scholarly journals Exploring the Phylogeography of Ancient Platycladus orientalis in China by Specific-Locus Amplified Fragment Sequencing

2019 ◽  
Vol 20 (16) ◽  
pp. 3871
Author(s):  
Ermei Chang ◽  
Yuxin Tian ◽  
Caiyun Wang ◽  
Nan Deng ◽  
Zeping Jiang ◽  
...  
Keyword(s):  
Genetic Resources ◽  
Phylogenetic Trees ◽  
De Novo ◽  
Climatic Factors ◽  
Geographical Location ◽  
Nucleotide Polymorphisms ◽  
Platycladus Orientalis ◽  
Sequencing Method ◽  
History Of ◽  
Specific Locus

Platycladus orientalis (i.e., Chinese thuja) is famous for its lifespan spanning hundreds, and even thousands, of years. Most ancient P. orientalis populations are widely distributed in China, with accessible historical records, making them valuable genetic resources. In this study, the distribution pattern of ancient P. orientalis in China was analyzed based on 13 bioclimatic factors. Additionally, a specific-locus amplified fragment (SLAF) sequencing method was applied to detect single nucleotide polymorphisms (SNPs) in the genomes of 100 accessions from 13 populations. The resulting data revealed that the suitable areas for the distribution of ancient P. orientalis populations were accurately predicted with four main climatic factors. A total of 81,722 SNPs were identified from 461,867 SLAFs for 100 individuals, with an average sequencing depth of 10.11-fold and a Q30 value of 82.75%. The pair-wise genetic distance and genetic differentiation of 13 populations indicated that the BT-T population exhibited the largest divergence from the other populations. A neighbor-joining phylogenetic tree suggested the relationship between many individuals was inconsistent with the geographical location, possibly indicative of a history of transplantation and cultivation. All individuals were clustered into nine genotypes according to a structural analysis and the relationships between individuals were clarified in phylogenetic trees. This study highlights the importance of the de novo genome sequencing of ancient P. orientalis and may provide the basis for the conservation of P. orientalis genetic resources, the identification of supergene families, and the evaluation of related genetic resources.

scholarly journals Investigation of Genetic Relationships within Miscanthus using SNP Markers Identified using SLAF-Seq

2021 ◽  
Author(s):  
ZHIYONG Chen ◽  
Yancen He ◽  
Yasir Iqbal ◽  
Yanlan Shi ◽  
Hongmei Huang ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Genetic Relationships ◽  
Female Parent ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Sequencing Method ◽  
Specific Locus

Abstract Background: Miscanthus, which is a leading dedicated-energy grass in Europe and in parts of Asia, is expected to play a key role in the development of the future bioeconomy. However, due to its complex genetic background, it is difficult to investigate phylogenetic relationships and the evolution of gene function in this genus. Here, we investigated 50 Miscanthus germplasms: 1 female parent (M. lutarioriparius), 30 candidate male parents (M. lutarioriparius, M. sinensis, and M. sacchariflorus), and 19 offspring. We used high-throughput Specific-Locus Amplified Fragment sequencing (SLAF-seq) to identify informative single nucleotide polymorphisms (SNPs) in all germplasms.Results: We identified 800,081 SLAF tags, of which 160,368 were polymorphic. Each tag was 264–364 bp long. The obtained SNPs were used to investigate genetic relationships within Miscanthus. We constructed a phylogenetic tree of the 50 germplasms using the obtained SNPs, and found that the germplasms fell into two clades: one clade of M. sinensis only and one clade that included the offspring, M. lutarioriparius, and M. sacchariflorus. Genetic cluster analysis indicated that M. lutarioriparius germplasm C3 was the most likely male parent of the offspring.Conclusions: As a high-throughput sequencing method, SLAF-seq can be used to identify informative SNPs in Miscanthus germplasms and to rapidly characterize genetic relationships within this genus. Our results will support the development of breeding programs utilizing Miscanthus cultivars with elite biomass- or fiber-production potential.

