 115 SNPs, respectively). Both species exhibit distinct lineages separating three regions: 1. Upper Guinea (UG, i.e. the West African forest block), 2. the area ranging from the DG to the Cameroon volcanic line (CVL), and 3. Lower Guinea (LG, the western part of the Central African forest block) where three lineages co-occur. In both species, the DG populations (including southern Nigeria west of Cross River) exhibit much lower genetic diversity than UG and LG populations, and their plastid lineages originate from the CVL, confirming the role of the CVL as an ancient forest refuge. Despite the similar phylogeographic structures displayed by A. macrophylla and D. benthamianus, molecular dating indicates very contrasting ages of lineage divergence (UG diverged from LG since c. 7 Ma and 0.7 Ma, respectively) and DG colonization (probably following the Mid Pleistocene Transition and the Last Glacial Maximum, respectively). The stability of forest refuge areas and repeated similar forest shrinking/expanding events during successive glacial periods might explain why similar phylogeographic patterns can be generated over contrasting timescales.


Assuntos
Fabaceae/classificação , Plastídeos/genética , Benin , Camarões , Fabaceae/genética , Variação Genética , Haplótipos , Filogenia , Filogeografia , Plastídeos/classificação , Floresta Úmida
7.
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
8.
Shokuhin Eiseigaku Zasshi ; 61(1): 22-30, 2020.
Artigo em Japonês | MEDLINE | ID: mdl-32336715

RESUMO

An identification method for testing contamination in products was assessed using various vegetables and fruits (70 types in total). DNA was extracted from plant fragments which are 1 to several millimeters long and the plastid rpl16-rpl14 linker sequence (approximately 550 base pairs) was amplified by PCR. The DNA nucleotide sequence was determined, and homology and SNP (single nucleotide polymorphism) analyses were carried out. Consequently, the test plants were difficult to distinguish between closely related species, but could be divided into 38 groups at the genus level or the species level. Although problems such as the accuracy of discrimination among some closely related plants and DNA stability under an acidic condition remain to be resolved, this method is considered to be expected to identify plant fragments mixed in products or raw materials.


Assuntos
DNA de Plantas/análise , Frutas/química , Plantas Comestíveis/genética , Plastídeos/genética , Verduras/química , Polimorfismo de Nucleotídeo Único
9.
PLoS One ; 15(3): e0229846, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32134967

RESUMO

The genome organization and gene content of plastome (plastid genome) are highly conserved among most flowering plant species. Plastome variation (in size and gene order) is rare in photosynthetic species but size variation, rearrangements and gene/intron losses is attributed to groups of seed plants. Fabaceae (legume family), in particular the subfamily Papilionoideae and the inverted repeat lacking clade (IRLC), a largest legume lineage, display the most dramatic and structural change which providing an excellent model for understanding of mechanisms of genomic evolution. The IRLC comprises 52 genera and ca 4000 species divided into seven tribes. In present study, we have sampled several representatives from each tribe across the IRLC from various herbaria and field. The ycf4 gene, which plays a role in regulating and assembly of photosystem I, is more variable in the tribe Fabeae than in other tribes. In certain species of Lathyrus, Pisum and Vavilovia, all belonging to Fabeae, the gene is either absent or a pseudogene. Our study suggests that ycf4 gene has undergone positive selection. Furthermore, the rapid evolution of the gene is locus and lineage specific and is not a shared character of the IRLC in legumes.


Assuntos
Fabaceae/genética , Genomas de Plastídeos , Plastídeos/genética , Pseudogenes , DNA de Plantas/genética , Evolução Molecular , Deleção de Genes , Filogenia , Seleção Genética
10.
Artigo em Inglês | MEDLINE | ID: mdl-32213457

