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1.
Ying Yong Sheng Tai Xue Bao ; 32(9): 3167-3176, 2021 Sep.
Artigo em Chinês | MEDLINE | ID: mdl-34658202

RESUMO

Niche shift between polyploid and diploid plants is an important requirement for the success of polyploid. Diploid, tetraploid, and hexaploid of kiwifruit distribute in different areas. Whether there is obvious niche differentiation and the major environmental factors which could influence the ecological niche of different ploidy kiwifruits are still unknown. Based on the natural distribution information collected from literature and by field works, the maximum entropy model (MaxEnt) was used to predict the potentially suitable ranges and the major climatic factors affecting distribution of different ploidy kiwifruits. Niche divergence between different ploidy kiwifruits was quantified by niche identity test. The results showed that there were obvious differences in the potential suitable areas of different ploidy kiwifruits. Diploid occurred in lower altitude Hunan foothills. Tetraploid nearly overlapped with diploid but tended to northern Guizhou and eastern Chongqing. Hexaploid were centered in Guizhou Plateau, northwestern Hunan, southwestern Hubei and southern Shanxi. Hexaploid kiwifruits preferred higher altitudes and latitudes. In addition, the hexaploid had wider highly suitable areas. Results of niche identity test showed overlapped niches between diploid and tetraploid, and different niches between diploid/tetraploid and hexaploid kiwifruits. Minimum temperature of the coldest month (Bio6) and precipitation of the driest month (Bio14) were key environmental factors driving the niche shift of ploidy kiwifruits. Polyploid kiwifruits could maintain a higher probability of existence under lower Bio6 and Bio14, which indicated more extreme niche in cold and arid mountains for polyploids.


Assuntos
Actinidia , Diploide , Actinidia/genética , Ecossistema , Plantas , Poliploidia
2.
Cells ; 10(10)2021 09 24.
Artigo em Inglês | MEDLINE | ID: mdl-34685505

RESUMO

The objective of this review is to describe the evolution of lung tissue-derived diploid progenitor cell applications, ranging from historical biotechnological substrate functions for vaccine production and testing to current investigations around potential therapeutic use in respiratory tract regenerative medicine. Such cell types (e.g., MRC-5 or WI-38 sources) were extensively studied since the 1960s and have been continuously used over five decades as safe and sustainable industrial vaccine substrates. Recent research and development efforts around diploid progenitor lung cells (e.g., FE002-Lu or Walvax-2 sources) consist in qualification for potential use as optimal and renewed vaccine production substrates and, alternatively, for potential therapeutic applications in respiratory tract regenerative medicine. Potentially effective, safe, and sustainable cell therapy approaches for the management of inflammatory lung diseases or affections and related symptoms (e.g., COVID-19 patients and burn patient severe inhalation syndrome) using local homologous allogeneic cell-based or cell-derived product administrations are considered. Overall, lung tissue-derived progenitor cells isolated and produced under good manufacturing practices (GMP) may be used with high versatility. They can either act as key industrial platforms optimally conforming to specific pharmacopoeial requirements or as active pharmaceutical ingredients (API) for potentially effective promotion of lung tissue repair or regeneration.


Assuntos
Biotecnologia/métodos , Diploide , Pulmão/citologia , Medicina Regenerativa/métodos , Infecções Respiratórias/terapia , Animais , Bancos de Espécimes Biológicos , Vacinas contra COVID-19 , Linhagem Celular , Terapia Baseada em Transplante de Células e Tecidos , História do Século XX , História do Século XXI , Humanos , Pulmão/fisiologia , Regeneração , Medicina Regenerativa/história , SARS-CoV-2 , Transplante de Células-Tronco , Células-Tronco/citologia , Transplante Homólogo
3.
An Acad Bras Cienc ; 93(4): e20201650, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34586322

