Genome-wide transcriptome analysis of the early developmental stages of Echinococcus granulosus protoscoleces reveals extensive alternative splicing events in the spliceosome pathway

Abstract Background The complex life cycle of Echinococcus granulosus involves numerous environmental conditions within different intermediate and definitive hosts. This requires adaptation at different levels of transcript regulation. Alternative splicing (AS) and the related cellular functions as one of the major fields of post-genomics has been poorly studied in tapeworms. In the present study, we investigated AS events and their potential biological effects in E. granulosus. Methods Whole transcriptome sequencing data of four groups of protoscoleces were prepared for RNA-seq library construction. Fresh protoscoleces were either used as non-induced controls (NT group) or incubated for 15 min with pepsin (PEP group) and cultivated in a biphasic medium for 12 and 24 h (12 and 24 h groups). The frequency and different types of AS events were identified using rMATS software. Functional annotations and gene ontology of differential AS (DAS) genes were performed using Blast2GO software. AS events were experimentally validated by PCR on the protoscolex cDNAs using specific primers for each gene. Results At least one AS event was found in 38.1% of the genes (3904 out of 10,245) in the protoscoleces during early strobilar development. The genes were associated primarily with cellular and metabolic processes and binding and catalytic activity. KEGG pathway analysis of DAS events revealed a number of genes belonging to different components of the spliceosome complex. These genes tended to belong to common SR proteins, U1-related factors, U2-related factors, complex A-specific factors and other splicing-related proteins. Conclusions The high number of AS events in the transcriptome regulatory mechanisms indicates the essential rapid molecular processes required by the parasite for adaptation in different environments. Graphical Abstract

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Transcriptome Analysis of Ginkgo biloba L. Leaves across Late Developmental Stages Based on RNA-Seq and Co-Expression Network

Forests ◽

10.3390/f12030315 ◽

2021 ◽

Vol 12 (3) ◽

pp. 315

Author(s):

Hailin Liu ◽

Xin Han ◽

Jue Ruan ◽

Lian Xu ◽

Bing He

Keyword(s):

Ginkgo Biloba ◽

Leaf Development ◽

Developmental Stages ◽

Leaf Growth ◽

Rna Seq ◽

Final Size ◽

Dioecious Species ◽

Related Factors ◽

New Genes ◽

Gene Modules

The final size of plant leaves is strictly controlled by environmental and genetic factors, which coordinate cell expansion and cell cycle activity in space and time; however, the regulatory mechanisms of leaf growth are still poorly understood. Ginkgo biloba is a dioecious species native to China with medicinally and phylogenetically important characteristics, and its fan-shaped leaves are unique in gymnosperms, while the mechanism of G. biloba leaf development remains unclear. In this study we studied the transcriptome of G. biloba leaves at three developmental stages using high-throughput RNA-seq technology. Approximately 4167 differentially expressed genes (DEGs) were obtained, and a total of 12,137 genes were structure optimized together with 732 new genes identified. More than 50 growth-related factors and gene modules were identified based on DEG and Weighted Gene Co-expression Network Analysis. These results could remarkably expand the existing transcriptome resources of G. biloba, and provide references for subsequent analysis of ginkgo leaf development.

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Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution

Scientific Reports ◽

10.1038/s41598-021-88160-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Jiawei Zhou ◽

Shuo Zhang ◽

Jie Wang ◽

Hongmei Shen ◽

Bin Ai ◽

...

