scholarly journals Chromosomal assembly of the nuclear genome of the endosymbiont-bearing trypanosomatid Angomonas deanei

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
John W Davey ◽  
Carolina M C Catta-Preta ◽  
Sally James ◽  
Sarah Forrester ◽  
Maria Cristina M Motta ◽  
...  
Keyword(s):  
Chromosome Number ◽  
Noncoding Rnas ◽  
Nuclear Genome ◽  
Supernumerary Chromosome ◽  
Ribosomal Rnas ◽  
Protein Coding ◽  
Transfer Rnas ◽  
Protein Coding Genes ◽  
Oxford Nanopore ◽  
Genome Assemblies

Abstract Angomonas deanei is an endosymbiont-bearing trypanosomatid with several highly fragmented genome assemblies and unknown chromosome number. We present an assembly of the A. deanei nuclear genome based on Oxford Nanopore sequence that resolves into 29 complete or close-to-complete chromosomes. The assembly has several previously unknown special features; it has a supernumerary chromosome, a chromosome with a 340-kb inversion, and there is a translocation between two chromosomes. We also present an updated annotation of the chromosomal genome with 10,365 protein-coding genes, 59 transfer RNAs, 26 ribosomal RNAs, and 62 noncoding RNAs.

Identify the critical protein‐coding genes and long noncoding RNAs in cardiac myxoma

2019 ◽  
Vol 120 (8) ◽  
pp. 13441-13452 ◽  
Author(s):  
Nan Cheng ◽  
Yuanbin Wu ◽  
Huajun Zhang ◽  
Yi Guo ◽  
Huimin Cui ◽  
...  
Keyword(s):  
Cardiac Myxoma ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Protein Coding ◽  
Protein Coding Genes

scholarly journals Mitochondrial Genome Sequences of Diorhabda carinata and Diorhabda carinulata, Two Beetle Species Introduced to North America for Biological Control

2019 ◽  
Vol 8 (35) ◽  
Author(s):  
A. R. Stahlke ◽  
A. Z. Ozsoy ◽  
D. W. Bean ◽  
P. A. Hohenlohe
Keyword(s):  
Biological Control ◽  
North America ◽  
Mitochondrial Genome ◽  
Noncoding Region ◽  
Beetle Species ◽  
Genome Sequences ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes ◽  
Genome Assemblies

We announce the complete circularized mitochondrial genome assemblies of Diorhabda carinata and Diorhabda carinulata, beetle species introduced to North America for the biological control of invasive shrubs of the genus Tamarix L. (Tamaricaceae). The assemblies (16,232 and 16,298 bp, respectively) each comprise 13 protein-coding genes, 22 tRNAs, two rRNAs, and a noncoding region.

scholarly journals Chronic lymphocytic leukemia: interplay between noncoding RNAs and protein-coding genes

Blood ◽  
2009 ◽  
Vol 114 (23) ◽  
pp. 4761-4770 ◽  
Author(s):  
George A. Calin ◽  
Carlo M. Croce
Keyword(s):  
Chronic Lymphocytic Leukemia ◽  
Noncoding Rnas ◽  
Malignant Potential ◽  
Lymphocytic Leukemia ◽  
Leukemic Cells ◽  
Cancer Genes ◽  
New Paradigm ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Molecular Oncology

Abstract One of the most unexpected and fascinating discoveries in oncology over the past few years is the interplay between abnormalities in protein-coding genes and noncoding RNAs (ncRNAs) that is causally involved in cancer initiation, progression, and dissemination. MicroRNAs (miRNAs), small regulatory ncRNAs, are involved in the pathogenesis of all types of human cancers, including leukemias, mainly via dysregulation of expression of cancer genes. Increasing evidence shows that miRNAs can work as tumor suppressors (inhibiting malignant potential) or oncogenes (activating malignant potential). Researchers first identified this new paradigm of molecular oncology in patients with chronic lymphocytic leukemia (CLL). Understanding the roles of miRNAs and other ncRNAs in leukemic cells is not only uncovering a new layer of gene regulation but also providing new markers for improved diagnosis and prognosis, as well as novel therapeutic options for CLL patients. Herein we focus on the roles of miRNAs and ultraconserved ncRNA genes in CLL, highlighting what is already known about their function, proposing a novel model of CLL predisposition and progression, and describing the challenges for the near future.

scholarly journals Complete Genome Sequence of Methanothermobacter sp. Strain THM-1, a Thermophilic and Hydrogenotrophic Methanogen Isolated from an Anaerobic Reactor in South Korea

2021 ◽  
Vol 10 (38) ◽  
Author(s):  
Byoung-Seung Jeon ◽  
Hyunjin Kim ◽  
Young Wook Go ◽  
Hyunook Kim ◽  
Okkyoung Choi ◽  
...  
Keyword(s):  
Complete Genome Sequence ◽  
Complete Genome ◽  
Noncoding Rnas ◽  
Gc Content ◽  
Its Sequence ◽  
Protein Coding ◽  
Content Type ◽  
Anaerobic Reactor ◽  
Hydrogenotrophic Methanogen ◽  
Protein Coding Genes

