scholarly journals Building a Reference Transcriptome for the Hexaploid Hard Fescue Turfgrass (Festuca brevipila) Using a Combination of PacBio Iso-Seq and Illumina Sequencing

2020 ◽  
Author(s):  
Yinjie Qiu ◽  
Ya Yang ◽  
Cory D. Hirsch ◽  
Eric Watkins
Keyword(s):  
Full Length ◽  
Gene Trees ◽  
Illumina Platform ◽  
Closely Related Species ◽  
Festuca Ovina ◽  
Reference Transcriptome ◽  
Sequencing Errors ◽  
Festuca Valesiaca ◽  
Close Relatives ◽  
Breeding And Genetics

AbstractBackgroundHard fescue (Festuca brevipila Tracey, 2n=6x=42) is a cool season turfgrass with a fine leaf texture that performs well under low-input management. Breeding and genetics studies of F. brevipila have been limited due to the complexity of its hexaploid genome. To advance our knowledge of F. brevipila genomics, we used PacBio isoform sequencing to develop a reference transcriptome for this species.ResultsHere, we report the F. brevipila reference transcriptome generated from root, crown, leaf, and inflorescence tissues. We obtained 59,510 full-length transcripts, of which 38,556 were non-redundant full-length transcripts. The longest and shortest transcripts were 11,487 and 58 bp, respectively. Distribution of synonymous distances among paralogs within F. brevipila suggested highly similar subgenomes that are difficult to distinguish from sequencing errors. To evaluate the phylogenetic relationships among F. brevipila and close relatives, we sequenced three additional transcriptomes using closely related species on an Illumina platform. The results of our phylotranscriptomic analysis supported the close relationships among F. brevipila (6x), Festuca ovina (4x), Festuca ovina subsp. ovina (2x), and Festuca valesiaca (2x), with high levels of discordance among gene trees.ConclusionsOverall, the F. brevipila PacBio Isoseq reference transcriptome provided the foundation for transcriptome studies and allowed breeders a resource for gene discovery in this important turfgrass species.

scholarly journals Building a Reference Transcriptome for the Hexaploid Hard Fescue Turfgrass (Festuca brevipila) Using a Combination of PacBio Isoseq and Illumina Sequencing

2020 ◽  
Author(s):  
Yinjie Qiu ◽  
Ya Yang ◽  
Cory D. Hirsch ◽  
Eric Watkins
Keyword(s):  
Full Length ◽  
Gene Trees ◽  
Illumina Platform ◽  
Closely Related Species ◽  
Festuca Ovina ◽  
Reference Transcriptome ◽  
Sequencing Errors ◽  
Festuca Valesiaca ◽  
Close Relatives ◽  
Breeding And Genetics

Abstract Background: Hard fescue (Festuca brevipila Tracey, 2n=6x=42) is a cool season turfgrass with a fine leaf texture that performs well under low-input management. Breeding and genetics studies of F. brevipila have been limited due to the complexity of its hexaploid genome. To advance our knowledge of F. brevipila genomics, we used PacBio isoform sequencing to develop a reference transcriptome for this species. Results: Here, we report the F. brevipila reference transcriptome generated from root, crown, leaf, and inflorescence tissues. We obtained 59,510 full-length transcripts, of which 38,556 were non-redundant full-length transcripts. The longest and shortest transcripts were 11,487 and 58 bp, respectively. Distribution of synonymous distances among paralogs within F. brevipila suggested highly similar subgenomes that are difficult to distinguish from sequencing errors. To evaluate the phylogenetic relationships among F. brevipila and close relatives, we sequenced three additional transcriptomes using closely related species on an Illumina platform. The results of our phylotranscriptomic analysis supported the close relationships among F. brevipila (6x), Festuca ovina (4x), Festuca ovina subsp. ovina (2x), and Festuca valesiaca (2x), with high levels of discordance among gene trees. Conclusions: Overall, the F. brevipila PacBio Isoseq reference transcriptome provided the foundation for transcriptome studies and allowed breeders a resource for gene discovery in this important turfgrass species.

scholarly journals Building a Reference Transcriptome for the Hexaploid Hard Fescue Turfgrass (Festuca brevipila) Using a Combination of PacBio Isoseq and Illumina Sequencing