Keyword(s):

Phylogenetic Analyses ◽

Population Level ◽

Gene Content ◽

Sequencing Data ◽

Cellular Functions ◽

Chloroplast Evolution ◽

Chloroplast Genomes ◽

Genome Features ◽

Genome Annotations ◽

Genome Analyses

AbstractThe chloroplast is one of two organelles containing a separate genome that codes for essential and distinct cellular functions such as photosynthesis. Given the importance of chloroplasts in plant metabolism, the genomic architecture and gene content have been strongly conserved through long periods of time and as such are useful molecular tools for evolutionary inferences. At present, complete chloroplast genomes from over 4000 species have been deposited into publicly accessible databases. Despite the large number of complete chloroplast genomes, comprehensive analyses regarding genome architecture and gene content have not been conducted for many lineages with complete species sampling. In this study, we employed the genus Populus to assess how more comprehensively sampled chloroplast genome analyses can be used in understanding chloroplast evolution in a broadly studied lineage of angiosperms. We conducted comparative analyses across Populus in order to elucidate variation in key genome features such as genome size, gene number, gene content, repeat type and number, SSR (Simple Sequence Repeat) abundance, and boundary positioning between the four main units of the genome. We found that some genome annotations were variable across the genus owing in part from errors in assembly or data checking and from this provided corrected annotations. We also employed complete chloroplast genomes for phylogenetic analyses including the dating of divergence times throughout the genus. Lastly, we utilized re-sequencing data to describe the variations of pan-chloroplast genomes at the population level for P. euphratica. The analyses used in this paper provide a blueprint for the types of analyses that can be conducted with publicly available chloroplast genomes as well as methods for building upon existing datasets to improve evolutionary inference.

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A survey of computational methods in transcriptome-wide alternative splicing analysis

BioMolecular Concepts ◽

10.1515/bmc-2014-0040 ◽

2015 ◽

Vol 6 (1) ◽

pp. 59-66 ◽

Cited By ~ 10

Author(s):

Jianbo Wang ◽

Zhenqing Ye ◽

Tim H.-M. Huang ◽

Huidong Shi ◽

Victor Jin

Keyword(s):

Alternative Splicing ◽

Experimental Validation ◽

Gene Diversity ◽

Exon Skipping ◽

Differential Splicing ◽

Sequencing Data ◽

Future Directions ◽

Specific Analysis ◽

Software Implementations ◽

Expected Outcomes

AbstractAlternative splicing is widely recognized for its roles in regulating genes and creating gene diversity. Consequently the identification and quantification of differentially spliced transcripts is pivotal for transcriptome analysis. Here, we review the currently available computational approaches for the analysis of RNA-sequencing data with a focus on exon-skipping events of alternative splicing and discuss the novelties as well as challenges faced to perform differential splicing analyses. In accordance with operational needs we have classified the software tools, which may be instrumental for a specific analysis based on the experimental objectives and expected outcomes. In addition, we also propose a framework for future directions by pinpointing more extensive experimental validation to assess the accuracy of the software predictions and improvements that would facilitate visualizations, data processing, and downstream analyses along with their associated software implementations.

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Regulation of Multiple Core Spliceosomal Proteins by Alternative Splicing-Coupled Nonsense-Mediated mRNA Decay

Molecular and Cellular Biology ◽

10.1128/mcb.00361-08 ◽

2008 ◽

Vol 28 (13) ◽

pp. 4320-4330 ◽

Cited By ~ 126

Author(s):

Arneet L. Saltzman ◽

Yoon Ki Kim ◽

Qun Pan ◽

Matthew M. Fagnani ◽

Lynne E. Maquat ◽

...

Keyword(s):

