scholarly journals Skim-Sequencing Reveals the Likely Origin of the Enigmatic Endangered Sunflower Helianthus schweinitzii

Genes ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 1040 ◽  
Author(s):  
Justin Anderson ◽  
Michael Kantar ◽  
Dan Bock ◽  
Kunsiri Chaw Grubbs ◽  
Edward Schilling ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
De Novo ◽  
Parental Species ◽  
Eastern United States ◽  
Nuclear Rdna ◽  
Reciprocal Monophyly ◽  
Phylogenetic Reconstructions ◽  
Evolutionary Studies ◽  
35S Rdna ◽  
Low Coverage

Resolving the origin of endangered taxa is an essential component of conservation. This information can be used to guide efforts of bolstering genetic diversity, and also enables species recovery and future evolutionary studies. Here, we used low-coverage whole genome sequencing to clarify the origin of Helianthus schweinitzii, an endangered tetraploid sunflower that is endemic to the Piedmont Plateau in the eastern United States. We surveyed four accessions representing four populations of H. schweinitzii and 38 accessions of six purported parental species. Using de novo approaches, we assembled 87,004 bp of the chloroplast genome and 6770 bp of the nuclear 35S rDNA. Phylogenetic reconstructions based on the chloroplast genome revealed no reciprocal monophyly of taxa. In contrast, nuclear rDNA data strongly supported the currently accepted sections of the genus Helianthus. Information from combined cpDNA and rDNA provided evidence that H. schweinitzii is likely an allo-tetraploid that formed as a result of hybridization between the diploids Helianthus giganteus and Helianthus microcephalus.

scholarly journals Complete chloroplast genome of Alternanthera philoxeroides by de novo sequencing

2021 ◽  
Vol 6 (7) ◽  
pp. 1826-1828
Author(s):  
Ping Jiang ◽  
Guangpei Xu ◽  
Yanfei He ◽  
Taotao Sun ◽  
Changli Liu ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
De Novo ◽  
De Novo Sequencing ◽  
Alternanthera Philoxeroides ◽  
Complete Chloroplast Genome

scholarly journals Sequencing an F1 hybrid of Silurus asotus and S. meridionalis enabled the assembly of high-quality parental genomes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Weitao Chen ◽  
Ming Zou ◽  
Yuefei Li ◽  
Shuli Zhu ◽  
Xinhui Li ◽  
...  
Keyword(s):  
De Novo ◽  
Parental Species ◽  
F1 Hybrids ◽  
Pelteobagrus Fulvidraco ◽  
F1 Hybrid ◽  
Short Reads ◽  
Final Assembly ◽  
Genome Complexity ◽  
Hybrid Genome ◽  
Silurus Asotus

AbstractGenome complexity such as heterozygosity may heavily influence its de novo assembly. Sequencing somatic cells of the F1 hybrids harboring two sets of genetic materials from both of the paternal and maternal species may avoid alleles discrimination during assembly. However, the feasibility of this strategy needs further assessments. We sequenced and assembled the genome of an F1 hybrid between Silurus asotus and S. meridionalis using the SequelII platform and Hi-C scaffolding technologies. More than 300 Gb raw data were generated, and the final assembly obtained 2344 scaffolds composed of 3017 contigs. The N50 length of scaffolds and contigs was 28.55 Mb and 7.49 Mb, respectively. Based on the mapping results of short reads generated for the paternal and maternal species, each of the 29 chromosomes originating from S. asotus and S. meridionalis was recognized. We recovered nearly 94% and 96% of the total length of S. asotus and S. meridionalis. BUSCO assessments and mapping analyses suggested that both genomes had high completeness and accuracy. Further analyses demonstrated the high collinearity between S. asotus, S. meridionalis, and the related Pelteobagrus fulvidraco. Comparison of the two genomes with that assembled only using the short reads from non-hybrid parental species detected a small portion of sequences that may be incorrectly assigned to the different species. We supposed that at least part of these situations may have resulted from mitotic recombination. The strategy of sequencing the F1 hybrid genome can recover the vast majority of the parental genomes and may improve the assembly of complex genomes.

scholarly journals A novel hybrid of Hypericum undulatum (Wavy-leaved St. John’s-wort, Hypericaceae) and its subsequent dispersal