2020 ◽  
Author(s):  
Yinjie Qiu ◽  
Ya Yang ◽  
Cory D. Hirsch ◽  
Eric Watkins
Keyword(s):  
Illumina Sequencing ◽  
Related Species ◽  
Gene Discovery ◽  
Full Length ◽  
Cool Season ◽  
Illumina Platform ◽  
Closely Related Species ◽  
Reference Transcriptome ◽  
Low Input ◽  
Breeding And Genetics

Abstract Background: Hard fescue (Festuca brevipila Tracey, 2n=6x=42) is a cool season turfgrass with a fine leaf texture that performs well under low-input management. Breeding and genetics studies of F. brevipila have been limited due to the complexity of its hexaploid genome. To advance our knowledge of F. brevipila genomics, we used PacBio isoform sequencing to develop a reference transcriptome for this species. Results: Here, we report the F. brevipila reference transcriptome generated from root, crown, leaf, and seed head tissues. We obtained 59,510 full-length transcripts, of which 38,595 were non-redundant full-length transcripts. The longest and shortest transcripts were 11,487 and 58 bp, respectively. To test the polyploid origin of F. brevipila, we sequenced three additional transcriptomes using closely related species on an Illumina platform. The results of our phylotranscriptomic analysis supported the allopolyploid origin of F. brevipila. Conclusions: Overall, the F. brevipila Pacbio Isoseq reference transcriptome provided the foundation for transcriptome studies and allowed breeders for gene discovery in this important turfgrass species.

Drosophila genomes and the development of affordable molecular markers for species genotyping

Genome ◽  
2011 ◽  
Vol 54 (4) ◽  
pp. 341-347 ◽  
Author(s):  
Leigh Minuk ◽  
Alberto Civetta
Keyword(s):  
Molecular Markers ◽  
Genome Sequence ◽  
Sequence Data ◽  
Closely Related Species ◽  
Genome Sequence Data ◽  
Sequencing Errors ◽  
Genome Data ◽  
Indel Polymorphisms ◽  
Partial Genome ◽  
Rule Out

The recent completion of genome sequencing of 12 species of Drosophila has provided a powerful resource for hypothesis testing, as well as the development of technical tools. Here we take advantage of genome sequence data from two closely related species of Drosophila, Drosophila simulans and Drosophila sechellia, to quickly identify candidate molecular markers for genotyping based on expected insertion or deletion (indel) differences between species. Out of 64 candidate molecular markers selected along the second and third chromosome of Drosophila, 51 molecular markers were validated using PCR and gel electrophoresis. We found that the 20% error rate was due to sequencing errors in the genome data, although we cannot rule out possible indel polymorphisms. The approach has the advantage of being affordable and quick, as it only requires the use of bioinformatics tools for predictions and a PCR and agarose gel based assay for validation. Moreover, the approach could be easily extended to a wide variety of taxa with the only limitation being the availability of complete or partial genome sequence data.

Genetic variation for monomer–dimer equilibria of esterase-5 in Drosophila pseudoobscura, Drosophila persimilis, and Drosophila miranda

1984 ◽  
Vol 26 (3) ◽  
pp. 374-381 ◽  
Author(s):  
David R. Townsend ◽  
Rama S. Singh
Keyword(s):  
Electrophoretic Mobility ◽  
Enzyme Stability ◽  
Good Deal ◽  
The Other ◽  
Drosophila Pseudoobscura ◽  
Closely Related Species ◽  
Speciation Event ◽  
Population Polymorphism ◽  
Drosophila Persimilis ◽  
Close Relatives

Esterase-5 is a highly polymorphic enzyme in Drosophila pseudoobscura and its close relatives. Numerous alleles have been identified by employing a number of physicochemical properties of the enzyme (e.g. electrophoretic mobility, enzyme stability, subunit dimerization, and variation in monomer–dimer equilibrium). Variation in the monomer–dimer equilibrium of esterase-5 leads to differences in electrophoretic mobility of monomers produced by dimers all of which have the same mobility. In this report we have used this criterion to study variation within, as well as between, four closely related species: D. pseudoobscura pseudoobscura, D. pseudoobscura bogotana. D. persimilis, and D. miranda. All lines were characterized for esterase-5 monomer and dimer mobility at a number of gel concentrations and the comparison was made by plotting log10 monomer – dimer mobility as a function of gel concentration. No variation was found within D. p. pseudoobscura or D. p. bogotana but some variation (two distinct alleles) did occur in D. persimilis. Drosophila miranda is segregating for two alleles, one of which is fixed in D. pseudoobscura and the other one is common in D. persimilis. Thus it seems that the variation in monomer–dimer equilibrium is a rather conservative criterion and that the variation in D. miranda is a good deal older than the speciation event(s) which gave rise to D. miranda and the lineage leading to D. pseudoobscura and D. persimilis.Key words: esterase-5, Drosophila pseudoobscura, monomer–dimer equilibrium, population, polymorphism, speciation, electrophoresis.