RESUMO

The genus Prunus contains many fruits used in the human diet, which exhibit a variety of different flavors. However, publications on the diversity of carotenoid profiles and sequestering structures in Prunus fruits are limited. In this study, carotenoids and their associated sequestering structures in mature fruits of four Prunus species, including peach [Prunus persica (L.) Batschi], nectarine [Prunus persica (L.) Batschi var. nucipersica], plum (Prunus salicina L.), and apricot (Prunus armeniaca L.) were investigated. HPLC-PAD analysis revealed that mature fruits all accumulated carotenoid esters, while their profiles and levels differed significantly. Transcription analysis suggested a positive correlation between carotenogenic genes and carotenoid profiles. Transmission electron microscopy (TEM) analysis revealed a common globular chromoplast in Prunus. However, the number and size of plastids and plastoglobules varied between species. Noticeably, the white-flesh Ruiguang 19 nectarine contained plastids similar to chromoplasts, except with smaller plastoglobules. In addition, it seemed like a lipid-dissolved ß-carotene form in apricot fruits, which is more effectively absorbed by humans than the solid-crystalline form. Moreover, the lowest transcriptions of plastid-related genes were found in Friar plum, and GLK2 and OR genes were presumed to be associated with the largest chromoplasts observed in apricot. We investigated the correlations among carotenoid accumulation, plastid characteristics and gene transcription and found that chromoplast development is likely more important in determining carotenoid accumulation than carotenogenic transcription in Prunus fruits. This study presents the first report on the diversity of carotenoid sequestering structures in Prunus fruits and suggests some crucial genes associated with diversity.


Assuntos
Carotenoides/análise , Frutas/química , Prunus/química , Transcrição Genética , Frutas/genética , Regulação da Expressão Gênica de Plantas , Plastídeos/genética , Prunus/genética
11.
Mol Phylogenet Evol ; 148: 106803, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32217168

RESUMO

Lepisoroid ferns (tribe Lepisoreae, Polypodiaceae) are arguably one of the most confusing fern groups in Polypodiaceae in terms of delimitation of genera largely because of their simple morphology. Previous molecular studies either had very small taxon sampling of the non-Lepisorus genera and did not well resolve the relationships among these genera, or had a relatively large sampling at species level but the critical species were missing or their relationships were not well resolved. A recent study resolved the newly sampled Lepisorus jakonensis as sister to the remaining genera in Lepisoreae excluding Paragramma, and the authors lumped all the six well recognized genera into Lepisorus. In the present study, to infer a phylogeny we used DNA sequences of five plastid markers (matK, rbcL, rbcL-atpB, rps4 &rps4-trnS, trnL &trnL-F) of 172 accessions representing ca. 44 species of non-Lepisorus genera and 54 accessions representing ca. 50 species of Lepisorus as ingroup, and 10 non-Lepisoreae accessions from the most closely related four genera (Leptochilus, Microsorum, Phymatosorus, and Goniophlebium) in Microsoroideae and one genus (Pyrrosia) in Platycerioideae. Our major results include: (1) All seven currently defined genera except Lepisorus in Lepisoreae are confirmed to be monophyletic; (2) The Lepisorus jakonensis clade is confirmed to be the second earliest diverged lineage in Lepisoreae; (3) Neolepisorus is resolved as sister to the rest in a clade containing all non-Lepisorus genera except Paragramma; (4) Lemmaphyllum is sister to a clade containing Lepidomicrosorium, Neocheiropteris, and Tricholepidium; and (5) Ellipinema gen. nov. is segregated from Lepisorus based on the phylogeny and morphology in order to stabilize the current usage of the existing six non-Lepisorus genera and species names in these genera. A key to all eight genera of Lepisoreae is provided.


Assuntos
Filogenia , Polypodiaceae/classificação , Funções Verossimilhança , Plastídeos/genética
12.
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
13.
PLoS One ; 15(2): e0228776, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32032368

RESUMO

The Mediterranean Basin is a biodiversity hotspot, where islands play a key role because of their high biological diversity, degree of endemicity and human pressure. One of these islands, Sardinia, is a good evolutionary laboratory, especially for the study of complex genera, such as Centaurea. In particular, endemic species of Centaurea sect. Centaurea from Sardinia provides an interesting case study of plant evolution on continental islands. We attempted to clarify the processes leading to the diversification of Centaurea species on Sardinia using bi-parentally inherited nuclear markers and maternally inherited plastid markers. Our plastid results revealed the presence of five lineages of sect. Centaurea on the island. Three of them were defined as three species: C. ferulacea, C. filiformis and C. horrida. The other two lineages highlighted the complex evolutionary history of the two polyploids C. corensis and C. magistrorum. Multiple colonization events from the mainland involving the C. deusta and C. paniculata lineages among others, have led to the diversity of sect. Centaurea on Sardinia. One colonization event likely followed a southern path via the land connection between the mainland, the Calabrian Plate and Sardinia. A second pathway likely followed a northern connection, probably through the Tuscan Archipelago. Implications of these findings on conservation efforts for Centaurea endemics on Sardinia are also discussed.


