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Solexa sequencing of small RNAs in Chinese Amphioxus

ABSTRACT: We applied Solexa sequencing technology to identify Amphioxus microRNA genes. We identified 113 amphioxus microRNA genes, 55 were conserved across species and coded for 45 nonredundant mature miRNAs, whereas 58 were amphioxus-specific and accounted for 53 mature miRNAs. Analyzing the evolutionary history of amphioxus miRNAs, we found amphioxus possessed many miRNAs that are also found in chordates and vertebrates, suggesting these miRNAs may represent cephalochordate lineage innovation. By detailed comparison of the miRNA phylogenetic histories, we further found that amphioxus is more vertebrate-like than tunicates. Keywords: Small RNA

ORGANISM(S): Branchiostoma belcheri

PROVIDER: GSE16859 | GEO | 2009/06/30

SECONDARY ACCESSION(S): PRJNA117563

REPOSITORIES: GEO

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Solexa sequencing of small RNAs in Chinese Amphioxus

Project description:We applied Solexa sequencing technology to identify Amphioxus microRNA genes. We identified 113 amphioxus microRNA genes, 55 were conserved across species and coded for 45 nonredundant mature miRNAs, whereas 58 were amphioxus-specific and accounted for 53 mature miRNAs. Analyzing the evolutionary history of amphioxus miRNAs, we found amphioxus possessed many miRNAs that are also found in chordates and vertebrates, suggesting these miRNAs may represent cephalochordate lineage innovation. By detailed comparison of the miRNA phylogenetic histories, we further found that amphioxus is more vertebrate-like than tunicates. Keywords: Small RNA 18-30 nt small RNAs from 12 adult Chinese Amphioxus were sequenced in one Solexa lane.

2009-06-29 | E-GEOD-16859 | biostudies-arrayexpress

microRNA expression changes after lipopolysaccharide treatment in gills of amphioxus Branchiostoma belcheri

Project description:Recently, amphioxus has served as a model for studying the origin and evolution of vertebrate immunity. However, little is known about how microRNAs (miRNAs) are involved in the immune defense in amphioxus. In this article, we identified the amphioxus miRNAs in the acute-phase response to Lipopolysaccharide (LPS). First, we determined the time point for the peak of immune response in amphioxus after LPS challenge by evaluating the expression of TLR4 and NF-κb(v-rel) which were commonly used immune response indicators. Then we performed miRNA microarray analysis on gill samples collected at the time point to select the differentially expressed miRNAs. Finally, we used real-time quantitative PCR to detect the expression patterns of amphioxus miRNAs under effective LPS challenge during the time course. The microarray data revealed that the miRNA expression file was significantly changed after LPS stimulation. The changes of the most upregulated and most downregualted miRNAs in gills of the amphioxus following challenge with LPS revealed a temporal induction kinetic. Our current study will provide valuable information to take an insight into molecular mechanism of innate immune and the evolution of the miRNA family.

2017-03-10 | GSE85326 | GEO

Identification of microRNA expression profiles in the gill, intestine and hepatic caecum of amphioxus

Project description:The amphioxus, as a simple basal chordate model, plays an important and unique role on providing insights into the evolution of tissues and organs of the vertebrates. To understand the unique features of the amphioxus during evolution, it’s important to identify the gene and microRNA (miRNA) expression profiles of amphioxus tissues or organs. However, the systematic examination of these expression profiles is not conducted. Here, we focused on characterizing the miRNA expression patterns of three amphioxus digestive organs (the gill, intestine and hepatic caecum) that are believed to be the first line of immune defense.

2016-12-08 | GSE87094 | GEO

A single 3D chromatin compartment in amphioxus Hox cluster suggests a stepwise evolutionary origin for vertebrate Hox bimodal regulatory topologies

Project description:Comparison among vertebrates and the cephalochordate amphioxus Hox clusters architectures 4C-seq experiments from promoters spanning the amphioxus Hox cluster and the zebrafish hoxd cluster and surrounnding areas,

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Identification and characterization of novel amphioxus microRNAs by Solexa sequencing.

