scholarly journals Transcriptome assembly and annotation of johnsongrass (Sorghum halepense) rhizomes identifies candidate rhizome-specific genes

2018 ◽  
Author(s):  
Nathan Ryder ◽  
Kevin M. Dorn ◽  
Mark Huitsing ◽  
Micah Adams ◽  
Jeff Ploegstra ◽  
...  
Keyword(s):  
De Novo ◽  
Tissue Sample ◽  
Transcriptome Assembly ◽  
Perennial Grass ◽  
Perennial Grasses ◽  
Sorghum Halepense ◽  
Protein Coding ◽  
Grain Crop ◽  
Perennial Grain ◽  
Rhizome Development

AbstractRhizomes facilitate the wintering and vegetative propagation of many perennial grasses. Sorghum halepense (johnsongrass) is an aggressive perennial grass that relies on a robust rhizome system to persist through winters and reproduce asexually from its rootstock nodes. This study aimed to sequence and assemble expressed transcripts within the johnsongrass rhizome. A de novo transcriptome assembly was generated from a single johnsongrass rhizome meristem tissue sample. A total of 141,176 probable protein-coding sequences from the assembly were identified and assigned gene ontology terms using Blast2GO. The johnsongrass assembly was compared to Sorghum bicolor, a related non-rhizomatous species, along with an assembly of similar rhizome tissue from the perennial grain crop Thinopyrum intermedium. The presence/absence analysis yielded a set of 259 johnsongrass contigs that are likely associated with rhizome development.

scholarly journals An Improved Human smORF Annnotation Workflow Combining De Novo Transcriptome Assembly and Ribo-Seq

2019 ◽  
Author(s):  
Thomas F. Martinez ◽  
Qian Chu ◽  
Cynthia Donaldson ◽  
Dan Tan ◽  
Maxim N. Shokhirev ◽  
...  
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Human Leukocyte ◽  
Open Reading Frames ◽  
Translation Efficiency ◽  
Proteomics Data ◽  
Protein Coding ◽  
Leukocyte Antigen ◽  
Human Genes ◽  
Small Open Reading Frames

Protein-coding small open reading frames (smORFs) are emerging as an important class of genes, however, the coding capacity of smORFs in the human genome is unclear. By integrating de novo transcriptome assembly and Ribo-Seq, we confidently annotate thousands of novel translated smORFs in three human cell lines. We find that smORF translation prediction is noisier than for annotated coding sequences, underscoring the importance of analyzing multiple experiments and footprinting conditions. These smORFs are located within non-coding and antisense transcripts, the UTRs of mRNAs, and unannotated transcripts. Analysis of RNA levels and translation efficiency during cellular stress identifies regulated smORFs, providing an approach to select smORFs for further investigation. Sequence conservation and signatures of positive selection indicate that encoded microproteins are likely functional. Additionally, proteomics data from enriched human leukocyte antigen complexes validates the translation of hundreds of smORFs and positions them as a source of novel antigens. Thus, smORFs represent a significant number of important, yet unexplored human genes.

scholarly journals Transcriptome Dynamics of Human Neuronal Differentiation From iPSC

2021 ◽  
Vol 9 ◽  
Author(s):  
Meltem Kuruş ◽  
Soheil Akbari ◽  
Doğa Eskier ◽  
Ahmet Bursalı ◽  
Kemal Ergin ◽  
...  
Keyword(s):  
Stem Cells ◽  
Neuronal Differentiation ◽  
De Novo ◽  
Neurological Diseases ◽  
Transcriptome Assembly ◽  
Embryonic Stem ◽  
Protein Coding ◽  
Regulatory Factors ◽  
Adult Cell ◽  
Induced Pluripotent

The generation and use of induced pluripotent stem cells (iPSCs) in order to obtain all differentiated adult cell morphologies without requiring embryonic stem cells is one of the most important discoveries in molecular biology. Among the uses of iPSCs is the generation of neuron cells and organoids to study the biological cues underlying neuronal and brain development, in addition to neurological diseases. These iPSC-derived neuronal differentiation models allow us to examine the gene regulatory factors involved in such processes. Among these regulatory factors are long non-coding RNAs (lncRNAs), genes that are transcribed from the genome and have key biological functions in establishing phenotypes, but are frequently not included in studies focusing on protein coding genes. Here, we provide a comprehensive analysis and overview of the coding and non-coding transcriptome during multiple stages of the iPSC-derived neuronal differentiation process using RNA-seq. We identify previously unannotated lncRNAs via genome-guided de novo transcriptome assembly, and the distinct characteristics of the transcriptome during each stage, including differentially expressed and stage specific genes. We further identify key genes of the human neuronal differentiation network, representing novel candidates likely to have critical roles in neurogenesis using coexpression network analysis. Our findings provide a valuable resource for future studies on neuronal differentiation.