scholarly journals Toward a comprehensive COI DNA barcode library for Swiss Stoneflies (Insecta: Plecoptera) with special emphasis on the genus Leuctra

Zoosymposia ◽  
2016 ◽  
Vol 11 ◽  
pp. 135-155 ◽  
Author(s):  
JEAN-LUC GATTOLLIAT ◽  
GILLES VINÇON ◽  
SOFIA WYLER ◽  
JAN PAWLOWSKI ◽  
MICHEL SARTORI
Keyword(s):  
Mitochondrial Gene ◽  
Dna Barcode ◽  
Pcr Amplification ◽  
Species Group ◽  
Genetic Distances ◽  
Gene Trees ◽  
Closely Related Species ◽  
Additional Tool ◽  
Non Destructive ◽  
Level Identification

The Swiss Barcode of Life initiative (SwissBOL) aims to inventory the genetic biodiversity in Switzerland using a short DNA sequence. DNA barcoding provides an additional tool for species identification that complements traditional morphological approaches. We report on the establishment of a DNA barcode library for Plecoptera, taxa that are of great importance as bioindicators of water quality and that often present difficulties in species-level identification for larvae and female specimens. Non-destructive DNA extraction, PCR amplification and sequencing of part of the mitochondrial gene Cytochrome Oxidase I (COI) was conducted for 440 individuals (one to eight per species) belonging to 90 species (of the 112 reported from Switzerland). Intra and interspecific distances were calculated and gene trees reconstructed. In most cases, COI was efficient in delimiting stonefly species. Some doubtful specimens were subsequently re-examined and a few misidentifications were found, especially in some problematic groups in the genus Leuctra Stephens, 1836. Larger genetic distances in some species (e.g. Leuctra nigra (Olivier 1811)) indicate the possible presence of sibling species, while in a few cases closely related species are genetically difficult to separate (within the Leuctra fusca species group).

scholarly journals Phylogenomic analyses using genomes and transcriptomes do not resolve relationships among major clades in Phrymaceae

2021 ◽  
Author(s):  
Diego F. Morales-Briones ◽  
Nan Lin ◽  
Eileen Y. Huang ◽  
Dena L. Grossenbacher ◽  
James M. Sobel ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Evolutionary Ecology ◽  
Gene Tree ◽  
Phylogenetic Network ◽  
Reticulate Evolution ◽  
Small Scale ◽  
Gene Trees ◽  
Network Analyses ◽  
Gene Tree Discordance ◽  
Close Relatives

Premise of the study: Phylogenomic datasets using genomes and transcriptomes provide rich opportunities beyond resolving bifurcating phylogenetic relationships. Monkeyflower (Phrymaceae) is a model system for evolutionary ecology. However, it lacks a well-supported phylogeny for a stable taxonomy and for macroevolutionary comparisons. Methods: We sampled 24 genomes and transcriptomes in Phrymaceae and closely related families, including eight newly sequenced transcriptomes. We reconstructed the phylogeny using IQ-TREE and ASTRAL, evaluated gene tree discordance using PhyParts, Quartet Sampling, and cloudogram, and carried out phylogenetic network analyses using PhyloNet and HyDe. We searched for whole genome duplication (WGD) events using chromosome numbers, synonymous distance, and gene duplication events. Key results: Most gene trees support the monophyly of Phrymaceae and each of its tribes. Most gene trees also support the tribe Mimuleae being sister to Phrymeae + Diplaceae + Leucocarpeae, with extensive gene tree discordance among the latter three. Despite the discordance, polyphyly of Mimulus s.l. is strongly supported, and no particular reticulation event among the Phrymaceae tribes is well supported. Reticulation likely occurred among Erythranthe bicolor and close relatives. No ancient WGD event was detected in Phrymaceae. Instead, small-scale duplications are among potential drivers of macroevolutionary diversification of Phrymaceae. Conclusions: We show that analysis of reticulate evolution is sensitive to taxon sampling and methods used. We also demonstrate that genome-scale data do not always fully "resolve" phylogenetic relationships. They present rich opportunities to investigate reticulate evolution, and gene and genome evolution involved in lineage diversification and adaptation.

