scholarly journals Transcriptomic basis for salt tolerance and disease resistance of silverleaf sunflower revealed by Iso-seq and RNA-seq

2019 ◽  
Author(s):  
Jing Bing ◽  
Yunhe Ling ◽  
Peipei An ◽  
Enshi Xiao ◽  
Chunlian Li ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Salt Tolerance ◽  
Reference Genome ◽  
Transcriptome Assembly ◽  
Future Research ◽  
Rna Seq ◽  
Gene Expressions ◽  
Breeding Programs ◽  
Genomic Variance ◽  
Cultivated Species

Abstract Background Silverleaf sunflower, Helianthus argophyllus , is one of the most important wild species that have been usually used for the improvement of cultivated sunflower. Although a reference genome is now available for the cultivated species, H. annuus , its effect in helping understanding the mechanisms underlying the traits of H. argophyllus is limited by the substantial genomic variance between these two species.Results In this study, we generated a high-quality reference transcriptome of H. argophyllus using Iso-seq strategy. This assembly contains 50,153 unique genes covering more than 91% of the whole genes. Among them, we find 205 genes that are absent in the cultivated species and 475 fusion genes containing components of coding or non-coding sequences from the genome of H. annuus . It is interesting that in line with the strong disease resistance observed for H. argophyllus , these H. argophyllus -specific genes are predominantly related to functions of resistance. We have also profiled the gene expressions in leaf and root under normal or salt stressed conditions and, as a result, find distinct transcriptomic responses to salt stress in leaf and root. Particularly, genes involved in several critical processes including the synthesis and metabolism of glutamate and carbohydrate transport are reversely regulated in leaf and root.Conclusions Overall, this study provided insights into the genomic mechanisms underlying the disease resistance and salt tolerance of silverleaf sunflower and the transcriptome assembly and the genes identified in this study can serve as a complement data resources for future research and breeding programs of sunflowers.

scholarly journals The value of genotype-specific reference for transcriptome analyses

2021 ◽  
Author(s):  
Wenbin Guo ◽  
Max Coulter ◽  
Robbie Waugh ◽  
Runxuan Zhang
Keyword(s):  
Alternative Splicing ◽  
Reference Genome ◽  
Transcriptome Assembly ◽  
Specific Reference ◽  
Rna Seq ◽  
High Quality ◽  
Common Reference ◽  
Transcript Quantification ◽  
Gene Level ◽  
Reference Transcript

High quality transcriptome assembly using short reads from RNA-seq data still heavily relies upon reference-based approaches, of which the primary step is to align RNA-seq reads to a single reference genome of haploid sequence. However, it is increasingly apparent that while different genotypes within a species share core genes, they also contain variable numbers of specific genes that are only present a subset of individuals. Using a common reference may thus lead to a loss of genotype-specific information in the assembled transcript dataset and the generation of erroneous, incomplete or misleading transcriptomics analysis results. With the recent development of pan-genome information in many species, it is important that we understand the limitations of single genotype references for transcriptomics analysis. In this study, we quantitively evaluated the advantages of using genotype-specific reference genomes for transcriptome assembly and analysis using cultivated barley as a model. We mapped barley cultivar Barke RNA-seq reads to the Barke genome and to the cultivar Morex genome (common barley genome reference) to construct a genotype specific Reference Transcript Dataset (sRTD) and a common Reference Transcript Datasets (cRTD), respectively. We compared the two RTDs according to their transcript diversity, transcript sequence and structure similarity and the accuracy they provided for transcript quantification and differential expression analysis. Our evaluation shows that the sRTD has a significantly higher diversity of transcripts and alternative splicing events. Despite using a high-quality reference genome for assembly of the cRTD, we miss ca. 40% transcripts present in the sRTD and cRTD only has ca. 70% true assemblies. We found that the sRTD is more accurate for transcript quantification as well as differential expression and differential alternative splicing analysis. However, gene level quantification and comparative expression analysis are less affected by the source RTD, which indicates that analysing transcriptomic data at the gene level may be a reasonable compromise when a high-quality genotype-specific reference is not available.

scholarly journals Siberian sturgeon multi-tissue reference transcriptome database