RESUMO

Taxonomic and cytogenetic aspects of Proceratophrys have not been thoroughly clarified in the literature; thus, the objective of the present study was to provide unprecedent karyotype data regarding P. schirchi, P. laticeps and P. melanopogon. Additionally, the karyotype of P. boiei (2n = 22) and its ZZ / ZW sex chromosome system was analyzed for different populations of southeastern and southern Brazil. All Proceratophrys species have a diploid number of 2n = 22 chromosomes. In P. schirchi, a strong C-band was found in the long arm in one of the homologues of the pair 8 in female metaphasic cells, denoting that this chromosome pair could represent the heteromorphic sex chromosome in a ZZ / ZW sex system. Despite the conserved number of chromosomes, there are considerable chromosomal differences in P. melanopogon and P. boiei (southern Brazil), strongly differentiating them cytogenetically from other species of the genus. Moreover, with the confirmation of chromosomal heteromorphism related to sexual differentiation in P. boiei and the possible description of this system in P. schirchi, the Proceratophrys genus can be regarded as an interesting group for evolutionary studies and sex chromosome differentiation in anurans.


Assuntos
Anuros , Diploide , Animais , Anuros/genética , Citogenética , Feminino , Cariotipagem , Cromossomos Sexuais/genética
4.
Nat Commun ; 12(1): 5508, 2021 09 17.
Artigo em Inglês | MEDLINE | ID: mdl-34535649

RESUMO

Perilla is a young allotetraploid Lamiaceae species widely used in East Asia as herb and oil plant. Here, we report the high-quality, chromosome-scale genomes of the tetraploid (Perilla frutescens) and the AA diploid progenitor (Perilla citriodora). Comparative analyses suggest post Neolithic allotetraploidization within 10,000 years, and nucleotide mutation in tetraploid is 10% more than in diploid, both of which are dominated by G:C → A:T transitions. Incipient diploidization is characterized by balanced swaps of homeologous segments, and subsequent homeologous exchanges are enriched towards telomeres, with excess of replacements of AA genes by fractionated BB homeologs. Population analyses suggest that the crispa lines are close to the nascent tetraploid, and involvement of acyl-CoA: lysophosphatidylcholine acyltransferase gene for high α-linolenic acid content of seed oil is revealed by GWAS. These resources and findings provide insights into incipient diploidization and basis for breeding improvement of this medicinal plant.


Assuntos
Diploide , Perilla/genética , Plantas Medicinais/genética , Sequência de Bases , Evolução Biológica , Genes de Plantas , Genética Populacional , Genoma de Planta , Estudo de Associação Genômica Ampla , Nucleotídeos/genética , Pigmentação/genética , Folhas de Planta/genética , Poliploidia
5.
G3 (Bethesda) ; 11(10)2021 09 27.
Artigo em Inglês | MEDLINE | ID: mdl-34568923

RESUMO

Genetic diversity is the raw material for germplasm enhancement. Landraces and wild species relatives of potato, which contain a rich gene pool of valuable agronomic traits, can provide insights into the genetic diversity behind the adaptability of the common potato. The diploid plant, Solanum stenotomum (Sst), is believed to have an ancestral relationship with modern potato cultivars and be a potential source of resistance against disease. Sequencing of the Sst genome generated an assembly of 852.85 Mb (N50 scaffold size, 3.7 Mb). Pseudomolecule construction anchored 788.75 Mb of the assembly onto 12 pseudochromosomes, with an anchor rate of 92.4%. Genome annotation yielded 41,914 high-confidence protein-coding gene models and comparative analyses with closely related Solanaceae species identified 358 Sst-specific gene families, 885 gene families with expansion along the Sst lineage, and 149 genes experiencing accelerated rates of protein sequence evolution in Sst, the functions of which were mainly associated with defense responses, particularly against bacterial and fungal infection. Insights into the Sst genome and the genomic variation of cultivated potato taxa are valuable in elaborating the impact of potato evolution in early landrace diploid and facilitate modern potato breeding.


