Draft genome of Meyerozyma guilliermondii strain vka1: a yeast strain with composting potential

Abstract Background Meyerozyma guilliermondii is a yeast which could be isolated from a variety of environments. The vka1 strain isolated and purified from the organic compost was found to have composting potential. To better understand the genes assisting the composting potential in this yeast, whole genome sequencing and sequence annotation were performed. Results The genome of M. guilliermondii vka1 strain was sequenced using a hybrid approach, on Illumina Hiseq-2500 platform at 100× coverage followed by Nanopore platform at 20× coverage. The de novo assembly using dual-fold approach had given draft genome of 10.8 Mb size. The genome was found to contain 5385 genes. The annotation of the genes was performed, and the enzymes identified to have roles in the degradation of macromolecules are discussed in relation to its composting potential. Annotation of the genome assembly of the related strains had revealed the unique biodegradation related genes in this strain. Phylogenetic analysis using the rDNA region has confirmed the position of this strain in the Ascomycota family. Raw reads are made public, and the genome wide proteome profile is presented to facilitate further studies on this organism. Conclusions Meyerozyma guilliermondii vka1 strain was sequenced through hybrid approach and the reads were de novo assembled. Draft genome size and the number of genes in the strain were assessed and discussed in relation to the related strains. Scientific insights into the composting potential of this strain are also presented in relation to the unique genes identified in this strain.

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Draft genome of Bugula neritina, a colonial animal packing powerful symbionts and potential medicines

Scientific Data ◽

10.1038/s41597-020-00684-y ◽

2020 ◽

Vol 7 (1) ◽

Author(s):

Mikhail Rayko ◽

Aleksey Komissarov ◽

Jason C. Kwan ◽

Grace Lim-Fong ◽

Adelaide C. Rhodes ◽

...

Keyword(s):

De Novo ◽

Draft Genome ◽

Transcriptome Data ◽

Biomedical Sciences ◽

Bugula Neritina ◽

Genome Sequences ◽

Illumina Hiseq ◽

Draft Assembly ◽

Metazoan Genome ◽

Animal Phyla

Abstract Many animal phyla have no representatives within the catalog of whole metazoan genome sequences. This dataset fills in one gap in the genome knowledge of animal phyla with a draft genome of Bugula neritina (phylum Bryozoa). Interest in this species spans ecology and biomedical sciences because B. neritina is the natural source of bioactive compounds called bryostatins. Here we present a draft assembly of the B. neritina genome obtained from PacBio and Illumina HiSeq data, as well as genes and proteins predicted de novo and verified using transcriptome data, along with the functional annotation. These sequences will permit a better understanding of host-symbiont interactions at the genomic level, and also contribute additional phylogenomic markers to evaluate Lophophorate or Lophotrochozoa phylogenetic relationships. The effort also fits well with plans to ultimately sequence all orders of the Metazoa.

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Draft genome of the Reindeer (Rangifer tarandus)

10.1101/154724 ◽

2017 ◽

Author(s):

Zhipeng Li ◽

Zeshan Lin ◽

Lei Chen ◽

Hengxing Ba ◽

Yongzhi Yang ◽

...

Keyword(s):

