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1.
Mitochondrial DNA B Resour ; 8(6): 695-698, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37389153

RESUMO

Porella grandiloba Lindb. is a liverwort species of Porellaceae, primarily distributed in East Asia. Here, we determined the complete chloroplast (cp) genome sequence of P. grandiloba. The complete cp genome was 121,433 bp in length with a typical quadripartite structure consisting of a large single-copy region (83,039 bp), a small single-copy region (19,586 bp), and two copies of inverted repeat regions (9,404 bp, each). Genome annotation predicted 131 genes, including 84 protein-coding, 36 tRNA, and eight rRNA genes. The maximum likelihood tree indicated that P. grandiloba was sister to P. perrottetiana, which species formed a clade with Radula japonica (Radulaceae).

2.
ACS Appl Mater Interfaces ; 15(20): 24670-24680, 2023 May 24.
Artigo em Inglês | MEDLINE | ID: mdl-37159422

RESUMO

To realize efficient, green solvent-processable organic solar cells (OSCs), considerable effort has been expended on the development of conjugated materials with both superior optoelectrical properties and processability. However, molecular design strategies that enhance solubility often reduce crystalline/electrical properties of the materials. In this study, we develop three new guest small-molecule acceptors (SMAs) (Y-4C-4O, Y-6C-4O, and Y-12C-4O) featuring inner side chains consisting of terminal oligo(ethylene glycol) (OEG) groups and alkyl spacers of different lengths. When a host SMA (Y6) and guest SMA (Y-nC-4O) are mixed, favorable interactions between these materials lead to the formation of "alloy-like" composites. The alloy-like SMA composites enable sufficient processing in o-xylene to afford suitable blend-film morphologies. It is also found that the lengths of the alkyl spacers in guest SMAs have a significant impact on the performance of the o-xylene-processed OSCs. The PM6:Y6:Y-4C-4O blend achieves a maximum power conversion efficiency (PCE) of 17.03%, outperforming PM6:Y6:Y-6C-4O (PCE = 15.85%) and PM6:Y6:Y-12C-4O (PCE = 12.12%) OSCs. The high PCE of the PM6:Y6:Y-4C-4O device is mainly attributed to the well-intermixed morphology and superior crystalline/electrical properties, which result from the high compatibility of the Y6:Y-4C-4O composites with PM6. Thus, we demonstrate that an alloy-like SMA composite based on well-designed OEG-incorporated Y-series SMAs can afford green solvent-processable, high-performance OSCs.

3.
Mitochondrial DNA B Resour ; 8(3): 461-465, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37006955

RESUMO

Amsonia elliptica (Apocynaceae), endangered species in Korea, is a perennial herb that is economically important as traditional medicine and used as ornamentals. Natural populations of this species are facing extinction due to small population size and isolated distribution. Here, we report the complete chloroplast (cp) genome of A. elliptica using Illumina HiSeq sequencing and its phylogenetic position in subfamily Rauvolfioideae based on 20 Apocynaceae cp genomes. The cp genome of A. elliptica was 154,242 bp in length with a pair of inverted repeats of 25,711 bp, separated by large single-copy and small single-copy regions of 85,382 bp and 17,438 bp, respectively. Our phylogenomic analyses revealed that A. elliptica was closely related to Rhazya stricta in Rauvolfioideae (Apocynaceae).

4.
Int J Med Robot ; 18(5): e2415, 2022 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-35512295

RESUMO

BACKGROUND: The camera of an endoscope is fixed to the device, and the image rotates together with the endoscope. This can lead to visual confusion for the user and incorrect image reading. The problem also occurs with endoscopic robots. Using a master device with the same degrees of freedom as the endoscope to control an endoscopic robot causes visual-motor misorientation, making intuitive control difficult. METHODS: The roll misorientation between the image and master device handle was removed by measuring and correcting for the roll axis displacement of the master device. This enabled intuitive manipulation of the master device. The work speed and number of mistakes were experimentally measured with and without image correction. RESULTS: The tasks were completed significantly faster and more accurately with image orientation correction than without. CONCLUSIONS: The proposed method enables intuitive manipulation of the master device by correcting the image orientation in endoscopic robot control.