Assuntos
Evolução Biológica , Centaurea/crescimento & desenvolvimento , Centaurea/classificação , Centaurea/genética , DNA de Plantas/química , DNA de Plantas/isolamento & purificação , DNA de Plantas/metabolismo , Ligação Genética , Ilhas , Itália , Filogenia , Plastídeos/genética , Poliploidia
14.
Mol Phylogenet Evol ; 145: 106738, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-32001365

RESUMO

We investigated species relationships in Astraea, a primarily Neotropical genus of tribe Crotoneae centered in Brazil, using data from the nuclear ribosomal ITS, and the plastid trnL-trnF and psbA-trnH spacers. With all species of Astraea sampled, along with representatives from across Crotoneae, the evolutionary history of Astraea was interpreted in a broader framework, as well as divergence time estimates and reconstructions of ancestral areas and morphological character states for Crotoneae. Our results show that Astraea is monophyletic, consisting of three main clades, and that most of its diversification took place from the Oligocene to the Pliocene, coincident with the formation of the South American "dry diagonal". As for Crotoneae, our data show incongruent phylogenetic positions between the nuclear and chloroplast data for most of its genera, and that the ancestor of the tribe was probably arborescent and might have occupied the Amazon Basin, most likely in moist forest, from which it spread throughout South America in the early Eocene. Ancestral state reconstruction recovered deeply lobed leaves and staminate petals bearing moniliform trichomes as putative synapomorphies for Astraea, whereas the absence or strong reduction of pistillate petals is widespread in Crotoneae and may be a synapomorphy for the tribe.


Assuntos
Evolução Biológica , Euphorbiaceae/classificação , Teorema de Bayes , Brasil , Euphorbiaceae/anatomia & histologia , Euphorbiaceae/genética , Florestas , Íntrons , Filogenia , Filogeografia , Plastídeos/genética
15.
Proc Natl Acad Sci U S A ; 117(10): 5364-5375, 2020 03 10.
Artigo em Inglês | MEDLINE | ID: mdl-32094181

RESUMO

Nucleomorphs are relic endosymbiont nuclei so far found only in two algal groups, cryptophytes and chlorarachniophytes, which have been studied to model the evolutionary process of integrating an endosymbiont alga into a host-governed plastid (organellogenesis). However, past studies suggest that DNA transfer from the endosymbiont to host nuclei had already ceased in both cryptophytes and chlorarachniophytes, implying that the organellogenesis at the genetic level has been completed in the two systems. Moreover, we have yet to pinpoint the closest free-living relative of the endosymbiotic alga engulfed by the ancestral chlorarachniophyte or cryptophyte, making it difficult to infer how organellogenesis altered the endosymbiont genome. To counter the above issues, we need novel nucleomorph-bearing algae, in which endosymbiont-to-host DNA transfer is on-going and for which endosymbiont/plastid origins can be inferred at a fine taxonomic scale. Here, we report two previously undescribed dinoflagellates, strains MGD and TGD, with green algal endosymbionts enclosing plastids as well as relic nuclei (nucleomorphs). We provide evidence for the presence of DNA in the two nucleomorphs and the transfer of endosymbiont genes to the host (dinoflagellate) genomes. Furthermore, DNA transfer between the host and endosymbiont nuclei was found to be in progress in both the MGD and TGD systems. Phylogenetic analyses successfully resolved the origins of the endosymbionts at the genus level. With the combined evidence, we conclude that the host-endosymbiont integration in MGD/TGD is less advanced than that in cryptophytes/chrorarachniophytes, and propose the two dinoflagellates as models for elucidating organellogenesis.


Assuntos
Cercozoários/ultraestrutura , Criptófitas/ultraestrutura , Dinoflagelados/ultraestrutura , Evolução Molecular , Genomas de Plastídeos , Plastídeos/fisiologia , Simbiose , Núcleo Celular/genética , Núcleo Celular/fisiologia , Cercozoários/classificação , Cercozoários/genética , Clorófitas/classificação , Clorófitas/fisiologia , Clorófitas/ultraestrutura , Criptófitas/classificação , Criptófitas/genética , Dinoflagelados/classificação , Dinoflagelados/genética , Modelos Biológicos , Filogenia , Plastídeos/genética
16.
Mol Biol Rep ; 47(3): 1713-1722, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-32020428