Assuntos
Solanum tuberosum , Solanum , Diploide , Genoma de Planta , Humanos , Melhoramento Vegetal , Solanum/genética , Solanum tuberosum/genética
6.
Elife ; 102021 09 15.
Artigo em Inglês | MEDLINE | ID: mdl-34523420

RESUMO

Although studies of Saccharomyces cerevisiae have provided many insights into mutagenesis and DNA repair, most of this work has focused on a few laboratory strains. Much less is known about the phenotypic effects of natural variation within S. cerevisiae's DNA repair pathways. Here, we use natural polymorphisms to detect historical mutation spectrum differences among several wild and domesticated S. cerevisiae strains. To determine whether these differences are likely caused by genetic mutation rate modifiers, we use a modified fluctuation assay with a CAN1 reporter to measure de novo mutation rates and spectra in 16 of the analyzed strains. We measure a 10-fold range of mutation rates and identify two strains with distinctive mutation spectra. These strains, known as AEQ and AAR, come from the panel's 'Mosaic beer' clade and share an enrichment for C > A mutations that is also observed in rare variation segregating throughout the genomes of several Mosaic beer and Mixed origin strains. Both AEQ and AAR are haploid derivatives of the diploid natural isolate CBS 1782, whose rare polymorphisms are enriched for C > A as well, suggesting that the underlying mutator allele is likely active in nature. We use a plasmid complementation test to show that AAR and AEQ share a mutator allele in the DNA repair gene OGG1, which excises 8-oxoguanine lesions that can cause C > A mutations if left unrepaired.


Assuntos
Variação Genética , Mutação Puntual , Saccharomyces cerevisiae/genética , Alelos , Sistemas de Transporte de Aminoácidos Básicos/genética , Reparo do DNA , Diploide , Teste de Complementação Genética , Haploidia , Taxa de Mutação , Fenótipo , Saccharomyces cerevisiae/classificação , Proteínas de Saccharomyces cerevisiae/genética
7.
An Acad Bras Cienc ; 93(suppl 3): e20201067, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34468489

RESUMO

The lowlands of mid-latitude South America comprise complex temperate ecoregions characterized by a unique biodiversity. However, the processes responsible for shaping its species diversity are still largely unknown. Turnera sidoides subsp. carnea is a variable subspecies occurring in the lowlands of northeastern Argentina and Uruguay, extending to southern Paraguay and Brazil. It constitutes a good model to perform evolutionary studies. Here we used an integrative approach to understand the process of diversification within this subspecies and to increase the knowledge concerning patterns and processes responsible for shaping the species diversity in the temperate lowlands of South America. The results provided strong evidences that this subspecies is an autopolyploid complex per se, being in an active process of intrasubspecific diversification. Morphological and genetic data show that the diversity of T. sidoides subsp. carnea is in congruence with the great past and present abiotic and biotic variability of the mid-latitude South American lowlands. The evolutionary history of this subspecies is consistent with past fragmentation and allopatric differentiation at diploid level. Geographic isolation and local adaptation would have promoted strong morphological, ecological, and genetic differentiation, resulting in two morphotypes and different genetic groups indicative of incipient speciation.


Assuntos
Turnera , Argentina , Biodiversidade , Brasil , Diploide , Filogenia , América do Sul
8.
Elife ; 102021 09 17.
Artigo em Inglês | MEDLINE | ID: mdl-34533136

RESUMO

Eukaryotic life cycles alternate between haploid and diploid phases and in phylogenetically diverse unicellular eukaryotes, expression of paralogous homeodomain genes in gametes primes the haploid-to-diploid transition. In the unicellular chlorophyte alga Chlamydomonas, KNOX and BELL TALE-homeodomain genes mediate this transition. We demonstrate that in the liverwort Marchantia polymorpha, paternal (sperm) expression of three of five phylogenetically diverse BELL genes, MpBELL234, and maternal (egg) expression of both MpKNOX1 and MpBELL34 mediate the haploid-to-diploid transition. Loss-of-function alleles of MpKNOX1 result in zygotic arrest, whereas a loss of either maternal or paternal MpBELL234 results in variable zygotic and early embryonic arrest. Expression of MpKNOX1 and MpBELL34 during diploid sporophyte development is consistent with a later role for these genes in patterning the sporophyte. These results indicate that the ancestral mechanism to activate diploid gene expression was retained in early diverging land plants and subsequently co-opted during evolution of the diploid sporophyte body.