Assuntos
Robótica , Endoscópios , Endoscopia/métodos , Desenho de Equipamento , Humanos
5.
Plant Divers ; 44(2): 170-180, 2022 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-35505990

RESUMO

Endemic plants are important for understanding phylogenetic relationships, biogeographical history, and genetic variation because of their restricted distribution and their role in conserving biodiversity. Here, we investigated the phylogenetic relationships of the Korean endemic Fraxinus chiisanensis by reconstructing the molecular phylogeny of Fraxinus based on two nuclear DNA (nrITS and phantastica) and two chloroplast DNA (psbA-trnH and rpl32-trnL) regions. Within our fossil-calibrated phylogenetic framework, we also inferred the biogeographical history of F. chiisanensis. To provide a scientific basis for the conservation of F. chiisanensis, we determined the levels of genetic diversity and genetic differentiation in this species. Combining information from nuclear and chloroplast DNA sequence data, our molecular phylogenetic analyses identified F. chiisanensis as a genetically distinct unit from its sister group, Fraxinus platypoda from Japan. Our molecular dating analyses using nuclear and chloroplast DNA data sets show F. chiisanensis diverged from its sister F. platypoda in the Early or Middle Miocene and differentiated in the Late Miocene on the Korean Peninsula. Our results suggest that the divergence of F. chiisanensis was associated with the submergence of the East China Sea land bridge and enhanced monsoons in East Asia. When compared to F. platypoda, F. chiisanensis exhibits low genetic diversity within populations and high genetic differentiation among populations. These results help us to understand the evolutionary history of F. chiisanensis and to develop a conservation strategy for this species.

6.
Int J Med Robot ; 18(4): e2402, 2022 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-35384304

RESUMO

BACKGROUND: Commercialised laparoscopic surgical robotic systems require a large operating room and can only be used in large hospitals. If the robotic system is to be used in a small- or medium-sized hospital, the occupied volume must be reduced further. METHODS: In this paper, we propose a bed-mounted system that can be installed in a general operating room. Furthermore, we proposed a novel positioning arm suitable for a bed-mounted surgical robot system. RESULTS: The surgical possibility of the proposed bed-mounted system has been verified. Furthermore, the surgical possibility of the proposed system was confirmed using in vivo animal experiments. CONCLUSIONS: A bed-mounted laparoscopic robotic system and a novel positioning arm was proposed. The study's ultimate goal is to enable robotic surgery in small and medium-sized hospitals by introducing the proposed bed-mounted laparoscopic robot system, allowing many people to receive high-quality medical services.


Assuntos
Laparoscopia , Procedimentos Cirúrgicos Robóticos , Robótica , Animais , Braço , Humanos
7.
Int J Med Robot ; 18(3): e2397, 2022 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-35349215

RESUMO

BACKGROUND: Master devices exclusively used for endoscopes with position control are being developed as an isomorphic form of endoscopes. These master devices are difficult to intuitively operate because the movement direction of the endoscopic image and control handle do not match. METHODS: To solve this problem, a master device was developed. Its movement direction is compatible with that of the endoscopic image. It analyzes image movements according to flexible endoscopic ureteroscope movements for each degree of freedom. A driving testbed experiment was conducted that modelled the internal structure of a kidney. RESULTS: The time taken in the experiment was shorter when using the proposed master device than the existing isomorphic master device. The proposed device yielded fewer mistakes. CONCLUSIONS: It was confirmed the proposed device is effective in exclusive use for endoscopes because of its feasibility of position control and movement direction's coinciding with that of the endoscopic image.


