scholarly journals The Genome of the “Sea Vomit” Didemnum vexillum

Life ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1377
Author(s):  
Ernesto Parra-Rincón ◽  
Cristian A. Velandia-Huerto ◽  
Adriaan Gittenberger ◽  
Jörg Fallmann ◽  
Thomas Gatter ◽  
...  
Keyword(s):  
Hybrid Approach ◽  
Sister Group ◽  
Total Size ◽  
High Genetic Diversity ◽  
Didemnum Vexillum ◽  
Protein Coding ◽  
Draft Assembly ◽  
Sea Squirt ◽  
Genome Duplications ◽  
Non Coding Rnas

Tunicates are the sister group of vertebrates and thus occupy a key position for investigations into vertebrate innovations as well as into the consequences of the vertebrate-specific genome duplications. Nevertheless, tunicate genomes have not been studied extensively in the past, and comparative studies of tunicate genomes have remained scarce. The carpet sea squirt Didemnum vexillum, commonly known as “sea vomit”, is a colonial tunicate considered an invasive species with substantial ecological and economical risk. We report the assembly of the D. vexillum genome using a hybrid approach that combines 28.5 Gb Illumina and 12.35 Gb of PacBio data. The new hybrid scaffolded assembly has a total size of 517.55 Mb that increases contig length about eightfold compared to previous, Illumina-only assembly. As a consequence of an unusually high genetic diversity of the colonies and the moderate length of the PacBio reads, presumably caused by the unusually acidic milieu of the tunic, the assembly is highly fragmented (L50 = 25,284, N50 = 6539). It is sufficient, however, for comprehensive annotations of both protein-coding genes and non-coding RNAs. Despite its shortcomings, the draft assembly of the “sea vomit” genome provides a valuable resource for comparative tunicate genomics and for the study of the specific properties of colonial ascidians.

scholarly journals The genome of the "Sea Vomit" Didemnum vexillum

2020 ◽  
Author(s):  
Ernesto Parra-Rincón ◽  
Cristian A Velandia-Huerto ◽  
Jörg Fallmann ◽  
Adriaan Gittenberger ◽  
Federico D Brown ◽  
...  
Keyword(s):  
Hybrid Approach ◽  
Sister Group ◽  
Total Size ◽  
Didemnum Vexillum ◽  
Protein Coding ◽  
Draft Assembly ◽  
The Past ◽  
Sequencing Technologies ◽  
Sea Squirt ◽  
Genome Duplications

Abstract Background: Tunicates are the sister group of vertebrates and thus occupy a key position for investigations into vertebrate innovations as well as into the consequences of the vertebrate-specific genome duplications. Nevertheless, tunicate genomes have not been studied extensively in the past and comparative studies of tunicate genomes have remained scarce. The carpet sea squirt Didemnum vexillum is a colonial tunicate considered an invasive species with substantial ecological and economical risk.Results: We report a newly re-assembled genome of Didemnum vexillum. We used a hybrid approach that combines two genome sequencing technologies and also its first transcriptome. Started from 28.5 Gb Illumina and 12.35 Gb of PacBio data a new hybrid scaffolded assembly was obtained comprised of a total size of 517.55 Mb that increases contig length about 8-fold compared to previous, Illumina-only assembly. While still highly fragmented (L50=25284, N50=6539), the assembly is suffcient for comprehensive annotations of both protein-coding genes and non-coding RNAs.Conclusions: The draft assembly of the "sea vomit" genome provides a valuable resource for comparative tunicate genomics and for the study of the specific properties of colonial ascidians.Availability: Genome and annotation data as well as a link to a UCSC Genome Browser hub are available at http://tunicatadvexillum.bioinf.uni-leipzig.de/.

scholarly journals Investigation of long non-coding RNAs as regulatory players of grapevine response to powdery and downy mildew infection

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Garima Bhatia ◽  
Santosh K. Upadhyay ◽  
Anuradha Upadhyay ◽  
Kashmir Singh
Keyword(s):  
Downy Mildew ◽  
Plasmopara Viticola ◽  
Defense Responses ◽  
Protein Coding ◽  
Functional Roles ◽  
Real Time Quantitative Pcr ◽  
Transcriptional Reprogramming ◽  
Sequencing Technologies ◽  
Non Coding Rnas ◽  
Fungal Phytopathogens

