scholarly journals The Distribution and Origins of Pyrus hopeiensis-“Wild Plant With Tiny Population” Using Whole Genome Resequencing

2021 ◽  
Vol 12 ◽  
Author(s):  
Yongtan Li ◽  
Jun Zhang ◽  
Shijie Wang ◽  
Yiwen Zhang ◽  
Minsheng Yang
Keyword(s):  
Morphological Characteristics ◽  
Principal Component ◽  
Sequencing Depth ◽  
Natural Hybridization ◽  
Wild Plant ◽  
Sphingolipid Metabolism ◽  
Whole Genome ◽  
Depth Range ◽  
Illumina Hiseq ◽  
Sequencing Platform

Pyrus hopeiensis is a valuable but endangered wild resource in the genus Pyrus. It has been listed as one of the 120 wild species with tiny population in China. The specie has been little studied. A preliminary study of propagation modes in P. hopeiensis was performed through seed propagation, hybridization, self-crossing trials, bud grafting, branch grafting, and investigations of natural growth. The results showed that the population size of P. hopeiensis was very small, the distribution range was limited, and the habitat was extremely degraded. In the wild population, natural hybridization and root tiller production were the major modes of propagation. Whole genome re-sequencing of the 23 wild and cultivated accessions from Pyrus species collected was performed using an Illumina HiSeq sequencing platform. The sequencing depth range was 26.56x−44.85x and the average sequencing depth was 32x. Phylogenetic tree and principal component analyses (PCA) based on SNPs showed that the wild Pyrus species, such as PWH06, PWH07, PWH09, PWH10, PWH13, and PWH17, were closely related to both P. hopeiensis HB-1 and P. hopeiensis HB-2. Using these results in combination with morphological characteristics, it speculated that P. hopeiensis populations may form a natural hybrid group with frequent gene exchanges between and within groups. A selective elimination analysis on the P. hopeiensis population were performed using Fst and π radio and a total of 381 overlapping genes including SAUR72, IAA20, HSFA2, and RKP genes were obtained. These genes were analyzed by gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) function enrichment. And four KEGG pathways, including lysine degradation, sphingolipid metabolism, other glycan degradation, and betaine biosynthesis were significantly enriched in the P. hopeiensis population. Our study provided information on genetic variation, evolutionary relationships, and gene enrichment in P. hopeiensis population. These data will help reveal the evolutionary history and origin of P. hopeiensis and provide guidelines for subsequent research on the locations of functional genes.

scholarly journals Population Evolution, Genetic Diversity and Structure of the Medicinal Legume, Glycyrrhiza uralensis and the Effects of Geographical Distribution on Leaves Nutrient Elements and Photosynthesis

2022 ◽  
Vol 12 ◽  
Author(s):  
Hanli Dang ◽  
Tao Zhang ◽  
Yuanyuan Li ◽  
Guifang Li ◽  
Li Zhuang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Unsaturated Fatty Acids ◽  
Principal Component ◽  
Glycyrrhiza Uralensis ◽  
Alpha Linolenic Acid ◽  
High Quality ◽  
Illumina Hiseq ◽  
Sequencing Platform ◽  
Population Evolution ◽  
Genetic Diversity And Structure

Glycyrrhiza uralensis is a valuable medicinal legume, which occurs widely in arid and semi-arid regions. G. uralensis demand has risen steeply due to its high medical and commercial value. Interpret genome-wide information can stimulate the G. uralensis development as far as its increased bioactive compound levels, and plant yield are concerned. In this study, leaf nutrient concentration and photosynthetic chlorophyll index of G. uralensis were evaluated to determine the G. uralensis growth physiology in three habitats. We observed that G. uralensis nutrient levels and photosynthesis differed significantly in three regions (p < 0.05). Whole-genome re-sequencing of the sixty G. uralensis populations samples from different habitats was performed using an Illumina HiSeq sequencing platform to elucidate the distribution patterns, population evolution, and genetic diversity of G. uralensis. 150.06 Gb high-quality clean data was obtained after strict filtering. The 895237686 reads were mapped against the reference genome, with an average 89.7% mapping rate and 87.02% average sample coverage rate. A total of 6985987 SNPs were identified, and 117970 high-quality SNPs were obtained after filtering, which were subjected to subsequent analysis. Principal component analysis (PCA) based on interindividual SNPs and phylogenetic analysis based on interindividual SNPs showed that the G. uralensis samples could be categorized into central, southern, and eastern populations, which reflected strong genetic differentiation due to long periods of geographic isolation. In this study, a total of 131 candidate regions were screened, and 145 candidate genes (such as Glyur001802s00036258, Glyur003702s00044485, Glyur001802s00036257, Glyur007364s00047495, Glyur000028s00003476, and Glyur000398s00034457) were identified by selective clearance analysis based on Fst and θπ values. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed significant enrichment of 110 GO terms including carbohydrate metabolic process, carbohydrate biosynthetic process, carbohydrate derivative biosynthetic process, and glucose catabolic process (p < 0.05). Alpha-linolenic acid metabolism, biosynthesis of unsaturated fatty acids, and fatty acid degradation pathways were significantly enriched (p < 0.05). This study provides information on the genetic diversity, genetic structure, and population adaptability of the medicinal legumes, G. uralensis. The data obtained in this study provide valuable information for plant development and future optimization of breeding programs for functional genes.

