Comprehensive Draft Genome Analyses of Three Rockfishes (Scorpaeniformes, Sebastiscus) via Genome Survey Sequencing

Sebastiscus species, marine rockfishes, are of essential economic value. However, the genomic data of this genus is lacking and incomplete. Here, whole genome sequencing of all species of Sebastiscus was conducted to provide fundamental genomic information. The genome sizes were estimated to be 802.49 Mb (S. albofasciatus), 786.79 Mb (S. tertius), and 776.00 Mb (S. marmoratus) by using k-mer analyses. The draft genome sequences were initially assembled, and genome-wide microsatellite motifs were identified. The heterozygosity, repeat ratios, and numbers of microsatellite motifs all suggested possibly that S. tertius is more closely related to S. albofasciatus than S. marmoratus at the genetic level. Moreover, the complete mitochondrial genome sequences were assembled from the whole genome data and the phylogenetic analyses genetically supported the validation of Sebastiscus species. This study provides an important genome resource for further studies of Sebastiscus species.

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Analysis of Draft Genome Resources of Thirty-Three Canadian Strains of Pseudomonas syringae pv. tomato isolated between 1992 and 2008 Reveals achromobactin virulence cluster that is absent in the reference strain DC3000

Phytopathology ◽

10.1094/phyto-08-21-0353-a ◽

2021 ◽

Author(s):

James Tambong ◽

Renlin Xu ◽

Diane Cuppels ◽

Julie T Chapados ◽

suzanne Gerdis ◽

...

Keyword(s):

Pseudomonas Syringae ◽

Draft Genome ◽

Genome Mining ◽

Gene Clusters ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Sequences ◽

Protein Coding ◽

Genome Data ◽

Bacterial Speck Disease

Pseudomonas syringae pv. tomato is the causal agent of bacterial speck disease of field and greenhouse tomato plants. Only one Canadian whole genome sequence of this economically important pathogen is publicly available in NCBI GenBank. Here, we report 33 whole genome sequences of Canadian strains of P. syringae pv. tomato isolated in Ontario, Canada, between 1992 and 2008. The genome sequences exhibited average nucleotide identity values of 98.64-98.72 % with P. syringae pv. tomato ICMP 2844PT and DC3000, validating the taxonomic standing of these Canadian strains. The genome sizes ranged from 6.20-6.39 Mbp with G+C content of 58.6% and comprised 5,889-6,166 protein-coding sequences (CDSs). The strains had pan- and core-genomes of 6808 and 4,993 gene clusters, respectively. Genome mining of the strains for virulence factors identified typical adherence genes, proteins related to antiphagocytosis, secretion system apparatuses and effectors. Also, partial or complete achromobactin biosynthetic cluster and iron transport genes were identified in all the Canadian strains but absent in P. syringae pv. tomato DC3000 or ICMP 2844 (pathotype). These new whole genome data of Canadian strains of P. syringae pv. tomato could be useful resources in understanding the evolution of this pathogen.

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Coniochaeta endophytica sp. nov., a foliar endophyte associated with healthy photosynthetic tissue of Platycladus orientalis (Cupressaceae)

Plant and Fungal Systematics ◽

10.2478/pfs-2019-0008 ◽

2019 ◽

Vol 64 (1) ◽

pp. 65-79

Author(s):

Alison H. Harrington ◽

Mariana del Olmo-Ruiz ◽

Jana M. U’Ren ◽

Kayla Garcia ◽

Daniela Pignatta ◽

...

Keyword(s):

New Species ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Type Specimen ◽

Whole Genome ◽

Platycladus Orientalis ◽

Genome Data ◽

Genome Analyses ◽

Close Relatives

AbstractThe ecologically diverse genus Coniochaeta (Coniochaetaceae, Ascomycota) contains numerous endophytic strains that occur in healthy leaves and lichen thalli in temperate and boreal North America. These endophytes frequently represent undescribed species. Here we examine two endophytic isolates of Coniochaeta from healthy photosynthetic tissue of Platycladus orientalis (Cupressaceae), a conifer cultivated for horticultural use in Arizona, USA. On the basis of morphology, in vitro assays, phylogenetic analyses of two loci, and analyses of whole genome data, we designate these endophytes as a novel species, Coniochaeta endophytica sp. nov. Strains of C. endophytica are closely related to an isolate from a native lichen in North Carolina, which we also characterize here. We compare C. endophytica with two known species that appear to be close relatives: C. prunicola, associated with wood necrosis in stonefruit trees in South Africa, and C. cephalothecoides, isolated from soil in Asia. The new species is distinct in phylogenetic, in vitro, and whole-genome analyses from C. prunicola, and differs slightly in conidiophore morphology from that species. Although available sequence data for C. cephalothecoides are of uncertain relation to the type specimen for that species, our results support the distinctiveness of C. endophytica on the basis of morphology, perithecial formation, and phylogenetic analyses. We discuss the challenge of identifying new species in the context of fungal ecology surveys, such as those for endophytes, which often rely only on a single locus and can misidentify taxa based on their closest matches in public databases or simple comparisons of barcode sequences alone.