Assuntos
Robótica , Endoscópios , Endoscopia/métodos , Desenho de Equipamento , Humanos
8.
Int J Med Robot ; 18(2): e2357, 2022 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-34962681

RESUMO

BACKGROUND: Control of the joints of robotic surgical instruments is difficult owing to hysteresis, and tendon twisting due to axial rotation of surgical tools also causes hysteresis. Therefore, a new mechanism is needed to prevent tendon twisting. METHODS: Tendon tension and hysteresis change were analysed by observing the movement of the joint depending on whether the tendons twisted for the same input signal. An anti-twist tendon mechanism to prevent twisting was developed. A 3-mm needle driver applied with the proposed mechanism was manufactured. RESULTS: The anti-twist mechanism makes no tension change because of twisting or friction between the tendon and the system, that is, the operating performance was the same regardless of rotation. CONCLUSION: The proposed mechanism has been verified and can be applied to small surgical instruments 3 mm in size. These findings can be applied in the development of instruments for precise surgeries such as microsurgery.


Assuntos
Procedimentos Cirúrgicos Robóticos , Robótica , Humanos , Rotação , Instrumentos Cirúrgicos , Tendões/cirurgia
9.
BMC Genomics ; 22(1): 231, 2021 Apr 02.
Artigo em Inglês | MEDLINE | ID: mdl-33794772

RESUMO

BACKGROUND: Commelinaceae (Commelinales) comprise 41 genera and are widely distributed in both the Old and New Worlds, except in Europe. The relationships among genera in this family have been suggested in several morphological and molecular studies. However, it is difficult to explain their relationships due to high morphological variations and low support values. Currently, many researchers have been using complete chloroplast genome data for inferring the evolution of land plants. In this study, we completed 15 new plastid genome sequences of subfamily Commelinoideae using the Mi-seq platform. We utilized genome data to reveal the structural variations and reconstruct the problematic positions of genera for the first time. RESULTS: All examined species of Commelinoideae have three pseudogenes (accD, rpoA, and ycf15), and the former two might be a synapomorphy within Commelinales. Only four species in tribe Commelineae presented IR expansion, which affected duplication of the rpl22 gene. We identified inversions that range from approximately 3 to 15 kb in four taxa (Amischotolype, Belosynapsis, Murdannia, and Streptolirion). The phylogenetic analysis using 77 chloroplast protein-coding genes with maximum parsimony, maximum likelihood, and Bayesian inference suggests that Palisota is most closely related to tribe Commelineae, supported by high support values. This result differs significantly from the current classification of Commelinaceae. Also, we resolved the unclear position of Streptoliriinae and the monophyly of Dichorisandrinae. Among the ten CDS (ndhH, rpoC2, ndhA, rps3, ndhG, ndhD, ccsA, ndhF, matK, and ycf1), which have high nucleotide diversity values (Pi > 0.045) and over 500 bp length, four CDS (ndhH, rpoC2, matK, and ycf1) show that they are congruent with the topology derived from 77 chloroplast protein-coding genes. CONCLUSIONS: In this study, we provide detailed information on the 15 complete plastid genomes of Commelinoideae taxa. We identified characteristic pseudogenes and nucleotide diversity, which can be used to infer the family evolutionary history. Also, further research is needed to revise the position of Palisota in the current classification of Commelinaceae.


Assuntos
Commelinaceae , Genoma de Cloroplastos , Teorema de Bayes , Europa (Continente) , Evolução Molecular , Filogenia
10.
PeerJ ; 9: e10687, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33520461