Assuntos
Diploide , Células Germinativas Vegetais , Marchantia/genética , Genes de Plantas , Haploidia , Filogenia
9.
Elife ; 102021 09 28.
Artigo em Inglês | MEDLINE | ID: mdl-34579806

RESUMO

KNOX and BELL transcription factors regulate distinct steps of diploid development in plants. In the green alga Chlamydomonas reinhardtii, KNOX and BELL proteins are inherited by gametes of the opposite mating types and heterodimerize in zygotes to activate diploid development. By contrast, in land plants such as Physcomitrium patens and Arabidopsis thaliana, KNOX and BELL proteins function in meristem maintenance and organogenesis during the later stages of diploid development. However, whether the contrasting functions of KNOX and BELL were acquired independently in algae and land plants is currently unknown. Here, we show that in the basal land plant species Marchantia polymorpha, gamete-expressed KNOX and BELL are required to initiate zygotic development by promoting nuclear fusion in a manner strikingly similar to that in C. reinhardtii. Our results indicate that zygote activation is the ancestral role of KNOX/BELL transcription factors, which shifted toward meristem maintenance as land plants evolved.


Assuntos
Evolução Biológica , Células Germinativas/fisiologia , Plantas/metabolismo , Fatores de Transcrição/metabolismo , Diploide
10.
Cells ; 10(9)2021 09 07.
Artigo em Inglês | MEDLINE | ID: mdl-34571992

RESUMO

The widely distributed ray-finned fish genus Carassius is very well known due to its unique biological characteristics such as polyploidy, clonality, and/or interspecies hybridization. These biological characteristics have enabled Carassius species to be successfully widespread over relatively short period of evolutionary time. Therefore, this fish model deserves to be the center of attention in the research field. Some studies have already described the Carassius karyotype, but results are inconsistent in the number of morphological categories for individual chromosomes. We investigated three focal species: Carassius auratus, C. carassius and C. gibelio with the aim to describe their standardized diploid karyotypes, and to study their evolutionary relationships using cytogenetic tools. We measured length (q+plength) of each chromosome and calculated centromeric index (i value). We found: (i) The relationship between q+plength and i value showed higher similarity of C. auratus and C. carassius. (ii) The variability of i value within each chromosome expressed by means of the first quartile (Q1) up to the third quartile (Q3) showed higher similarity of C. carassius and C. gibelio. (iii) The fluorescent in situ hybridization (FISH) analysis revealed higher similarity of C. auratus and C. gibelio. (iv) Standardized karyotype formula described using median value (Q2) showed differentiation among all investigated species: C. auratus had 24 metacentric (m), 40 submetacentric (sm), 2 subtelocentric (st), 2 acrocentric (a) and 32 telocentric (T) chromosomes (24m+40sm+2st+2a+32T); C. carassius: 16m+34sm+8st+42T; and C. gibelio: 16m+22sm+10st+2a+50T. (v) We developed R scripts applicable for the description of standardized karyotype for any other species. The diverse results indicated unprecedented complex genomic and chromosomal architecture in the genus Carassius probably influenced by its unique biological characteristics which make the study of evolutionary relationships more difficult than it has been originally postulated.


