scholarly journals The draft genome of an octocoral, Dendronephthya gigantea

2018 ◽  
Author(s):  
Yeonsu Jeon ◽  
Seung Gu Park ◽  
Nayun Lee ◽  
Jessica A. Weber ◽  
Hui-Su Kim ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Soft Coral ◽  
Environmental Changes ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Sea Anemones ◽  
High Quality ◽  
Stony Corals ◽  
Dendronephthya Gigantea

Background: Coral reefs composed of stony corals are threatened by global marine environmental changes. However, soft coral communities composed of octocorallian species, appear more resilient. The genomes of several species of cnidarians have been published, including stony corals, sea anemones, and hydra, but as of yet no octocoral species. To fill this phylogenetic gap within the cnidarian, we sequenced the octocoral, Dendronephthya gigantea, a non-symbiotic soft coral, commonly known as the carnation coral. Findings: The D. gigantea genome size is approximately 276 Mb. A high-quality genome assembly was constructed using 29.85Gb (108x coverage) of PacBio long reads and 35.54Gb (128x coverage) of Illumina short paired-end reads resulting in the largest N50 value reported among cnidarian of 1.4 Mb. About 12 % of the genome consisted of repetitive elements. We found 28,879 protein-coding genes. This gene set contained about 94% metazoan single-copy orthologs, indicating the gene models were predicted with high quality compared to other cnidarians. Based on molecular phylogenetic analysis, octocoral and hexacoral divergence occurred approximately 544 million years ago. Moreover, there is a clear difference in Hox gene composition: unlike in hexacorals, Antp superclass member Evx gene was absent in D. gigantea. Conclusions: We present the first genome assembly of a non-symbiotic octocoral, D. gigantea to aid in the comparative genomic analysis of cnidarians, including comparisons of stony and soft corals and symbiotic and non-symbiotic corals. In addition, the genome of this species may provide clues about differential genetic coping mechanisms between soft and stony coral regarding the global warming.

scholarly journals Genome assembly of the JD17 soybean provides a new reference genome for Comparative genomics

2021 ◽  
Author(s):  
Xinxin Yi ◽  
Jing Liu ◽  
Shengcai Chen ◽  
Hao Wu ◽  
Min Liu ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Genome Assembly ◽  
Reference Genome ◽  
De Novo ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
High Quality ◽  
Genome Wide ◽  
A Genome ◽  
Cultivated Soybean

Cultivated soybean (Glycine max) is an important source for protein and oil. Many elite cultivars with different traits have been developed for different conditions. Each soybean strain has its own genetic diversity, and the availability of more high-quality soybean genomes can enhance comparative genomic analysis for identifying genetic underpinnings for its unique traits. In this study, we constructed a high-quality de novo assembly of an elite soybean cultivar Jidou 17 (JD17) with chromsome contiguity and high accuracy. We annotated 52,840 gene models and reconstructed 74,054 high-quality full-length transcripts. We performed a genome-wide comparative analysis based on the reference genome of JD17 with three published soybeans (WM82, ZH13 and W05) , which identified five large inversions and two large translocations specific to JD17, 20,984 - 46,912 PAVs spanning 13.1 - 46.9 Mb in size, and 5 - 53 large PAV clusters larger than 500kb. 1,695,741 - 3,664,629 SNPs and 446,689 - 800,489 Indels were identified and annotated between JD17 and them. Symbiotic nitrogen fixation (SNF) genes were identified and the effects from these variants were further evaluated. It was found that the coding sequences of 9 nitrogen fixation-related genes were greatly affected. The high-quality genome assembly of JD17 can serve as a valuable reference for soybean functional genomics research.

scholarly journals A high-quality draft genome for Melaleuca alternifolia (tea tree): a new platform for evolutionary genomics of myrtaceous terpene-rich species

Gigabyte ◽  
2021 ◽  
Vol 2021 ◽  
pp. 1-15
Author(s):  
Julia Voelker ◽  
Mervyn Shepherd ◽  
Ramil Mauleon
Keyword(s):  
Genome Assembly ◽  
De Novo ◽  
Genome Structure ◽  
Draft Genome ◽  
Gene Family Evolution ◽  
Comparative Genomic ◽  
Melaleuca Alternifolia ◽  
High Quality ◽  
Tea Tree ◽  
Prediction Approach

