scholarly journals Comprehensive transcriptome analysis provides new insights into nutritional strategies and phylogenetic relationships of chrysophytes

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2832 ◽  
Author(s):  
Daniela Beisser ◽  
Nadine Graupner ◽  
Christina Bock ◽  
Sabina Wodniok ◽  
Lars Grossmann ◽  
...  
Keyword(s):  
Illumina Hiseq ◽  
Chlorophyll Metabolism ◽  
Eukaryotic Diversity ◽  
Alignment Free ◽  
Illumina Hiseq Platform ◽  
Photosynthesis Genes ◽  
Lipid Transporters ◽  
Nutritional Strategies ◽  
Environmental Information Processing ◽  
Bacterial Food

BackgroundChrysophytes are protist model species in ecology and ecophysiology and important grazers of bacteria-sized microorganisms and primary producers. However, they have not yet been investigated in detail at the molecular level, and no genomic and only little transcriptomic information is available. Chrysophytes exhibit different trophic modes: while phototrophic chrysophytes perform only photosynthesis, mixotrophs can gain carbon from bacterial food as well as from photosynthesis, and heterotrophs solely feed on bacteria-sized microorganisms. Recent phylogenies and megasystematics demonstrate an immense complexity of eukaryotic diversity with numerous transitions between phototrophic and heterotrophic organisms. The question we aim to answer is how the diverse nutritional strategies, accompanied or brought about by a reduction of the plasmid and size reduction in heterotrophic strains, affect physiology and molecular processes.ResultsWe sequenced the mRNA of 18 chrysophyte strains on the Illumina HiSeq platform and analysed the transcriptomes to determine relations between the trophic mode (mixotrophic vs. heterotrophic) and gene expression. We observed an enrichment of genes for photosynthesis, porphyrin and chlorophyll metabolism for phototrophic and mixotrophic strains that can perform photosynthesis. Genes involved in nutrient absorption, environmental information processing and various transporters (e.g., monosaccharide, peptide, lipid transporters) were present or highly expressed only in heterotrophic strains that have to sense, digest and absorb bacterial food. We furthermore present a transcriptome-based alignment-free phylogeny construction approach using transcripts assembled from short reads to determine the evolutionary relationships between the strains and the possible influence of nutritional strategies on the reconstructed phylogeny. We discuss the resulting phylogenies in comparison to those from established approaches based on ribosomal RNA and orthologous genes. Finally, we make functionally annotated reference transcriptomes of each strain available to the community, significantly enhancing publicly available data on Chrysophyceae.ConclusionsOur study is the first comprehensive transcriptomic characterisation of a diverse set of Chrysophyceaen strains. In addition, we showcase the possibility of inferring phylogenies from assembled transcriptomes using an alignment-free approach. The raw and functionally annotated data we provide will prove beneficial for further examination of the diversity within this taxon. Our molecular characterisation of different trophic modes presents a first such example.

The mitochondrial genome and phylogenetic analysis of the tick Haemaphysalis qinghaiensis Teng, 1980 (Acari:Ixodidae)

2022 ◽  
Author(s):  
Tianhong Wang ◽  
Zihao Wang ◽  
Ruwei Bai ◽  
Zhijun Yu ◽  
Jingze Liu
Keyword(s):  
Phylogenetic Analysis ◽  
Mitochondrial Genome ◽  
Complete Mitochondrial Genome ◽  
Rrna Genes ◽  
Trna Genes ◽  
Illumina Hiseq ◽  
Protein Coding ◽  
Haemaphysalis Qinghaiensis ◽  
Mitogenome Sequence ◽  
Illumina Hiseq Platform

Haemaphysalis qinghaiensis is an endemic species and mainly inhabiting in the northwestern plateau of China, which can transmit many zoonotic pathogens and cause great harm to animals. In this study, the complete mitochondrial genome (mitogenome) of H. qinghaiensis was assembled through the Illumina HiSeq platform. The mitogenome was 14,533 bp in length, consisting of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes and 3 noncoding regions (NCRs). The bias towards a high A+T content with 77.65% in mitogenome of H. qinghaiensis. The rearrangement of mitochondrial genes in H. qinghaiensis was consistent with other hard ticks. The phylogenetic analysis based on the concatenation of 13 PCGs from 65 tick mitogenomes showed that the H. qinghaiensis was clustered into a well-supported clade within the Haemaphysalis genus. This is the first complete mitogenome sequence of H. qinghaiensis, which provides a useful reference for understanding of the taxonomic and genetics of ticks.

scholarly journals A Cluster of Colistin- and Carbapenem-Resistant Klebsiella pneumoniae Carrying blaNDM-1 and mcr-8.2