Database ◽  
2020 ◽  
Vol 2020 ◽  
Author(s):  
Christophe Klopp ◽  
Cédric Cabau ◽  
Gonzalo Greif ◽  
André Lasalle ◽  
Santiago Di Landro ◽  
...  
Keyword(s):  
Reference Genome ◽  
Transcriptome Assembly ◽  
Fish Farming ◽  
Siberian Sturgeon ◽  
Supplementary Information ◽  
Rna Seq ◽  
High Quality ◽  
Reference Transcriptome ◽  
Functional Studies ◽  
Transcriptome Database

Abstract Motivation: Siberian sturgeon is a long lived and late maturing fish farmed for caviar production in 50 countries. Functional genomics enable to find genes of interest for fish farming. In the absence of a reference genome, a reference transcriptome is very useful for sequencing based functional studies. Results: We present here a high-quality transcriptome assembly database built using RNA-seq reads coming from brain, pituitary, gonadal, liver, stomach, kidney, anterior kidney, heart, embryonic and pre-larval tissues. It will facilitate crucial research on topics such as puberty, reproduction, growth, food intake and immunology. This database represents a major contribution to the publicly available sturgeon transcriptome reference datasets. Availability: The database is publicly available at http://siberiansturgeontissuedb.sigenae.org Supplementary information:  Supplementary data are available at Database online.

scholarly journals Full-length transcriptome assembly from RNA-Seq data without a reference genome

2011 ◽  
Vol 29 (7) ◽  
pp. 644-652 ◽  
Author(s):  
Manfred G Grabherr ◽  
Brian J Haas ◽  
Moran Yassour ◽  
Joshua Z Levin ◽  
Dawn A Thompson ◽  
...  
Keyword(s):  
Reference Genome ◽  
Transcriptome Assembly ◽  
Full Length ◽  
Rna Seq

scholarly journals The Bellerophon pipeline, improving de novo transcriptomes and removing chimeras

2018 ◽  
Author(s):  
Jesse Kerkvliet ◽  
Arthur de Fouchier ◽  
Michiel van Wijk ◽  
Astrid T. Groot
Keyword(s):  
Quality Control ◽  
Quality Assessment ◽  
Reference Genome ◽  
Assessment Tool ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Rna Seq ◽  
Quality Assessment Tool ◽  
Chimeric Sequences

AbstractTranscriptome quality control is an important step in RNA-seq experiments. However, the quality of de novo assembled transcriptomes is difficult to assess, due to the lack of reference genome to compare the assembly to. We developed a method to assess and improve the quality of de novo assembled transcriptomes by focusing on the removal of chimeric sequences. These chimeric sequences can be the result of faulty assembled contigs, merging two transcripts into one. The developed method is incorporated into a pipeline, that we named Bellerophon, which is broadly applicable and easy to use. Bellerophon first uses the quality-assessment tool TransRate to indicate the quality, after which it uses a Transcripts Per Million (TPM) filter to remove lowly expressed contigs and CD-HIT-EST to remove highly identical contigs. To validate the quality of this method, we performed three benchmark experiments: 1) a computational creation of chimeras, 2) identification of chimeric contigs in a transcriptome assembly, 3) a simulated RNAseq experiment using a known reference transcriptome. Overall, the Bellerophon pipeline was able to remove between 40 to 91.9% of the chimeras in transcriptome assemblies and removed more chimeric than non-chimeric contigs. Thus, the Bellerophon sequence of filtration steps is a broadly applicable solution to improve transcriptome assemblies.

Widening the genetic base of cultivated lentil through hybridization of Lens culinaris ‘Eston’ and L. ervoides accession IG 72815

2013 ◽  
Vol 93 (6) ◽  
pp. 1037-1047 ◽  
Author(s):  
A. Tullu ◽  
K. Bett ◽  
S. Banniza ◽  
S. Vail ◽  
A. Vandenberg
Keyword(s):  
Genetic Variation ◽  
Disease Resistance ◽  
Seed Weight ◽  
Lens Culinaris ◽  
Agronomic Traits ◽  
Breeding Programs ◽  
Genetic Base ◽  
Recessive Genes ◽  
Cultivated Species ◽  
Transgressive Segregations