RESUMO

A conversion of amyloplasts into chloroplasts in the potato tuber after light exposure is known as tuber greening and is one of the major causes of tuber loss. We report here the first mapping of the factors affecting tuber greening in potato. We used an F1 mapping population of diploid potatoes and DArTseq™ markers to construct a genetic map. The individuals of the mapping population, parents and standards were phenotyped for two tuber greening parameters: external tuber greening and internal greening depth on 0-5 scales in three years 2015, 2016 and 2018. The results were used for the analysis of Quantitative Trait Loci (QTLs) by an interval QTL mapping. Two most important QTLs were covering large regions of chromosomes VII and X and had the strongest effect on both greening parameters in data sets obtained in particular years and in the mean data set. Variance observed in the mean tuber greening could be ascribed in 16.9% to the QTL on chromosome VII and in 23.4% to the QTL on chromosome X. The QTL on chromosome VII explained 13.1%, while the QTL on chromosome X explained up to 17.7% of the variance in the mean tuber greening depth. Additional, minor QTLs were year- and/or trait-specific. The QTLs on chromosomes VII and X determine big parts of the observed tuber greening variation and should be investigated further in order to identify the genes underlying their effects but also should be taken into account when selecting non-greening potato lines in the breeding process.


Assuntos
Cloroplastos/genética , Tubérculos/genética , Plastídeos/genética , Locos de Características Quantitativas/genética , Solanum tuberosum/genética , Cloroplastos/metabolismo , Cloroplastos/efeitos da radiação , Mapeamento Cromossômico , Cromossomos de Plantas/genética , Genes de Plantas/genética , Genótipo , Luz , Fenótipo , Tubérculos/metabolismo , Plastídeos/metabolismo , Plastídeos/efeitos da radiação , Solanum tuberosum/classificação , Solanum tuberosum/metabolismo , Especificidade da Espécie
17.
Biomed Res Int ; 2020: 3465380, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32025518

RESUMO

The lengths of intergenic regions between neighboring genes that are convergent, divergent, or unidirectional were calculated for plastids of the rhodophytic branch and complete archaeal and bacterial genomes. Statistically significant linear relationships between any pair of the medians of these three length types have been revealed in each genomic group. Exponential relationships between the optimal growth temperature and each of the three medians have been revealed as well. The leading coefficients of the regression equations relating all pairs of the medians as well as temperature and any of the medians have the same sign and order of magnitude. The results obtained for plastids, archaea, and bacteria are also similar at the qualitative level. For instance, the medians are always low at high temperatures. At low temperatures, the medians tend to statistically significant greater values and scattering. The original model was used to test our hypothesis that the intergenic distances are optimized in particular to decrease the competition of RNA polymerases within the locus that results in transcribing shortened RNAs. Overall, this points to an effect of temperature for both remote and close genomes.


Assuntos
Archaea/crescimento & desenvolvimento , Archaea/genética , Bactérias/crescimento & desenvolvimento , Bactérias/genética , Plastídeos/genética , Plastídeos/fisiologia , Temperatura , Archaea/metabolismo , Proteínas Arqueais/genética , Bactérias/metabolismo , Proteínas de Bactérias/genética , Técnicas de Cultura de Células , Proteínas de Cloroplastos/genética , Evolução Molecular , Genoma Arqueal , Genoma Bacteriano , Genomas de Plastídeos , Modelos Lineares , Plastídeos/metabolismo
18.
Sci Rep ; 10(1): 2720, 2020 02 17.
Artigo em Inglês | MEDLINE | ID: mdl-32066766

RESUMO

The study of intracellular gene transfer may allow for the detection of interesting evolutionary processes such as ancient polyploidization. We compared 24 plastid genomes (plastomes) from tribe Delphinieae, one from tribe Nigelleae and one from tribe Ranunculeae, including five newly sequenced genomes. The functional transfers of the plastids rpl32 and rps16 to the nucleus in tribe Delphinieae were identified. Unexpectedly, we discovered multiple divergent copies of the nuclear-encoded plastid rpl32 in the genus Aconitum. Phylogenetic and synonymous substitution rate analyses revealed that the nuclear-encoded plastid rpl32 underwent two major duplication events. These ancient gene duplication events probably occurred via multiple polyploidization events in Aconitum between 11.9 and 24.7 Mya. Furthermore, our sequence rate analysis indicated that the eight plastid-encoded rpl subunits in Aconitum had a significantly accelerated evolutionary rate compared to those in other genera, suggesting that highly divergent paralogs targeted to the plastid may contribute to an elevated rate of evolution in plastid rpl genes. In addition, heteroplasmy of the plastid matK from two Aconitum species suggested the existence of potentially functional plastid maturases in its plastome. Our results provide insight into the evolutionary history of the tribe Delphinieae.


