scholarly journals De novo Transcriptome Characterization of Iris atropurpurea (the Royal Iris, Iris section Oncocyclus) and Phylogenetic Analysis of MADS-box and R2R3-MYB Gene Families

2019 ◽  
Author(s):  
Bar-Lev Yamit ◽  
Senden Esther ◽  
Pasmanik-Chor Metsada ◽  
Sapir Yuval
Keyword(s):  
Molecular Markers ◽  
Transcriptome Sequencing ◽  
De Novo ◽  
Major Gene ◽  
Middle Eastern ◽  
Gene Families ◽  
Model Organisms ◽  
Gene Trees ◽  
Mads Box ◽  
Valuable Resource

AbstractThe Royal Irises, Iris section Oncocyclus, are a Middle-Eastern group of irises, characterized by extremely large flowers with a huge range of flower colors and a unique pollination system. The Royal Irises are considered to be in the course of speciation and serve as a model for evolutionary processes of speciation and pollination ecology. However, no transcriptomic and genomic data for molecular characterization are available for these plants.Transcriptome sequencing is a valuable resource for determining the genetic basis of ecological-meaningful traits, especially in non-model organisms. Here we describe the de novo transcriptome sequencing and assembly of Iris atropurpurea, an endangered species, endemic to Israel’s coastal plain. We employed RNA sequencing to analyze the transcriptomes of roots, leaves, and three stages of developing flower buds. To identify genes involved in developmental processes we generated phylogenetic gene trees for two major gene families, the MADS-box and MYB transcription factors, which play an important role in plant development. In addition, we identified 1,503 short sequence repeats that can be developed for molecular markers for population genetics in irises.In the era of large genetic datasets, the Iris transcriptome sequencing provides a valuable resource for studying adaptation-associated traits in this non-model plant. This first reported transcriptome for the Royal Irises, and the data generated from this study, will facilitate gene discovery, functional genomic studies, and development of molecular markers in irises, to complete the intensive eco-evolutionary studies of this group.

scholarly journals De novo transcriptome characterization of Iris atropurpurea (the Royal Iris) and phylogenetic analysis of MADS-box and R2R3-MYB gene families

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Bar-Lev Yamit ◽  
Senden Esther ◽  
Pasmanik-Chor Metsada ◽  
Sapir Yuval
Keyword(s):  
Molecular Markers ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Major Gene ◽  
Gene Families ◽  
Model Organisms ◽  
Gene Trees ◽  
Mads Box ◽  
Valuable Resource ◽  
De Novo Transcriptome

AbstractThe Royal Irises (section Oncocyclus) are a Middle-Eastern group of irises, characterized by extremely large flowers with a huge range of flower colors and a unique pollination system. The Royal Irises are considered to be in the course of speciation and serve as a model for evolutionary processes of speciation and pollination ecology. However, no transcriptomic and genomic data are available for these plants. Transcriptome sequencing is a valuable resource for determining the genetic basis of ecological-meaningful traits, especially in non-model organisms. Here we describe the de novo transcriptome assembly of Iris atropurpurea, an endangered species endemic to Israel’s coastal plain. We sequenced and analyzed the transcriptomes of roots, leaves, and three stages of developing flower buds. To identify genes involved in developmental processes we generated phylogenetic gene trees for two major gene families, the MADS-box and MYB transcription factors, which play an important role in plant development. In addition, we identified 1503 short sequence repeats that can be developed for molecular markers for population genetics in irises. This first reported transcriptome for the Royal Irises, and the data generated, provide a valuable resource for this non-model plant that will facilitate gene discovery, functional genomic studies, and development of molecular markers in irises, to complete the intensive eco-evolutionary studies of this group.

scholarly journals Reference Genome for the Highly Transformable Setaria viridis ME034V

2020 ◽  
Vol 10 (10) ◽  
pp. 3467-3478 ◽  
Author(s):  
Peter M. Thielen ◽  
Amanda L. Pendleton ◽  
Robert A. Player ◽  
Kenneth V. Bowden ◽  
Thomas J. Lawton ◽  
...  
Keyword(s):  
De Novo ◽  
Gene Families ◽  
Model Organisms ◽  
Phylogenomic Analysis ◽  
Setaria Viridis ◽  
Sequencing Technology ◽  
Protein Coding ◽  
Genotype Frequencies ◽  
Green Foxtail ◽  
Genome Assemblies