The economically important Melaleuca alternifolia (tea tree) is the source of a terpene-rich essential oil with therapeutic and cosmetic uses around the world. Tea tree has been cultivated and bred in Australia since the 1990s. It has been extensively studied for the genetics and biochemistry of terpene biosynthesis. Here, we report a high quality de novo genome assembly using Pacific Biosciences and Illumina sequencing. The genome was assembled into 3128 scaffolds with a total length of 362 Mb (N50  = 1.9 Mb), with significantly higher contiguity than a previous assembly (N50  = 8.7 Kb). Using a homology-based, RNA-seq evidence-based and ab initio prediction approach, 37,226 protein-coding genes were predicted. Genome assembly and annotation exhibited high completeness scores of 98.1% and 89.4%, respectively. Sequence contiguity was sufficient to reveal extensive gene order conservation and chromosomal rearrangements in alignments with Eucalyptus grandis and Corymbia citriodora genomes. This new genome advances currently available resources to investigate the genome structure and gene family evolution of M. alternifolia. It will enable further comparative genomic studies in Myrtaceae to elucidate the genetic foundations of economically valuable traits in this crop.

scholarly journals High-quality genome assembly of Cinnamomum burmami (chvar. Borneol) provides insights into the natural borneol biosynthesis

2021 ◽  
Author(s):  
Fangping Li ◽  
Shilin Huang ◽  
Yu Mei ◽  
Bingqi Wu ◽  
Zhuangwei Hou ◽  
...  
Keyword(s):  
Single Molecule ◽  
Genome Assembly ◽  
Herbal Medicines ◽  
Genomic Analysis ◽  
Biological Tissues ◽  
Industrial Plant ◽  
Size Difference ◽  
Comparative Genomic ◽  
High Quality ◽  
Genome Database

Cinnamomum burmami (chvar. Borneol) is a well-known medicinal and industrial plant cultivated in the Lingnan region of China. It is the key source from organism of natural borneol (D-borneol), one of the precious and widely used Chinese herbal medicines with a variety of medicinal effects. Here, we report a high-quality chromosome-scale genome assembly of C. burmami (chvar. Borneol) using Pacbio single-molecule sequencing and Hi-C technology. The assembled genome size was 1.14 GB with a scaffold N50 of 94.30 Mb, while 98.77% of the assembled sequences were anchored on 12 pseudochromosomes including 41549 protein-coding genes. Genomic evolution analysis revealed C. burmami and C. micranthum shared two Lauraceae unique ancestral whole-genome duplication (WGD) events. Likewise, comparative genomic analysis showed strong collinearity between these two species. Besides, the analysis for Long Terminal Repeat Retrotransposons (LTR-RTs) indicated the outbreak of LTR-RTs insertion made a great contribution to the size difference of genomes between C. burmami and C. micranthum. Furthermore, the candidate genes in pathway associated with natural borneol synthesis were identified on the genome and their differential expressions were analyzed in various biological tissues. We considered that several of genes in Mevalonate (MVA) Methylerythritol Phosphate (MEP) pathways or in downstream pathway have the potential to be the key factors in the biosynthesis of D-borneol. We also constructed the genome database (CAMD; http://www.cinnamomumdatabase.com/) of Cinnamomum species for a better data utilization in the future. All these results will enrich the genomic data of Lauraceae plants and facilitate genetic improvement of this commercially important plant.

scholarly journals Draft Genome Sequence of Mesosutterella multiformis JCM 32464T, a Member of the Family Sutterellaceae, Isolated from Human Feces

2019 ◽  
Vol 8 (24) ◽  
Author(s):  
Nao Ikeyama ◽  
Moriya Ohkuma ◽  
Mitsuo Sakamoto
Keyword(s):  
Genome Sequence ◽  
Genome Assembly ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Draft Genome Sequence ◽  
Human Feces ◽  
The Family ◽  
Metabolic Activities

Here, we report the draft genome sequence of Mesosutterella multiformis JCM 32464T, a new member of the family Sutterellaceae that was isolated from human feces. The genome assembly comprised 2,621,983 bp, with a G+C content of 56.9%. This genomic analysis will be useful for understanding the metabolic activities of this asaccharolytic bacterium.

scholarly journals Draft Genome Sequence ofBacillus subtilisIa1a, a New Strain for Poly-γ-Glutamic Acid and Exopolysaccharide Production

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Mohammad H. A. Ibrahim ◽  
Brady F. Cress ◽  
Robert J. Linhardt ◽  
Mattheos A. G. Koffas ◽  
Richard A. Gross
Keyword(s):  
Bacillus Subtilis ◽  
Glutamic Acid ◽  
Genome Sequence ◽  
Genome Assembly ◽  
Draft Genome ◽  
Carbon Sources ◽  
Draft Genome Sequence ◽  
High Quality ◽  
Exopolysaccharide Production ◽  
Draft Genome Assembly

We report here the 4.092-Mb high-quality draft genome assembly of a newly isolated poly-γ-glutamic acid–producing strain,Bacillus subtilisIa1a. The genome sequence is considered a critical tool to facilitate the engineering of improved production strains. Exopolysaccharides and many industrially important enzymes can be produced by this new strain utilizing different carbon sources.