Tullu, A., Bett, K., Banniza, S., Vail, S. and Vandenberg, A. 2013. Widening the genetic base of cultivated lentil through hybridization of Lens culinaris ‘Eston’ and L . ervoides accession IG 72815. Can. J. Plant Sci. 93: 1037–1047. Lentil (Lens culinaris Medik.) is affected by many stresses and the genetic variation for resistance to some of these stresses is limited in the cultivated germplasm. Introgression of genes from diverse sources for the improvement of disease resistance and agronomic performance is urgently needed. An interspecific recombinant inbred line (RIL) population designated LR-26 was developed from a cross of L. culinaris ‘Eston’ and L. ervoides (Brign.) Grande accession IG 72815. RILs were phenotyped (1) to examine the inheritance of resistance to the more aggressive race 0 of Colletotrichum truncatum (Schwein.) Andus & W.D. Moore, causal agent of anthracnose, for which resistance is lacking in the cultivated species and (2) to study the genetic variation in agronomic traits and their relationships to each other. Greenhouse studies were conducted to screen for resistance to race 0 of C. truncatum and evaluate RILs for variations of agronomic characters. Two recessive genes conferred resistance in L. ervoides accession IG 72815. Traits varied significantly and showed transgressive segregations. Seed yield had a significant and positive relationship with biomass, straw yield, seed weight and harvest index. About 20 lines that performed better than Eston in terms of podding ability, lodging, and stand at maturity can be used in a breeding program. LR-26-180 had an 8% greater seed weight than Eston, suggesting that IG 72815 has alleles contributing positively to seed size. Overall, results show that IG 72815 can be used in breeding programs to improve disease resistance and quantitative traits of lentil.

scholarly journals Compacting and correcting Trinity and Oases RNA-Seq de novo assemblies

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2988 ◽  
Author(s):  
Cédric Cabau ◽  
Frédéric Escudié ◽  
Anis Djari ◽  
Yann Guiguen ◽  
Julien Bobe ◽  
...  
Keyword(s):  
Reference Genome ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Error Rates ◽  
Rna Seq ◽  
Software Packages ◽  
Redundancy Reduction ◽  
Assembly Pipeline ◽  
Free Open Source

Background De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is still possible to improve them in several ways including redundancy reduction or error correction. Trinity and Oases are two commonly used de novo transcriptome assemblers. The contig sets they produce are of good quality. Still, their compaction (number of contigs needed to represent the transcriptome) and their quality (chimera and nucleotide error rates) can be improved. Results We built a de novo RNA-Seq Assembly Pipeline (DRAP) which wraps these two assemblers (Trinity and Oases) in order to improve their results regarding the above-mentioned criteria. DRAP reduces from 1.3 to 15 fold the number of resulting contigs of the assemblies depending on the read set and the assembler used. This article presents seven assembly comparisons showing in some cases drastic improvements when using DRAP. DRAP does not significantly impair assembly quality metrics such are read realignment rate or protein reconstruction counts. Conclusion Transcriptome assembly is a challenging computational task even if good solutions are already available to end-users, these solutions can still be improved while conserving the overall representation and quality of the assembly. The de novo RNA-Seq Assembly Pipeline (DRAP) is an easy to use software package to produce compact and corrected transcript set. DRAP is free, open-source and available under GPL V3 license at http://www.sigenae.org/drap.

scholarly journals Transcriptome profiling of Finnsheep ovaries during out-of-season breeding period

2015 ◽  
Vol 24 (1) ◽  
pp. 1-9 ◽  
Author(s):  
Kisun Pokharel ◽  
Jaana Peippo ◽  
Göran Andersson ◽  
Meng-Hua Li ◽  
Juha Kantanen
Keyword(s):  
Candidate Genes ◽  
Reference Genome ◽  
Transcriptome Assembly ◽  
Transcriptome Profiling ◽  
Breeding Period ◽  
Rna Seq ◽  
Sequence Coverage ◽  
Bioinformatics Pipeline ◽  
Two Samples ◽  
The World

Finnsheep is one of the most prolific sheep breeds in the world. We sequenced RNA-Seq libraries from the ovaries of Finnsheep ewes collected during out of season breeding period at about 30X sequence coverage. A total of 86 966 348 and 105 587 994 reads from two samples were mapped against latest available ovine reference genome (Oarv3.1). The transcriptome assembly revealed 14 870 known ovine genes, including the 15 candidate genes for fertility and out-of-season breeding. In this study we successfully used our bioinformatics pipeline to assemble the first ovarian transcriptome of Finnsheep.

