scholarly journals Draft genome of the aquatic moss Fontinalis antipyretica (Fontinalaceae, Bryophyta)

Gigabyte ◽  
2020 ◽  
Vol 2020 ◽  
pp. 1-9
Author(s):  
Jin Yu ◽  
Linzhou Li ◽  
Sibo Wang ◽  
Shanshan Dong ◽  
Ziqiang Chen ◽  
...  
Keyword(s):  
Vascular Plants ◽  
Aquatic Plant ◽  
De Novo ◽  
Draft Genome ◽  
Nuclear Genome ◽  
Sister Group ◽  
Plant Genome ◽  
Fontinalis Antipyretica ◽  
Aquatic Moss ◽  
Colonization Of Land

Mosses comprise one of three lineages forming a sister group to extant vascular plants. Having emerged from an early split in the diversification of embryophytes, mosses may offer complementary insights into the evolution of traits following the transition to, and colonization of, land. Here, we report the draft nuclear genome of Fontinalis antipyretica (Fontinalaceae, Hypnales), a charismatic aquatic moss that is widespread in temperate regions of the Northern Hemisphere. We sequenced and de novo-assembled its genome using the 10X Genomics method. The genome comprises 385.2 Mbp, with a scaffold N50 of 45.8 Kbp. The assembly captured 87.2% of the 430 genes in the BUSCO Viridiplantae odb10 dataset. The newly generated F. antipyretica genome is the third moss genome, and the second seedless aquatic plant genome, to be sequenced and assembled to date.

scholarly journals Draft genome of the aquatic moss Fontinalis antipyretica (Fontinalaceae, Bryophyta)

2020 ◽  
Author(s):  
Jin Yu ◽  
Linzhou Li ◽  
Sibo Wang ◽  
Shanshan Dong ◽  
Ziqiang Chen ◽  
...  
Keyword(s):  
Vascular Plants ◽  
Aquatic Plant ◽  
De Novo ◽  
Draft Genome ◽  
Nuclear Genome ◽  
Sister Group ◽  
Fontinalis Antipyretica ◽  
Aquatic Moss ◽  
The Third ◽  
Colonization Of Land

AbstractBackgroundMosses compose one of the three lineages that form the sister group to extant vascular plants. Having emerged from an early split in the diversification of embryophytes, mosses may offer complementary insights into the evolution of traits following the transition to and colonization of land. Here, we report the draft nuclear genome of Fontinalis antipyretica (Fontinalaceae, Hypnales), a charismatic aquatic moss widespread in temperate regions of the Northern Hemisphere. We sequenced and de novo assembled its genome using the 10 × genomics method. The genome comprises 486.3 Mb, with a scaffold N50 of 38.8 kb. The assembly captured 89.4% of the 303 genes in the BUSCO eukaryote dataset. The newly generated F. antipyretica genome is the third genome of mosses, and the second genome for a seedless aquatic plant.

scholarly journals The draft nuclear genome assembly of Eucalyptus pauciflora: new approaches to comparing de novo assemblies

2019 ◽  
Author(s):  
Weiwen Wang ◽  
Ashutosh Das ◽  
David Kainer ◽  
Miriam Schalamun ◽  
Alejandro Morales-Suarez ◽  
...  
Keyword(s):  
Error Rate ◽  
Genome Assembly ◽  
De Novo ◽  
Sequence Similarity ◽  
Draft Genome ◽  
Nuclear Genome ◽  
Single Species ◽  
Test Case ◽  
High Coverage ◽  
Validation Set

