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

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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De Novo Genome Assembly of the Meadow Brown Butterfly, Maniola jurtina

G3 Genes|Genome|Genetics ◽

10.1534/g3.120.401071 ◽

2020 ◽

Vol 10 (5) ◽

pp. 1477-1484

Author(s):

Kumar Saurabh Singh ◽

David J. Hosken ◽

Nina Wedell ◽

Richard ffrench-Constant ◽

Chris Bass ◽

...

Keyword(s):

De Novo ◽

Draft Genome ◽

Single Copy ◽

De Novo Genome Assembly ◽

Modern Biology ◽

Final Assembly ◽

Gene Sets ◽

Gene Count ◽

In The Wild ◽

Maniola Jurtina

Meadow brown butterflies (Maniola jurtina) on the Isles of Scilly represent an ideal model in which to dissect the links between genotype, phenotype and long-term patterns of selection in the wild - a largely unfulfilled but fundamental aim of modern biology. To meet this aim, a clear description of genotype is required. Here we present the draft genome sequence of M. jurtina to serve as a founding genetic resource for this species. Seven libraries were constructed using pooled DNA from five wild caught spotted females and sequenced using Illumina, PacBio RSII and MinION technology. A novel hybrid assembly approach was employed to generate a final assembly with an N50 of 214 kb (longest scaffold 2.9 Mb). The sequence assembly described here predicts a gene count of 36,294 and includes variants and gene duplicates from five genotypes. Core BUSCO (Benchmarking Universal Single-Copy Orthologs) gene sets of Arthropoda and Insecta recovered 90.5% and 88.7% complete and single-copy genes respectively. Comparisons with 17 other Lepidopteran species placed 86.5% of the assembled genes in orthogroups. Our results provide the first high-quality draft genome and annotation of the butterfly M. jurtina.

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

Journal of Genetic Engineering and Biotechnology ◽

10.1186/s43141-020-00074-2 ◽

2020 ◽

Vol 18 (1) ◽

Author(s):

Ravisankar Valsalan ◽

Deepu Mathew

Keyword(s):

De Novo ◽

Draft Genome ◽

Hybrid Approach ◽

Sequence Annotation ◽

Illumina Hiseq ◽

Meyerozyma Guilliermondii ◽

Genome Wide ◽

Number Of Genes ◽

Proteome Profile ◽

Organic Compost

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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Genome Report: De novo genome assembly and annotation for the Taita white-eye (Zosterops silvanus)

10.1101/2020.03.06.980599 ◽

2020 ◽

Author(s):

Jan O. Engler ◽

Yvonne Lawrie ◽

Yannick Gansemans ◽

Filip Van Nieuwerburgh ◽

Alexander Suh ◽

...

Keyword(s):

Genome Assembly ◽

De Novo ◽

Draft Genome ◽

Wild Female ◽

De Novo Genome Assembly ◽

Small Areas ◽

Fragmented Forest ◽

Draft Genome Assembly ◽

Taita Hills ◽

Genomic Resource

AbstractThe Taita White-eye (Zosterops silvanus) is an endangered songbird endemic to the Taita Hills of Southern Kenya, where it is confined to small areas of fragmented forest. With diversification rates exceeding those reported in most other vertebrates, White-eyes are a prime example of a ‘great speciator’. Nevertheless, we still know surprisingly little about the genomic underpinnings leading to this extraordinary fast radiation. Here, we present a draft genome assembly (ZSil_MB_1.0) for the Taita White-eye generated from a blood sample of a wild, female bird captured in the Taita Hills, Kenya. By performing a de novo assembly with linked-reads and annotation of the assembly with the MAKER pipeline, we generated a 1.069 Gb assembly with a scaffold N50 of 1.105 Mb and an L50 of 244. After quality evaluation of the assembly, we identified 92.1% of BUSCOs complete or fragmented, indicating that our de novo assembly is of high quality. This new assembly provides a genomic resource for future studies into the evolutionary and comparative genomics of this rapidly diversifying group of birds.

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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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De novo genome assembly of the meadow brown butterfly, Maniola jurtina

10.1101/715243 ◽

2019 ◽

Author(s):

Kumar Saurabh Singh ◽

David J. Hosken ◽

Nina Wedell ◽

Richard ffrench-Constant ◽

Chris Bass ◽

...

Keyword(s):

De Novo ◽

Draft Genome ◽

Single Copy ◽

De Novo Genome Assembly ◽

Modern Biology ◽

Final Assembly ◽

Gene Sets ◽

In The Wild ◽

Maniola Jurtina

AbstractBackgroundMeadow brown butterflies (Maniola jurtina) on the Isles of Scilly represent an ideal model in which to dissect the links between genotype, phenotype and long-term patterns of selection in the wild - a largely unfulfilled but fundamental aim of modern biology. To meet this aim, a clear description of genotype is required.FindingsHere we present the draft genome sequence of M. jurtina to serve as an initial genetic resource for this species. Seven libraries were constructed using DNA from multiple wild caught females and sequenced using Illumina, PacBio RSII and MinION technology. A novel hybrid assembly approach was employed to generate a final assembly with an N50 of 214 kb (longest scaffold 2.9 Mb). The genome encodes a total of 36,294 genes. 90.3% and 88.7% of core BUSCO (Benchmarking Universal Single-Copy Orthologs) Arthropoda and Insecta gene sets were recovered as complete single-copies from this assembly. Comparisons with 17 other Lepidopteran species placed 86.5% of the assembled genes in orthogroups.ConclusionsOur results provide the first high-quality draft genome and annotation of the butterfly M. jurtina.