2020 ◽  
Vol 2 (3) ◽  
Author(s):  
Andrew Jones ◽  
Fred Rumsey
Keyword(s):  
De Novo ◽  
Parental Species ◽  
Species Range ◽  
The Novel ◽  
The Core ◽  
St John’S Wort ◽  
St John's Wort ◽  
Core Site

The novel hybrid Hypericum undulatum Schousb. ex. Willd. x H. perforatum L. is described from Cardiganshire (v.c.46) and given the name H. x cereticae R.A. Jones, F.J. Rumsey & N. Robson.  Despite reduced fertility it shows indications of ongoing introgression and signs of recent dispersal up to 5 km from the core site. The hybrid has arisen recently at the northern extremes of the rarer (H. undulatum) parental species’ range, although at neither site are the parents currently sympatric and in the outlying population both are absent, supporting the belief that here it has not arisen de novo but has colonised through unknown agencies.

scholarly journals Copy Number Signatures Predict Chromothripsis and Poor Clinical Outcome in Newly Diagnosed Multiple Myeloma Patients

Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 52-53
Author(s):  
Kylee H Maclachlan ◽  
Binbin Zheng-Lin ◽  
Venkata Yellapantula ◽  
Andriy Derkach ◽  
Even H Rustad ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Clinical Trials ◽  
Research Funding ◽  
De Novo ◽  
Data Monitoring ◽  
Signature Analysis ◽  
Independent Data ◽  
Genetics Research ◽  
Manual Curation ◽  
Low Coverage