Rangifer Tarandus ◽

Reference Genome ◽

De Novo ◽

Bos Taurus ◽

Repetitive Sequences ◽

Draft Genome ◽

Divergence Time ◽

Capra Hircus ◽

High Quality ◽

Illumina Hiseq

AbstractBackgroundReindeer (Rangifer tarandus) is the only fully domesticated species in the Cervidae family, and is the only cervid with a circumpolar distribution. Unlike all other cervids, female reindeer regularly grow cranial appendages (antlers, the defining characteristics of cervids), as well as males. Moreover, reindeer milk contains more protein and less lactose than bovids’ milk. A high quality reference genome of this specie will assist efforts to elucidate these and other important features in the reindeer.FindingsWe obtained 723.2 Gb (Gigabase) of raw reads by an Illumina Hiseq 4000 platform, and a 2.64 Gb final assembly, representing 95.7% of the estimated genome (2.76 Gb according to k-mer analysis), including 92.6% of expected genes according to BUSCO analysis. The contig N50 and scaffold N50 sizes were 89.7 kilo base (kb) and 0.94 mega base (Mb), respectively. We annotated 21,555 protein-coding genes and 1.07 Gb of repetitive sequences by de novo and homology-based prediction. Homology-based searches detected 159 rRNA, 547 miRNA, 1,339 snRNA and 863 tRNA sequences in the genome of R. tarandus. The divergence time between R. tarandus, and ancestors of Bos taurus and Capra hircus, is estimated to be 29.55 million years ago (Mya).ConclusionsOur results provide the first high-quality reference genome for the reindeer, and a valuable resource for studying evolution, domestication and other unusual characteristics of the reindeer.

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The draft genome sequence of Eucalyptus polybractea based on hybrid assembly with short- and long-reads reads

10.1101/2021.05.18.444652 ◽

2021 ◽

Author(s):

Teng Li ◽

David Kainer ◽

William J Foley ◽

Allen Rodrigo ◽

Carsten Kuelheim

Keyword(s):

Population Genomics ◽

De Novo ◽

Draft Genome ◽

Hybrid Assembly ◽

Illumina Hiseq ◽

Protein Coding ◽

Genome Coverage ◽

Protein Coding Genes ◽

Long Reads ◽

Long Read

Eucalyptus polybractea is a small, multi-stemmed tree, which is widely cultivated in Australia for the production of Eucalyptus oil. We report the hybrid assembly of the E. polybractea genome utilizing both short- and long-read technology. We generated 44 Gb of Illumina HiSeq short reads and 8 Gb of Nanopore long reads, representing approximately 83 and 15 times genome coverage, respectively. The hybrid-assembled genome, after polishing, contained 24,864 scaffolds with an accumulated length of 523 Mb (N50 = 40.3 kb; BUSCO-calculated genome completeness of 94.3%). The genome contained 35,385 predicted protein-coding genes detected by combining homology-based and de novo approaches. We have provided the first assembled genome based on hybrid sequences from the highly diverse Eucalyptus subgenus Symphyomyrtus, and revealed the value of including long-reads from Nanopore technology for enhancing the contiguity of the assembled genome, as well as for improving its completeness. We anticipate that the E. polybractea genome will be an invaluable resource supporting a range of studies in genetics, population genomics and evolution of related species in Eucalyptus.

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First draft genome assembly of the Argane tree (Argania spinosa)

F1000Research ◽

10.12688/f1000research.15719.2 ◽

2020 ◽

Vol 7 ◽

pp. 1310

Author(s):

Slimane Khayi ◽

Nour Elhouda Azza ◽

Fatima Gaboun ◽

Stacy Pirro ◽

Oussama Badad ◽

...

Keyword(s):

Genome Assembly ◽

Environmental Changes ◽

De Novo ◽

Arid Zone ◽

Draft Genome ◽

Illumina Hiseq ◽

Argania Spinosa ◽

Draft Genome Assembly ◽

Food And Feed ◽

Tree Genetics

Background: The Argane tree ( Argania spinosa L. Skeels) is an endemic tree of mid-western Morocco that plays an important socioeconomic and ecologic role for a dense human population in an arid zone. Several studies confirmed the importance of this species as a food and feed source and as a resource for both pharmaceutical and cosmetic compounds. Unfortunately, the argane tree ecosystem is facing significant threats from environmental changes (global warming, over-population) and over-exploitation. Limited research has been conducted, however, on argane tree genetics and genomics, which hinders its conservation and genetic improvement. Methods: Here, we present a draft genome assembly of A. spinosa. A reliable reference genome of A. spinosa was created using a hybrid de novo assembly approach combining short and long sequencing reads. Results: In total, 144 Gb Illumina HiSeq reads and 7.6 Gb PacBio reads were produced and assembled. The final draft genome comprises 75 327 scaffolds totaling 671 Mb with an N50 of 49 916 kb. The draft assembly is close to the genome size estimated by k-mers distribution and covers 89% of complete and 4.3 % of partial Arabidopsis orthologous groups in BUSCO. Conclusion: The A. spinosa genome will be useful for assessing biodiversity leading to efficient conservation of this endangered endemic tree. Furthermore, the genome may enable genome-assisted cultivar breeding, and provide a better understanding of important metabolic pathways and their underlying genes for both cosmetic and pharmacological.