Assuntos
Aconitum/genética , Evolução Biológica , Delphinium/genética , Genomas de Plastídeos , Nigella/genética , Proteínas de Plantas/genética , Plastídeos/genética , Aconitum/classificação , Sequência de Bases , Núcleo Celular/genética , Delphinium/classificação , Endorribonucleases/genética , Duplicação Gênica , Genoma de Planta , Nigella/classificação , Nucleotidiltransferases/genética , Poliploidia , Proteínas Ribossômicas/genética , Alinhamento de Sequência , Homologia de Sequência do Ácido Nucleico
19.
Sci Rep ; 10(1): 2048, 2020 02 06.
Artigo em Inglês | MEDLINE | ID: mdl-32029782

RESUMO

Among the brown algal lineages, Ectocarpales species have isogamous fertilization in which male and female gametes are morphologically similar. In contrast, female gametes are much larger than male gametes in the oogamous species found in many other brown algal lineages. It has been reported that the plastids of isogamous species are biparentally inherited whereas the plastids of oogamous species are maternally inherited. In contrast, in both isogamous and oogamous species, the mitochondria are usually inherited maternally. To investigate whether there is any relationship between the modes of inheritance and organellar genome architecture, we sequenced six plastid genomes (ptDNA) and two mitochondrial genomes (mtDNA) of isogamous species from the Ectocarpales and compared them with previously sequenced organellar genomes. We found that the biparentally inherited ptDNAs of isogamous species presented distinctive structural rearrangements whereas maternally inherited ptDNAs of oogamous species showed no rearrangements. Our analysis permits the hypothesis that structural rearrangements in ptDNAs may be a consequence of the mode of inheritance.


Assuntos
Genoma Mitocondrial , Genomas de Plastídeos , Padrões de Herança , Feófitas/genética , DNA Mitocondrial/genética , Evolução Molecular , Rearranjo Gênico , Genômica , Plastídeos/genética , Análise de Sequência de DNA
20.
PLoS One ; 15(1): e0227991, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31990943

RESUMO

This study reports complete plastome sequences for six species of Neotropical Cranichideae and focuses on identification of the most variable regions (hotspots) in this group of orchids. These structure of these six plastomes is relatively conserved, exhibiting lengths ranging between 142,599 to 154,562 bp with 36.7% GC on average and exhibiting typical quadripartite arrangement (LSC, SSC and two IRs). Variation detected in the LSC/IR and SSC/IR junctions is explained by the loss of ndhF and ycf1 length variation. For the two genera of epiphytic clade in Spiranthinae, almost whole sets of the ndh-gene family were missing. Eight mutation hotspots were identified based on nucleotide diversity, sequence variability and parsimony-informative sites. Three of them (rps16-trnQ, trnT-trnL, rpl32-trnL) seem to be universal hotspots in the family, and the other five (trnG-trnR, trnR-atpA, trnP-psaJ, rpl32-infA, and rps15-ycf1) are described for the first time as orchid molecular hotspots. These regions have much more variation than all those used previously in phylogenetics of the group and offer useful plastid markers for phylogenetic, barcoding and population genetic studies. The use of whole plastomes or exclusive no-gap matrices also positioned with high support the holomycotrophic Rhizanthella among Orchidoideae plastomes in model-based analyses, showing the utility of plastomes for phylogenetic placement of this unusual genus.


Assuntos
Regulação da Expressão Gênica de Plantas , Variação Genética , Genoma , Orchidaceae/genética , Filogenia , Plastídeos/genética , Composição de Bases , Brasil , Mapeamento Cromossômico , Código de Barras de DNA Taxonômico/métodos , Ontologia Genética , Anotação de Sequência Molecular , NADH Desidrogenase/genética , NADH Desidrogenase/metabolismo , Orchidaceae/classificação , Orchidaceae/metabolismo , Folhas de Planta/genética , Folhas de Planta/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo
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