Setaria viridis (green foxtail) is an important model system for improving cereal crops due to its diploid genome, ease of cultivation, and use of C4 photosynthesis. The S. viridis accession ME034V is exceptionally transformable, but the lack of a sequenced genome for this accession has limited its utility. We present a 397 Mb highly contiguous de novo assembly of ME034V using ultra-long nanopore sequencing technology (read N50 = 41kb). We estimate that this genome is largely complete based on our updated k-mer based genome size estimate of 401 Mb for S. viridis. Genome annotation identified 37,908 protein-coding genes and >300k repetitive elements comprising 46% of the genome. We compared the ME034V assembly with two other previously sequenced Setaria genomes as well as to a diversity panel of 235 S. viridis accessions. We found the genome assemblies to be largely syntenic, but numerous unique polymorphic structural variants were discovered. Several ME034V deletions may be associated with recent retrotransposition of copia and gypsy LTR repeat families, as evidenced by their low genotype frequencies in the sampled population. Lastly, we performed a phylogenomic analysis to identify gene families that have expanded in Setaria, including those involved in specialized metabolism and plant defense response. The high continuity of the ME034V genome assembly validates the utility of ultra-long DNA sequencing to improve genetic resources for emerging model organisms. Structural variation present in Setaria illustrates the importance of obtaining the proper genome reference for genetic experiments. Thus, we anticipate that the ME034V genome will be of significant utility for the Setaria research community.

scholarly journals CAARS: comparative assembly and annotation of RNA-Seq data

2018 ◽  
Vol 35 (13) ◽  
pp. 2199-2207 ◽  
Author(s):  
Carine Rey ◽  
Philippe Veber ◽  
Bastien Boussau ◽  
Marie Sémon
Keyword(s):  
Gene Family ◽  
De Novo ◽  
Sequence Similarity ◽  
Gene Families ◽  
Supplementary Information ◽  
Model Organisms ◽  
Difficult Case ◽  
Rna Seq ◽  
Comparative Analyses ◽  
Family Reconstruction

Abstract Motivation RNA sequencing (RNA-Seq) is a widely used approach to obtain transcript sequences in non-model organisms, notably for performing comparative analyses. However, current bioinformatic pipelines do not take full advantage of pre-existing reference data in related species for improving RNA-Seq assembly, annotation and gene family reconstruction. Results We built an automated pipeline named CAARS to combine novel data from RNA-Seq experiments with existing multi-species gene family alignments. RNA-Seq reads are assembled into transcripts by both de novo and assisted assemblies. Then, CAARS incorporates transcripts into gene families, builds gene alignments and trees and uses phylogenetic information to classify the genes as orthologs and paralogs of existing genes. We used CAARS to assemble and annotate RNA-Seq data in rodents and fishes using distantly related genomes as reference, a difficult case for this kind of analysis. We showed CAARS assemblies are more complete and accurate than those assembled by a standard pipeline consisting of de novo assembly coupled with annotation by sequence similarity on a guide species. In addition to annotated transcripts, CAARS provides gene family alignments and trees, annotated with orthology relationships, directly usable for downstream comparative analyses. Availability and implementation CAARS is implemented in Python and Ocaml and is freely available at https://github.com/carinerey/caars. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Reference genome for the highly transformable Setaria viridis cultivar ME034V

2020 ◽  
Author(s):  
Peter M. Thielen ◽  
Amanda L. Pendleton ◽  
Robert A. Player ◽  
Kenneth V. Bowden ◽  
Thomas J. Lawton ◽  
...  
Keyword(s):  
De Novo ◽  
Gene Families ◽  
Model Organisms ◽  
Phylogenomic Analysis ◽  
Setaria Viridis ◽  
Sequencing Technology ◽  
Protein Coding ◽  
Genotype Frequencies ◽  
Green Foxtail ◽  
Genome Assemblies