Chromothripsis is emerging as a strong and independent prognostic factor in multiple myeloma (MM), predicting shorter progression-free (PFS) and overall survival (Rustad BioRxiv 2019). Reliable detection requires whole genome sequencing (WGS), with 24% prevalence in 752 newly diagnosed multiple myeloma (NDMM) from CoMMpass (NCT01454297, Rustad BioRxiv 2019) compared with 1.3% by array-based techniques (Magrangeas Blood 2011). In MM, chromothripsis presents differently to solid cancers. Although the biological impact is similar across malignancies, in MM the structural complexity of chromothriptic events is typically lower. In addition, chromothripsis can occur early in MM development and remain stable over time (Maura Nat Comm 2019). Computational algorithms for chromothripsis detection (e.g. ShatterSeek; Cortes-Ciriano Nat Gen 2018) were developed in solid cancers and are accurate in that setting. Running ShatterSeek on 752 NDMM patients with low coverage WGS from CoMMpass, we observed a high specificity for chromothripsis (98.3%) but poor sensitivity (30.2%). ShatterSeek detected chromothripsis in 64/752 samples (8.5%), with 85% confirmed on manual curation; however, missed 114 cases located by manual curation. This indicates that MM-specific computational methods are required. We hypothesized that a signature analysis approach using copy number variation (CNV) may provide an accurate estimation of chromothripsis. We adapted CNV signature analysis, developed in ovarian cancer (Macintyre Nat Gen 2018), to now detect MM-specific CNV and structural features. The analysis utilizes 6 fundamental CN features: i) absolute CN of segments, ii) difference in CN in adjacent segments, iii) breakpoints per 10 Mb, iv) breakpoints per chromosome arm, v) lengths of oscillating CN segment chains, and vi) the size of segments. The optimal number of categories in each CNV feature was established using a mixed effect model (mclust R package). Using CoMMpass low-coverage WGS, de novo extraction using the hierarchical dirichlet process defined 5 signatures, 2 of which (CNV-SIG 4 and CNV-SIG 5) contain features associated with chromothripsis: longer lengths of oscillating CN states, higher numbers of breakpoints / chromosome arm, and higher total numbers of small segments of CN change. Next, we demonstrate that CNV signatures are highly predictive of chromothripsis (average area-under-the-curve /AUC = 0.9, based on 10-fold cross validation). Chromothripsis-associated CNV signatures are correlated with biallelic TP53 inactivation (p= 0.01) and gain1q21 (p<0.001) and show negative association with t(11;14) (p<0.001). Chromothriptic signatures were associated with shorter PFS, with multivariate analysis after correction for ISS, age, biallelic TP53 inactivation, t(4;14) and gain1q21 producing a hazard ratio of 2.9 (95% CI 1.07-7.7, p = 0.036). A validation set of 29 NDMM WGS confirmed the ability of CNV signatures to predict chromothripsis (AUC 0.87). As WGS is currently too expensive and computationally intensive to employ in routine practice, we investigated if CNV signatures can predict chromothripsis without using WGS. First, we performed de novo signature extraction using whole exome data from 865 CoMMpass samples. CNV signatures extracted without reference to WGS produced an AUC = 0.81 for predicting chromothripsis (in those with WGS to confirm; n =752), and the chromothriptic-signatures confirmed the association with a shorter PFS (HR=7.2, 95%CI 1.32-39.4, p = 0.022). Second, we applied CNV signature analysis to NDMM having either the myTYPE targeted sequencing panel (n= 113; Yellapantula, Blood Can J 2019) or a single nucleotide polymorphism (SNP) array (n= 217). CNV signature assessment by each technology was predictive of clinical outcome, likely due to the detection of chromothripsis. As with WGS, multivariate analysis confirmed CNV signatures to be independently prognostic (myTYPE; p = 0.003, SNP; p = 0.004). Overall, we demonstrate that CNV signature analysis in NDMM provides a highly accurate prediction of chromothripsis. CNV signature assessment remains reliable by multiple surrogate measures, without requiring WGS. Chromothripsis-associated CNV signatures are an independent and adverse prognostic factor, potentially allowing refinement of standard prognostic scores for NDMM patients and providing a more accurate risk stratification for clinical trials. Disclosures Hultcrantz: Amgen: Research Funding; Daiichi Sankyo: Research Funding; GSK: Research Funding; Intellisphere LLC: Consultancy. Dogan:Takeda: Consultancy; National Cancer Institute: Research Funding; Roche: Consultancy, Research Funding; Seattle Genetics: Consultancy; AbbVie: Consultancy; EUSA Pharma: Consultancy; Physicians Education Resource: Consultancy; Corvus Pharmaceuticals: Consultancy. Morgan:Bristol-Myers Squibb: Consultancy, Honoraria; Janssen: Research Funding; Karyopharm: Consultancy, Honoraria; Amgen: Consultancy, Honoraria; Takeda: Consultancy, Honoraria; Celgene: Consultancy, Honoraria, Research Funding; Roche: Consultancy, Honoraria; GSK: Consultancy, Honoraria. Landgren:Cellectis: Consultancy, Honoraria; Takeda: Other: Independent Data Monitoring Committees for clinical trials, Research Funding; BMS: Consultancy, Honoraria; Adaptive: Consultancy, Honoraria; Takeda: Other: Independent Data Monitoring Committees for clinical trials, Research Funding; Glenmark: Consultancy, Honoraria, Research Funding; Seattle Genetics: Research Funding; Binding Site: Consultancy, Honoraria; Karyopharma: Research Funding; Merck: Other; BMS: Consultancy, Honoraria; Karyopharma: Research Funding; Merck: Other; Pfizer: Consultancy, Honoraria; Celgene: Consultancy, Honoraria, Research Funding; Seattle Genetics: Research Funding; Juno: Consultancy, Honoraria; Juno: Consultancy, Honoraria; Janssen: Consultancy, Honoraria, Other: Independent Data Monitoring Committees for clinical trials, Research Funding; Celgene: Consultancy, Honoraria, Research Funding; Janssen: Consultancy, Honoraria, Other: Independent Data Monitoring Committees for clinical trials, Research Funding; Pfizer: Consultancy, Honoraria; Amgen: Consultancy, Honoraria, Research Funding; Cellectis: Consultancy, Honoraria; Glenmark: Consultancy, Honoraria, Research Funding; Binding Site: Consultancy, Honoraria.

scholarly journals The complete chloroplast genome of Saxifraga sinomontana (Saxifragaceae) and comparative analysis with other Saxifragaceae species

2019 ◽  
Vol 42 (4) ◽  
pp. 601-611 ◽  
Author(s):  
Yan Li ◽  
Liukun Jia ◽  
Zhihua Wang ◽  
Rui Xing ◽  
Xiaofeng Chi ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Phylogenetic Relationships ◽  
De Novo ◽  
Single Copy ◽  
Bootstrap Support ◽  
Protein Coding ◽  
Complete Chloroplast Genome ◽  
Protein Coding Genes ◽  
Chloroplast Genomes