Gene Expression ◽

Alternative Splicing ◽

Mrna Decay ◽

Splice Variants ◽

Cellular Functions ◽

Regulate Gene Expression ◽

Premature Termination Codons ◽

Microarray Profiling ◽

Nonsense Mediated Mrna Decay ◽

Regulate Gene

ABSTRACT Alternative splicing (AS) can regulate gene expression by introducing premature termination codons (PTCs) into spliced mRNA that subsequently elicit transcript degradation by the nonsense-mediated mRNA decay (NMD) pathway. However, the range of cellular functions controlled by this process and the factors required are poorly understood. By quantitative AS microarray profiling, we find that there are significant overlaps among the sets of PTC-introducing AS events affected by individual knockdown of the three core human NMD factors, Up-Frameshift 1 (UPF1), UPF2, and UPF3X/B. However, the levels of some PTC-containing splice variants are less or not detectably affected by the knockdown of UPF2 and/or UPF3X, compared with the knockdown of UPF1. The intron sequences flanking the affected alternative exons are often highly conserved, suggesting important regulatory roles for these AS events. The corresponding genes represent diverse cellular functions, and surprisingly, many encode core spliceosomal proteins and assembly factors. We further show that conserved, PTC-introducing AS events are enriched in genes that encode core spliceosomal proteins. Where tested, altering the expression levels of these core spliceosomal components affects the regulation of PTC-containing splice variants from the corresponding genes. Together, our results show that AS-coupled NMD can have different UPF factor requirements and is likely to regulate many general components of the spliceosome. The results further implicate general spliceosomal components in AS regulation.

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Photothermal modulation of human stem cells using light-responsive 2D nanomaterials

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1914345117 ◽

2020 ◽

Vol 117 (24) ◽

pp. 13329-13338

Author(s):

James K. Carrow ◽

Kanwar Abhay Singh ◽

Manish K. Jaiswal ◽

Adelina Ramirez ◽

Giriraj Lokhande ◽

...

Keyword(s):

Stem Cells ◽

Near Infrared ◽

Global Gene Expression ◽

Cellular Migration ◽

Human Stem Cells ◽

Cellular Functions ◽

Nir Light ◽

Whole Transcriptome Sequencing ◽

Whole Transcriptome ◽

Stimulation Of

Two-dimensional (2D) molybdenum disulfide (MoS2) nanomaterials are an emerging class of biomaterials that are photoresponsive at near-infrared wavelengths (NIR). Here, we demonstrate the ability of 2D MoS2to modulate cellular functions of human stem cells through photothermal mechanisms. The interaction of MoS2and NIR stimulation of MoS2with human stem cells is investigated using whole-transcriptome sequencing (RNA-seq). Global gene expression profile of stem cells reveals significant influence of MoS2and NIR stimulation of MoS2on integrins, cellular migration, and wound healing. The combination of MoS2and NIR light may provide new approaches to regulate and direct these cellular functions for the purposes of regenerative medicine as well as cancer therapy.

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AStrap: identification of alternative splicing from transcript sequences without a reference genome

Bioinformatics ◽

10.1093/bioinformatics/bty1008 ◽

2018 ◽

Vol 35 (15) ◽

pp. 2654-2656 ◽

Cited By ~ 5

Author(s):

Guoli Ji ◽

Wenbin Ye ◽

Yaru Su ◽

Moliang Chen ◽

Guangzao Huang ◽

...

Keyword(s):

Machine Learning ◽

Alternative Splicing ◽

Single Molecule ◽

Reference Genome ◽

De Novo ◽

Supplementary Information ◽

Model Organisms ◽

Sequencing Data ◽

Extensive Evaluation ◽

Reference Genomes

Abstract Summary Alternative splicing (AS) is a well-established mechanism for increasing transcriptome and proteome diversity, however, detecting AS events and distinguishing among AS types in organisms without available reference genomes remains challenging. We developed a de novo approach called AStrap for AS analysis without using a reference genome. AStrap identifies AS events by extensive pair-wise alignments of transcript sequences and predicts AS types by a machine-learning model integrating more than 500 assembled features. We evaluated AStrap using collected AS events from reference genomes of rice and human as well as single-molecule real-time sequencing data from Amborella trichopoda. Results show that AStrap can identify much more AS events with comparable or higher accuracy than the competing method. AStrap also possesses a unique feature of predicting AS types, which achieves an overall accuracy of ∼0.87 for different species. Extensive evaluation of AStrap using different parameters, sample sizes and machine-learning models on different species also demonstrates the robustness and flexibility of AStrap. AStrap could be a valuable addition to the community for the study of AS in non-model organisms with limited genetic resources. Availability and implementation AStrap is available for download at https://github.com/BMILAB/AStrap. Supplementary information Supplementary data are available at Bioinformatics online.