scholarly journals De novo assembly and annotation of the eastern fence lizard (Sceloporus undulatus) transcriptome

2017 ◽  
Author(s):  
Mariana B. Grizante ◽  
Marc Tollis ◽  
Juan J. Rodriguez ◽  
Ofir Levy ◽  
Michael J. Angilletta ◽  
...  
Keyword(s):  
Complex Traits ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Single Copy ◽  
Genomic Research ◽  
Sceloporus Undulatus ◽  
Protein Coding ◽  
Average Contig Length ◽  
Green Anole Lizard ◽  
Eastern Fence Lizard

AbstractBackgroundThe eastern fence lizard (Sceloporus undulatus) has been a model species for ecological and evolutionary research. Genomic and transcriptomic resources for this species would promote investigation of genetic mechanisms that underpin plastic responses to environmental stress, such as climate warming. Moreover, such resources would aid comparative studies of complex traits at the molecular level, such as the transition from oviparous to viviparous reproduction, which happened at least four times within Sceloporus.FindingsA de novo transcriptome assembly for Sceloporus undulatus, Sund_v1.0, was generated using over 179 million Illumina reads obtained from three tissues (whole brain, skeletal muscle, and embryo) as well as previously reported liver sequences. The Sund_v1.0 assembly had an average contig length of 782 nucleotides and an E90N50 statistic of 2,550 nucleotides. Comparing S. undulatus transcripts with the benchmarking universal single-copy orthologs (BUSCO) for tetrapod species yielded 97.2% gene representation. A total of 13,422 protein-coding orthologs were identified in comparison to the genome of the green anole lizard, Anolis carolinensis, which is the closest related species with genomic data available.ConclusionsThe multi-tissue transcriptome of S. undulatus is the first for a member of the family Phrynosomatidae, offering an important resource to advance studies of adaptation in this species and genomic research in reptiles.

scholarly journals CONTROL OF PERENNIAL GRASSES ON CULTIVATED AND UNCULTIVATED LAND

HortScience ◽  
1990 ◽  
Vol 25 (9) ◽  
pp. 1078d-1078
Author(s):  
Bakir A. Al-Juboory
Keyword(s):  
Cynodon Dactylon ◽  
Perennial Grass ◽  
Cyperus Rotundus ◽  
Perennial Grasses ◽  
Bermuda Grass ◽  
Sorghum Halepense ◽  
Johnson Grass ◽  
Successful Control ◽  
Major Factors ◽  
Uncultivated Land

This experiment was conducted to determine effects of herbicides on the control of noxious perennial grass weeds. The results indicate that the rate, timing, duration and number of applications employed were the major factors in the successful control of perennial grass weeds such as Cogon Grass (Imperala cylindrica), Johnson Grass (Sorghum halepense), Bermuda Grass (Cynodon dactylon), Nut Grass (Cyperus rotundus) and Common Red (Phragmites spp.), commonly found in Iraq growing both in cultivated fields and wild on uncultivated land.

scholarly journals De novo transcriptome assembly of the Italian white truffle (Tuber magnatum Pico)

2018 ◽  
Author(s):  
Federico Vita ◽  
Amedeo Alpi ◽  
Edoardo Bertolini
Keyword(s):  
Molecular Mechanisms ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Rna Seq ◽  
Genetic Studies ◽  
Protein Coding ◽  
Important Species ◽  
White Truffle ◽  
Tuber Magnatum ◽  
Insight Into

AbstractThe Italian white truffle (Tuber magnatum Pico) is a gastronomic delicacy that dominates the worldwide truffle market. Despite its importance, the genomic resources currently available for this species are still limited. Here we present the first de novo transcriptome assembly of T. magnatum. Illumina RNA-seq data were assembled using a single-k-mer approach into 22,932 transcripts with N50 of 1,524 bp. Our approach allowed to predict and annotate 12,367 putative protein coding sequences, reunited in 6,723 loci. In addition, we identified 2,581 gene-based SSR markers. This work provides the first publicly available reference transcriptome for genomics and genetic studies providing insight into the molecular mechanisms underlying the biology of this important species.