scholarly journals Comparative analysis of novel MGISEQ-2000 sequencing platform vs Illumina HiSeq 2500 for whole-genome sequencing

2019 ◽  
Author(s):  
Dmitriy Korostin ◽  
Nikolay Kulemin ◽  
Vladimir Naumov ◽  
Vera Belova ◽  
Dmitriy Kwon ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Variant Calling ◽  
Advanced Technology ◽  
Lower Sensitivity ◽  
Its Sequencing ◽  
Whole Genome ◽  
Illumina Hiseq ◽  
Sequencing Platform ◽  
Wide Range

AbstractBackgroundMGISEQ-2000 developed by MGI Tech Co. Ltd. (a subsidiary of the BGI Group) is a new competitor of such next-generation sequencing platforms as NovaSeq and HiSeq (Illumina). Its sequencing principle is based on the DNB and cPAS technologies, which were also used in the previous version of the BGISEQ-500 device. However, the reagents for MGISEQ-2000 have been refined and the platform utilizes updated software. The cPAS method is an advanced technology based on cPAL previously created by Complete Genomics.ResultIn this paper, the authors compare the results of the whole-genome sequencing of a DNA sample from a Russian female donor performed on MGISEQ-2000 and Illumina HiSeq 2500 (both PE150). Two platforms were compared in terms of sequencing quality, number of errors and performance. Additionally, we performed variant calling using four different software packages: Samtools mpileaup, Strelka2, Sentieon, and GATK. The accuracy of single nucleotide polymorphism (SNP) detection was similar in the data generated by MGISEQ-2000 and HiSeq 2500, which was used as a reference. At the same time, a separate indel analysis of the overall error rate revealed similar FPR values and lower sensitivity.Conclusionsit may be concluded with confidence that the data generated by the analyzed sequencing systems is characterized by comparable magnitudes of error and that MGISEQ-2000 can be used for a wide range of research tasks on par with HiSeq 2500.

scholarly journals Application of Principal Component Analysis in distinguishing three species of ‘jernang’ (Daemonorops spp.)

2021 ◽  
Vol 918 (1) ◽  
pp. 012026
Author(s):  
R Andini ◽  
L A Yanti ◽  
S Rasnovi ◽  
M I Sulaiman ◽  
R Moulana ◽  
...  
Keyword(s):  
Morphological Characteristics ◽  
Field Performance ◽  
Principal Component ◽  
Forest Products ◽  
Wild Plant ◽  
Land Area ◽  
Animal Products ◽  
Morphological Variations ◽  
The Past ◽  
Non Timber Forest Products

Abstract The province of Aceh at the northern tip of Sumatra has a total area of 5,75 million hectares. Its forest resources are considerably extensive as 60% of its total land area is still considered as ‘forest area’. Non-Timber Forest Products (NTFP) are defined as any wild plant and animal products harvested from forests, e.g., ‘jernang’ or dragon blood (Daemonorops spp.). It is classified as one of the valuable NTFP’s harvested from the forests in Aceh. Its morphological features resemble that of rattan (Calamus spp.), both of which belong to Aracaceae. The red resin of Daemonorops spp. is highly valued in Chinese medicine and possesses anti-inflammatory, anti-tumor, and anti-hemostatic properties. Almost 112 species of Daemonorops spp. exist. However, only 10% produces the red resin. Daemonorops draco, D. mattanensis, D. didymophylla are considered to have significant economic values. Over the past decade, a farmer living in central and western Aceh has cultivated dragon blood plants in small farms and sold the seedlings. In this study, the morphological variations of dragon blood (N=11) from Kuta Panang in central Aceh were assessed, and the Principal Component Analyses (PCA) were applied in order to distinguish the three species. Up to 92% of total variations were significantly explained with PC1, while the remaining were explained with PC2. Among the three species measured with PCA, Daemonorops draco or known as super ‘jernang’, appeared to have more distinctive morphological characteristics, e.g., fruit-, and stem diameter, as well as a number of fruit per trunk. These characteristics would contribute to better yield and field performance.