scholarly journals Chromosome-level genome assembly of the female western mosquitofish (Gambusia affinis)

GigaScience ◽  
2020 ◽  
Vol 9 (8) ◽  
Author(s):  
Feng Shao ◽  
Arne Ludwig ◽  
Yang Mao ◽  
Ni Liu ◽  
Zuogang Peng
Keyword(s):  
Dna Sequences ◽  
Genome Assembly ◽  
Gambusia Affinis ◽  
Comparative Genomic ◽  
Suitable Model ◽  
High Quality ◽  
Western Mosquitofish ◽  
Poeciliid Fish ◽  
Oxford Nanopore ◽  
Chromosome Level

Abstract Background The western mosquitofish (Gambusia affinis) is a sexually dimorphic poeciliid fish known for its worldwide biological invasion and therefore an important research model for studying invasion biology. This organism may also be used as a suitable model to explore sex chromosome evolution and reproductive development in terms of differentiation of ZW sex chromosomes, ovoviviparity, and specialization of reproductive organs. However, there is a lack of high-quality genomic data for the female G. affinis; hence, this study aimed to generate a chromosome-level genome assembly for it. Results The chromosome-level genome assembly was constructed using Oxford nanopore sequencing, BioNano, and Hi-C technology. G. affinis genomic DNA sequences containing 217 contigs with an N50 length of 12.9 Mb and 125 scaffolds with an N50 length of 26.5 Mb were obtained by Oxford nanopore and BioNano, respectively, and the 113 scaffolds (90.4% of scaffolds containing 97.9% nucleotide bases) were assembled into 24 chromosomes (pseudo-chromosomes) by Hi-C. The Z and W chromosomes of G. affinis were identified by comparative genomic analysis of female and male G. affinis, and the mechanism of differentiation of the Z and W chromosomes was explored. Combined with transcriptome data from 6 tissues, a total of 23,997 protein-coding genes were predicted and 23,737 (98.9%) genes were functionally annotated. Conclusions The high-quality female G. affinis reference genome provides a valuable omics resource for future studies of comparative genomics and functional genomics to explore the evolution of Z and W chromosomes and the reproductive developmental biology of G. affinis.

scholarly journals Phylogenomic analysis shows that Bacillus amyloliquefaciens subsp. plantarum is a later heterotypic synonym of Bacillus methylotrophicus

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2104-2109 ◽  
Author(s):  
Christopher A. Dunlap ◽  
Soo-Jin Kim ◽  
Soon-Wo Kwon ◽  
Alejandro P. Rooney
Keyword(s):  
Bacillus Amyloliquefaciens ◽  
Type Strain ◽  
Plant Pathogens ◽  
Phylogenetic Analyses ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Phylogenomic Analysis ◽  
Growth Promoters ◽  
Bacillus Methylotrophicus

The rhizosphere-isolated bacteria belonging to the Bacillus amyloliquefaciens subsp. plantarum and Bacillus methylotrophicus clades are an important group of strains that are used as plant growth promoters and antagonists of plant pathogens. These properties have made these strains the focus of commercial interest. Here, we present the draft genome sequence of B. methylotrophicus KACC 13105T ( = CBMB205T). Comparative genomic analysis showed only minor differences between this strain and the genome of the B. amyloliquefaciens subsp. plantarum type strain, with the genomes sharing approximately 95 % of the same genes. The results of morphological, physiological, chemotaxonomic and phylogenetic analyses indicate that the type strains of these two taxa are highly similar. In fact, our results show that the type strain of B. amyloliquefaciens subsp. plantarum FZB42T ( = DSM 23117T = BGSC 10A6T) does not cluster with other members of the B. amyloliquefaciens taxon. Instead, it clusters well within a clade of strains that are assigned to B. methylotrophicus, including the type strain of that species. Therefore, we propose that the subspecies B. amyloliquefaciens subsp. plantarum should be reclassified as a later heterotypic synonym of B. methylotrophicus.

scholarly journals A Highly Contiguous Genome Assembly of a Major Forest Pest, the Eurasian Spruce Bark Beetle Ips Typographus

2021 ◽  
Author(s):  
Daniel Powell ◽  
Ewald Grosse-Wilde ◽  
Paal Krokene ◽  
Amit Roy ◽  
Amrita Chakraborty ◽  
...  
Keyword(s):  
Bark Beetle ◽  
Genome Assembly ◽  
Bark Beetles ◽  
Plant Cell Wall ◽  
Draft Genome ◽  
Ips Typographus ◽  
Whole Genome Sequence ◽  
Comparative Genomic ◽  
Spruce Bark Beetle ◽  
Spruce Bark