RESUMO

BACKGROUND: Carduus, commonly known as plumeless thistles, is a genus in the Asteraceae family that exhibits both medicinal value and invasive tendencies. However, the genomic data of Carduus (i.e., complete chloroplast genomes) have not been sequenced. METHODS: We sequenced and assembled the chloroplast genome (cpDNA) sequences of three Carduus species using the Illumina Miseq sequencing system and Geneious Prime. Phylogenetic relationships between Carduus and related taxa were reconstructed using Maximum Likelihood and Bayesian Inference analyses. In addition, we used a single nucleotide polymorphism (SNP) in the protein coding region of the matK gene to develop molecular markers to distinguish C. crispus from C. acanthoides and C. tenuiflorus. RESULTS: The cpDNA sequences of C. crispus, C. acanthoides, and C. tenuiflorus ranged from 152,342 bp to 152,617 bp in length. Comparative genomic analysis revealed high conservation in terms of gene content (including 80 protein-coding, 30 tRNA, and four rRNA genes) and gene order within the three focal species and members of subfamily Carduoideae. Despite their high similarity, the three species differed with respect to the number and content of repeats in the chloroplast genome. Additionally, eight hotspot regions, including psbI-trnS_GCU, trnE_UUC-rpoB, trnR_UCU-trnG_UCC, psbC-trnS_UGA, trnT_UGU-trnL_UAA, psbT-psbN, petD-rpoA, and rpl16-rps3, were identified in the study species. Phylogenetic analyses inferred from 78 protein-coding and non-coding regions indicated that Carduus is polyphyletic, suggesting the need for additional studies to reconstruct relationships between thistles and related taxa. Based on a SNP in matK, we successfully developed a molecular marker and protocol for distinguishing C. crispus from the other two focal species. Our study provides preliminary chloroplast genome data for further studies on plastid genome evolution, phylogeny, and development of species-level markers in Carduus.

11.
Sci Rep ; 11(1): 3262, 2021 02 05.
Artigo em Inglês | MEDLINE | ID: mdl-33547390

RESUMO

Allioideae includes economically important bulb crops such as garlic, onion, leeks, and some ornamental plants in Amaryllidaceae. Here, we reported the complete chloroplast genome (cpDNA) sequences of 17 species of Allioideae, five of Amaryllidoideae, and one of Agapanthoideae. These cpDNA sequences represent 80 protein-coding, 30 tRNA, and four rRNA genes, and range from 151,808 to 159,998 bp in length. Loss and pseudogenization of multiple genes (i.e., rps2, infA, and rpl22) appear to have occurred multiple times during the evolution of Alloideae. Additionally, eight mutation hotspots, including rps15-ycf1, rps16-trnQ-UUG, petG-trnW-CCA, psbA upstream, rpl32-trnL-UAG, ycf1, rpl22, matK, and ndhF, were identified in the studied Allium species. Additionally, we present the first phylogenomic analysis among the four tribes of Allioideae based on 74 cpDNA coding regions of 21 species of Allioideae, five species of Amaryllidoideae, one species of Agapanthoideae, and five species representing selected members of Asparagales. Our molecular phylogenomic results strongly support the monophyly of Allioideae, which is sister to Amaryllioideae. Within Allioideae, Tulbaghieae was sister to Gilliesieae-Leucocoryneae whereas Allieae was sister to the clade of Tulbaghieae- Gilliesieae-Leucocoryneae. Molecular dating analyses revealed the crown age of Allioideae in the Eocene (40.1 mya) followed by differentiation of Allieae in the early Miocene (21.3 mya). The split of Gilliesieae from Leucocoryneae was estimated at 16.5 mya. Biogeographic reconstruction suggests an African origin for Allioideae and subsequent spread to Eurasia during the middle Eocene. Cool and arid conditions during the late Eocene led to isolation between African and Eurasian species. African Allioideae may have diverged to South American taxa in the late Oligocene. Rather than vicariance, long-distance dispersal is the most likely explanation for intercontinental distribution of African and South American Allioideae species.