scholarly journals Fine-scale morphological, genomic, reproductive, and symbiont differences delimit the Caribbean octocorals Plexaura homomalla and P. kükenthali

Coral Reefs ◽  
2021 ◽  
Author(s):  
Jessie A. Pelosi ◽  
Moisés A. Bernal ◽  
Trevor J. Krabbenhoft ◽  
Samantha Galbo ◽  
Carlos Prada ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
De Novo ◽  
Nucleotide Polymorphisms ◽  
Marine Fauna ◽  
Single Nucleotide ◽  
Nuclear Introns ◽  
Multiple Sampling ◽  
History Of ◽  
The Caribbean ◽  
The Relationship

AbstractOctocorals are conspicuous members of coral reefs and deep-sea ecosystems. Yet, species boundaries and taxonomic relationships within this group remain poorly understood, hindering our understanding of this essential component of the marine fauna. We used a multifaceted approach to revisit the systematics of the Caribbean octocorals Plexaura homomalla and Plexaura kükenthali, two taxa that have a long history of taxonomic revisions. We integrated morphological and reproductive analyses with high-throughput sequencing technology to clarify the relationship between these common gorgonians. Although size and shape of the sclerites are significantly different, there is overlap in the distributions making identification based on sclerites alone difficult. Differences in reproductive timing and mode of larval development were detected, suggesting possible mechanisms of pre-zygotic isolation. Furthermore, there are substantial genetic differences and clear separation of the two species in nuclear introns and single-nucleotide polymorphisms obtained from de novo assembled transcriptomes. Despite these differences, analyses with SNPs suggest that hybridization is still possible between the two groups. The two nascent species also differed in their symbiont communities (genus Breviolum) across multiple sampling sites in the Caribbean. Despite a complicated history of taxonomic revisions, our results support the differentiation of P. homomalla and P. kükenthali, emphasizing that integrative approaches are essential for Anthozoan systematics.

scholarly journals Analysis of phylogenetic relationships and genome size evolution of the Amaranthus genus using GBS indicates the ancestors of an ancient crop

2016 ◽  
Author(s):  
Markus G. Stetter ◽  
Karl J Schmid
Keyword(s):  
Phylogenetic Trees ◽  
De Novo ◽  
Geographic Origin ◽  
Genotyping By Sequencing ◽  
South American ◽  
Amaranthus Hypochondriacus ◽  
Multispecies Coalescent ◽  
Genome Size Evolution ◽  
History Of ◽  
Weedy Species

AbstractThe genus Amaranthus consists of 50 to 70 species and harbors several cultivated and weedy species of great economic importance. A small number of suitable traits, phenotypic plasticity, gene flow and hybridization made it difficult to establish the taxonomy and phylogeny of the whole genus despite various studies using molecular markers. We inferred the phylogeny of the Amaranthus genus using genotyping by sequencing (GBS) of 94 genebank accessions representing 35 Amaranthus species and measured their genome sizes. SNPs were called by de novo and reference-based methods, for which we used the distant sugarbeet Beta vulgaris and the closely related Amaranthus hypochondriacus as references. SNP counts and proportions of missing data differed between methods, but the resulting phylogenetic trees were highly similar. A distance-based neighbor joing tree of individual accessions and a species tree calculated with the multispecies coalescent supported a previous taxonomic classification into three subgenera although the subgenus A. Acnida consists of two highly differentiated clades. The analysis of the Hybridus complex within the A. Amaranthus subgenus revealed insights on the history of cultivated grain amaranths. The complex includes the three cultivated grain amaranths and their wild relatives and was well separated from other species in the subgenus. Wild and cultivated amaranth accessions did not differentiate according to the species assignment but clustered by their geographic origin from South and Central America. Different geographically separated populations of Amaranthus hybridus appear to be the common ancestors of the three cultivated grain species and A. quitensis might be additionally be involved in the evolution of South American grain amaranth (A. caudatus). We also measured genome sizes of the species and observed little variation with the exception of two lineages that showed evidence for a recent polyploidization. With the exception of two lineages, genome sizes are quite similar and indicate that polyploidization did not play a major role in the history of the genus.