Abstract Conifer-feeding bark beetles are important herbivores and decomposers in forest ecosystems. These species have evolved specializations to complete their life cycle in nutritionally poor wooden substrates and some can overwhelm tree defences and kill enormous numbers of trees during population outbreaks. The Eurasian spruce bark beetle (Ips typographus) is one tree-killing species; during a recent epidemic it destroyed >100 million m3 of spruce in a single year. We report a 236 Mb, highly contiguous I. typographus genome assembly using PacBio long-read sequencing. The final phased assembly had a contig N50 of 6.65 Mb in 272 contigs and was predicted to contain 23,923 protein-coding genes. Comparative genomic analysis including 11 additional coleopterans revealed expanded gene families associated with plant cell wall degradation, including pectinases, aspartyl proteases, and glycosyl hydrolases. This first whole-genome sequence from the genus Ips provides timely resources to address important questions about the evolutionary biology of the true weevils (Curculionidae), one of the most species-rich animal families. This resource will also allow for improved studies of functional genomics of both fundamental and applied value. In forests of today, increasingly stressed by global warming, this draft genome may ultimately assist in developing novel pest control strategies to mitigate outbreaks.

scholarly journals Analysis of microsatellites from the transcriptome of downy mildew pathogens and their application for characterization of Pseudoperonospora populations

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3266 ◽  
Author(s):  
Emma C. Wallace ◽  
Lina M. Quesada-Ocampo
Keyword(s):  
Downy Mildew ◽  
Draft Genome ◽  
Model Organism ◽  
Genomic Analysis ◽  
Population Level ◽  
Comparative Genomic ◽  
Pathogen Population ◽  
Pseudoperonospora Humuli ◽  
Hyaloperonospora Arabidopsidis

Downy mildew pathogens affect several economically important crops worldwide but, due to their obligate nature, few genetic resources are available for genomic and population analyses. Draft genomes for emergent downy mildew pathogens such as the oomycete Pseudoperonospora cubensis, causal agent of cucurbit downy mildew, have been published and can be used to perform comparative genomic analysis and develop tools such as microsatellites to characterize pathogen population structure. We used bioinformatics to identify 2,738 microsatellites in the P. cubensis predicted transcriptome and evaluate them for transferability to the hop downy mildew pathogen, Pseudoperonospora humuli, since no draft genome is available for this species. We also compared the microsatellite repertoire of P. cubensis to that of the model organism Hyaloperonospora arabidopsidis, which causes downy mildew in Arabidopsis. Although trends in frequency of motif-type were similar, the percentage of SSRs identified from P. cubensis transcripts differed significantly from H. arabidopsidis. The majority of a subset of microsatellites selected for laboratory validation (92%) produced a product in P. cubensis isolates, and 83 microsatellites demonstrated transferability to P. humuli. Eleven microsatellites were found to be polymorphic and consistently amplified in P. cubensis isolates. Analysis of Pseudoperonospora isolates from diverse hosts and locations revealed higher diversity in P. cubensis compared to P. humuli isolates. These microsatellites will be useful in efforts to better understand relationships within Pseudoperonospora species and P. cubensis on a population level.

scholarly journals Comparative genomics: Dominant coral-bacterium Endozoicomonas acroporae metabolizes dimethylsulfoniopropionate (DMSP)

2019 ◽  
Author(s):  
Kshitij Tandon ◽  
Pei-Wen Chiang ◽  
Chih-Ying Lu ◽  
Naohisa Wada ◽  
Shan-Hua Yang ◽  
...  
Keyword(s):  
Sole Carbon Source ◽  
Genomic Analysis ◽  
Sulfur Cycle ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
High Quality ◽  
Coa Transferase ◽  
Complete Genomes ◽  
Central Carbon

AbstractDominant coral-associated Endozoicomonas bacteria species are hypothesized to play a role in the coral-sulfur cycle by metabolizing Dimethylsulfoniopropionate (DMSP) into Dimethylsulfide (DMS); however, no sequenced genome to date harbors genes for this process. In this study, we assembled high-quality (>95% complete) genomes of strains of a recently added species Endozoicomonas acroporae (Acr-14T, Acr-1 and Acr-5) isolated from the coral Acropora muricata and performed comparative genomic analysis on genus Endozoicomonas. We identified the first DMSP CoA-transferase/lyase—a dddD gene homolog found in all E. acroporae strains—and functionally characterized bacteria capable of metabolizing DMSP into DMS via the DddD cleavage pathway using RT-qPCR and gas chromatography (GC). Furthermore, we demonstrated that E. acroporae strains can use DMSP as the sole carbon source and have genes arranged in an operon-like manner to link DMSP metabolism to the central carbon cycle. This study confirms the role of Endozoicomonas in the coral sulfur cycle.

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