Abstract Saxifraga sinomontana J.-T. Pan & Gornall belongs to Saxifraga sect. Ciliatae subsect. Hirculoideae, a lineage containing ca. 110 species whose phylogenetic relationships are largely unresolved due to recent rapid radiations. Analyses of complete chloroplast genomes have the potential to significantly improve the resolution of phylogenetic relationships in this young plant lineage. The complete chloroplast genome of S. sinomontana was de novo sequenced, assembled and then compared with that of other six Saxifragaceae species. The S. sinomontana chloroplast genome is 147,240 bp in length with a typical quadripartite structure, including a large single-copy region of 79,310 bp and a small single-copy region of 16,874 bp separated by a pair of inverted repeats (IRs) of 25,528 bp each. The chloroplast genome contains 113 unique genes, including 79 protein-coding genes, four rRNAs and 30 tRNAs, with 18 duplicates in the IRs. The gene content and organization are similar to other Saxifragaceae chloroplast genomes. Sixty-one simple sequence repeats were identified in the S. sinomontana chloroplast genome, mostly represented by mononucleotide repeats of polyadenine or polythymine. Comparative analysis revealed 12 highly divergent regions in the intergenic spacers, as well as coding genes of matK, ndhK, accD, cemA, rpoA, rps19, ndhF, ccsA, ndhD and ycf1. Phylogenetic reconstruction of seven Saxifragaceae species based on 66 protein-coding genes received high bootstrap support values for nearly all identified nodes, suggesting a promising opportunity to resolve infrasectional relationships of the most species-rich section Ciliatae of Saxifraga.

scholarly journals Complete Chloroplast Genome Sequence of Broomcorn Millet (Panicum miliaceum L.) and Comparative Analysis with Other Panicoideae Species

Agronomy ◽  
2018 ◽  
Vol 8 (9) ◽  
pp. 159 ◽  
Author(s):  
Xiaojun Nie ◽  
Xian Zhao ◽  
Sue Wang ◽  
Ting Zhang ◽  
Chong Li ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Chloroplast Genome ◽  
Panicum Virgatum ◽  
Genome Structure ◽  
Structural Features ◽  
Panicum Miliaceum ◽  
Genomic Knowledge ◽  
Broomcorn Millet ◽  
Evolutionary Studies ◽  
Cp Genome

Broomcorn millet (Panicum miliaceum L.) is one of the earliest domesticated cereals worldwide, holding significant agricultural, historical, and evolutionary importance. However, our genomic knowledge of it is rather limited at present, hampering further genetic and evolutionary studies. Here, we sequenced and assembled the chloroplast genome (cp) of broomcorn millet and compared it with five other Panicoideae species. Results showed that the cp genome of broomcorn millet was 139,826 bp in size, with a typical quadripartite structure. In total, 108 genes were annotated and 18 genes were duplicated in the IR (inverted region) region, which was similar to other Panicoideae species. Comparative analysis showed a rather conserved genome structure between them, with three common regions. Furthermore, RNA editing, codon usage, and expansion of the IR, as well as simple sequence repeat (SSR) elements, were systematically investigated and 13 potential DNA markers were developed for Panicoideae species identification. Finally, phylogenetic analysis implied that broomcorn millet was a sister species to Panicum virgatum within the tribe Paniceae, and supported a monophyly of the Panicoideae. This study has reported for the first time the genome organization, gene content, and structural features of the chloroplast genome of broomcorn millet, which provides valuable information for genetic and evolutionary studies in the genus Panicum and beyond.

scholarly journals An evaluation of the PacBio RS platform for sequencing and de novo assembly of a chloroplast genome

BMC Genomics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 670 ◽  
Author(s):  
Marco Ferrarini ◽  
Marco Moretto ◽  
Judson A Ward ◽  
Nada Šurbanovski ◽  
Vladimir Stevanović ◽  
...  
Keyword(s):  
Chloroplast Genome ◽  
De Novo Assembly ◽  
De Novo

scholarly journals Sequencing and De Novo Assembly of the Complete Chloroplast Genome of the Peruvian Carrot (Arracacia xanthorrhiza Bancroft)