2019 ◽  
Vol 221 (Supplement_2) ◽  
pp. S237-S242 ◽  
Author(s):  
Ke Ma ◽  
Yu Feng ◽  
Lu Liu ◽  
Zhihong Yao ◽  
Zhiyong Zong
Keyword(s):  
Klebsiella Pneumoniae ◽  
Nucleotide Polymorphisms ◽  
Illumina Hiseq ◽  
Carbapenem Resistant ◽  
Interhospital Transfer ◽  
Transmissible Plasmid ◽  
New Variant ◽  
Long Read ◽  
Illumina Hiseq Platform ◽  
Resistant Strains

Abstract Background Klebsiella pneumoniae resistant to both carbapenems and colistin imposes severe challenges for management. In this study, we report a cluster of 5 carbapenem-resistant K pneumoniae clinical strains belonging to ST1 and K57 types, 4 of which were also resistant to colistin, from 2 hospitals. Methods The 5 strains were subjected to whole-genome sequencing (WGS) using the short-read Illumina HiSeq platform, and 2 strains were also selected for long-read WGS using MinION. Clonal relatedness of the 5 strains was determined based on single-nucleotide polymorphisms (SNPs). Conjugation experiments were performed to obtain self-transmissible plasmids. Results All 5 strains carried the carbapenemase-encoding gene blaNDM-1, whereas the 4 colistin-resistant strains also harbored a new variant of the mcr-8 colistin resistance gene, namely, mcr-8.2. MCR-8.2 differs from MCR-8.1 by four amino acid substitutions (A51V, A232S, N365Y, and N480K). mcr-8.2 was located on a large, hybrid, nonself-transmissible plasmid containing IncQ, IncR, and IncFII replicons, whereas blaNDM-1 was carried by self-transmissible IncX3 plasmids. Phylogenetic analysis based on SNPs revealed that the 5 strains were likely to have a common origin. Conclusions Both the intra- and interhospital transfer of strains carrying mcr-8 and blaNDM-1 were identified, which represents an emerging threat for clinical management and infection control.

scholarly journals Software updates in the Illumina HiSeq platform affect whole-genome bisulfite sequencing

BMC Genomics ◽  
2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Hidehiro Toh ◽  
Kenjiro Shirane ◽  
Fumihito Miura ◽  
Naoki Kubo ◽  
Kenji Ichiyanagi ◽  
...  
Keyword(s):  
Bisulfite Sequencing ◽  
Whole Genome ◽  
Illumina Hiseq ◽  
Whole Genome Bisulfite Sequencing ◽  
Genome Bisulfite Sequencing ◽  
Software Updates ◽  
Illumina Hiseq Platform

scholarly journals De novo transcriptome sequencing of Rhododendron molle and identification of genes involved in the biosynthesis of secondary metabolites

2020 ◽  
Author(s):  
Guolin Zhou ◽  
Ping Zhu
Keyword(s):  
Secondary Metabolites ◽  
Transcriptome Sequencing ◽  
De Novo ◽  
Illumina Hiseq ◽  
Medicinal Value ◽  
Relieve Pain ◽  
Chemical Studies ◽  
Illumina Hiseq Platform ◽  
Differential Gene ◽  
First Time

Abstract Background: Rhododendron molle (Ericaceae) is a traditional Chinese medicinal plant, its flower and root have been widely used to treat rheumatism and relieve pain for thousands of years in China. Chemical studies have revealed that R. molle contains abundant secondary metabolites such as terpenoinds, flavonoids and lignans, some of which have exhibited various bioactivities including antioxidant, hypotension and analgesic activity. In spite of immense pharmaceutical importance, the mechanism underlying the biosynthesis of secondary metabolites remains unknown and the genomic information is unavailable. Results: To gain molecular insight into this plant, especially on the information of pharmaceutically important secondary metabolites including grayanane diterpenoids, we conducted deep transcriptome sequencing for R. molle flower and root using the Illumina Hiseq platform. In total, 100,603 unigenes were generated through de novo assembly with mean length of 778 bp, 57.1% of these unigenes were annotated in public databases and 17,906 of those unigenes showed significant match in the KEGG database. Unigenes involved in the biosynthesis of secondary metabolites were annotated, including the TPSs and CYPs that were potentially responsible for the biosynthesis of grayanoids. Moreover, 3,376 transcription factors and 10,828 simple sequence repeats (SSRs) were also identified. Additionally, we further performed differential gene expression (DEG) analysis of the flower and root transcriptome libraries and identified numerous genes that were specifically expressed or up-regulated in flower.Conclusions: To the best of our knowledge, this is the first time to generate and thoroughly analyze the transcriptome data of both R. molle flower and root. This study provided an important genetic resource which will shed light on elucidating various secondary metabolite biosynthetic pathways in R. molle, especially for those with medicinal value and allow for drug development in this plant.