Assuntos
Amaryllidaceae/genética , Genoma de Cloroplastos , DNA de Plantas/genética , Evolução Molecular , Filogenia , RNA de Plantas/genética
12.
ACS Appl Mater Interfaces ; 12(50): 56240-56250, 2020 Dec 16.
Artigo em Inglês | MEDLINE | ID: mdl-33280373

RESUMO

The aggregation properties of conjugated polymers can play a crucial role in their thin film structures and performance of electronic devices. Control of these aggregated structures is particularly important in producing efficient all-polymer solar cells (all-PSCs), considering that strong demixing of the polymer donor and polymer acceptor typically occurs during film formation because of the low entropic contribution to the thermodynamics of the system. Here, three naphthalenediimide (NDI)-based polymer acceptors with different backbone chlorination patterns are developed to investigate the effect of the chlorination patterns on the aggregation tendencies of the polymer acceptors, which greatly influence their crystalline structures, electrical properties, and device performances of the resultant all-PSCs and organic field-effect transistors (OFETs). The counterparts of NDI units, dichlorinated bithiophene (Cl2T2), monochlorinated bithiophene (ClT2), and dichlorinated thienylene-vinylene-thienylene (Cl2TVT), are employed to synthesize a series of P(NDIOD-Cl2T2), P(NDIOD-ClT2), and P(NDIOD-Cl2TVT) polymers. The P(NDIOD-Cl2T2) polymer takes advantage of strong noncovalent bonding induced by its chlorine substituents, resulting in the formation of optimal face-on oriented crystalline structures which are suitable for efficient all-PSC devices. In comparison, the P(NDIOD-Cl2TVT) polymer forms bimodal crystalline structures in thin films to yield optimal performances in the resultant OFETs. When the three chlorinated polymers are applied to all-PSCs with the PBDTTTPD polymer donor, P(NDIOD-Cl2T2) achieves a maximum power conversion efficiency (PCE) of 7.22% with an appropriate blend morphology and high fill factor, outperforming P(NDIOD-ClT2) (PCE = 4.80%) and P(NDIOD-Cl2TVT) (PCE = 5.78%). Our observations highlight the effectiveness of the chlorination strategy for developing efficient polymer acceptors and demonstrate the important role of polymer aggregation in modulating the blend morphology and all-PSC performance.

13.
ACS Nano ; 14(11): 14493-14527, 2020 Nov 24.
Artigo em Inglês | MEDLINE | ID: mdl-33103903

RESUMO

Despite the recent breakthroughs of polymer solar cells (PSCs) exhibiting a power conversion efficiency of over 17%, toxic and hazardous organic solvents such as chloroform and chlorobenzene are still commonly used in their fabrication, which impedes the practical application of PSCs. Thus, the development of eco-friendly processing methods suitable for industrial-scale production is now considered an imperative research focus. This Review provides a roadmap for the design of efficient photoactive materials that are compatible with non-halogenated green solvents (e.g., xylenes, toluene, and tetrahydrofuran). We summarize the recent development of green processing solvents and the processing methods to match with the efficient photoactive materials used in non-fullerene solar cells. We further review progress in the use of more eco-friendly solvents (i.e., water or alcohol) for achieving truly sustainable and eco-friendly PSC fabrication. For example, the concept of water- or alcohol-dispersed nanoparticles made of conjugated materials is introduced. Also, recent important progress and strategies to develop water/alcohol-soluble photoactive materials that completely eliminate the use of conventional toxic solvents are discussed. Finally, we provide our perspectives on the challenges facing the current green processing methods and materials, such as large-area coating techniques and long-term stability. We believe this Review will inform the development of PSCs that are truly clean and renewable energy sources.