2017 ◽  
Vol 5 (7) ◽  
Author(s):  
Javier Santiago Alvarado ◽  
Diane Hinojosa López ◽  
Isaury Maldonado Torres ◽  
María Margarita Meléndez ◽  
Rosalinda Aybar Batista ◽  
...  
Keyword(s):  
Puerto Rico ◽  
South America ◽  
Chloroplast Genome ◽  
De Novo ◽  
Crop Protection ◽  
Food Crop ◽  
Storage Roots ◽  
Complete Chloroplast Genome ◽  
Improvement Strategies ◽  
Chloroplast Genome Sequence

ABSTRACT Arracacia xanthorrhiza is an important secondary food crop in South America and Puerto Rico. The lack of crop protection and improvement strategies leads to infections damaging the storage roots. Here, we report the annotated complete chloroplast genome sequence of A. xanthorrhiza as a step toward developing genomic resources for this crop.

scholarly journals Social behavior in bees influences the abundance of Sodalis (Enterobacteriaceae) symbionts

2017 ◽  
Author(s):  
Benjamin E. Rubin ◽  
Jon G. Sanders ◽  
Kyle M. Turner ◽  
Naomi E. Pierce ◽  
Sarah D. Kocher
Keyword(s):  
Social Interactions ◽  
Bacterial Communities ◽  
Bacterial Abundance ◽  
De Novo ◽  
Amplicon Sequencing ◽  
Social Forms ◽  
Phylogenetic Reconstructions ◽  
16S Amplicon Sequencing ◽  
Species Specific ◽  
Genome Assemblies

AbstractSocial interactions can facilitate transmission of microbes between individuals, reducing variation in gut communities within social groups. Thus, the evolution of social behaviors and symbiont community composition have the potential to be tightly linked. We explored this connection by characterizing the diversity of bacteria associated with both social and solitary bee species within the behaviorally variable family Halictidae using 16S amplicon sequencing. Contrary to expectations, we found few differences in bacterial abundance or variation between social forms, and most halictid species appear to share similar gut bacterial communities. However, several strains of Sodalis, a genus described as a symbiont in a variety of insects but yet to be characterized in bees, differ in abundance between social and solitary bees. Phylogenetic reconstructions based on whole-genome alignments indicate that Sodalis has independently colonized halictids at least three times. These strains appear to be mutually exclusive within individual bees, although they are not host-species-specific and no signatures of vertical transmission were observed, suggesting that Sodalis strains compete for access to hosts. De novo genome assemblies indicate that these three lineages are subject to widespread relaxed selection and that Sodalis is undergoing genome degeneration during the colonization of these hosts.

scholarly journals Molecular Delineation of De Novo Small Supernumerary Marker Chromosomes in Prenatal Diagnosis, A Retrospective Study

2021 ◽  
Author(s):  
Shuang Hu ◽  
Xiangdong Kong
Keyword(s):  
Genetic Counseling ◽  
Prenatal Diagnosis ◽  
De Novo ◽  
Snp Array ◽  
Chromosome 9 ◽  
Marker Chromosomes ◽  
Number Variation ◽  
Low Coverage ◽  
Small Supernumerary Marker Chromosomes ◽  
Supernumerary Marker Chromosomes

Abstract Background To define the genotype-phenotype correlation of small supernumerary marker chromosomes (sSMCs) and conduct precise genetic counseling, we retrospectively searched and reviewed de novo sSMC cases detected during prenatal diagnosis at The First Affiliated Hospital of Zhengzhou University. Chromosome karyotypes of 20,314 cases of amniotic fluid from pregnant women were performed. For 16 samples with de novo sSMCs, 10 were subjected to single-nucleotide polymorphism (SNP) array or low-coverage massively parallel copy number variation sequencing (CNV-seq) analysis. Results Among the 10 sSMC cases, two sSMCs derived from chromosome 9, and three sSMCs derived from chromosomes 12, 18 and 22. The remaining 5 cases were not identified by SNP array or CNV-seq because they lacked euchromatin or had a low proportion of mosaicism. Four of them with a karyotype of 47,XN,+mar presented normal molecular cytogenetic results (seq[hg19] 46,XN), and the remaining patient with a karyotype of 46,XN,+mar presented with Turner syndrome (seq[hg19] 45,X). Five sSMC samples were mosaics of all 16 cases. Conclusion Considering the variable origins of sSMCs, further genetic testing of sSMCs should be performed by SNP array or CNV-seq. Detailed molecular characterization would allow precise genetic counseling for prenatal diagnosis.

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