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Sequencing, de novo assembly and annotation of the genome of the scleractinian coral, Pocillopora acuta

10.1101/698688 ◽

2019 ◽

Cited By ~ 1

Author(s):

Jeremie Vidal-Dupiol ◽

Cristian Chaparro ◽

Marine Pratlong ◽

Pierre Pontarotti ◽

Christoph Grunau ◽

...

Keyword(s):

Coral Reefs ◽

De Novo ◽

Marine Ecosystem ◽

Draft Genome ◽

Global Changes ◽

Insert Size ◽

Modern Biology ◽

Genome Wide ◽

Sequencing Strategy ◽

Genomic Resource

AbstractCoral reefs are the most divers marine ecosystem. However, under the pressure of global changes and anthropogenic disturbances corals and coral reefs are declining worldwide. In order to better predict and understand the future of these organisms all the tools of modern biology are needed today. However, many NGS based approaches are not feasible in corals because of the lack of reference genomes. Therefore we have sequenced, de novo assembled, and annotated, the draft genome of one of the most studied coral species, Pocillopora acuta (ex damicornis). The sequencing strategy was based on four libraries with complementary insert size and sequencing depth (180pb, 100x; 3Kb, 25x; 8kb, 12x and 20 kb, 12x). The de novo assembly was performed with Platanus (352 Mb; 25,553 scaffolds; N50 171,375 bp). 36,140 genes were annotated by RNA-seq data and 64,558 by AUGUSTUS (Hidden-Markov model). Gene functions were predicted through Blast and orthology based approaches. This new genomic resource will enable the development of a large array of genome wide studies but also shows that the de novo assembly of a coral genome is now technically feasible and economically realistic.

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Whole-genome sequencing of Nicotiana glauca

10.1101/211482 ◽

2017 ◽

Author(s):

Galina Khafizova ◽

Pavel Dobrynin ◽

Dmitrii Polev ◽

Tatyana Matveeva

Keyword(s):

Dna Analysis ◽

De Novo ◽

Draft Genome ◽

Full Genome ◽

Nicotiana Glauca ◽

Illumina Hiseq ◽

Genome Data ◽

Dna Insertion ◽

Ngs Data ◽

Ct Dna

AbstractBackgroundNicotiana glauca (tree tobacco) is a member of the Solanaceae family, which includes important crops (potato, tomato, eggplant, pepper) and many medicinal plants. This diploid plant is native to South America and is one of the first Nicotiana species with Agrobacterium cellular T-DNA (cT-DNA). Its cT-DNA is a partial, inverted repeat, called gT. Tree tobacco belongs to the section Noctiflorae. Sequencing of the genomes of N. tomentosiformis and N. otophora (section Tomentosae) and N. tabacum (section Nicotiana) allowed the detection of previously unknown multiple cT-DNAs, raising the question whether there are other T-DNA insertions in the N. glauca. NGS data can help answer this question. Besides, N. glauca contains a profile of alkaloids different from N. tabacum. The plant is used for medicinal purposes. Comparative analysis of genomic data of phylogenetically distant tobacco species will provide valuable information on the genetic basis for various traits, especially secondary metabolism.FindingsWe report a high-depth sequencing and de novo assembly of N. glauca full genome, which was obtained from 210 Gb Illumina HiSeq data. The final draft genome is 3.2 Gb, with N50 size of 31.1 kbp. T-DNA analysis confirmed the presence of the previously described gT insertion and the absence of other ones.ConclusionWe provide the first comprehensive de novo full genome assembly of three tobacco, and a cT-DNA insertion analysis. These genome data could be used in pharmacological and in phylogenetic studies.