scholarly journals InTransBo: An Integrative Transcript Library to Enable Genome-Free Systematic Exploration of Bougainvillea

2020 ◽  
Author(s):  
Qi Luo ◽  
Ziliang Chen ◽  
Tingting Xu ◽  
Dangzheng Huang ◽  
Haitao Hou ◽  
...  
Keyword(s):  
Large Scale ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Genomic Information ◽  
Protein Coding ◽  
Traditional Medicines ◽  
Systematic Exploration ◽  
Genomic Resource ◽  
Better Than ◽  
Complete Genomic

Abstract Members of the genus Bougainvillea are rich sources of natural dyes, pigments, and traditional medicines. They are also commonly used as ornamentals in roadside landscape construction. However, the horticultural development of Bougainvillea flowers with extended growth periods and coloration is not always feasible. One reason is limited molecular knowledge and no genomic information for Bougainvillea. Here, we compiled an expressed transcript sequence library for Bougainvillea by integrating 20 Illumina-sequencing RNA transcriptomes. The library consisted of 97,623 distinct transcripts. Of these, 47,006 were protein-coding, 31,109 were lncRNA, and 19,508 were unannotated. We also confirmed that the library is an alternative genomic reference for accurate transcriptome assembly and its performance was substantially better than that of the de novo method. We also curated the Integrative Transcript Library database for Bougainvillea known as InTransBo (http://www.bio-add.org/InTransBo/index.jsp). To the best of our knowledge, the present study is the first large scale genomic resource for Bougainvillea. Overall, the library helps fill the genomic gap and elucidate the transcriptional nature of Bougainvillea. It may also advance progress in the precise regulation of flowering in horticulture. The same strategy can be readily applied toward the systematic exploration of other plant species lacking complete genomic information.

scholarly journals An ethnobotanical study of the genus Elymus

2019 ◽  
Author(s):  
Emma S. Frawley ◽  
Claudia Ciotir ◽  
Brooke Micke ◽  
Matthew J. Rubin ◽  
Allison J. Miller
Keyword(s):  
De Novo ◽  
Perennial Grass ◽  
Size Variation ◽  
Perennial Grasses ◽  
Grass Species ◽  
Ethnobotanical Study ◽  
Agricultural Systems ◽  
Ethnobotanical Survey ◽  
Ethnobotanical Uses ◽  
Sustainable Agricultural Systems

AbstractGrains of domesticated grasses (Poaceae) have long been a global food source and constitute the bulk of calories in the human diet. Recent efforts to establish more sustainable agricultural systems have focused in part on the development of herbaceous, perennial crops. Perennial plants have extensive root systems that stabilize soil and absorb water and nutrients at greater rates than their annual counterparts; consequently, perennial grasses are important potential candidates for grain domestication. While most contemporary grass domesticates consumed by humans are annual plants, there are over 7,000 perennial grass species that remain largely unexplored for domestication purposes. Documenting ethnobotanical uses of wild perennial grasses could aid in the evaluation of candidate species for de novo crop development. The objectives of this study are 1) to provide an ethnobotanical survey of the grass genus Elymus; and 2) to investigate floret size variation in species used by people. Elymus includes approximately 150 perennial species distributed in temperate and subtropical regions, of which at least 21 taxa have recorded nutritional, medicinal, and/or material uses. Elymus species used for food by humans warrant pre-breeding and future analyses to assess potential utility in perennial agricultural systems.

scholarly journals Regulatory Potential of Long Non-Coding RNAs (lncRNAs) in Boar Spermatozoa with Good and Poor Freezability

Life ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 300
Author(s):  
Leyland Fraser ◽  
Łukasz Paukszto ◽  
Anna Mańkowska ◽  
Paweł Brym ◽  
Przemysław Gilun ◽  
...  
Keyword(s):  
Target Genes ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Biological Processes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Potential Target ◽  
Non Coding Rnas