scholarly journals The evolutionary history of the current globalRamularia collo-cygniepidemic

2017 ◽  
Author(s):  
Remco Stam ◽  
Hind Sghyer ◽  
Martin Münsterkötter ◽  
Saurabh Pophaly ◽  
Aurélien Tellier ◽  
...  
Keyword(s):  
World Wide ◽  
De Novo ◽  
Geographical Location ◽  
Control Measures ◽  
Genomic Comparison ◽  
Ramularia Leaf Spot ◽  
The World ◽  
Genome Features ◽  
History Of ◽  
Species Specific

AbstractRamularia Leaf Spot (RLS) has emerged as a threat for barley production in many regions of the world. Late appearance of unspecific symptoms caused thatRamularia collo-cygnicould only by molecular diagnostics be detected as the causal agent of RLS. Although recent research has shed more light on the biology and genomics of the pathogen, the cause of the recent global spread remains unclear.To address urgent questions, especially on the emergence to a major disease, life-cycle, transmission, and quick adaptation to control measures, we de-novo sequenced the genome ofR. collo-cygni(urug2 isolate). Additionally, we sequenced fungal RNA from 6 different conditions, which allowed for an improved genome annotation. This resulted in a high quality draft assembly of about 32 Mb, with only 78 scaffolds with an N50 of 2.1 Mb. The overall annotation enabled the prediction of 12.346 high confidence genes. Genomic comparison revealed thatR. collo-cygnihas significantly diverged from relatedDothidiomycetes, including gain and loss of putative effectors, however without obtaining species-specific genome features.To evaluate the species-wide genetic diversity, we sequenced the genomes of 19R. collo-cygniisolates from multiple geographic locations and diverse hosts and mapped sequences to our reference genome. Admixture analyses show thatR. collo-cygniis world-wide genetically uniform and that samples do not show a strong clustering on either geographical location or host species. To date, the teleomorph ofR. collo-cygnihas not been observed. Analysis of linkage disequilibrium shows that in the world-wide sample set there are clear signals of recombination and thus sexual reproduction, however these signals largely disappear when excluding three outliers samples, suggesting that the main global expansion ofR. collo-cygnicomes from mixed or clonally propagating populations. We further analysed the historic population size (Ne) ofR. collo-cygniusing Bayesian simulations.We discuss how our genomic data and population genetics analysis can help understand the currentR. collo-cygniepidemic and provide different hypothesis that are supported by our data. We specifically highlight how recombination, clonal spreading and lack of host-specificity could further support global epidemics of this increasingly recognized plant disease and suggest specific approaches to combat this pathogen.

Transcriptome based genetic resources from Rabbiteye and Southern Highbush blueberries

2021 ◽  
pp. 1-13
Author(s):  
Chuyan Wang ◽  
Jie Yu ◽  
Jun Wang ◽  
Jigang Zhang ◽  
Liuqing Yang ◽  
...  
Keyword(s):  
Genetic Resources ◽  
De Novo ◽  
Present Report ◽  
Rapid Development ◽  
Homology Search ◽  
Nucleotide Polymorphisms ◽  
High Quality ◽  
Wide Range ◽  
Highbush Blueberries ◽  
Southern Highbush