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Splicing Express: a software suite for alternative splicing analysis using next-generation sequencing data

PeerJ ◽

10.7717/peerj.1419 ◽

2015 ◽

Vol 3 ◽

pp. e1419 ◽

Cited By ~ 6

Author(s):

Jose E. Kroll ◽

Jihoon Kim ◽

Lucila Ohno-Machado ◽

Sandro J. de Souza

Keyword(s):

Alternative Splicing ◽

Dna Sequencing ◽

Next Generation Sequencing Data ◽

Next Generation ◽

Sequencing Data ◽

Software Suite ◽

Next Generation Dna Sequencing ◽

Sequencing Technologies ◽

Body Map ◽

Sequencing Platforms

Motivation.Alternative splicing events (ASEs) are prevalent in the transcriptome of eukaryotic species and are known to influence many biological phenomena. The identification and quantification of these events are crucial for a better understanding of biological processes. Next-generation DNA sequencing technologies have allowed deep characterization of transcriptomes and made it possible to address these issues. ASEs analysis, however, represents a challenging task especially when many different samples need to be compared. Some popular tools for the analysis of ASEs are known to report thousands of events without annotations and/or graphical representations. A new tool for the identification and visualization of ASEs is here described, which can be used by biologists without a solid bioinformatics background.Results.A software suite namedSplicing Expresswas created to perform ASEs analysis from transcriptome sequencing data derived from next-generation DNA sequencing platforms. Its major goal is to serve the needs of biomedical researchers who do not have bioinformatics skills.Splicing Expressperforms automatic annotation of transcriptome data (GTF files) using gene coordinates available from the UCSC genome browser and allows the analysis of data from all available species. The identification of ASEs is done by a known algorithm previously implemented in another tool namedSplooce. As a final result,Splicing Expresscreates a set of HTML files composed of graphics and tables designed to describe the expression profile of ASEs among all analyzed samples. By using RNA-Seq data from the Illumina Human Body Map and the Rat Body Map, we show thatSplicing Expressis able to perform all tasks in a straightforward way, identifying well-known specific events.Availability and Implementation.Splicing Expressis written in Perl and is suitable to run only in UNIX-like systems. More details can be found at:http://www.bioinformatics-brazil.org/splicingexpress.

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Divergent and convergent evolution of housekeeping genes in human–pig lineage

PeerJ ◽

10.7717/peerj.4840 ◽

2018 ◽

Vol 6 ◽

pp. e4840 ◽

Cited By ~ 4

Author(s):

Kai Wei ◽

Tingting Zhang ◽

Lei Ma

Keyword(s):

Active Sites ◽

Evolutionary Dynamics ◽

Purifying Selection ◽

Housekeeping Genes ◽

Neutral Evolution ◽

Structure Evolution ◽

Tissue Cell ◽

Sequencing Data ◽

Cellular Functions ◽

Species Specific

Housekeeping genes are ubiquitously expressed and maintain basic cellular functions across tissue/cell type conditions. The present study aimed to develop a set of pig housekeeping genes and compare the structure, evolution and function of housekeeping genes in the human–pig lineage. By using RNA sequencing data, we identified 3,136 pig housekeeping genes. Compared with human housekeeping genes, we found that pig housekeeping genes were longer and subjected to slightly weaker purifying selection pressure and faster neutral evolution. Common housekeeping genes, shared by the two species, achieve stronger purifying selection than species-specific genes. However, pig- and human-specific housekeeping genes have similar functions. Some species-specific housekeeping genes have evolved independently to form similar protein active sites or structure, such as the classical catalytic serine–histidine–aspartate triad, implying that they have converged for maintaining the basic cellular function, which allows them to adapt to the environment. Human and pig housekeeping genes have varied structures and gene lists, but they have converged to maintain basic cellular functions essential for the existence of a cell, regardless of its specific role in the species. The results of our study shed light on the evolutionary dynamics of housekeeping genes.