scholarly journals Comparative analysis of novel MGISEQ-2000 sequencing platform vs Illumina HiSeq 2500 for whole-genome sequencing

PLoS ONE ◽  
2020 ◽  
Vol 15 (3) ◽  
pp. e0230301 ◽  
Author(s):  
Dmitriy Korostin ◽  
Nikolay Kulemin ◽  
Vladimir Naumov ◽  
Vera Belova ◽  
Dmitriy Kwon ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Illumina Hiseq ◽  
Sequencing Platform

scholarly journals Autism Spectrum Disorder (ASD) with and without Mental Regression is Associated with Changes in the Fecal Microbiota

Nutrients ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 337 ◽  
Author(s):  
Julio Plaza-Díaz ◽  
Antonio Gómez-Fernández ◽  
Natalia Chueca ◽  
María Torre-Aguilar ◽  
Ángel Gil ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
Present Report ◽  
Principal Component ◽  
Autism Spectrum ◽  
Control Group ◽  
Healthy Group ◽  
Sequencing Platform ◽  
Preliminary Results ◽  
Children With Asd ◽  
Mental Regression

New microbiome sequencing technologies provide novel information about the potential interactions among intestinal microorganisms and the host in some neuropathologies as autism spectrum disorders (ASD). The microbiota–gut–brain axis is an emerging aspect in the generation of autistic behaviors; evidence from animal models suggests that intestinal microbial shifts may produce changes fitting the clinical picture of autism. The aim of the present study was to evaluate the fecal metagenomic profiles in children with ASD and compare them with healthy participants. This comparison allows us to ascertain how mental regression (an important variable in ASD) could influence the intestinal microbiota profile. For this reason, a subclassification in children with ASD by mental regression (AMR) and no mental regression (ANMR) phenotype was performed. The present report was a descriptive observational study. Forty-eight children aged 2–6 years with ASD were included: 30 with ANMR and 18 with AMR. In addition, a control group of 57 normally developing children was selected and matched to the ASD group by sex and age. Fecal samples were analyzed with a metagenomic approach using a next-generation sequencing platform. Several differences between children with ASD, compared with the healthy group, were detected. Namely, Actinobacteria and Proteobacteria at phylum level, as well as, Actinobacteria, Bacilli, Erysipelotrichi, and Gammaproteobacteria at class level were found at higher proportions in children with ASD. Additionally, Proteobacteria levels showed to be augmented exclusively in AMR children. Preliminary results, using a principal component analysis, showed differential patterns in children with ASD, ANMR and AMR, compared to healthy group, both for intestinal microbiota and food patterns. In this study, we report, higher levels of Actinobacteria, Proteobacteria and Bacilli, aside from Erysipelotrichi, and Gammaproteobacteria in children with ASD compared to healthy group. Furthermore, AMR children exhibited higher levels of Proteobacteria. Further analysis using these preliminary results and mixing metagenomic and other “omic” technologies are needed in larger cohorts of children with ASD to confirm these intestinal microbiota changes.

scholarly journals Estimating sequencing error rates using families

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Kelley Paskov ◽  
Jae-Yoon Jung ◽  
Brianna Chrisman ◽  
Nate T. Stockham ◽  
Peter Washington ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Exome Sequencing ◽  
Genome Sequencing ◽  
Variant Calling ◽  
Error Rates ◽  
Sequencing Error ◽  
Whole Genome ◽  
Sequencing Data ◽  
Sequencing Platform ◽  
Whole Exome

Abstract Background As next-generation sequencing technologies make their way into the clinic, knowledge of their error rates is essential if they are to be used to guide patient care. However, sequencing platforms and variant-calling pipelines are continuously evolving, making it difficult to accurately quantify error rates for the particular combination of assay and software parameters used on each sample. Family data provide a unique opportunity for estimating sequencing error rates since it allows us to observe a fraction of sequencing errors as Mendelian errors in the family, which we can then use to produce genome-wide error estimates for each sample. Results We introduce a method that uses Mendelian errors in sequencing data to make highly granular per-sample estimates of precision and recall for any set of variant calls, regardless of sequencing platform or calling methodology. We validate the accuracy of our estimates using monozygotic twins, and we use a set of monozygotic quadruplets to show that our predictions closely match the consensus method. We demonstrate our method’s versatility by estimating sequencing error rates for whole genome sequencing, whole exome sequencing, and microarray datasets, and we highlight its sensitivity by quantifying performance increases between different versions of the GATK variant-calling pipeline. We then use our method to demonstrate that: 1) Sequencing error rates between samples in the same dataset can vary by over an order of magnitude. 2) Variant calling performance decreases substantially in low-complexity regions of the genome. 3) Variant calling performance in whole exome sequencing data decreases with distance from the nearest target region. 4) Variant calls from lymphoblastoid cell lines can be as accurate as those from whole blood. 5) Whole-genome sequencing can attain microarray-level precision and recall at disease-associated SNV sites. Conclusion Genotype datasets from families are powerful resources that can be used to make fine-grained estimates of sequencing error for any sequencing platform and variant-calling methodology.