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Faculty Opinions recommendation of Genome-wide profiling of heritable and de novo STR variations.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.727556430.793546826 ◽

2018 ◽

Author(s):

Melanie Bahlo

Keyword(s):

De Novo ◽

Genome Wide

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A study of transposable element-associated structural variations (TASVs) using a de novo-assembled Korean genome

Experimental & Molecular Medicine ◽

10.1038/s12276-021-00586-y ◽

2021 ◽

Author(s):

Seyoung Mun ◽

Songmi Kim ◽

Wooseok Lee ◽

Keunsoo Kang ◽

Thomas J. Meyer ◽

...

Keyword(s):

Genome Sequencing ◽

Genome Assembly ◽

De Novo ◽

Personal Genome ◽

Human Populations ◽

Whole Genome ◽

Structural Variations ◽

Insert Size ◽

Human Genomes ◽

Next Generation Sequencing Ngs

AbstractAdvances in next-generation sequencing (NGS) technology have made personal genome sequencing possible, and indeed, many individual human genomes have now been sequenced. Comparisons of these individual genomes have revealed substantial genomic differences between human populations as well as between individuals from closely related ethnic groups. Transposable elements (TEs) are known to be one of the major sources of these variations and act through various mechanisms, including de novo insertion, insertion-mediated deletion, and TE–TE recombination-mediated deletion. In this study, we carried out de novo whole-genome sequencing of one Korean individual (KPGP9) via multiple insert-size libraries. The de novo whole-genome assembly resulted in 31,305 scaffolds with a scaffold N50 size of 13.23 Mb. Furthermore, through computational data analysis and experimental verification, we revealed that 182 TE-associated structural variation (TASV) insertions and 89 TASV deletions contributed 64,232 bp in sequence gain and 82,772 bp in sequence loss, respectively, in the KPGP9 genome relative to the hg19 reference genome. We also verified structural differences associated with TASVs by comparative analysis with TASVs in recent genomes (AK1 and TCGA genomes) and reported their details. Here, we constructed a new Korean de novo whole-genome assembly and provide the first study, to our knowledge, focused on the identification of TASVs in an individual Korean genome. Our findings again highlight the role of TEs as a major driver of structural variations in human individual genomes.

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Genome-wide methylation sequencing identifies progression-related epigenetic drivers in myelodysplastic syndromes

Cell Death and Disease ◽

10.1038/s41419-020-03213-2 ◽

2020 ◽

Vol 11 (11) ◽

Author(s):

Jing-dong Zhou ◽

Ting-juan Zhang ◽

Zi-jun Xu ◽

Zhao-qun Deng ◽

Yu Gu ◽

...

Keyword(s):

Cancer Progression ◽

Myelodysplastic Syndromes ◽

Bisulfite Sequencing ◽

De Novo ◽

Dna Hypermethylation ◽

Reduced Representation ◽

Targeted Bisulfite Sequencing ◽

Specific Pcr ◽

Genome Wide ◽

Potential Biomarker

AbstractThe potential mechanism of myelodysplastic syndromes (MDS) progressing to acute myeloid leukemia (AML) remains poorly elucidated. It has been proved that epigenetic alterations play crucial roles in the pathogenesis of cancer progression including MDS. However, fewer studies explored the whole-genome methylation alterations during MDS progression. Reduced representation bisulfite sequencing was conducted in four paired MDS/secondary AML (MDS/sAML) patients and intended to explore the underlying methylation-associated epigenetic drivers in MDS progression. In four paired MDS/sAML patients, cases at sAML stage exhibited significantly increased methylation level as compared with the matched MDS stage. A total of 1090 differentially methylated fragments (DMFs) (441 hypermethylated and 649 hypomethylated) were identified involving in MDS pathogenesis, whereas 103 DMFs (96 hypermethylated and 7 hypomethylated) were involved in MDS progression. Targeted bisulfite sequencing further identified that aberrant GFRA1, IRX1, NPY, and ZNF300 methylation were frequent events in an additional group of de novo MDS and AML patients, of which only ZNF300 methylation was associated with ZNF300 expression. Subsequently, ZNF300 hypermethylation in larger cohorts of de novo MDS and AML patients was confirmed by real-time quantitative methylation-specific PCR. It was illustrated that ZNF300 methylation could act as a potential biomarker for the diagnosis and prognosis in MDS and AML patients. Functional experiments demonstrated the anti-proliferative and pro-apoptotic role of ZNF300 overexpression in MDS-derived AML cell-line SKM-1. Collectively, genome-wide DNA hypermethylation were frequent events during MDS progression. Among these changes, ZNF300 methylation, a regulator of ZNF300 expression, acted as an epigenetic driver in MDS progression. These findings provided a theoretical basis for the usage of demethylation drugs in MDS patients against disease progression.

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