AbstractBackgroundSelecting the best genome assembly from a collection of draft assemblies for the same species remains a difficult task. Here, we combine new and existing approaches to help to address this, using the non-model plant Eucalyptus pauciflora (snow gum) as a test case. Eucalyptus pauciflora is a long-lived tree with high economic and ecological importance. Currently, little genomic information for Eucalyptus pauciflora is available.FindingsWe generated high coverage of long-(Nanopore, 174x) and short-(Illumina, 228x) read data from a single Eucalyptus pauciflora individual and compared assemblies from four assemblers with a variety of settings: Canu, Flye, Marvel, and MaSuRCA. A key component of our approach is to keep a randomly selected collection of ~10% of both long- and short-reads separate from the assemblies to use as a validation set with which to assess the assemblies. Using this validation set along with a range of existing tools, we compared the assemblies in eight ways: contig N50, BUSCO scores, LAI scores, assembly ploidy, base-level error rate, computing genome assembly likelihoods, structural variation and genome sequence similarity. Our result showed that MaSuRCA generated the best assembly, which is 594.87 Mb in size, with a contig N50 of 3.23 Mb, and an estimated error rate of ~0.006 errors per base.ConclusionsWe report a draft genome of Eucalyptus pauciflora, which will be a valuable resource for further genomic studies of eucalypts. These approaches for assessing and comparing genomes should help in assessing and choosing among many potential genome assemblies for a single species.

Protocols for "Draft genome of the aquatic moss Fontinalis antipyretica (Fontinalaceae, Bryophyta)" v1 (protocols.io.bn7jmhkn)

protocols.io ◽  
2020 ◽  
Author(s):  
Yang Liu ◽  
Huan Liu ◽  
Hongfeng Chen ◽  
Bernard Goffinet ◽  
Nikisha Patel ◽  
...  
Keyword(s):  
Draft Genome ◽  
Fontinalis Antipyretica ◽  
Aquatic Moss

scholarly journals Genomic and transcriptomic resources for assassin flies including the complete genome sequence ofProctacanthus coquilletti(Insecta: Diptera: Asilidae) and 16 representative transcriptomes

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2951 ◽  
Author(s):  
Rebecca B. Dikow ◽  
Paul B. Frandsen ◽  
Mauren Turcatel ◽  
Torsten Dikow
Keyword(s):  
Life Histories ◽  
Large Scale ◽  
De Novo ◽  
Draft Genome ◽  
Sister Group ◽  
Sister Group Relationship ◽  
Fossil Calibration ◽  
A Genome ◽  
Relationship Of ◽  
Illumina Library

A high-quality draft genome forProctacanthus coquilletti(Insecta: Diptera: Asilidae) is presented along with transcriptomes for 16 Diptera species from five families: Asilidae, Apioceridae, Bombyliidae, Mydidae, and Tabanidae. Genome sequencing reveals thatP. coquillettihas a genome size of approximately 210 Mbp and remarkably low heterozygosity (0.47%) and few repeats (15%). These characteristics helped produce a highly contiguous (N50 = 862 kbp) assembly, particularly given that only a single 2 × 250 bp PCR-free Illumina library was sequenced. A phylogenomic hypothesis is presented based on thousands of putative orthologs across the 16 transcriptomes. Phylogenetic relationships support the sister group relationship of Apioceridae + Mydidae to Asilidae. A time-calibrated phylogeny is also presented, with seven fossil calibration points, which suggests an older age of the split among Apioceridae, Asilidae, and Mydidae (158 mya) and Apioceridae and Mydidae (135 mya) than proposed in the AToL FlyTree project. Future studies will be able to take advantage of the resources presented here in order to produce large scale phylogenomic and evolutionary studies of assassin fly phylogeny, life histories, or venom. The bioinformatics tools and workflow presented here will be useful to others wishing to generatede novogenomic resources in species-rich taxa without a closely-related reference genome.

scholarly journals DNA Methylation Diversification at the Integrated Organellar DNA-Like Sequence

Genes ◽  
2018 ◽  
Vol 9 (12) ◽  
pp. 602 ◽  
Author(s):  
Takanori Yoshida ◽  
Yoshiaki Tarutani ◽  
Tetsuji Kakutani ◽  
Akira Kawabe
Keyword(s):  
Dna Methylation ◽  
De Novo ◽  
Epigenetic Modification ◽  
Natural Populations ◽  
Nuclear Genome ◽  
Amplicon Sequencing ◽  
Epigenetic Modifications ◽  
Plant Genome ◽  
Organellar Dna ◽  
Epigenetic Diversity