ABSTRACTSetaria viridis (green foxtail) is an important model system for improving cereal crops due to its diploid genome, ease of cultivation, and use of C4 photosynthesis. The S. viridis cultivar ME034V is exceptionally transformable, but the lack of a sequenced genome for this cultivar has limited its utility. We present a 397 Mb highly contiguous de novo assembly of ME034V using ultra-long nanopore sequencing technology (read N50=41kb). We estimate that this genome is largely complete based on our updated k-mer based genome size estimate of 401 Mb for S. viridis. Genome annotation identified 37,908 protein-coding genes and >300k repetitive elements comprising 46% of the genome. We compared the ME034V assembly with two other previously sequenced Setaria genomes as well as to a diversity panel of 235 S. viridis cultivars. We found the genome assemblies to be largely syntenic, but numerous unique polymorphic structural variants were discovered. Several ME034V deletions may be associated with recent retrotransposition of copia and gypsy LTR repeat families, as evidenced by their low genotype frequencies in the sampled population. Lastly, we performed a phylogenomic analysis to identify gene families that have expanded in Setaria, including those involved in specialized metabolism and plant defense response. The high continuity of the ME034V genome assembly validates the utility of ultra-long DNA sequencing to improve genetic resources for emerging model organisms. Structural variation present in Setaria illustrates the importance of obtaining the proper genome reference for genetic experiments. Thus, we anticipate that the ME034V genome will be of significant utility for the Setaria research community.

scholarly journals Evolution of anisogamy in the early diverging fungus, Allomyces

2017 ◽  
Author(s):  
Sujal S. Phadke ◽  
Shawn M. Rupp ◽  
Melissa A. Wilson Sayres
Keyword(s):  
Mating Systems ◽  
De Novo ◽  
Model Organisms ◽  
Character State ◽  
Gene Trees ◽  
Male And Female ◽  
Individual Gene ◽  
Genomic Changes ◽  
Molecular Events ◽  
Gamete Size

AbstractGamete size dimorphism between sexes (anisogamy) is predicted to have evolved from an isogamous system in which sexes have equal-sized, monomorphic gametes. Although adaptive explanations for the evolution of anisogamy abound, we lack comparable insights into molecular changes that bring about the transition from monomorphism to dimorphism. The basal fungal clade Allomyces provides unique opportunities to investigate genomic changes that are associated with this transition in closely related species that show either isogamous or anisogamous mating systems. The anisogamous species show sexual dimorphism in gamete size, number, pigmentation and motility. We sequenced transcriptomes of five Allomyces isolates representing the two mating systems, including both male and female phenotypes in the anisogamous species. Maximum likelihood ancestral character state reconstruction performed in MESQUITE using the de-novo assembled transcriptomes indicated that anisogamy likely evolved once in Allomyces, and is a derived character as predicted in theory. We found that sexual stages of Allomyces express homologs of several genes known to be involved in sex determination in model organisms including Drosophila and humans. Furthermore, expression of CatSper homologs in male- and female-biased samples in our analysis support the hypothesis that gamete interaction in the anisogamous species of Allomyces may involve similar molecular events as the egg-sperm interaction in animals, including humans. Although the strains representing either mating system shared much of the transcriptome, supporting recent common ancestry, the analysis of rate of evolution using individual gene trees indicates high substitution rates and divergence between the strains. In summary, we find that anisogamy likely evolved once in Allomyces, using convergent mechanisms to those in other taxa.

scholarly journals Comparability of reference-based and reference-free transcriptome analysis approaches at the gene expression level

2021 ◽  
Vol 22 (S11) ◽  
Author(s):  
Sung-Gwon Lee ◽  
Dokyun Na ◽  
Chungoo Park
Keyword(s):  
Gene Expression ◽  
De Novo ◽  
Expression Profiles ◽  
Gene Families ◽  
Cell Types ◽  
Model Organisms ◽  
Expression Levels ◽  
Large Gene ◽  
Gene Expression Quantification ◽  
Gene Expression Levels