Abstract Background Long non-coding RNAs (lncRNAs) are regulatory transcripts of length > 200 nt. Owing to the rapidly progressing RNA-sequencing technologies, lncRNAs are emerging as considerable nodes in the plant antifungal defense networks. Therefore, we investigated their role in Vitis vinifera (grapevine) in response to obligate biotrophic fungal phytopathogens, Erysiphe necator (powdery mildew, PM) and Plasmopara viticola (downy mildew, DM), which impose huge agro-economic burden on grape-growers worldwide. Results Using computational approach based on RNA-seq data, 71 PM- and 83 DM-responsive V. vinifera lncRNAs were identified and comprehensively examined for their putative functional roles in plant defense response. V. vinifera protein coding sequences (CDS) were also profiled based on expression levels, and 1037 PM-responsive and 670 DM-responsive CDS were identified. Next, co-expression analysis-based functional annotation revealed their association with gene ontology (GO) terms for ‘response to stress’, ‘response to biotic stimulus’, ‘immune system process’, etc. Further investigation based on analysis of domains, enzyme classification, pathways enrichment, transcription factors (TFs), interactions with microRNAs (miRNAs), and real-time quantitative PCR of lncRNAs and co-expressing CDS pairs suggested their involvement in modulation of basal and specific defense responses such as: Ca2+-dependent signaling, cell wall reinforcement, reactive oxygen species metabolism, pathogenesis related proteins accumulation, phytohormonal signal transduction, and secondary metabolism. Conclusions Overall, the identified lncRNAs provide insights into the underlying intricacy of grapevine transcriptional reprogramming/post-transcriptional regulation to delay or seize the living cell-dependent pathogen growth. Therefore, in addition to defense-responsive genes such as TFs, the identified lncRNAs can be further examined and leveraged to candidates for biotechnological improvement/breeding to enhance fungal stress resistance in this susceptible fruit crop of economic and nutritional importance.

scholarly journals Non-Coding RNAs as Prognostic Markers for Endometrial Cancer

2021 ◽  
Vol 22 (6) ◽  
pp. 3151 ◽  
Author(s):  
Roberto Piergentili ◽  
Simona Zaami ◽  
Anna Franca Cavaliere ◽  
Fabrizio Signore ◽  
Giovanni Scambia ◽  
...  
Keyword(s):  
Endometrial Cancer ◽  
Prognostic Markers ◽  
Classification Systems ◽  
Prognostic Role ◽  
Protein Coding ◽  
Pathological Characteristics ◽  
Epigenetic Events ◽  
Cancer Types ◽  
Non Coding Rnas

Endometrial cancer (EC) has been classified over the years, for prognostic and therapeutic purposes. In recent years, classification systems have been emerging not only based on EC clinical and pathological characteristics but also on its genetic and epigenetic features. Noncoding RNAs (ncRNAs) are emerging as promising markers in several cancer types, including EC, for which their prognostic value is currently under investigation and will likely integrate the present prognostic tools based on protein coding genes. This review aims to underline the importance of the genetic and epigenetic events in the EC tumorigenesis, by expounding upon the prognostic role of ncRNAs.

scholarly journals Insights into the Genome Sequence ofChromobacterium amazonenseIsolated from a Tropical Freshwater Lake

2018 ◽  
Vol 2018 ◽  
pp. 1-10
Author(s):  
Alexandre Bueno Santos ◽  
Patrícia Silva Costa ◽  
Anderson Oliveira do Carmo ◽  
Gabriel da Rocha Fernandes ◽  
Larissa Lopes Silva Scholte ◽  
...  
Keyword(s):  
De Novo ◽  
Genomic Diversity ◽  
Protein Coding ◽  
Biotechnological Potential ◽  
Draft Assembly ◽  
Functional Studies ◽  
Alpha Hemolysin ◽  
Type Iv ◽  
Nudix Hydrolases ◽  
Colicin V

Members of the genusChromobacteriumhave been isolated from geographically diverse ecosystems and exhibit considerable metabolic flexibility, as well as biotechnological and pathogenic properties in some species. This study reports the draft assembly and detailed sequence analysis ofChromobacterium amazonensestrain 56AF. The de novo-assembled genome is 4,556,707 bp in size and contains 4294 protein-coding and 95 RNA genes, including 88 tRNA, six rRNA, and one tmRNA operon. A repertoire of genes implicated in virulence, for example, hemolysin, hemolytic enterotoxins, colicin V, lytic proteins, and Nudix hydrolases, is present. The genome also contains a collection of genes of biotechnological interest, including esterases, lipase, auxins, chitinases, phytoene synthase and phytoene desaturase, polyhydroxyalkanoates, violacein, plastocyanin/azurin, and detoxifying compounds. Importantly, unlike otherChromobacteriumspecies, the 56AF genome contains genes for pore-forming toxin alpha-hemolysin, a type IV secretion system, among others. The analysis of theC. amazonensestrain 56AF genome reveals the versatility, adaptability, and biotechnological potential of this bacterium. This study provides molecular information that may pave the way for further comparative genomics and functional studies involvingChromobacterium-related isolates and improves our understanding of the global genomic diversity ofChromobacteriumspecies.