14.
Mol Phylogenet Evol ; 148: 106818, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32294543

RESUMO

The families of the monocot order Liliales exhibit highly contrasting characteristic of photosynthetic and mycoheterotrophic life histories. Although previous phylogenetic and morphological studies of Liliales have been conducted, they have not examined molecular evolution associated with this contrasting phenomenon. Here, we conduct the first comparative plastome study of all ten families of Liliales using 29 newly sequenced plastid genomes analyzed together with previously published data. We also present a phylogenetic analysis for Liliales of 78 plastid genes combined with 22 genes from all three genomes (nuclear 18S rDNA and phyC; 17 plastid genes; and mitochondrial matR, atpA, and cob). Within the newly generated phylogenetic tree of Liliales, we evaluate the ancestral state changes of selected morphological traits in the order. There are no significant differences in plastid genome features among species that show divergent characteristics correlated with family circumscriptions. However, the results clearly differentiate between photosynthetic and mycoheterotrophic taxa of Liliales in terms of genome structure, and gene content and order. The newly sequenced plastid genomes and combined three-genome data revealed Smilacaceae as sister to Liliaceae instead of Philesiaceae and Ripogonaceae. Additionally, we propose a revised familial classification system of Liliales that consists of nine families, considering Ripogonaceae a synonym of Philesiaceae. The ancestral state reconstruction indicated synapomorphies for each family of Liliales, except Liliaceae, Melanthiaceae and Colchicaceae. A taxonomic key for all nine families of Liliales is also provided.


Assuntos
Evolução Molecular , Genomas de Plastídeos , Lilium/genética , Sequência de Bases , Teorema de Bayes , DNA de Cloroplastos/genética , Lilium/anatomia & histologia , Fases de Leitura Aberta/genética , Fotossíntese , Filogenia , Especificidade da Espécie
15.
Mitochondrial DNA B Resour ; 5(3): 3269-3271, 2020 Aug 31.
Artigo em Inglês | MEDLINE | ID: mdl-33458135

RESUMO

Habenaria cruciformis (Orchidaceae), endemic to South Korea, is a perennial herb and its local population sizes are declined because of the destruction caused by human activity and the invasion of exotic species in their habitats. Here, we report the complete chloroplast (cp) genome sequence of H. cruciformis, which will provide valuable information for its biological conservation and future studies for the cp genome evolution of endemic plants on the Korean Peninsula. The cp genome of H. cruciformis is 155,708 bp in length, containing a large single-copy region of 85,131 bp and a small single-copy region of 17,659 bp which are separated by a pair of inverted repeats of 26,459 bp. The H. cruciformis cp genome encodes 131 genes, of which 113 are unique, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. The overall GC content is 36.6%, which is consistent with the Habenaria species previously reported. Our phylogenomic analyses identified the sister relationship between H. cruciformis and H. linearfolia in the genus.

16.
Front Plant Sci ; 10: 396, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31019522

RESUMO

Intercontinental floristic disjunction between East Asia and North America in the Northern Hemisphere has received much attention during the past decades, but few studies have focused on the family level. Melanthiaceae, containing 196 species and 17 genera circumscribed in five tribes, is disjunctly distributed in Eurasia and North America. It is one of the foremost models for studying the evolution of biogeographic patterns in this region. Here, we present a fossil-calibrated, molecular phylogeny of Melanthiaceae based on two chloroplast DNA datasets: one dataset includes extensive sampling (94 species representing all 17 genera of Melanthiaceae) of four chloroplast DNA regions (atpB, rbcL, matK, and ndhF) and the other includes six species representing all tribes of the family for 78 coding genes of the chloroplast genome. Within this framework, we infer the historical biogeography of Melanthiaceae. Both datasets produce well-resolved phylogenies of Melanthiaceae showing the monophyly of the family and the relationships among the five tribes. Melanthieae is found to be sister to the rest of the tribes of the family and the remaining taxa are divided into two major clades consisting of the Chionographideae + Heloniadeae clade and the Parideae + Xerophylleae clade. The molecular dating and the ancestral area analyses suggest that Melanthiaceae most likely originated in North America with its crown group dated at 92.1 mya in the late Cretaceous. The favored ancestral areas at the crown lineages of tribes are also in North America. In the family, seven independent migrations into East Asia from North America are inferred to have occurred in the Oligocene and the Miocene-Pliocene via historical paleo-land bridge connections. Cooling trends during the Oligocene resulted in the present East Asia-North America disjunct distribution, while the warm period during the middle Miocene and habitat heterogeneity stimulated diversification in East Asia. Our study provides the phylogenetic and biogeographical history of the Melanthiaceae and adds an example of "out of North America" migration in the biogeographic history of the Northern Hemisphere.