scholarly journals A novel post hoc method for detecting index switching finds no evidence for increased switching on the Illumina HiSeq X

2017 ◽  
Author(s):  
Gregory L. Owens ◽  
Marco Todesco ◽  
Emily B. M. Drummond ◽  
Sam Yeaman ◽  
Loren H. Rieseberg
Keyword(s):  
Allele Frequency ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Sequence Data ◽  
Molecular Ecology ◽  
Whole Genome Shotgun ◽  
Whole Genome ◽  
Illumina Hiseq ◽  
Illumina Hiseq Platform ◽  
Post Hoc

AbstractHigh throughput sequencing using the Illumina HiSeq platform is a pervasive and critical molecular ecology resource, and has provided the data underlying many recent advances. A recent study has suggested that ‘index switching’, where reads are misattributed to the wrong sample, may be higher in new versions of the HiSeq platform. This has the potential to invalidate both published and in-progress work across the field. Here, we test for evidence of index switching in an exemplar whole genome shotgun dataset sequenced on both the Illumina HiSeq 2500, which should not have the problem, and the Illumina HiSeq X, which may. We leverage unbalanced heterozygotes, which may be produced by index switching, and ask whether the under-sequenced allele is more likely to be found in other samples in the same lane than expected based on the allele frequency. Although we validate the sensitivity of this method using simulations, we find that neither the HiSeq 2500 nor the HiSeq X have evidence of index switching. This suggests that, thankfully, index switching may not be a ubiquitous problem in HiSeq X sequence data. Lastly, we provide scripts for applying our method so that index switching can be tested for in other datasets.

scholarly journals De novo transcriptome sequencing of Rhododendron molle and identification of genes involved in the biosynthesis of secondary metabolites

2020 ◽  
Author(s):  
Guolin Zhou ◽  
Ping Zhu
Keyword(s):  
Secondary Metabolites ◽  
Transcriptome Sequencing ◽  
De Novo ◽  
Illumina Hiseq ◽  
Medicinal Value ◽  
Relieve Pain ◽  
Chemical Studies ◽  
Illumina Hiseq Platform ◽  
Differential Gene ◽  
First Time

Abstract Background: Rhododendron molle (Ericaceae) is a traditional Chinese medicinal plant, its flower and root have been widely used to treat rheumatism and relieve pain for thousands of years in China. Chemical studies have revealed that R. molle contains abundant secondary metabolites such as terpenoinds, flavonoids and lignans, some of which have exhibited various bioactivities including antioxidant, hypotension and analgesic activity. In spite of immense pharmaceutical importance, the mechanism underlying the biosynthesis of secondary metabolites remains unknown and the genomic information is unavailable. Results: To gain molecular insight into this plant, especially on the pharmaceutically important secondary metabolic information, we conducted deep transcriptome sequencing for R. molle flower and root using the Illumina Hiseq platform. In total, 100,603 unigenes were generated through de novo assembly with mean length of 778 bp, 57.1% of these unigenes were annotated in public databases and 17,906 of those unigenes showed significant match in the KEGG database. Unigenes involved in the biosynthesis of secondary metabolites were annotated, including the TPSs and CYPs that were potentially responsible for the biosynthesis of grayanoids. Moreover, 3,376 transcription factors and 10,828 simple sequence repeats (SSRs) were also identified. Additionally, we further performed differential gene expression (DEG) analysis of the flower and root transcriptome libraries and identified numerous genes that were specifically expressed or up-regulated in flower.Conclusions: To the best of our knowledge, this is the first time to generate and thoroughly analyze the transcriptome data of both R. molle flower and root. This study provided an important genetic resource which will shed light on elucidating various secondary metabolite biosynthetic pathways in R. molle, especially for those with medicinal value and allow for drug development in this plant.

scholarly journals Insights into the Gryllus bimaculatus Immune-Related Transcriptomic Profiling to Combat Naturally Invading Pathogens

2020 ◽  
Vol 6 (4) ◽  
pp. 232 ◽  
Author(s):  
Abid Hussain ◽  
Muhammad Waqar Ali ◽  
Ahmed Mohammed AlJabr ◽  
Saad Naser AL-Kahtani
Keyword(s):  
Defense Mechanism ◽  
Immune Defense ◽  
Cdna Libraries ◽  
Gryllus Bimaculatus ◽  
Illumina Hiseq ◽  
Field Crickets ◽  
Wide Range ◽  
Illumina Hiseq Platform ◽  
Immune Related Genes ◽  
First Time