scholarly journals Clover: a clustering-oriented de novo assembler for Illumina sequences

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Ming-Feng Hsieh ◽  
Chin Lung Lu ◽  
Chuan Yi Tang
Keyword(s):  
De Novo Assembly ◽  
De Novo ◽  
Low Cost ◽  
De Bruijn Graph ◽  
Illumina Platform ◽  
Sequencing Errors ◽  
Sequencing Technologies ◽  
String Graph ◽  
Clustering Approach ◽  
De Bruijn

Abstract Background Next-generation sequencing technologies revolutionized genomics by producing high-throughput reads at low cost, and this progress has prompted the recent development of de novo assemblers. Multiple assembly methods based on de Bruijn graph have been shown to be efficient for Illumina reads. However, the sequencing errors generated by the sequencer complicate analysis of de novo assembly and influence the quality of downstream genomic researches. Results In this paper, we develop a de Bruijn assembler, called Clover (clustering-oriented de novo assembler), that utilizes a novel k-mer clustering approach from the overlap-layout-consensus concept to deal with the sequencing errors generated by the Illumina platform. We further evaluate Clover’s performance against several de Bruijn graph assemblers (ABySS, SOAPdenovo, SPAdes and Velvet), overlap-layout-consensus assemblers (Bambus2, CABOG and MSR-CA) and string graph assembler (SGA) on three datasets (Staphylococcus aureus, Rhodobacter sphaeroides and human chromosome 14). The results show that Clover achieves a superior assembly quality in terms of corrected N50 and E-size while remaining a significantly competitive in run time except SOAPdenovo. In addition, Clover was involved in the sequencing projects of bacterial genomes Acinetobacter baumannii TYTH-1 and Morganella morganii KT. Conclusions The marvel clustering-based approach of Clover that integrates the flexibility of the overlap-layout-consensus approach and the efficiency of the de Bruijn graph method has high potential on de novo assembly. Now, Clover is freely available as open source software from https://oz.nthu.edu.tw/~d9562563/src.html.

Ribosomal internal transcribed spacer regions are not suitable for intra- or inter-specific phylogeny reconstruction in haplosclerid sponges (Porifera: Demospongiae)

2009 ◽  
Vol 89 (6) ◽  
pp. 1251-1256 ◽  
Author(s):  
Niamh E. Redmond ◽  
Grace P. McCormack
Keyword(s):  
Internal Transcribed Spacer ◽  
Phylogenetic Trees ◽  
Population Level ◽  
Single Species ◽  
Its Sequences ◽  
Closely Related Species ◽  
Internal Transcribed Spacer Regions ◽  
Species Specific ◽  
Close Relatives ◽  
Number Of Individuals

Sequences of the ribosomal internal transcribed spacer regions 1 and 2 (ITS-1 and ITS-2) were employed to investigate relationships between putatively very closely related species of marine haplosclerids and to investigate the species status of Haliclona cinerea. Results indicate that intra-genomic and intra-specific levels of diversity are equivalent, and sequences from multiple clones from a number of individuals of a single species could not be separated on phylogenetic trees. As a result, the ITS regions are not suitable markers for population level studies in marine haplosclerids. Sequences of these regions were highly species specific, and large differences were found between species. ITS sequences from three Callyspongia and three Haliclona species could not be aligned successfully and therefore this locus could not be used to investigate relationships between these putative close relatives. However, ITS sequences retrieved from one H. cinerea were very different from sequences generated from other H. cinerea individuals indicating that this species comprises more than one taxon.