BACKGROUND: Blueberry is among the fastest growing fruit crops in the world, which is beneficial to human health and attracts extensive interests. In contrast to its rapid development and utilization, availability of molecular and genetic resources for blueberries are still scarce. OBJECTIVE: In present report, transcriptomic profiling of four widely cultivated varieties of Rabbiteye and Southern Highbush blueberries were characterized to assist the breeding programs. METHODS: Both de novo and reference-based assembly were conducted to generate the genetic resources that can be used in the further functional and breeding studies. RESULTS: De novo and reference-based assembly found average 136,350 and 158,123 non-redundant transcripts, respectively. Average 57,668 de novo assembled transcripts can be functionally annotated by homology search with different databases. We further detected 6,268 polymorphic simple sequence repeats, 566,913 high-quality single nucleotide polymorphisms and 88,662 insertion and deletions among the four varieties with comparison to a recently released reference genome of blueberry. Differentially expressed genes analysis showed that varieties of same species show less differences within species but larger differences between species. CONCLUSIONS: These comprehensive and high-quality genetic resources will contribute to a wide range of genetics and molecular breeding studies in blueberries.

scholarly journals Investigation of genetic relationships within three Miscanthus species using SNP markers identified with SLAF-seq

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Zhiyong Chen ◽  
Yancen He ◽  
Yasir Iqbal ◽  
Yanlan Shi ◽  
Hongmei Huang ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Genetic Relationships ◽  
Female Parent ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Sequencing Method ◽  
Specific Locus

Abstract Background Miscanthus, which is a leading dedicated-energy grass in Europe and in parts of Asia, is expected to play a key role in the development of the future bioeconomy. However, due to its complex genetic background, it is difficult to investigate phylogenetic relationships in this genus. Here, we investigated 50 Miscanthus germplasms: 1 female parent (M. lutarioriparius), 30 candidate male parents (M. lutarioriparius, M. sinensis, and M. sacchariflorus), and 19 offspring. We used high-throughput Specific-Locus Amplified Fragment sequencing (SLAF-seq) to identify informative single nucleotide polymorphisms (SNPs) in all germplasms. Results We identified 257,889 SLAF tags, of which 87,162 were polymorphic. Each tag was 264–364 bp long. The obtained 724,773 population SNPs were used to investigate genetic relationships within three species of Miscanthus. We constructed a phylogenetic tree of the 50 germplasms using the obtained SNPs and grouped them into two clades: one clade comprised of M. sinensis alone and the other one included the offspring, M. lutarioriparius, and M. sacchariflorus. Genetic cluster analysis had revealed that M. lutarioriparius germplasm C3 was the most likely male parent of the offspring. Conclusions As a high-throughput sequencing method, SLAF-seq can be used to identify informative SNPs in Miscanthus germplasms and to rapidly characterize genetic relationships within this genus. Our results will support the development of breeding programs with the focus on utilizing Miscanthus cultivars with elite biomass- or fiber-production potential for the developing bioeconomy.

Parafia unicka w Rachaniach do 1811 roku/ The Uniate Parish in Rachanie until 1811

2012 ◽  
Vol 67 (2) ◽  
Author(s):  
Janusz Adam Frykowski
Keyword(s):  
Hierarchical Structure ◽  
Geographical Location ◽  
Historical Sources ◽  
Holy Communion ◽  
The Hierarchical Structure ◽  
History Of ◽  
The Church ◽  
Ancillary Equipment

AbstractThe following paper depicts the history of Saint Simeon Stylites Uniate Parish in Rachanie since it became known in historical sources until 1811- that is the time it ceased to be an independent church unit. The introduction of the article contains the geographical location of the parish, its size and the position within the hierarchical structure of the Church. Having analysed post-visit inspection protocols left by Chelm Bishops, the appearance as well as fittings and ancillary equipment of the church in Rachanie in that particular period are reported. Moreover, the list of 4 local clergymen is recreated and their benefice is determined. As far as possible, both the number of worshipers and the number of Holy Communion receivers is determined.