Natural pathogen pressure is an important factor that shapes the host immune defense mechanism. The current study primarily aimed to explore the molecular basis of the natural immune defense mechanism of a sporadic pest, Gryllus bimaculatus, during swarming by constructing cDNA libraries of the female mid-gut, male mid-gut, testes, and ovaries. The Illumina HiSeq platform generated an average of 7.9 G, 11.77 G, 10.07 G, and 10.07 G bases of outputs from the male mid-gut, female mid-gut, testes, and ovaries and libraries, respectively. The transcriptome of two-spotted field crickets was assembled into 233,172 UniGenes, which yielded approximately 163.58 million reads. On the other hand, there were 43,055 genes in common that were shared among all the biological samples. Gene Ontology analysis successfully annotated 492 immune-related genes, which comprised mainly Pattern Recognition Receptors (62 genes), Signal modulators (57 genes), Signal transduction (214 genes), Effectors (36 genes), and another immune-related 123 genes. In summary, the identified wide range of immune-related genes from G. bimaculatus indicates the existence of a sophisticated and specialized broad spectrum immune mechanism against invading pathogens, which provides, for the first time, insights into the molecular mechanism of disease resistance among two-spotted field crickets.

scholarly journals Characterization of mRNA Profiles of Exosomes from Diverse Forms of M2 Macrophages

2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
Yuan Yue ◽  
Suiqing Huang ◽  
Zixuan Wu ◽  
Keke Wang ◽  
Huayang Li ◽  
...  
Keyword(s):  
Messenger Rnas ◽  
M2 Macrophages ◽  
Cellular Functions ◽  
Nf Kappa B ◽  
Illumina Hiseq ◽  
Illumina Hiseq Platform ◽  
High Level ◽  
Culture Supernatants ◽  
Necrosis Factor

Exosomes transmit certain amounts of molecules to specific recipient cells for intercellular communication. Among these molecules, messenger RNAs (mRNAs) may be delivered and translated into proteins in the recipient cells, and these mRNAs are thought to be critical mediators of exosomal functions. There are three subtypes of M2 macrophages (M2Ф), M2aФ, M2bФ, and M2cФ, which have different specific functional programs. The aim of the present study was to screen the mRNA profiles in the exosomes of these macrophage subtypes and to analyze the transcriptomic profile features associated with their specific functions. The mRNA contents of the exosomes isolated from the culture supernatants of the M2Ф subtypes were analyzed and compared using the Illumina HiSeq platform. The results indicated that the exosomes contained particular mRNAs from their source cells and were messengers of cellular functions. Bioinformatics analysis suggested that the exosomal mRNAs from M2bФs are enriched in the Toll-like receptor (TLR), tumor necrosis factor (TNF), NOD-like receptor (NLR), and NF-kappa B (NF-κB) signaling pathways. The mRNA profile of exosomes from M2bФ was distinctly different from that of exosomes from M2aФ and M2cФ and was consistent with the M2bФ cytological characteristic of maintaining a high level of proinflammatory cytokine and regulatory factor production. Therefore, the mRNA profiles revealed several characteristics of the exosomes from diverse forms of M2Ф. Further functional investigations based on these results may advance the understanding of the physiological roles of exosome-transferred mRNAs in MФ functions.

Development of nuclear microsatellite markers in Stizophyllum (Bignoniaceae) using next-generation sequencing

2019 ◽  
Vol 17 (04) ◽  
pp. 382-385 ◽  
Author(s):  
Maila Beyer ◽  
Alison Gonçalvez Nazareno ◽  
Lúcia G. Lohmann
Keyword(s):  
Microsatellite Markers ◽  
Polymorphic Information Content ◽  
Nuclear Markers ◽  
Illumina Hiseq ◽  
Closely Related Species ◽  
Widespread Species ◽  
Genomic Dataset ◽  
Nuclear Microsatellite ◽  
Illumina Hiseq Platform ◽  
Generation Sequencing

AbstractHere we developed the first set of nuclear microsatellite markers (nSSRs) for Stizophyllum riparium (Bignoniaceae), a widespread species of Neotropical liana. Thirty-two sets of primers were isolated from a genomic dataset obtained with an Illumina HiSeq Platform, and characterized for 57 individuals of S. riparium from three populations. Nine nSSRs were polymorphic and the number of alleles ranged from eight to 29. The unbiased expected heterozygosity per locus ranged from 0.724 to 0.952 and the polymorphic information content values ranged from 0.717 to 0.944. All nine primer pairs also amplified for two closely related species (S. inaequilaterum and S. perforatum). The new set of nuclear markers will be useful for population genetics studies of Stizophyllum as a whole.

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