scholarly journals Transcriptomic Analysis of Betula halophila in Response to Salt Stress

2018 ◽  
Vol 19 (11) ◽  
pp. 3412 ◽  
Author(s):  
Fenjuan Shao ◽  
Lisha Zhang ◽  
Iain Wilson ◽  
Deyou Qiu
Keyword(s):  
Cell Wall ◽  
Salt Stress ◽  
Salt Tolerance ◽  
Expression Patterns ◽  
Soil Salinization ◽  
Sphingolipid Metabolism ◽  
Sequencing Platform ◽  
Resistant Varieties ◽  
High Salt Tolerance ◽  
Salt Overly Sensitive

Soil salinization is a matter of concern worldwide. It can eventually lead to the desertification of land and severely damage local agricultural production and the ecological environment. Betula halophila is a tree with high salt tolerance, so it is of importance to understand and discover the salt responsive genes of B. halophila for breeding salinity resistant varieties of trees. However, there is no report on the transcriptome in response to salt stress in B. halophila. Using Illumina sequencing platform, approximately 460 M raw reads were generated and assembled into 117,091 unigenes. Among these unigenes, 64,551 unigenes (55.12%) were annotated with gene descriptions, while the other 44.88% were unknown. 168 up-regulated genes and 351 down-regulated genes were identified, respectively. These Differentially Expressed Genes (DEGs) involved in multiple pathways including the Salt Overly Sensitive (SOS) pathway, ion transport and uptake, antioxidant enzyme, ABA signal pathway and so on. The gene ontology (GO) enrichments suggested that the DEGs were mainly involved in a plant-type cell wall organization biological process, cell wall cellular component, and structural constituent of cell wall molecular function. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment showed that the top-four enriched pathways were ‘Fatty acid elongation’, ‘Ribosome’, ‘Sphingolipid metabolism’ and ‘Flavonoid biosynthesis’. The expression patterns of sixteen DEGs were analyzed by qRT-PCR to verify the RNA-seq data. Among them, the transcription factor AT-Hook Motif Nuclear Localized gene and dehydrins might play an important role in response to salt stress in B. halophila. Our results provide an important gene resource to breed salt tolerant plants and useful information for further elucidation of the molecular mechanism of salt tolerance in B. halophila.

scholarly journals To the question of the origin of the cultural assortment   of Dagestan apricots through assessing the variability   of leaf morphological characteristics

2019 ◽  
Vol 14 (3) ◽  
pp. 17-24
Author(s):  
D. M. Anatov ◽  
Z. M. Аsadulaev ◽  
R. M. Osmanov ◽  
K. I. Akhmedova
Keyword(s):  
Leaf Shape ◽  
Morphological Characteristics ◽  
Principal Component ◽  
Leaf Size ◽  
Shape Index ◽  
Botanical Garden ◽  
Mahalanobis Distances ◽  
Traditional Cultivars ◽  
Academy Of Sciences ◽  
Degree Of Similarity

Aim. The paper presents the results of assessment of the indigenous nature and  degree of similarity of apricot cultivars growing in the collection of the Mountain  Botanical Garden, Gunib, Dagestan, Russia based on a comparative analysis of the  variability of leaf morphological characteristics.   Material and Methods. The material assessed consisted of 33 apricot cultivars of  various ecological and geographical origins aggregated in the following groups: (a)  Dagestan – traditional cultivars; (b) Moscow ‐ selection from the Tsytsin Main Moscow Botanical Garden, Russian Academy of Sciences based on wild forms of Tajikistan and Kyrgyzstan; (c) European and (d) Asian ‐ from Central Asia, Tajikistan, China  and Altai.   Results. The closeness of Dagestan and European varieties in comparison with Asian  and Moscow varieties was shown. Most Dagestan (16 of 19) and European varieties  have round‐shaped leaves (leaf shape index 80‐ 100%), while those from Asia and  the Moscow Botanical Garden have leaves which are elongated elliptical and oval  (60‐80%). Using the method of principal component analysis (PCA), it was established that most cultivars of Dagestan origin have similar leaf shapes and sizes, of  which Tlama kurak (wide‐round), Hekobarsh (elongated) were distinguished by leaf  shape and Esdelik by leaf size.   Conclusion. Based on a discriminant analysis (Squared Mahalanobis Distances), it  was found that the indices of indicators of leaf attributes (width/length of leaf lamina; petiole length/length of lamina; apex angle/corner of leaf base) are more reliable criteria for differentiating apricot varieties into ecological and geographical  groups than their morphological characteristics.  