Methanothermobacter sp. strain THM-1, a thermophilic and hydrogenotrophic methanogen, was isolated from an anaerobic reactor enriched with thermophilic methanogens. The genome of THM-1 shares 98.81% of its sequence with Methanothermobacter wolfeii isolate SIV6 and consists of 1,724,502 bp with 1,665 protein-coding genes, 50 noncoding RNAs, and a GC content of 48.6%.

scholarly journals Genome Sequence of Lactobacillus fermentum 47-7, a Good In Vitro Probiotic Strain Isolated from a Healthy Thai Infant

2019 ◽  
Vol 8 (39) ◽  
Author(s):  
Atthaphon Konyanee ◽  
Panjamaporn Yotpanya ◽  
Marutpong Panya ◽  
Chulapan Engchanil ◽  
Namfon Suebwongsa ◽  
...  
Keyword(s):  
Genome Size ◽  
Genome Sequence ◽  
Noncoding Rnas ◽  
Probiotic Strain ◽  
Lactobacillus Fermentum ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes

We report the genome sequence of Lactobacillus fermentum 47-7, a good in vitro probiotic strain isolated from an infant. Its genome size is 1.83 Mb, it is assembled from 180 contigs, and it consists of 1,636 protein-coding genes, 15 rRNAs, 57 tRNAs, and 4 noncoding RNAs. This genome sequence will be useful for a variety of applications.

scholarly journals Near Chromosome-Level Genome Assembly and Annotation of Rhodotorula babjevae Strains Reveals High Intraspecific Divergence

2021 ◽  
Author(s):  
Giselle C. Martin-Hernandez ◽  
Bettina Müller ◽  
Christian Brandt ◽  
Martin Hölzer ◽  
Adrian Viehweger ◽  
...  
Keyword(s):  
Gc Content ◽  
Pairwise Identity ◽  
Protein Coding ◽  
Intraspecific Divergence ◽  
Protein Coding Genes ◽  
Fungal Evolution ◽  
Lignocellulose Hydrolysate ◽  
Long Read ◽  
Genome Assemblies ◽  
High Quality Genome

The genus Rhodotorula includes basidiomycetous oleaginous yeast species. R. babjevae can produce compounds of biotechnological interest such as lipids, carotenoids and biosurfactants from low value substrates such as lignocellulose hydrolysate. High-quality genome assemblies are needed to develop genetic tools and to understand fungal evolution and genetics. Here, we combined short- and long-read sequencing to resolve the genomes of two R. babjevae strains, CBS 7808 (type strain) and DBVPG 8058 at chromosomal level. Both genomes have a size of 21 Mbp and a GC content of 68.2%. Allele frequency analysis indicated tetraploidy in both strains. They harbor 21 putative chromosomes with sizes ranging from 0.4 to 2.4 Mb. In both assemblies, the mitochondrial genome was recovered in a single contig, which shared 97% pairwise identity. The pairwise identity between the majority of chromosomes ranges from 82% to 87%. We found indications for strain-specific extrachromosomal endogenous DNA. 7,591 protein-coding genes and 7,607 associated transcripts were annotated in CBS 7808 and 7,481 protein-coding genes and 7,516 associated transcripts in DBVPG 8058. CBS 7808 has accumulated a higher number of tandem duplications than DBVPG 8058. We identified large translocation events between putative chromosomes and a high genetic divergence between the two strains.

scholarly journals Bacterial Noncoding RNAs Excised from within Protein-Coding Transcripts

mBio ◽  
2018 ◽  
Vol 9 (5) ◽  
Author(s):  
Daniel Dar ◽  
Rotem Sorek
Keyword(s):  
Expression Patterns ◽  
Noncoding Rnas ◽  
Large Set ◽  
Rna Structures ◽  
Protein Coding ◽  
Small Noncoding Rnas ◽  
Coding Regions ◽  
Protein Coding Genes ◽  
Evolutionarily Conserved ◽  
Intergenic Regions

ABSTRACT Prokaryotic genomes encode a plethora of small noncoding RNAs (ncRNAs) that fine-tune the expression of specific genes. The vast majority of known bacterial ncRNAs are encoded from within intergenic regions, where their expression is controlled by promoter and terminator elements, similarly to protein-coding genes. In addition, recent studies have shown that functional ncRNAs can also be derived from gene 3′ untranslated regions (3′UTRs) via an alternative biogenesis pathway, in which the ncRNA segment is separated from the mRNA via RNase cleavage. Here, we report the detection of a large set of decay-generated noncoding RNAs (decRNAs), many of which are completely embedded within protein-coding mRNA regions rather than in the UTRs. We show that these decRNAs are “carved out” of the mRNA through the action of RNase E and that they are predicted to fold into highly stable RNA structures, similar to those of known ncRNAs. A subset of these decRNAs is predicted to interact with Hfq or ProQ or both, which act as ncRNA chaperones, and some decRNAs display evolutionarily conserved sequences and conserved expression patterns between different species. These results suggest that mRNA protein-coding regions may harbor a large set of potentially functional small RNAs. IMPORTANCE Bacteria and archaea utilize regulatory small noncoding RNAs (ncRNAs) to control the expression of specific genetic programs. These ncRNAs are almost exclusively encoded within intergenic regions and are independently transcribed. Here, we report on a large set ncRNAs that are “carved out” from within the protein-coding regions of Escherichia coli mRNAs by cellular RNases. These protected mRNA fragments fold into energetically stable RNA structures, reminiscent of those of intergenic regulatory ncRNAs. In addition, a subset of these ncRNAs coprecipitate with the major ncRNA chaperones Hfq and ProQ and display evolutionarily conserved sequences and conserved expression patterns between different bacterial species. Our data suggest that protein-coding genes can potentially act as a reservoir of regulatory ncRNAs.