Assuntos
Carpas/genética , Carpa Dourada/genética , Animais , Mapeamento Cromossômico/métodos , Cromossomos/genética , Diploide , Feminino , Peixes/genética , Variação Genética/genética , Genoma/genética , Hibridização in Situ Fluorescente/métodos , Cariótipo , Cariotipagem/métodos , Masculino , Filogenia , Poliploidia
11.
Proc Biol Sci ; 288(1958): 20211127, 2021 09 08.
Artigo em Inglês | MEDLINE | ID: mdl-34493080

RESUMO

Inbreeding depression, that is the decrease in fitness of inbred relative to outbred individuals, was shown to increase strongly as life expectancy increases in plants. Because plants are thought to not have a separated germline, it was proposed that this pattern could be generated by somatic mutations accumulating during growth, since larger and more long-lived species have more opportunities for mutations to accumulate. A key determinant of the role of somatic mutations is the rate at which they occur, which probably differs between species because mutation rates may evolve differently in species with constrasting life histories. In this paper, I study the evolution of the mutation rates in plants, and consider the population-level consequences of inheritable somatic mutations given this evolution. I show that despite substantially lower somatic and meiotic mutation rates, more long-lived species still tend to accumulate larger amounts of deleterious mutations because of the increased number of opportunities they have to acquire mutations during growth, leading to higher levels of inbreeding depression in these species. However, the magnitude of this increase depends strongly on how mutagenic meiosis is relative to growth, to the point of being close to non-existent in some situations.


Assuntos
Depressão por Endogamia , Taxa de Mutação , Diploide , Mutação , Plantas/genética
12.
Plant Physiol Biochem ; 167: 366-375, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34404007

RESUMO

Polyploid plants often show improved resistance against many diseases, but whether they show increased resistance to grey mould, a devastating disease caused by Botrytis spp. fungi, is seldom reported. Stomata and reactive oxygen species (ROS) play dual roles in defence against grey mould, and it is unclear how their roles change after polyploidization. We addressed these questions in diploid and colchicine-induced Lilium rosthornii after B. elliptica infection. Tetraploids were less susceptible to grey mould, with lower morality rates in naturally infected plants. Before the stomata closed in artificially infected leaves, tetraploids, with larger stomatal apertures, were more easily invaded by the pathogen than diploids. However, the lesion area increased more slowly in tetraploids than in diploids, which may be explained by three causes based on histological and physiological characteristics. First, the pathogen required more time to penetrate the epidermis and closed stomata in tetraploids than in diploids. Second, the pathogen penetrated the reopened stomata more easily than the epidermis, and stomatal density was lower in tetraploids than in diploids. Third, tetraploids showed faster ROS accumulation, a more effective ROS-scavenging system and less malondialdehyde (MDA) accumulation than diploids. Stomatal starch and abnormal guard cell nuclei were present in the infected leaves. This phenomenon may be caused by oxalic acid, a pathogenic factor for many pathogens that promotes stomatal starch degradation and stomatal reopening in Sclerotinia spp., a pathogen closely related to Botrytis spp. This suggestion was primarily confirmed by immersing healthy leaves in oxalic acid solution.


Assuntos
Botrytis , Lilium , Diploide , Lilium/genética , Estômatos de Plantas , Espécies Reativas de Oxigênio , Tetraploidia
13.
Plant Physiol Biochem ; 167: 385-389, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34404009

RESUMO

Lippia alba (Mill.) N.E. Brown (Verbenaceae), popularly known as "lemon balm" or "bushy matgrass", is widely used in folk medicine due to its anti-inflammatory, antispasmodic, analgesic, and digestive properties. It was described as an autopolyploid complex with five cytotypes (2n = 30, 38, 45, 60 and 90). To enhance our understanding of the biological variation of the species, we investigated, comparatively, the proteomic profile of all ploidal levels (diploid, aneuploid, triploid, tetraploid, and hexaploid). Leaf proteins were extracted with subsequent separation by two-dimensional electrophoresis, spot analysis, and protein identification by mass spectrometry. By comparing the proteomic profile of diploid accession to the profile of the other ploidal levels we identified differential expression between the analysed spots. We identified 34 proteins with differential expression between the ploidal levels in comparison with the diploid. The identified proteins seem to play relevant roles in the primary metabolism of L. alba suggesting that a specific set of proteins was selected during the polyploidization process, being the triploid the most different one. Given that protein composition can substantially affect the desired therapeutic effect, we posit that further combination of proteomic and metabolomic studies may help to unravel genetic variations and phenotypic profiles in L. alba.