scholarly journals RNA sequencing of transcriptomes in human brain regions: protein-coding and non-coding RNAs, isoforms and alleles

BMC Genomics ◽  
2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Amy Webb ◽  
Audrey C. Papp ◽  
Amanda Curtis ◽  
Leslie C. Newman ◽  
Maciej Pietrzak ◽  
...  
Keyword(s):  
Human Brain ◽  
Rna Sequencing ◽  
Brain Regions ◽  
Protein Coding ◽  
Non Coding Rnas

scholarly journals CALINCA—A Novel Pipeline for the Identification of lncRNAs in Podocyte Disease

Cells ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 692
Author(s):  
Sweta Talyan ◽  
Samantha Filipów ◽  
Michael Ignarski ◽  
Magdalena Smieszek ◽  
He Chen ◽  
...  
Keyword(s):  
Cell Biology ◽  
Mammalian Cells ◽  
De Novo ◽  
Depth Information ◽  
Gene Products ◽  
Classical Analysis ◽  
Protein Coding ◽  
Bioinformatic Pipeline ◽  
Non Coding Rnas ◽  
Filtration Unit

Diseases of the renal filtration unit—the glomerulus—are the most common cause of chronic kidney disease. Podocytes are the pivotal cell type for the function of this filter and focal-segmental glomerulosclerosis (FSGS) is a classic example of a podocytopathy leading to proteinuria and glomerular scarring. Currently, no targeted treatment of FSGS is available. This lack of therapeutic strategies is explained by a limited understanding of the defects in podocyte cell biology leading to FSGS. To date, most studies in the field have focused on protein-coding genes and their gene products. However, more than 80% of all transcripts produced by mammalian cells are actually non-coding. Here, long non-coding RNAs (lncRNAs) are a relatively novel class of transcripts and have not been systematically studied in FSGS to date. The appropriate tools to facilitate lncRNA research for the renal scientific community are urgently required due to a row of challenges compared to classical analysis pipelines optimized for coding RNA expression analysis. Here, we present the bioinformatic pipeline CALINCA as a solution for this problem. CALINCA automatically analyzes datasets from murine FSGS models and quantifies both annotated and de novo assembled lncRNAs. In addition, the tool provides in-depth information on podocyte specificity of these lncRNAs, as well as evolutionary conservation and expression in human datasets making this pipeline a crucial basis to lncRNA studies in FSGS.

393 DECONVOLUTING THE COMPLEXITY OF LONG NON-CODING RNAS AND ESOPHAGEAL CARCINOMA FOR POTENTIAL CLINICAL IMPLICATIONS

2021 ◽  
Vol 34 (Supplement_1) ◽  
Author(s):  
Siyuan Luan ◽  
Yushang Yang ◽  
Shouyue Zhang ◽  
Xiaoxi Zeng ◽  
Xin Xiao ◽  
...  
Keyword(s):  
Esophageal Carcinoma ◽  
Rapid Development ◽  
Direct Interaction ◽  
Clinical Applications ◽  
Regulatory Mechanisms ◽  
Protein Coding ◽  
Functional Roles ◽  
Cancer Hallmarks ◽  
Clinical Scenarios ◽  
Non Coding Rnas