scholarly journals An integrative proteogenomics approach reveals peptides encoded by annotated lincRNA in the mouse kidney inner medulla

2020 ◽  
Vol 52 (10) ◽  
pp. 485-491
Author(s):  
Cameron T. Flower ◽  
Lihe Chen ◽  
Hyun Jun Jung ◽  
Viswanathan Raghuram ◽  
Mark A. Knepper ◽  
...  
Keyword(s):  
Noncoding Rnas ◽  
Peptide Identification ◽  
Mouse Kidney ◽  
Open Reading Frames ◽  
Specific Expression ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Peptide Database ◽  
Liquid Chromatography Tandem Mass ◽  
Spectrum Matching

Long noncoding RNAs (lncRNAs) are intracellular transcripts longer than 200 nucleotides and lack protein-coding information. A subclass of lncRNA known as long intergenic noncoding RNAs (lincRNAs) are transcribed from genomic regions that share no overlap with annotated protein-coding genes. Increasing evidence has shown that some annotated lincRNA transcripts do in fact contain open reading frames (ORFs) encoding functional short peptides in the cell. Few robust methods for lincRNA-encoded peptide identification have been reported, and the tissue-specific expression of these peptides has been largely unexplored. Here we propose an integrative workflow for lincRNA-encoded peptide discovery and test it on the mouse kidney inner medulla (IM). In brief, low molecular weight protein fractions were enriched from homogenate of IMs and trypsinized into shorter peptides, which were sequenced by high resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS). To curate a hypothetical lincRNA-encoded peptide database for peptide-spectrum matching following LC-MS/MS, we performed RNA-Seq on IMs, computationally removed reads overlapping with annotated protein-coding genes, and remapped the remaining reads to a database of mouse noncoding transcripts to infer lincRNA expression. Expressed lincRNAs were searched for ORFs by an existing rule-based algorithm, and translated ORFs were used for peptide-spectrum matching. Peptides identified by LC-MS/MS were further evaluated by using several quality control criteria and bioinformatics methods. We discovered three novel lincRNA-encoded peptides, which are conserved in mouse, rat, and human. The workflow can be adapted for discovery of small protein-coding genes in any species or tissue where noncoding transcriptome information is available.

scholarly journals Draft Genome Sequence of Lactobacillus fermentum BFE 6620, a Potential Starter Culture for African Vegetable Foods, Isolated from Fermented Cassava

2017 ◽  
Vol 5 (33) ◽  
Author(s):  
Eliud N. Wafula ◽  
Erik Brinks ◽  
Biserka Becker ◽  
Melanie Huch ◽  
Bernhard Trierweiler ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Draft Genome ◽  
Starter Culture ◽  
Noncoding Rnas ◽  
Lactobacillus Fermentum ◽  
Draft Genome Sequence ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes ◽  
Vegetable Foods

ABSTRACT We report the draft genome sequence of Lactobacillus fermentum BFE 6620 from fermented cassava used as a potential starter culture for African vegetable fermentation. Sequence analysis showed the assembled genome size to be 1,982,893 bp, encoding a predicted total of 2,003 protein-coding genes, 14 rRNAs, 54 tRNAs, and 3 noncoding RNAs (ncRNAs).

scholarly journals When Long Noncoding RNAs Meet Genome Editing in Pluripotent Stem Cells

2017 ◽  
Vol 2017 ◽  
pp. 1-13
Author(s):  
Fuquan Chen ◽  
Jiaojiao Ji ◽  
Jian Shen ◽  
Xinyi Lu
Keyword(s):  
Stem Cells ◽  
Transcriptional Regulation ◽  
Genome Editing ◽  
Pluripotent Stem Cells ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Biological Processes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
The Past

Most of the human genome can be transcribed into RNAs, but only a minority of these regions produce protein-coding mRNAs whereas the remaining regions are transcribed into noncoding RNAs. Long noncoding RNAs (lncRNAs) were known for their influential regulatory roles in multiple biological processes such as imprinting, dosage compensation, transcriptional regulation, and splicing. The physiological functions of protein-coding genes have been extensively characterized through genome editing in pluripotent stem cells (PSCs) in the past 30 years; however, the study of lncRNAs with genome editing technologies only came into attentions in recent years. Here, we summarize recent advancements in dissecting the roles of lncRNAs with genome editing technologies in PSCs and highlight potential genome editing tools useful for examining the functions of lncRNAs in PSCs.

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