scholarly journals Identification of microRNA-like RNAs from Trichoderma asperellum DQ-1 during its interaction with tomato roots using bioinformatic analysis and high-throughput sequencing

PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0254808
Author(s):  
Weiwei Wang ◽  
Fengtao Zhang ◽  
Jia Cui ◽  
Di Chen ◽  
Zhen Liu ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Plant Growth ◽  
Plant Disease Resistance ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Illumina Hiseq ◽  
Stem Loop ◽  
Sequencing Platform ◽  
Srna Library ◽  
Tomato Roots

MicroRNA-like small RNAs (milRNAs) and their regulatory roles in the interaction between plant and fungus have recently aroused keen interest of plant pathologists. Trichoderma spp., one of the widespread biocontrol fungi, can promote plant growth and induce plant disease resistance. To investigate milRNAs potentially involved in the interaction between Trichoderma and tomato roots, a small RNA (sRNA) library expressed during the interaction of T. asperellum DQ-1 and tomato roots was constructed and sequenced using the Illumina HiSeqTM 2500 sequencing platform. From 13,464,142 sRNA reads, we identified 21 milRNA candidates that were similar to other known microRNAs in the miRBase database and 22 novel milRNA candidates that possessed a stable microRNA precursor hairpin structure. Among them, three milRNA candidates showed different expression level in the interaction according to the result of stem-loop RT-PCR indicating that these milRNAs may play a distinct regulatory role in the interaction between Trichoderma and tomato roots. The potential transboundary milRNAs from T. asperellum and their target genes in tomato were predicted by bioinformatics analysis. The results revealed that several interesting proteins involved in plant growth and development, disease resistance, seed maturation, and osmotic stress signal transduction might be regulated by the transboundary milRNAs. To our knowledge, this is the first report of milRNAs taking part in the process of interaction of T. asperellum and tomato roots and associated with plant promotion and disease resistance. The results might be useful to unravel the mechanism of interaction between Trichoderma and tomato.

scholarly journals Morphological evaluation of common bean diversity in Bosnia and Herzegovina using the discriminant analysis of principal components (DAPC) multivariate method

Genetika ◽  
2013 ◽  
Vol 45 (3) ◽  
pp. 963-977 ◽  
Author(s):  
Jasmin Grahic ◽  
Fuad Gasi ◽  
Mirsad Kurtovic ◽  
Lutvija Karic ◽  
Mirha Djikic ◽  
...  
Keyword(s):  
Discriminant Analysis ◽  
Common Bean ◽  
Bosnia And Herzegovina ◽  
Principal Components ◽  
Morphological Characteristics ◽  
Principal Component ◽  
Discriminant Functions ◽  
Factor Loadings ◽  
Geographical Regions ◽  
High Level

In order to analyze morphological characteristics of locally cultivated common bean landraces from Bosnia and Herzegovina (B&H), thirteen quantitative and qualitative traits of 40 P. vulgaris accessions, collected from four geographical regions (Northwest B&H, Northeast B&H, Central B&H and Sarajevo) and maintained at the Gene bank of the Faculty of Agriculture and Food Sciences in Sarajevo, were examined. Principal component analysis (PCA) showed that the proportion of variance retained in the first two principal components was 54.35%. The first principal component had high contributing factor loadings from seed width, seed height and seed weight, whilst the second principal component had high contributing factor loadings from the analyzed traits seed per pod and pod length. PCA plot, based on the first two principal components, displayed a high level of variability among the analyzed material. The discriminant analysis of principal components (DAPC) created 3 discriminant functions (DF), whereby the first two discriminant functions accounted for 90.4% of the variance retained. Based on the retained DFs, DAPC provided group membership probabilities which showed that 70% of the accessions examined were correctly classified between the geographically defined groups. Based on the taxonomic distance, 40 common bean accessions analyzed in this study formed two major clusters, whereas two accessions Acc304 and Acc307 didn?t group in any of those. Acc360 and Acc362, as well as Acc324 and Acc371 displayed a high level of similarity and are probably the same landrace. The present diversity of Bosnia and Herzegovina?s common been landraces could be useful in future breeding programs.

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