scholarly journals Comprehensive Transcriptome Profiling and Identification of Potential Genes Responsible for Salt Tolerance in Tall Fescue Leaves under Salinity Stress

Genes ◽  
2018 ◽  
Vol 9 (10) ◽  
pp. 466 ◽  
Author(s):  
Erick Amombo ◽  
Xiaoning Li ◽  
Guangyang Wang ◽  
Shao An ◽  
Wei Wang ◽  
...  
Keyword(s):  
Salt Tolerance ◽  
Dna Sequences ◽  
Tall Fescue ◽  
Molecular Mechanisms ◽  
De Novo ◽  
Interaction Analysis ◽  
Quantitative Polymerase Chain Reaction ◽  
Future Research ◽  
Salt Treatment ◽  
Gene Expressions

Soil salinity is a serious threat to plant growth and crop productivity. Tall fescue utilization in saline areas is limited by its inferior salt tolerance. Thus, a transcriptome study is a prerequisite for future research aimed at providing deeper insights into the molecular mechanisms of tall fescue salt tolerance as well as molecular breeding. Recent advances in sequencing technology offer a platform to achieve this. Here, Illumina RNA sequencing of tall fescue leaves generated a total of 144,339 raw reads. After de novo assembly, unigenes with a total length of 129,749,938 base pairs were obtained. For functional annotations, the unigenes were aligned to various databases. Further structural analyses revealed 79,352 coding DNA sequences and 13,003 microsatellites distributed across 11,277 unigenes as well as single nucleotide polymorphisms. In total, 1862 unigenes were predicted to encode for 2120 transcription factors among which most were key salt-responsive. We determined differential gene expression and distribution per sample and most genes related to salt tolerance and photosynthesis were upregulated in 48 h vs. 24 h salt treatment. Protein interaction analysis revealed a high interaction of chaperonins and Rubisco proteins in 48 h vs. 24 h salt treatment. The gene expressions were finally validated using quantitative polymerase chain reaction (qPCR), which was coherent with sequencing results.

Looking to the horizon: the role of bilirubin in the development and prevention of age-related chronic diseases

2015 ◽  
Vol 129 (1) ◽  
pp. 1-25 ◽  
Author(s):  
Karl-Heinz Wagner ◽  
Marlies Wallner ◽  
Christine Mölzer ◽  
Silvia Gazzin ◽  
Andrew Cameron Bulmer ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Chronic Diseases ◽  
Elevated Serum ◽  
Future Research ◽  
Bile Pigment ◽  
Therapeutic Modalities ◽  
Age Related ◽  
All Cause Mortality ◽  
Novel Biomarkers ◽  
Future Research Directions

Bilirubin, the principal tetrapyrrole, bile pigment and catabolite of haem, is an emerging biomarker of disease resistance, which may be related to several recently documented biological functions. Initially believed to be toxic in infants, the perception of bilirubin has undergone a transformation: it is now considered to be a molecule that may promote health in adults. Data from the last decade demonstrate that mildly elevated serum bilirubin levels are strongly associated with reduced prevalence of chronic diseases, particularly cardiovascular diseases (CVDs), as well as CVD-related mortality and risk factors. Recent data also link bilirubin to other chronic diseases, including cancer and Type 2 diabetes mellitus, and to all-cause mortality. Therefore, there is evidence to suggest that bilirubin is a biomarker for reduced chronic disease prevalence and a predictor of all-cause mortality, which is of important clinical significance. In the present review, detailed information on the association between bilirubin and all-cause mortality, as well as the pathological conditions of CVD, cancer, diabetes and neurodegenerative diseases, is provided. The mechanistic background concerning how bilirubin and its metabolism may influence disease prevention and its clinical relevance is also discussed. Given that the search for novel biomarkers of these diseases, as well as for novel therapeutic modalities, is a key research objective for the near future, bilirubin represents a promising candidate, meeting the criteria of a biomarker, and should be considered more carefully in clinical practice as a molecule that might provide insights into disease resistance. Clearly, however, greater molecular insight is warranted to support and strengthen the conclusion that bilirubin can prevent disease, with future research directions also proposed.

Sign in / Sign up

Export Citation Format

Share Document