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Alternative RNA splicing that is spatially regulated: generation of transcripts from the Antennapedia gene of Drosophila melanogaster with different protein-coding regions

Molecular and Cellular Biology ◽

10.1128/mcb.8.10.4143-4154.1988 ◽

1988 ◽

Vol 8 (10) ◽

pp. 4143-4154

Author(s):

V L Stroeher ◽

J C Gaiser ◽

R L Garber

Keyword(s):

Alternative Splicing ◽

Rna Splicing ◽

Developmental Stages ◽

Molecular Evidence ◽

Rnase Protection ◽

Protein Coding ◽

Spatial Regulation ◽

Coding Regions ◽

Imaginal Disks ◽

Isolated Tissues

We have shown previously that transcription of the Drosophila homeotic gene Antennapedia results in four major RNA species which differ in long 5'- and 3'-untranslated sequences. The protein-coding portion of these transcripts, however, is located in exons common to all. Using RNase protection assays and further cDNA clone isolation, we have now detected two alternative splicing events between exons of this region. These result in four RNA variations which, if translated, would encode a family of Antennapedia proteins. By analyzing transcripts from various developmental stages and isolated tissues, we show that alternative splicing is under strict temporal and spatial regulation. For example, while similar patterns of splicing were found for all wild-type thoracic imaginal disks examined, these differed distinctly from the patterns observed in neural tissues. Our results suggest that individual RNAs may be associated with different biological roles, and provide molecular evidence that the Antennapedia gene is involved in multiple functions.

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Whirling Disease: Reviews and Current Topics

Whirling Disease: Reviews and Current Topics ◽

10.47886/9781888569377.ch4 ◽

2002 ◽

Keyword(s):

Life Cycle ◽

Developmental Stages ◽

Small Subunit ◽

Fish Host ◽

Complex Life Cycle ◽

Developmental Cycle ◽

Myxobolus Cerebralis ◽

Rdna Sequences ◽

Complex Development ◽

The One

ABSTRACT. Myxobolus cerebralis possesses unique phenotypic and genotypic characteristics when compared with other histozoic parasites from the phylum Myxozoa. The parasite infects the cartilage and thereby induces a serious and potentially lethal disease in salmonid fish. Comparisons of the small subunit ribosomal DNA (ssu rDNA) sequences of M. cerebralis to other myxozoans demonstrate that the parasite has evolved separately from other Myxobolus spp. that may appear in cartilage or nervous tissues of the fish host. Myxobolus cerebralis has a complex life cycle involving two hosts and numerous developmental stages that may divide by mitosis, endogeny, or plasmotomy, and, at one stage, by meiosis. In the salmonid host, the parasite undergoes extensive migration from initial sites of attachment to the epidermis, through the nervous system, to reach cartilage, the site where sporogenesis occurs. During this migration, parasite numbers may increase by replication. Sporogenesis is initiated by autogamy, a process typical of pansporoblastic myxosporean development that involves the union of the one cell (pericyte) with another (sporogonic). Following this union, the sporogonic cell will give rise to all subsequent cells that differentiate into the lenticular shaped spore with a diameter of approximately 10 µm. This spore or myxospore is an environmentally resistant stage characterized by two hardened valves surrounding two polar capsules with coiled filaments and a binucleate sporoplasm cell. In the fish, these spores are found only in cartilage where they reside until released from fish that die or are consumed by other fish or fish-eating animals (e.g., birds). Spores reaching the aquatic sediments can be ingested and hatch in susceptible oligochaete hosts. The released sporoplasm invades and then resides between cells of the intestinal mucosa. In contrast to the parasite in the fish host, the parasite in the oligochaete undergoes the entire developmental cycle in this location. This developmental cycle involves merogony, gametogamy or the formation of haploid gametes, and sporogony. The actinosporean spores, formed at the culmination of this development, are released into the lumen of the intestine, prior to discharging into the aquatic environment. The mechanisms underlying the complex development of M. cerebralis, and its interactions with both hosts, are poorly understood. Recent advances, however, are providing insights into the factors that mediate certain phases of the infection. In this review, we consider known and recently obtained information on the taxonomy, development, and life cycle of the parasite.

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