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Genome description and inventory of immune-related genes of the endangered pen shell Pinna nobilis: a giant bivalve experiencing a mass mortality event

10.21203/rs.2.15332/v1 ◽

2019 ◽

Author(s):

Robert Bunet ◽

Jean-Marc Prévot ◽

Nardo Vicente ◽

José Rafa García-March ◽

Rajko Martinović ◽

...

Keyword(s):

De Novo ◽

Draft Genome ◽

Gc Content ◽

Innate Immune ◽

Trna Genes ◽

Ecological Value ◽

Illumina Hiseq ◽

Late 20Th Century ◽

Pinna Nobilis ◽

Pen Shell

Abstract Background: The noble pen shell Pinna nobilis is a Mediterranean endemic and emblematic giant bivalve. Already registered as an endangered species in the late 20th century, it is facing a dramatic and rapidly expanding epizooty that decimates its populations since mid-2016. The ecological value of P. nobilis has urged important investigations for conservation purposes. In light of this, we report here the first draft genome of this animal. Results: The whole-genome sequencing has been performed on an Illumina HiSeq X platform using a single paired-end library of short fragments (2x150 bp). The de novo contig assembly accounted for a total size of 584 Mb (96,738 contigs, N50 = 7.6 kb, with 0.4% of “N” nucleotides), representing 77.5% of the predicted genome size of 754 Mb. The pen shell genome is very AT-rich, with a GC-content of 35.6 %. Heterozygosity was found to be in the range of other sequenced bivalves (1%). Over one third (36.2 %) of the genome consisted of repeated elements with a surprising larger number of SINEs elements compared to other molluscan genomes. We were also able to reconstruct the full mitochondrial genome (~19 kb, with 12 protein-coding genes, 2 rRNA and 22 tRNA genes). In relation with the outbreak that affects P. nobilis, we paid a special attention on the innate immune and stress-related genes found in the sequence. We revealed that P. nobilis disposes of a complete chemical defensome, and a relatively sophisticated innate immune system. Conclusion: In addition to offering a valuable resource for further research in comparative biology and evolution, access to the draft genome sequence is central to deepen our understanding of the vulnerability of P. nobilis to new diseases, which are likely to occur more often in the current scenario of a rapidly changing environment.

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Draft Genome Sequence and Annotation of the Lichen-Forming Fungus Arthonia radiata

Genome Announcements ◽

10.1128/genomea.00281-18 ◽

2018 ◽

Vol 6 (14) ◽

Cited By ~ 5

Author(s):

Ellie E. Armstrong ◽

Stefan Prost ◽

Damien Ertz ◽

Martin Westberg ◽

Andreas Frisch ◽

...

Keyword(s):

Genome Sequence ◽

Genome Assembly ◽

Type Species ◽

De Novo ◽

Transcriptome Assembly ◽

Draft Genome ◽

Draft Genome Sequence ◽

Illumina Hiseq ◽

Content Type ◽

Mate Pair

ABSTRACT We report here the draft de novo genome assembly, transcriptome assembly, and annotation of the lichen-forming fungus Arthonia radiata (Pers.) Ach., the type species for Arthoniomycetes, a class of lichen-forming, lichenicolous, and saprobic Ascomycota. The genome was assembled using overlapping paired-end and mate pair libraries and sequenced on an Illumina HiSeq 2500 instrument.