Project description:BACKGROUND: microRNAs (miRNAs) are endogenous small non-coding RNAs that regulate gene expression at the post-transcriptional level. While the number of known human and murine miRNAs is continuously increasing, information regarding miRNAs from other species such as amphioxus remains limited. RESULTS: We combined Solexa sequencing with computational techniques to identify novel miRNAs in the amphioxus species B. belcheri (Gray). This approach allowed us to identify 113 amphioxus miRNA genes. Among them, 55 were conserved across species and encoded 45 non-redundant mature miRNAs, whereas 58 were amphioxus-specific and encoded 53 mature miRNAs. Validation of our results with microarray and stem-loop quantitative RT-PCR revealed that Solexa sequencing is a powerful tool for miRNA discovery. Analyzing the evolutionary history of amphioxus miRNAs, we found that amphioxus possesses many miRNAs unique to chordates and vertebrates, and these may thus represent key steps in the evolutionary progression from cephalochordates to vertebrates. We also found that amphioxus is more similar to vertebrates than are tunicates with respect to their miRNA phylogenetic histories. CONCLUSIONS: Taken together, our results indicate that Solexa sequencing allows the successful discovery of novel miRNAs from amphioxus with high accuracy and efficiency. More importantly, our study provides an opportunity to decipher how the elaboration of the miRNA repertoire that occurred during chordate evolution contributed to the evolution of the vertebrate body plan.

| S-EPMC2728532 | biostudies-literature

Insights into deuterostome evolution from the biphasic transcriptional programmes of hemichordates [RNA-Seq]

Project description:Evolutionary history of deuterostomes has remained unsolved and is intimately related to how chordates originated. Within the clade of deuterostomes, hemichordates and echinoderms (together called Ambulacraria) are sister groups of chordates; comparative studies among the three are insightful for understanding deuterostome evolution. Indirect-developing hemichordates, such as Ptychodera flava, develop into planktonic larvae, which are morphologically similar to echinoderm larvae, before metamorphosing into the adult body plan that retains an anteroposterior polarity homologous to that of chordates. Therefore, deciphering developmental programmes of indirect-developing hemichordates may provide a key for understanding the evolution of deuterostomes and chordate origins. Here, we characterise transcriptomes and chromatin accessibility across multiple developmental stages of P. flava and uncover biphasic developmental programmes controlled by different sets of transcription factors and their corresponding cis-regulatory elements. Transcriptome age and network analyses reveal that the gastrula transcriptome is relatively ancient and highly connected. By comparing developmental transcriptomes of hemichordate, sea urchin and amphioxus, a high conservation of gene expression during gastrulation is identified and extended to neurula stages of amphioxus, in addition to the highly similar larval transcriptomes among the three species. Moreover, P. flava possesses conserved interactions of transcription factors required for the development of echinoderm endomesoderm and chordate axial mesoderm. These results suggest a deuterostome phylotypic stage during gastrulation (corresponding to amphioxus gastrulation and neurulation) controlled by gene regulatory networks with conserved cis-regulatory interactions, and support the hypothesis that the deuterostome ancestor is an indirect-developer.

2024-07-31 | GSE207834 | GEO

Insights into deuterostome evolution from the biphasic transcriptional programmes of hemichordates [ATAC-Seq]

2024-07-31 | GSE207833 | GEO

A single 3D chromatin compartment in amphioxus Hox cluster suggests a stepwise evolutionary origin for vertebrate Hox bimodal regulatory topologies

Project description:Comparison among vertebrates and the cephalochordate amphioxus Hox clusters architectures

2015-12-16 | GSE68737 | GEO

A Comparative Profile of the MicroRNA Transcriptome in Immature and Mature Porcine Testes using Solexa Deep Sequencing

Project description:MicroRNAs (miRNAs) are small non-coding regulatory RNAs that play key roles in many diverse biological processes such as spermatogenesis. However, no study has been performed on the miRNA transcriptome of developing porcine testes. Here, we employed Solexa deep sequencing technology to extend the repertoire of porcine testis miRNAs and extensively compare the expression patterns of the sexually immature and mature porcine testes. Solexa sequencing of two small RNA libraries derived from immature (30 days) and mature (180 days) pig testis samples yielded over 25 million high-quality reads. Overall, the two developmental stages had significantly different small RNA compositions. A custom data analysis pipeline identified 398 known and/or homologous conserved porcine miRNAs, 15 novel pig-specific miRNAs, and 56 novel candidate miRNAs. We further observed multiple mature miRNA variants (isomiRs) and identified a new bidirectional transcribed miRNA locus, ssc-mir-181a. One hundred twenty-two miRNAs were differentially expressed in the immature and mature testes, and 10 were validated using quantitative RT-PCR. Furthermore, GO and KEGG pathway analyses of the predicted miRNA targets further illustrate the likely roles for these differentially expressed miRNAs in spermatogenesis. This study is the first comparative profile of the miRNA transcriptome in immature and mature porcine testes using a deep sequencing approach, and it provides a useful resource for future studies on the role of miRNAs in spermatogenesis and male infertility treatment. microRNA profiling and discovery in two small RNA cDNA libraries derived from sexually immature (30-day) and mature (180-day) pig testes.

2011-09-23 | E-GEOD-28169 | biostudies-arrayexpress

ATAC-seq data of control and Activin-treated amphioxus ectodermal explants at 11 hpf and 19 hpf.

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2022-01-24 | GSE166495 | GEO

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