Assuntos
Lippia , Diploide , Poliploidia , Proteínas , Proteômica
14.
Sci Rep ; 11(1): 15592, 2021 08 02.
Artigo em Inglês | MEDLINE | ID: mdl-34341414

RESUMO

A near-complete diploid nuclear genome and accompanying circular mitochondrial and chloroplast genomes have been assembled from the elite commercial diatom species Nitzschia inconspicua. The 50 Mbp haploid size of the nuclear genome is nearly double that of model diatom Phaeodactylum tricornutum, but 30% smaller than closer relative Fragilariopsis cylindrus. Diploid assembly, which was facilitated by low levels of allelic heterozygosity (2.7%), included 14 candidate chromosome pairs composed of long, syntenic contigs, covering 93% of the total assembly. Telomeric ends were capped with an unusual 12-mer, G-rich, degenerate repeat sequence. Predicted proteins were highly enriched in strain-specific marker domains associated with cell-surface adhesion, biofilm formation, and raphe system gliding motility. Expanded species-specific families of carbonic anhydrases suggest potential enhancement of carbon concentration efficiency, and duplicated glycolysis and fatty acid synthesis pathways across cytosolic and organellar compartments may enhance peak metabolic output, contributing to competitive success over other organisms in mixed cultures. The N. inconspicua genome delivers a robust new reference for future functional and transcriptomic studies to illuminate the physiology of benthic pennate diatoms and harness their unique adaptations to support commercial algae biomass and bioproduct production.


Assuntos
Biomassa , Diatomáceas/genética , Diploide , Genoma , Anidrases Carbônicas/genética , Mapeamento de Sequências Contíguas , Diatomáceas/classificação , Tamanho do Genoma , Genoma de Cloroplastos , Genoma Mitocondrial , Fases de Leitura Aberta/genética , Filogenia , Sequências Repetitivas de Ácido Nucleico/genética , Análise de Sequência de DNA , Sintenia/genética
15.
J Mol Evol ; 89(8): 554-564, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34341836

RESUMO

Gene duplication is a fundamental process that has the potential to drive phenotypic differences between populations and species. While evolutionarily neutral changes have the potential to affect phenotypes, detecting selection acting on gene duplicates can uncover cases of adaptive diversification. Existing methods to detect selection on duplicates work mostly inter-specifically and are based upon selection on coding sequence changes, here we present a method to detect selection directly on a copy number variant segregating in a population. The method relies upon expected relationships between allele (new duplication) age and frequency in the population dependent upon the effective population size. Using both a haploid and a diploid population with a Moran Model under several population sizes, the neutral baseline for copy number variants is established. The ability of the method to reject neutrality for duplicates with known age (measured in pairwise dS value) and frequency in the population is established through mathematical analysis and through simulations. Power is particularly good in the diploid case and with larger effective population sizes, as expected. With extension of this method to larger population sizes, this is a tool to analyze selection on copy number variants in any natural or experimentally evolving population. We have made an R package available at https://github.com/peterbchi/CNVSelectR/ which implements the method introduced here.


Assuntos
Diploide , Duplicação Gênica , Alelos , Fenótipo , Seleção Genética
16.
Int J Mol Sci ; 22(16)2021 Aug 12.
Artigo em Inglês | MEDLINE | ID: mdl-34445371

RESUMO

The lizards of the species-rich clade Scincoidea including cordylids, gerrhosaurids, skinks, and xantusiids, show an almost cosmopolitan geographical distribution and a remarkable ecological and morphological divergence. However, previous studies revealed limited variability in cytogenetic traits. The sex determination mode was revealed only in a handful of gerrhosaurid, skink, and xantusiid species, which demonstrated either ZZ/ZW or XX/XY sex chromosomes. In this study, we explored the karyotypes of six species of skinks, two species of cordylids, and one gerrhosaurid. We applied conventional and molecular cytogenetic methods, including C-banding, fluorescence in situ hybridization with probes specific for telomeric motifs and rDNA loci, and comparative genomic hybridization. The diploid chromosome numbers are rather conserved among these species, but the chromosome morphology, the presence of interstitial telomeric sequences, and the topology of rDNA loci vary significantly. Notably, XX/XY sex chromosomes were identified only in Tiliqua scincoides, where, in contrast to the X chromosome, the Y chromosome lacks accumulations of rDNA loci. We confirm that within the lizards of the scincoidean clade, sex chromosomes remained in a generally poor stage of differentiation.