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Genome-Wide Characterization and Expression Analyses of Pleurotus ostreatus MYB Transcription Factors during Developmental Stages and under Heat Stress Based on de novo Sequenced Genome

International Journal of Molecular Sciences ◽

10.3390/ijms19072052 ◽

2018 ◽

Vol 19 (7) ◽

pp. 2052 ◽

Cited By ~ 5

Author(s):

Lining Wang ◽

Wei Gao ◽

Xiangli Wu ◽

Mengran Zhao ◽

Jibin Qu ◽

...

Keyword(s):

Heat Stress ◽

Pleurotus Ostreatus ◽

Developmental Stages ◽

De Novo ◽

Draft Genome ◽

Myb Transcription Factor ◽

Entire Genome ◽

Mushroom Species ◽

Genome Wide ◽

Myb Genes

Pleurotus ostreatus is a commercially grown mushroom species in China. However, studies on the mechanisms of the fruiting body development and stress response of P. ostreatus are still at a primary stage. In this study, we report the entire genome sequence of P. ostreatus CCMSSC03989. Then, we performed comprehensive genome-wide characterization and expression analysis of the MYB transcription factor family during a series of developmental stages and under the condition of heat stress. A 34.76 Mb genome was obtained through next-generation sequencing (NGS) and Bionano optical mapping approaches. The genome has a scaffold N50 of 1.1 Mb and contains 10.11% repeats, and 10,936 gene models were predicted. A total of 20 MYB genes (PoMYB) were identified across the genome, and the full-length open reading frames were isolated. The PoMYBs were classified into 1 repeat (1R), 2R, and 3R-MYB groups according to their MYB domain repeat numbers, and 3R-MYBs possessed relatively more introns than 1R and 2R-MYBs. Based on phylogenetic analysis, the PoMYBs were divided into four groups and showed close relationships with the MYB genes of plants and fungi. RNA-sequencing (RNA-Seq) and quantitative PCR (qPCR) analyses revealed that PoMYB expression showed stage-specific patterns in reproductive stages and could be induced by heat stress. The P. ostreatus draft genome will promote genome-wide analysis, and our study of PoMYBs will promote further functional analysis of MYB genes in mushrooms.

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Transcriptomic Profiling of Fruit Development in Black Raspberry Rubus coreanus

International Journal of Genomics ◽

10.1155/2018/8084032 ◽

2018 ◽

Vol 2018 ◽

pp. 1-13

Author(s):

Qing Chen ◽

Xunju Liu ◽

Yueyang Hu ◽

Bo Sun ◽

Yaodong Hu ◽

...

Keyword(s):

Developmental Stages ◽

De Novo ◽

Developmental Regulation ◽

Draft Genome ◽

Pathogen Resistance ◽

Flavonoid Biosynthesis ◽

Great Promise ◽

Protein Coding ◽

Genome Wide ◽

Phenylpropanoid Biosynthesis

The wild Rubus species R. coreanus, which is widely distributed in southwest China, shows great promise as a genetic resource for breeding. One of its outstanding properties is adaptation to high temperature and humidity. To facilitate its use in selection and breeding programs, we assembled de novo 179,738,287 R. coreanus reads (125 bp in length) generated by RNA sequencing from fruits at three representative developmental stages. We also used the recently released draft genome of R. occidentalis to perform reference-guided assembly. We inferred a final 95,845-transcript reference for R. coreanus. Of these genetic resources, 66,597 (69.5%) were annotated. Based on these results, we carried out a comprehensive analysis of differentially expressed genes. Flavonoid biosynthesis, phenylpropanoid biosynthesis, plant hormone signal transduction, and cutin, suberin, and wax biosynthesis pathways were significantly enriched throughout the ripening process. We identified 23 transcripts involved in the flavonoid biosynthesis pathway whose expression perfectly paralleled changes in the metabolites. Additionally, we identified 119 nucleotide-binding site leucine-rich repeat (NBS-LRR) protein-coding genes, involved in pathogen resistance, of which 74 were in the completely conserved domain. These results provide, for the first time, genome-wide genetic information for understanding developmental regulation of R. coreanus fruits. They have the potential for use in breeding through functional genetic approaches in the near future.

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