USTURSHANA IN EASTERN SOURCES

2019 ◽  
Vol 20 (2) ◽  
pp. 18-23
Author(s):  
Ziyodulla Xolboev ◽  
Keyword(s):  
Geographical Location ◽  
Medieval History ◽  
History Of

This article contains description of works which give information about the ancient and medieval history of Usturshana such as Chinese chronicles , Soghd documents from the Mugh hill and also Arabian historian-geographers' works. It provides valuable information on the historical geographical location of Usturshana and traditions of the population , the struggle for Arab invasion and the genealogy of Afshins

Liepājai – veltījuma dzejas / dziesmu piemēri mūsdienās un 19. gadsimta baltvācu literārajā mantojumā

2020 ◽  
pp. 26-34
Author(s):  
Ivars Orehovs
Keyword(s):  
Travel Literature ◽  
Geographical Location ◽  
Geographical Environment ◽  
Comparative Aspect ◽  
Literary Heritage ◽  
History Of ◽  
Native Place ◽  
History Of Literature ◽  
The 19Th Century ◽  
The Town

In a literary heritage with a developed tradition of genres, works whose main purpose is to attract the attention of readers to a selected geographical location, are of particular culture-historical and culture-geographical interest. The most widespread in this respect is travel literature, which is usually written by travellers and consist of impressions portrayed in prose after visits to foreign lands. Another type of literary depiction with an expressed poetic orientation, but a similar goal, is characteristic of dedicatory poetry. The author’s position is usually saturated with emotional expressiveness as well as the artistry of symbols, encouraging the reader or listener to feel the formation of a spontaneous attitude. It is possible to gain confidence in the engagement of the author of the poetry as an individual in the depicted cultural-geographical environment, which can be conceptually expressed by words or pairs of words ‘resident’, ‘native place’, ‘patriot’. With regard to the devotional depictions on the Latvian urban environment, one of the earliest examples known in the history of literature is the dedicatory poem in German by Christian Bornmann to the town Jelgava with its ancient name (Mitau, 1686/1802). The name of Liepāja town in this tradition of the genre has become an embodiment later – in the poetry selection in German, also using the ancient name of the town (Libausche Dichtungen, 1853), but in terms of contemporary literary practice with Imants Kalniņš’ music, there is a convincing dominance of songs with words of poetry. The aim of the article is, looking at the poetry devoted to Liepāja in the 19th century and at the turn of the 20th/21st century in the comparative aspect, to present textually thematic peculiarities as well as to provide the analytical interpretative summary of those.

scholarly journals R1352Q CACNA1A Variant in a Patient with Sporadic Hemiplegic Migraine, Ataxia, Seizures and Cerebral Oedema: A Case Report

2021 ◽  
pp. 123-130
Author(s):  
Anker Stubberud ◽  
Emer O’Connor ◽  
Erling Tronvik ◽  
Henry Houlden ◽  
Manjit Matharu
Keyword(s):  
Mental Retardation ◽  
Case Report ◽  
Genetic Testing ◽  
Head Trauma ◽  
Cerebral Oedema ◽  
De Novo ◽  
Minor Head Trauma ◽  
Hemiplegic Migraine ◽  
Wide Range ◽  
History Of

Mutations in the <i>CACNA1A</i> gene show a wide range of neurological phenotypes including hemiplegic migraine, ataxia, mental retardation and epilepsy. In some cases, hemiplegic migraine attacks can be triggered by minor head trauma and culminate in encephalopathy and cerebral oedema. A 37-year-old male without a family history of complex migraine experienced hemiplegic migraine attacks from childhood. The attacks were usually triggered by minor head trauma, and on several occasions complicated with encephalopathy and cerebral oedema. Genetic testing of the proband and unaffected parents revealed a de novo heterozygous nucleotide missense mutation in exon 25 of the <i>CACNA1A</i> gene (c.4055G&#x3e;A, p.R1352Q). The R1352Q <i>CACNA1A</i> variant shares the phenotype with other described <i>CACNA1A</i> mutations and highlights the interesting association of trauma as a precipitant for hemiplegic migraine. Subjects with early-onset sporadic hemiplegic migraine triggered by minor head injury or associated with seizures, ataxia or episodes of encephalopathy should be screened for mutations. These patients should also be advised to avoid activities that may result in head trauma, and anticonvulsants should be considered as prophylactic migraine therapy.

Sign in / Sign up

Export Citation Format

Share Document