scholarly journals Morphology captures diet and locomotor types in rodents

2017 ◽  
Vol 4 (1) ◽  
pp. 160957 ◽  
Author(s):  
Luis D. Verde Arregoitia ◽  
Diana O. Fisher ◽  
Manuel Schweizer
Keyword(s):  
Evolutionary History ◽  
Morphological Features ◽  
Museum Specimens ◽  
Museum Collections ◽  
Morphological Similarity ◽  
Closely Related Species ◽  
Phylogenetic Relatedness ◽  
Ecological Relevance ◽  
Ecological Literature ◽  
Close Relatives

To understand the functional meaning of morphological features, we need to relate what we know about morphology and ecology in a meaningful, quantitative framework. Closely related species usually share more phenotypic features than distant ones, but close relatives do not necessarily have the same ecologies. Rodents are the most diverse group of living mammals, with impressive ecomorphological diversification. We used museum collections and ecological literature to gather data on morphology, diet and locomotion for 208 species of rodents from different bioregions to investigate how morphological similarity and phylogenetic relatedness are associated with ecology. After considering differences in body size and shared evolutionary history, we find that unrelated species with similar ecologies can be characterized by a well-defined suite of morphological features. Our results validate the hypothesized ecological relevance of the chosen traits. These cranial, dental and external (e.g. ears) characters predicted diet and locomotion and showed consistent differences among species with different feeding and substrate use strategies. We conclude that when ecological characters do not show strong phylogenetic patterns, we cannot simply assume that close relatives are ecologically similar. Museum specimens are valuable records of species' phenotypes and with the characters proposed here, morphology can reflect functional similarity, an important component of community ecology and macroevolution.

scholarly journals Horizontal gene transfer and recombination analysis of SARS-CoV-2 genes helps discover its close relatives and shed light on its origin

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Vladimir Makarenkov ◽  
Bogdan Mazoure ◽  
Guillaume Rabusseau ◽  
Pierre Legendre
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Intermediate Host ◽  
Close Relative ◽  
Intragenic Recombination ◽  
Recombination Analysis ◽  
Gene Trees ◽  
Intermediate Hosts ◽  
Evolutionary Patterns ◽  
Close Relatives

Abstract Background The SARS-CoV-2 pandemic is one of  the greatest  global medical and social challenges that have emerged in recent history. Human coronavirus strains discovered during previous SARS outbreaks have been hypothesized to pass from bats to humans using intermediate hosts, e.g. civets for SARS-CoV and camels for MERS-CoV. The discovery of an intermediate host of SARS-CoV-2 and the identification of specific mechanism of its emergence in humans are topics of primary evolutionary importance. In this study we investigate the evolutionary patterns of 11 main genes of SARS-CoV-2. Previous studies suggested that the genome of SARS-CoV-2 is highly similar to the horseshoe bat coronavirus RaTG13 for most of the genes and to some Malayan pangolin coronavirus (CoV) strains for the receptor binding (RB) domain of the spike protein. Results We provide a detailed list of statistically significant horizontal gene transfer and recombination events (both intergenic and intragenic) inferred for each of 11 main genes of the SARS-CoV-2 genome. Our analysis reveals that two continuous regions of genes S and N of SARS-CoV-2 may result from intragenic recombination between RaTG13 and Guangdong (GD) Pangolin CoVs. Statistically significant gene transfer-recombination events between RaTG13 and GD Pangolin CoV have been identified in region [1215–1425] of gene S and region [534–727] of gene N. Moreover, some statistically significant recombination events between the ancestors of SARS-CoV-2, RaTG13, GD Pangolin CoV and bat CoV ZC45-ZXC21 coronaviruses have been identified in genes ORF1ab, S, ORF3a, ORF7a, ORF8 and N. Furthermore, topology-based clustering of gene trees inferred for 25 CoV organisms revealed a three-way evolution of coronavirus genes, with gene phylogenies of ORF1ab, S and N forming the first cluster, gene phylogenies of ORF3a, E, M, ORF6, ORF7a, ORF7b and ORF8 forming the second cluster, and phylogeny of gene ORF10 forming the third cluster. Conclusions The results of our horizontal gene transfer and recombination analysis suggest that SARS-CoV-2 could not only be a chimera virus resulting from recombination of the bat RaTG13 and Guangdong pangolin coronaviruses but also a close relative of the bat CoV ZC45 and ZXC21 strains. They also indicate that a GD pangolin may be an intermediate host of this dangerous virus. 

Sign in / Sign up

Export Citation Format

Share Document