17.
Genome Biol ; 19(1): 127, 2018 09 04.
Artigo em Inglês | MEDLINE | ID: mdl-30180884

RESUMO

BACKGROUND: Hybridization is an important evolutionary process that results in increased plant diversity. Flowering Prunus includes popular cherry species that are appreciated worldwide for their flowers. The ornamental characteristics were acquired both naturally and through artificially hybridizing species with heterozygous genomes. Therefore, the genome of hybrid flowering Prunus presents important challenges both in plant genomics and evolutionary biology. RESULTS: We use long reads to sequence and analyze the highly heterozygous genome of wild Prunus yedoensis. The genome assembly covers > 93% of the gene space; annotation identified 41,294 protein-coding genes. Comparative analysis of the genome with 16 accessions of six related taxa shows that 41% of the genes were assigned into the maternal or paternal state. This indicates that wild P. yedoensis is an F1 hybrid originating from a cross between maternal P. pendula f. ascendens and paternal P. jamasakura, and it can be clearly distinguished from its confusing taxon, Yoshino cherry. A focused analysis of the S-locus haplotypes of closely related taxa distributed in a sympatric natural habitat suggests that reduced restriction of inter-specific hybridization due to strong gametophytic self-incompatibility is likely to promote complex hybridization of wild Prunus species and the development of a hybrid swarm. CONCLUSIONS: We report the draft genome assembly of a natural hybrid Prunus species using long-read sequencing and sequence phasing. Based on a comprehensive comparative genome analysis with related taxa, it appears that cross-species hybridization in sympatric habitats is an ongoing process that facilitates the diversification of flowering Prunus.


Assuntos
Genoma de Planta , Hibridização Genética , Prunus/genética , Flores/genética , Frutas/genética , Expressão Gênica , Genes de Plantas , Genômica , Haplótipos , Prunus/metabolismo , Análise de Sequência de DNA , Simpatria
18.
Front Plant Sci ; 9: 99, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29459880

RESUMO

Tribe Forsythieae (Oleaceae), containing two genera (Abeliophyllum and Forsythia) and 13 species, is economically important plants used as ornamentals and in traditional medicine. This tribe species occur primarily in mountainous regions of Eurasia with the highest species diversity in East Asia. Here, we examine 11 complete chloroplast genome and nuclear cycloidea2 (cyc2) DNA sequences of 10 Forsythia species and Abeliophyllum distichum using Illumina platform to provide the phylogeny and biogeographic history of the tribe. The chloroplast genomes of the 11 Forsythieae species are highly conserved, except for a deletion of about 400 bp in the accD-psaI region detected only in Abeliophyllum. Within Forsythieae species, analysis of repetitive sequences revealed a total of 51 repeats comprising 26 forward repeats, 22 palindromic repeats, and 3 reverse repeats. Of those, 19 repeats were common and 32 were unique to one or more Forsythieae species. Our phylogenetic analyses supported the monophyly of Forsythia and its sister group is Abeliophyllum using the concatenated dataset of 78 chloroplast genes. Within Forsythia, Forsythia likiangensis and F. giraldiana were basal lineages followed by F. europaea; the three species are characterized by minutely serrate or entire leaf margins. The remaining species, which are distributed in East Asia, formed two major clades. One clade included F. ovata, F. velutina, and F. japonica; they are morphologically supported by broadly ovate leaves. Another clade of F. suspensa, F. saxatilis, F. viridissima, and F. koreana characterized by lanceolate leaves (except F. suspensa which have broad ovate leaves). Although cyc2 phylogeny is largely congruent to chloroplast genome phylogeny, we find the discordance between two phylogenies in the position of F. ovata suggesting that introgression of the chloroplast genome from one species into the nuclear background of another by interspecific hybridization in East Asian Forsythia species. Molecular dating and biogeographic reconstructions suggest an origin of the Forsythieae species in East China in the Miocene. Distribution patterns in Forsythia indicated that the species were radially differentiated from East China, and the speciation of the European F. europaea was the result of both vicariance and dispersal in the late Miocene to Pliocene.