Abstract Background Lately, high-throughput RNA sequencing has been extensively used to elucidate the transcriptome landscape and dynamics of cell types of different species. In particular, for most non-model organisms lacking complete reference genomes with high-quality annotation of genetic information, reference-free (RF) de novo transcriptome analyses, rather than reference-based (RB) approaches, are widely used, and RF analyses have substantially contributed toward understanding the mechanisms regulating key biological processes and functions. To date, numerous bioinformatics studies have been conducted for assessing the workflow, production rate, and completeness of transcriptome assemblies within and between RF and RB datasets. However, the degree of consistency and variability of results obtained by analyzing gene expression levels through these two different approaches have not been adequately documented. Results In the present study, we evaluated the differences in expression profiles obtained with RF and RB approaches and revealed that the former tends to be satisfactorily replaced by the latter with respect to transcriptome repertoires, as well as from a gene expression quantification perspective. In addition, we urge cautious interpretation of these findings. Several genes that are lowly expressed, have long coding sequences, or belong to large gene families must be validated carefully, whenever gene expression levels are calculated using the RF method. Conclusions Our empirical results indicate important contributions toward addressing transcriptome-related biological questions in non-model organisms.

scholarly journals Author Correction: De novo transcriptome characterization of Iris atropurpurea (the Royal Iris) and phylogenetic analysis of MADS-box and R2R3-MYB gene families

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yamit Bar-Lev ◽  
Esther Senden ◽  
Metsada Pasmanik-Chor ◽  
Yuval Sapir
Keyword(s):  
Phylogenetic Analysis ◽  
De Novo ◽  
Gene Families ◽  
Mads Box ◽  
De Novo Transcriptome ◽  
Myb Gene ◽  
R2r3 Myb

scholarly journals Removing the bad apples: A simple bioinformatic method to improve loci‐recovery in de novo RADseq data for non‐model organisms

2021 ◽  
Author(s):  
José Cerca ◽  
Marius F. Maurstad ◽  
Nicolas C. Rochette ◽  
Angel G. Rivera‐Colón ◽  
Niraj Rayamajhi ◽  
...  
Keyword(s):  
De Novo ◽  
Model Organisms

scholarly journals Dissecting the chromosome-level genome of the Asian Clam (Corbicula fluminea)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tongqing Zhang ◽  
Jiawen Yin ◽  
Shengkai Tang ◽  
Daming Li ◽  
Xiankun Gu ◽  
...  
Keyword(s):  
De Novo ◽  
Corbicula Fluminea ◽  
Gene Families ◽  
Ruditapes Philippinarum ◽  
Genomic Sequences ◽  
Future Research ◽  
Asian Clam ◽  
Sequencing Technologies ◽  
East And Southeast Asia ◽  
Clam Corbicula

AbstractThe Asian Clam (Corbicula fluminea) is a valuable commercial and medicinal bivalve, which is widely distributed in East and Southeast Asia. As a natural nutrient source, the clam is rich in protein, amino acids, and microelements. The genome of C. fluminea has not yet been characterized; therefore, genome-assisted breeding and improvements cannot yet be implemented. In this work, we present a de novo chromosome-scale genome assembly of C. fluminea using PacBio and Hi-C sequencing technologies. The assembled genome comprised 4728 contigs, with a contig N50 of 521.06 Kb, and 1,215 scaffolds with a scaffold N50 of 70.62 Mb. More than 1.51 Gb (99.17%) of genomic sequences were anchored to 18 chromosomes, of which 1.40 Gb (92.81%) of genomic sequences were ordered and oriented. The genome contains 38,841 coding genes, 32,591 (83.91%) of which were annotated in at least one functional database. Compared with related species, C. fluminea had 851 expanded gene families and 191 contracted gene families. The phylogenetic tree showed that C. fluminea diverged from Ruditapes philippinarum, ~ 228.89 million years ago (Mya), and the genomes of C. fluminea and R. philippinarum shared 244 syntenic blocks. Additionally, we identified 2 MITF members and 99 NLRP members in C. fluminea genome. The high-quality and chromosomal Asian Clam genome will be a valuable resource for a range of development and breeding studies of C. fluminea in future research.

Sign in / Sign up

Export Citation Format

Share Document