Assuntos
Análise Citogenética/métodos , Lagartos/classificação , Cromossomos Sexuais/genética , Animais , Hibridização Genômica Comparativa , DNA Ribossômico/genética , Diploide , Evolução Molecular , Feminino , Hibridização in Situ Fluorescente , Cariotipagem , Lagartos/genética , Masculino , Processos de Determinação Sexual
17.
Planta ; 254(3): 62, 2021 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-34459999

RESUMO

MAIN CONCLUSION: Majority of differentially expressed miRNAs with functional attributes have been recruited independently and parallelly during allopolyploidy followed by the millennia of human selection of both domesticated G. hirsutum and G. barbadense. The genus Gossypium is a marvelous evolutionary model for studying allopolyploidy and morpho-evolution of long-spinnable fibers from the ancestral wild-fuzz. Many genes, transcription factors, and notably, the regulatory miRNAs essentially govern such remarkable modern fiber phenotypes. To comprehend the impact of allopolyploidy on the evolutionary selection of transcriptional dynamicity of key miRNAs, comparative transcriptome profiling of vegetative and fiber tissues of domesticated diploid G. arboreum (A2) and allopolyploid cotton species G. hirsutum (AD1), and G. barbadense (AD2) identified > 300 differentially expressed miRNAs (DEmiRs) within or between corresponding tissues of A2, AD1 and AD2 species. Up to 49% and 32% DEmiRs were up- and down-regulated at fiber initiation stage of AD1 and AD2 species, respectively, whereas 50% and 18% DEmiRs were up- and down-regulated at fiber elongation stage of both the allopolyploid species. Interestingly, A-subgenome-specific DEmiRs exhibit expression dominance in the allopolyploid genetic backgrounds. Comparative spatio-temporal expression analyses of AD1 and AD2 species discovered that a majority of DEmiRs were recruited independently under millennia of human selection during domestication. Functional annotations of these DEmiRs revealed selection of associated molecular functions such as hormone-signaling, calcium-signaling and reactive oxygen species (ROS) signaling during fiber initiation and elongation. To validate the functional attributes of annotated DEmiRs, we demonstrated for the first time that the target-mimicry-based constitutive diminution of auxin-signaling associated miR167 directly affected the differentiation of floral and fiber tissues of transgenic cotton. These results strongly suggested that the evolutionarily favored DEmiRs including miR167 were involved in the transcriptional regulation of numerous genes during cotton evolution for enhanced fiber-associated agronomic traits.


Assuntos
Gossypium , MicroRNAs , Fibra de Algodão , Diploide , Domesticação , Regulação da Expressão Gênica de Plantas , Gossypium/genética , MicroRNAs/genética
18.
Nat Ecol Evol ; 5(10): 1367-1381, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34413506

RESUMO

Most diploid organisms have polyploid ancestors. The evolutionary process of polyploidization is poorly understood but has frequently been conjectured to involve some form of 'genome shock', such as genome reorganization and subgenome expression dominance. Here we study polyploidization in Arabidopsis suecica, a post-glacial allopolyploid species formed via hybridization of Arabidopsis thaliana and Arabidopsis arenosa. We generated a chromosome-level genome assembly of A. suecica and complemented it with polymorphism and transcriptome data from all species. Despite a divergence around 6 million years ago (Ma) between the ancestral species and differences in their genome composition, we see no evidence of a genome shock: the A. suecica genome is colinear with the ancestral genomes; there is no subgenome dominance in expression; and transposon dynamics appear stable. However, we find changes suggesting gradual adaptation to polyploidy. In particular, the A. thaliana subgenome shows upregulation of meiosis-related genes, possibly to prevent aneuploidy and undesirable homeologous exchanges that are observed in synthetic A. suecica, and the A. arenosa subgenome shows upregulation of cyto-nuclear processes, possibly in response to the new cytoplasmic environment of A. suecica, with plastids maternally inherited from A. thaliana. These changes are not seen in synthetic hybrids, and thus are likely to represent subsequent evolution.