19.
Am J Bot ; 104(6): 939-952, 2017 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-28634256

RESUMO

PREMISE OF THE STUDY: Understanding the underlying mechanisms for the evolution of intercontinental disjunct patterns has long fascinated botanists. We present a molecular phylogenetic reconstruction of Maianthemum s.l. (including Smilacina) with a focus on Maianthemum s.s. species, which have a disjunct distribution between Eurasia and North America. Within this evolutionary framework, we clarify the systematic classification and biogeographical history of Maianthemum s.s. METHOD: Data from two nuclear and five chloroplast DNA regions were analyzed using the programs PAUP*, RAxML, MrBayes, BEAST, and RASP. KEY RESULTS: Our molecular phylogeny supports Maianthemum s.s. as monophyletic. Maianthemum bifolium and M. canadense are grouped according to their taxonomic species, but the accessions of M. dilatatum are divided into two well-defined groups, i.e., one comprising western North American accessions, and the other composed of northeast Asian accessions. Molecular dating and biogeographic reconstructions suggest a northeast Asian origin for Maianthemum s.s. and that a complicated pattern of divergent evolution began approximately in the late Miocene. Intercontinental disjunctions of Maianthemum s.s. in the Northern Hemisphere appear to have occurred two times during the Pliocene. CONCLUSIONS: Based on our results, two possible ways to treat Maianthemum s.s. species can be envisioned: (1) elevate Asian populations of M. dilatatum to specific rank; or (2) combine the three Maianthemum s.s. species into a broadly defined single species. We recommend treatment of Maianthemum s.s. as a single species. The biogeographic patterns of Maianthemum s.s. coupled with molecular dating suggest both vicariance and long-distance dispersal events as key mechanisms for diversification of the clade.


Assuntos
Evolução Biológica , Maianthemum/classificação , Filogenia , DNA de Cloroplastos/genética , DNA de Plantas/genética , América do Norte , Análise de Sequência de DNA
20.
PLoS One ; 11(10): e0163581, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27783628

RESUMO

Mazus sunhangii, a new species of Mazaceae from central China is described and illustrated based on evidence from morphology and molecular phylogeny. This new species is morphologically similar to M. puchellus and M. omeiensis but differs in erect habit, inflorescence position, leaf pattern and corolla color. Phylogenetic analysis based on four chloroplast DNA regions (rbcL, rps16, trnL-F, and psbA-trnH) identified the new species as the independent lineage sister to the other East Asian Mazus species. The new species is known only from a single location in Mt. Shennongjia area in northwest Hubei province, at the elevation of 760 m. The species grows on the limestone cliff, and, because a tourist arterial highway is located along this cliff, its habitat can be easily disturbed or destroyed. We propose that the only known species location is recognized as critical habitat (i.e., as the habitat required to ensure the persistence of a species) and the species listed as Critically Endangered based on the International Union for Conservation of Nature Red List Categories and Criteria B2a.


Assuntos
Magnoliopsida/genética , China , Cloroplastos/genética , DNA de Cloroplastos/química , DNA de Cloroplastos/isolamento & purificação , DNA de Cloroplastos/metabolismo , Ecossistema , Espécies em Perigo de Extinção , Magnoliopsida/classificação , Filogenia , Folhas de Planta/genética , Análise de Sequência de DNA
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