Abstract   Long non-coding RNAs (lncRNAs), a type of transcriptional products with more than 200 nucleotides in length, have been less characterized compared to protein-coding RNAs so far. However, it is increasingly evident that lncRNAs are key players involved in multiple genetic and epigenetic activities during the carcinogenesis of neoplastic diseases. Currently, accumulating data have pointed out the close connection between lncRNAs and esophageal carcinoma (EC), shedding light on further unravelling the complexity of lncRNAs and EC. Methods In this review, we thoroughly collect the evidence regarding original studies on EC-related lncRNAs by searching in MEDLINE/PubMed, Embase and WOS/SCI. We especially focus on summarizing EC-related lncRNAs based upon more updated evidence, and further discuss their different features from various perspectives, including regulatory mechanisms, functional roles in cancer hallmarks, as well as potential diagnostic and therapeutic applications, which would together reveal the complexity of lncRNAs and EC for potential clinical applications. Results We discuss over thirty EC-related lncRNAs in total, most of which function as oncogenes that promote cancer development, while the others function as tumor suppressors. Regulatory mechanisms included sponging miRNAs, direct interaction with proteins, and exosome visicle-based intercellular communication. Based upon these modes of actions, lncRNAs play multiple roles in cancer hallmarks such as uncontrolled cell growth, evasion of programmed cell death, invasion and metastasis. Moreover, lncRNAs packaged in exosomes have unique potency to serve as diagnostic biomarkers; some lncRNAs show great potential to predict patients' chemical resistance and may be crucial targets to improve chemoradiotherapy and targeted therapy. Conclusion Over the past few years, the research of EC-related lncRNAs maintain obviously rapid development, yet further exploration of exact mechanisms and clinical applications that lncRNAs can offer need to be done. Indeed, LncRNAs hold the promise of being applied in multiple clinical scenarios, especially early diagnosis of EC, improvement of sensitivity to chemotherapy/radiotherapy, and development of small-molecule targeted drugs.

scholarly journals Non-Coding RNAs in Breast Cancer: Intracellular and Intercellular Communication

2018 ◽  
Vol 4 (4) ◽  
pp. 40 ◽  
Author(s):  
Carolyn Klinge
Keyword(s):  
Breast Cancer ◽  
Intercellular Communication ◽  
Intracellular Signaling ◽  
Colorectal Neoplasia ◽  
Breast Tumors ◽  
Estrogen Receptor Α ◽  
Circular Rnas ◽  
Intercellular Signaling ◽  
Protein Coding ◽  
Non Coding Rnas

Non-coding RNAs (ncRNAs) are regulators of intracellular and intercellular signaling in breast cancer. ncRNAs modulate intracellular signaling to control diverse cellular processes, including levels and activity of estrogen receptor α (ERα), proliferation, invasion, migration, apoptosis, and stemness. In addition, ncRNAs can be packaged into exosomes to provide intercellular communication by the transmission of microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) to cells locally or systemically. This review provides an overview of the biogenesis and roles of ncRNAs: small nucleolar RNA (snRNA), circular RNAs (circRNAs), PIWI-interacting RNAs (piRNAs), miRNAs, and lncRNAs in breast cancer. Since more is known about the miRNAs and lncRNAs that are expressed in breast tumors, their established targets as oncogenic drivers and tumor suppressors will be reviewed. The focus is on miRNAs and lncRNAs identified in breast tumors, since a number of ncRNAs identified in breast cancer cells are not dysregulated in breast tumors. The identity and putative function of selected lncRNAs increased: nuclear paraspeckle assembly transcript 1 (NEAT1), metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), steroid receptor RNA activator 1 (SRA1), colon cancer associated transcript 2 (CCAT2), colorectal neoplasia differentially expressed (CRNDE), myocardial infarction associated transcript (MIAT), and long intergenic non-protein coding RNA, Regulator of Reprogramming (LINC-ROR); and decreased levels of maternally-expressed 3 (MEG3) in breast tumors have been observed as well. miRNAs and lncRNAs are considered targets of therapeutic intervention in breast cancer, but further work is needed to bring the promise of regulating their activities to clinical use.

scholarly journals Long noncoding RNAs: fine-tuners hidden in the cancer signaling network

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Shanshan Zhao ◽  
Xue Zhang ◽  
Shuo Chen ◽  
Song Zhang
Keyword(s):  
Signaling Pathways ◽  
Cancer Progression ◽  
Biological Activities ◽  
Noncoding Rnas ◽  
Fine Tuning ◽  
Multiple Perspectives ◽  
Sequencing Technology ◽  
Protein Coding ◽  
Abnormal Signal ◽  
Non Coding Rnas

AbstractWith the development of sequencing technology, a large number of long non-coding RNAs (lncRNAs) have been identified in addition to coding genes. LncRNAs, originally considered as junk RNA, are dysregulated in various types of cancer. Although protein-coding signaling pathways underlie various biological activities, and abnormal signal transduction is a key trigger and indicator for tumorigenesis and cancer progression, lncRNAs are sparking keen interest due to their versatile roles in fine-tuning signaling pathways. We are just beginning to scratch the surface of lncRNAs. Therefore, despite the fact that lncRNAs drive malignant phenotypes from multiple perspectives, in this review, we focus on important signaling pathways modulated by lncRNAs in cancer to demonstrate an up-to-date understanding of this emerging field.

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