Long non-coding RNAs (lncRNAs) are suggested to play an important role in the sperm biological processes. We performed de novo transcriptome assembly to characterize lncRNAs in spermatozoa, and to investigate the role of the potential target genes of the differentially expressed lncRNAs (DElncRNAs) in sperm freezability. We detected approximately 4007 DElncRNAs, which were differentially expressed in spermatozoa from boars classified as having good and poor semen freezability (GSF and PSF, respectively). Most of the DElncRNAs were upregulated in boars of the PSF group and appeared to significantly affect the sperm’s response to the cryopreservation conditions. Furthermore, we predicted that the potential target genes were regulated by DElncRNAs in cis or trans. It was found that DElncRNAs of both freezability groups had potential cis- and trans-regulatory effects on different protein-coding genes, such as COX7A2L, TXNDC8 and SOX-7. Gene Ontology (GO) enrichment revealed that the DElncRNA target genes are associated with numerous biological processes, including signal transduction, response to stress, cell death (apoptosis), motility and embryo development. Significant differences in the de novo assembled transcriptome expression profiles of the DElncRNAs between the freezability groups were confirmed by quantitative real-time PCR analysis. This study reveals the potential effects of protein-coding genes of DElncRNAs on sperm functions, which could contribute to further research on their relevance in semen freezability.

scholarly journals The neurotranscriptome of the Aedes aegypti mosquito

2015 ◽  
Author(s):  
Benjamin J Matthews ◽  
Carolyn S McBride ◽  
Matthew DeGennaro ◽  
Orion Despo ◽  
Leslie B Vosshall
Keyword(s):  
Gene Expression ◽  
Aedes Aegypti ◽  
Vector Control ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Molecular Genetic ◽  
Blood Feeding ◽  
Model Organisms ◽  
Protein Coding ◽  
Male And Female

Background A complete genome sequence and the advent of genome editing open up non-traditional model organisms to mechanistic genetic studies. The mosquito Aedes aegypti is an important vector of infectious diseases such as dengue, chikungunya, and yellow fever, and has a large and complex genome, which has slowed annotation efforts. We used comprehensive transcriptomic analysis of adult gene expression to improve the genome annotation and to provide a detailed tissue-specific catalogue of neural gene expression at different adult behavioral states. Results We carried out deep RNA sequencing across all major peripheral male and female sensory tissues, the brain, and (female) ovary. Furthermore, we examined gene expression across three important phases of the female reproductive cycle, a remarkable example of behavioral switching in which a female mosquito alternates between obtaining blood-meals from humans and laying eggs. Using genome-guided alignments and de novo transcriptome assembly, our re-annotation includes 572 new putative protein-coding genes and updates to 13.5% and 50.3% of existing transcripts within coding sequences and untranslated regions, respectively. Using this updated annotation, we detail gene expression in each tissue, identifying large numbers of transcripts regulated by blood-feeding and sexually dimorphic transcripts that may provide clues to the biology of male- and female-specific behaviors, such as mating and blood-feeding, which are areas of intensive study for those interested in vector control. Conclusions This neurotranscriptome forms a strong foundation for the study of genes in the mosquito nervous system and investigation of sensory-driven behaviors and their regulation. Furthermore, understanding the molecular genetic basis of mosquito chemosensory behavior has important implications for vector control.

scholarly journals Translational landscape in tomato revealed by transcriptome assembly and ribosome profiling

2019 ◽  
Author(s):  
Hsin-Yen Larry Wu ◽  
Gaoyuan Song ◽  
Justin W. Walley ◽  
Polly Yingshan Hsu
Keyword(s):  
De Novo ◽  
Transcriptome Assembly ◽  
Mrna Translation ◽  
Ribosome Profiling ◽  
In Planta ◽  
Protein Coding ◽  
Tomato Roots ◽  
Translation Start ◽  
High Throughput Method ◽  
And Control

mRNA translation is a critical step in gene expression, but our understanding of the landscape and control of translation in diverse crops remains lacking. Here, we combined de novo transcriptome assembly and ribosome profiling to study global mRNA translation in tomato roots. Taking advantage of the 3-nucleotide periodicity displayed by translating ribosomes, we identified 354 novel small ORFs (sORFs) translated from previously unannotated transcripts, as well as 1329 upstream ORFs (uORFs) translated within the 5-prime UTRs of annotated protein-coding genes. Proteomic analysis confirmed that some of these novel uORFs and sORFs generate stable proteins in planta. Compared with the annotated ORFs, the uORFs use more flexible Kozak sequences around translation start sites. Interestingly, uORF-containing genes are enriched for protein phosphorylation/dephosphorylation and signaling transduction pathways, suggesting a regulatory role for uORFs in these processes. We also demonstrated that ribosome profiling is useful to facilitate the annotation of translated ORFs and noncanonical translation initiation sites. In addition to defining the translatome, our results revealed the global control of mRNA translation by uORFs and microRNAs in tomato. In summary, our approach provides a high-throughput method to discover unannotated ORFs, elucidates evolutionarily conserved translational features, and identifies new regulatory mechanisms hidden in a crop genome.

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