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 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 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 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 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 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.

Systematic studies in Paniceae (Poaceae): Homopholis and Whalleya gen. et sp. nov.

2000 ◽  
Vol 13 (3) ◽  
pp. 437 ◽  
Author(s):  
Karen E. Wills ◽  
R. D. B. Whalley ◽  
Jeremy J. Bruhl
Keyword(s):  
Sister Group ◽  
The Other ◽  
Sister Species ◽  
Parsimonious Tree ◽  
The Third ◽  
Putative Species ◽  
Anatomical Data ◽  
Cladistic Analyses

The taxonomy ofHomopholis C.E.Hubb. is revised, and anew genus Whalleya K.E.Wills & J.J.Bruhl isdescribed. Relationships among the known species ofHomopholis (H. belsonii C.E.Hubb.,H. proluta F.Muell., and a putative species,H. sp. nov.), and the relationships betweenHomopholis and other genera within the Paniceae were investigated. Morphological and anatomical data forHomopholis and selected species ofDigitaria and Panicum were analysed phenetically and cladistically. The value and contribution ofcharacters to the findings were assessed. In the phenetic analyses, threedistinct clusters of species were formed. The first cluster includedDigitaria coenicola (F.Muell.) Hughes,D. divaricatissima (R.Br.) Hughes andD. papposa (R.Br.) P.Beauv.; the second,Panicum effusum R.Br.,P. queenslandicum Domin var.queenslandicum and P. simileDomin; and the third, H. sp. nov.,H. proluta, H. belsonii andP. subxerophilum Domin. Specimens ofH. belsonii noticeably separated from the other threespecies. For the cladistic analyses, species ofEntolasia and Thyridolepis were used as outgroup taxa. One most parsimonious tree was produced.Homopholis belsonii was well supported as the most basalmember of the ingroup. The three species ofDigitariaformed a well-supported clade.Panicum effusum, P. queenslandicumvar. queenslandicum and P. simileformed a well-supported clade, and were the sister group toEntolasia marginata (R.Br.) Hughes andE. stricta (R.Br.) Hughes.Panicum subxerophilum was in a clade (=Whalleya) with H. sp. nov. andH. proluta, with P. subxerophilumand H. proluta as sister species.

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 The genome of the blind soil-dwelling and ancestrally wingless dipluran Campodea augens, a key reference hexapod for studying the emergence of insect innovations

2019 ◽  
Author(s):  
Mosè Manni ◽  
Felipe A. Simao ◽  
Hugh M. Robertson ◽  
Marco A. Gabaglio ◽  
Robert M. Waterhouse ◽  
...  
Keyword(s):  
Draft Genome ◽  
Gene Families ◽  
Sister Group ◽  
Sensu Stricto ◽  
Comparative Genomic ◽  
Gene Repertoire ◽  
Animal Group ◽  
Origin And Evolution ◽  
Genomic Analyses ◽  
Metabolism Gene

AbstractThe dipluran two-pronged bristletail Campodea augens is a blind ancestrally wingless hexapod with the remarkable capacity to regenerate lost body appendages such as its long antennae. As sister group to Insecta (sensu stricto), Diplura are key to understanding the early evolution of hexapods and the origin and evolution of insects. Here we report the 1.2-Gbp draft genome of C. augens and results from comparative genomic analyses with other arthropods. In C. augens we uncovered the largest chemosensory gene repertoire of ionotropic receptors in the animal kingdom, a massive expansion which might compensate for the loss of vision. We found a paucity of photoreceptor genes mirroring at the genomic level the secondary loss of an ancestral external photoreceptor organ. Expansions of detoxification and carbohydrate metabolism gene families might reflect adaptations for foraging behaviour, and duplicated apoptotic genes might underlie its high regenerative potential.The C. augens genome represents one of the key references for studying the emergence of genomic innovations in insects, the most diverse animal group, and opens up novel opportunities to study the under-explored biology of diplurans.

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