Assuntos
Arabidopsis , Arabidopsis/genética , Diploide , Genoma de Planta , Humanos , Hibridização Genética , Poliploidia
19.
Heredity (Edinb) ; 127(3): 253-265, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34331028

RESUMO

Tuber dormancy and sprouting are commercially important potato traits as long-term tuber storage is necessary to ensure year-round availability. Premature dormancy release and sprout growth in tubers during storage can result in a significant deterioration in product quality. In addition, the main chemical sprout suppressant chlorpropham has been withdrawn in Europe, necessitating alternative approaches for controlling sprouting. Breeding potato cultivars with longer dormancy and slower sprout growth is a desirable goal, although this must be tempered by the needs of the seed potato industry, where dormancy break and sprout vigour are required for rapid emergence. We have performed a detailed genetic analysis of tuber sprout growth using a diploid potato population derived from two highly heterozygous parents. A dual approach employing conventional QTL analysis allied to a combined bulk-segregant analysis (BSA) using a novel potato whole-exome capture (WEC) platform was evaluated. Tubers were assessed for sprout growth in storage at six time-points over two consecutive growing seasons. Genetic analysis revealed the presence of main QTL on five chromosomes, several of which were consistent across two growing seasons. In addition, phenotypic bulks displaying extreme sprout growth phenotypes were subjected to WEC sequencing for performing BSA. The combined BSA and WEC approach corroborated QTL locations and served to narrow the associated genomic regions, while also identifying new QTL for further investigation. Overall, our findings reveal a very complex genetic architecture for tuber sprouting and sprout growth, which has implications both for potato and other root, bulb and tuber crops where long-term storage is essential.


Assuntos
Solanum tuberosum , Diploide , Exoma , Melhoramento Vegetal , Tubérculos/genética , Solanum tuberosum/genética
20.
J Phycol ; 57(5): 1648-1658, 2021 10.
Artigo em Inglês | MEDLINE | ID: mdl-34260752

RESUMO

In the life cycle of Neopyropia yezoensis, a potential model system for marine macroalgae, both asexual archeospores and meiosis-related conchospores develop into thalli (gametophyte). To understand this special life phenomenon in macroalgae, we picked out the two kinds of spores (10-30 cells in each sample) and conducted RNA-seq using Smart-seq2. Comparative analysis showed that light capture and carbon fixation associated differentially expressed genes (DEGs) were upregulated in archeospores, thus indicating that archeospores are in a state of rapid vegetative growth. In conchospores, protein synthesis and degradation, especially molecular chaperone, associated DEGs were up-regulated, indicating that complex life activities might be occurring in conchospores. There were 68 genes related to DNA replication and repair expressed in conchospores, showing that active DNA replication might occur in conchospores. Moreover, we found that one conchospore specifically expressed DEG (py04595: DNA helicase) only in diploid stages (conchocelis, sporangial filament) and three archeospores specifically expressed DEGs only in haploid stages (thalli). These molecular level results indicated that conchospores were closer to diploid, and might be the meiotic mother cells of N. yezoensis. In addition, we found that the knotted-like homeobox gene (PyKNOX), which might relate to the transition of gametophyte from sporophyte, was only expressed in sporophyte generation but not expressed in conchospores, archeospores and thalli, indicating the morphogenesis of gametophyte sin N. yezoensis might require the inactivation of PyKNOX.


Assuntos
Células Germinativas Vegetais , Alga Marinha , Diploide , Meiose , RNA-Seq
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