Plants have a lot of diversity in epigenetic modifications such as DNA methylation in their natural populations or cultivars. Although many studies observing the epigenetic diversity within and among species have been reported, the mechanisms how these variations are generated are still not clear. In addition to the de novo spontaneous epi-mutation, the intra- and inter-specific crossing can also cause a change of epigenetic modifications in their progenies. Here we report an example of diversification of DNA methylation by crossing and succeeding selfing. We traced the inheritance pattern of epigenetic modification during the crossing experiment between two natural strains Columbia (Col), and Landsberg electa (Ler) in model plant Arabidopsis thaliana to observe the inheritance of DNA methylation in two organellar DNA-like sequence regions in the nuclear genome. Because organellar DNA integration to the nuclear genome is common in flowering plants and these sequences are occasionally methylated, such DNA could be the novel source of plant genome evolution. The amplicon sequencing, using bisulfite-converted DNA and a next-generation auto-sequencer, was able to efficiently track the heredity of DNA methylation in F1 and F2 populations. One region showed hypomethylation in the F1 population and succeeding elevation of DNA methylation with large variance in the F2 population. The methylation level of Col and Ler alleles in F2 heterozygotes showed a significant positive correlation, implying the trans-chromosomal effect on DNA methylation. The results may suggest the possible mechanism causing the natural epigenetic diversity within plant populations.

scholarly journals The draft nuclear genome assembly of Eucalyptus pauciflora: a pipeline for comparing de novo assemblies

GigaScience ◽  
2020 ◽  
Vol 9 (1) ◽  
Author(s):  
Weiwen Wang ◽  
Ashutosh Das ◽  
David Kainer ◽  
Miriam Schalamun ◽  
Alejandro Morales-Suarez ◽  
...  
Keyword(s):  
Error Rate ◽  
Genome Assembly ◽  
De Novo ◽  
Sequence Similarity ◽  
Draft Genome ◽  
Nuclear Genome ◽  
Read Length ◽  
High Coverage ◽  
Ecological Importance ◽  
Validation Set

Abstract Background Eucalyptus pauciflora (the snow gum) is a long-lived tree with high economic and ecological importance. Currently, little genomic information for E. pauciflora is available. Here, we sequentially assemble the genome of Eucalyptus pauciflora with different methods, and combine multiple existing and novel approaches to help to select the best genome assembly. Findings We generated high coverage of long- (Nanopore, 174×) and short- (Illumina, 228×) read data from a single E. pauciflora individual and compared assemblies from 5 assemblers (Canu, SMARTdenovo, Flye, Marvel, and MaSuRCA) with different read lengths (1 and 35 kb minimum read length). A key component of our approach is to keep a randomly selected collection of ∼10% of both long and short reads separated from the assemblies to use as a validation set for assessing assemblies. Using this validation set along with a range of existing tools, we compared the assemblies in 8 ways: contig N50, BUSCO scores, LAI (long terminal repeat assembly index) scores, assembly ploidy, base-level error rate, CGAL (computing genome assembly likelihoods) scores, structural variation, and genome sequence similarity. Our result showed that MaSuRCA generated the best assembly, which is 594.87 Mb in size, with a contig N50 of 3.23 Mb, and an estimated error rate of ∼0.006 errors per base. Conclusions We report a draft genome of E. pauciflora, which will be a valuable resource for further genomic studies of eucalypts. The approaches for assessing and comparing genomes should help in assessing and choosing among many potential genome assemblies from a single dataset.

scholarly journals De Novo Sporophyte Transcriptome Assembly and Functional Annotation in the Endangered Fern Species Vandenboschia speciosa (Willd.) G. Kunkel

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 1017
Author(s):  
Mohammed Bakkali ◽  
Rubén Martín-Blázquez ◽  
Mercedes Ruiz-Estévez ◽  
Manuel A. Garrido-Ramos
Keyword(s):  
Functional Annotation ◽  
Vascular Plants ◽  
De Novo ◽  
Transcriptome Assembly ◽  
Systematic Position ◽  
Important Data ◽  
Ecological Requirements ◽  
Physiological Adaptations ◽  
Fern Species ◽  
Go Terms

We sequenced the sporophyte transcriptome of Killarney fern (Vandenboschia speciosa (Willd.) G. Kunkel). In addition to being a rare endangered Macaronesian-European endemism, this species has a huge genome (10.52 Gb) as well as particular biological features and extreme ecological requirements. These characteristics, together with the systematic position of ferns among vascular plants, make it of high interest for evolutionary, conservation and functional genomics studies. The transcriptome was constructed de novo and contained 36,430 transcripts, of which 17,706 had valid BLAST hits. A total of 19,539 transcripts showed at least one of the 7362 GO terms assigned to the transcriptome, whereas 6547 transcripts showed at least one of the 1359 KEGG assigned terms. A prospective analysis of functional annotation results provided relevant insights on genes involved in important functions such as growth and development as well as physiological adaptations. In this context, a catalogue of genes involved in the genetic control of plant development, during the vegetative to reproductive transition, in stress response as well as genes coding for transcription factors is given. Altogether, this study provides a first step towards understanding the gene expression of a significant fern species and the in silico functional and comparative analyses reported here provide important data and insights for further comparative evolutionary studies in ferns and land plants in general.

scholarly journals Draft Genome Sequence of Leifsonia xyli subsp. xyli Strain gdw1

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Jihua Wang ◽  
Li Wang ◽  
Gan Cao ◽  
Muqing Zhang ◽  
Ying Guo
Keyword(s):  
Genome Sequence ◽  
Genetic Improvement ◽  
De Novo ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Coding Sequences ◽  
Ratoon Stunting Disease

Here, we report the draft genome sequence of Leifsonia xyli subsp. xyli strain gdw1, isolated from the stem of Badila sugarcane located at the Guangdong Key Laboratory for Crops Genetic Improvement (Guanzhou, China), that causes ratoon stunting disease of sugarcane. The de novo genome of Leifsonia xyli subsp. xyli was assembled with 48 scaffolds and a G+C content of 67.68%, and contained 2.6 Mb bp and 2,838 coding sequences.

scholarly journals Nuclear-cytoplasmic balance: whole genome duplications induce elevated organellar genome copy number

2021 ◽  
Author(s):  
Matheus Fernandes Gyorfy ◽  
Emma R Miller ◽  
Justin L Conover ◽  
Corrinne E Grover ◽  
Jonathan F Wendel ◽  
...  
Keyword(s):  
Copy Number ◽  
Nuclear Genome ◽  
Plant Genome ◽  
Whole Genome ◽  
Genome Copy ◽  
Relative Copy Number ◽  
Organellar Genome ◽  
Plastid Genomes ◽  
Copy Numbers ◽  
Genome Copy Number

The plant genome is partitioned across three distinct subcellular compartments: the nucleus, mitochondria, and plastids. Successful coordination of gene expression among these organellar genomes and the nuclear genome is critical for plant function and fitness. Whole genome duplication events (WGDs) in the nucleus have played a major role in the diversification of land plants and are expected to perturb the relative copy number (stoichiometry) of nuclear, mitochondrial, and plastid genomes. Thus, elucidating the mechanisms whereby plant cells respond to the cytonuclear stoichiometric imbalance that follow WGDs represents an important yet underexplored question in understanding the evolutionary consequences of genome doubling. We used droplet digital PCR (ddPCR) to investigate the relationship between nuclear and organellar genome copy numbers in allopolyploids and their diploid progenitors in both wheat and Arabidopsis. Polyploids exhibit elevated organellar genome copy numbers per cell, largely preserving the cytonuclear stoichiometry observed in diploids despite the change in nuclear genome copy number. To investigate the timescale over which cytonuclear stoichiometry may respond to WGD, we also estimated organellar genome copy number in Arabidopsis synthetic autopolyploids and in a haploid-induced diploid line. We observed corresponding changes in organellar genome copy number in these laboratory-generated lines, indicating that at least some of the cellular response to cytonuclear stoichiometric imbalance is immediate following WGD. We conclude that increases in organellar genome copy numbers represent a common response to polyploidization, suggesting that maintenance of cytonuclear stoichiometry is an important component in establishing polyploid lineages.

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