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Molecular Epidemiology and Whole-Genome Analysis of Bovine Foamy Virus in Japan

Viruses ◽

10.3390/v13061017 ◽

2021 ◽

Vol 13 (6) ◽

pp. 1017

Author(s):

Hirohisa Mekata ◽

Tomohiro Okagawa ◽

Satoru Konnai ◽

Takayuki Miyazawa

Keyword(s):

Phylogenetic Analyses ◽

Foamy Virus ◽

Pcr Analysis ◽

Whole Genome ◽

Genome Sequences ◽

Whole Genome Analysis ◽

Virus Family ◽

Bovine Foamy Virus ◽

Novel Genotype

Bovine foamy virus (BFV) is a member of the foamy virus family in cattle. Information on the epidemiology, transmission routes, and whole-genome sequences of BFV is still limited. To understand the characteristics of BFV, this study included a molecular survey in Japan and the determination of the whole-genome sequences of 30 BFV isolates. A total of 30 (3.4%, 30/884) cattle were infected with BFV according to PCR analysis. Cattle less than 48 months old were scarcely infected with this virus, and older animals had a significantly higher rate of infection. To reveal the possibility of vertical transmission, we additionally surveyed 77 pairs of dams and 3-month-old calves in a farm already confirmed to have BFV. We confirmed that one of the calves born from a dam with BFV was infected. Phylogenetic analyses revealed that a novel genotype was spread in Japan. In conclusion, the prevalence of BFV in Japan is relatively low and three genotypes, including a novel genotype, are spread in Japan.

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Draft Genome Sequences of Lactobacillus salivarius A3iob and Lactobacillus johnsonii CRL1647, Novel Potential Probiotic Strains for Honeybees (Apis mellifera L.)

Microbiology Resource Announcements ◽

10.1128/mra.00975-18 ◽

2018 ◽

Vol 7 (6) ◽

Cited By ~ 3

Author(s):

Marcela Carina Audisio ◽

Leonardo Albarracín ◽

Maria Julia Torres ◽

Lucila Saavedra ◽

Elvira Maria Hebert ◽

...

Keyword(s):

Apis Mellifera ◽

Genome Sequencing ◽

Draft Genome ◽

Illumina Miseq ◽

Whole Genome ◽

Genome Sequences ◽

Lactobacillus Johnsonii ◽

Lactobacillus Salivarius ◽

Content Type ◽

Probiotic Strains

This report describes the draft genome sequences of Lactobacillus salivarius A3iob and Lactobacillus johnsonii CRL1647, probiotic strains isolated from the gut of honeybee Apis mellifera workers. The reads were generated by a whole-genome sequencing (WGS) strategy on an Illumina MiSeq sequencer and were assembled into contigs with total sizes of 2,054,490 and 2,137,413 bp for the A3iob and CRL1647 strains, respectively.

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Draft Genome Sequences of Six Skin Isolates of Streptococcus pyogenes

Genome Announcements ◽

10.1128/genomea.00592-18 ◽

2018 ◽

Vol 6 (26) ◽

Cited By ~ 1

Author(s):

Zhong Liang ◽

Melissa Stephens ◽

Victoria A. Ploplis ◽

Shaun W. Lee ◽

Francis J. Castellino

Keyword(s):

Streptococcus Pyogenes ◽

Draft Genome ◽

Whole Genome Shotgun ◽

Whole Genome ◽

Genome Sequences ◽

Bottom Up ◽

Content Type

Whole-genome shotgun sequences and bottom-up assembly of contigs of six skin isolates of Streptococcus pyogenes, viz., NS88.3 (emm98.1), NS223 (emm91), NS455 (emm52), SS1448 (emm86.2), SS1572 (emm223), and SS1574 (emm224), are presented here. All contigs were annotated, and the gene arrangements and the inferred proteins were consistent with a pattern D classification.

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Draft Whole-Genome Sequences of Seven Listeria monocytogenes Strains with Variations in Virulence and Stress Responses

Microbiology Resource Announcements ◽

10.1128/mra.01038-18 ◽

2018 ◽

Vol 7 (13) ◽

Cited By ~ 1

Author(s):

Yanhong Liu ◽

Aixia Xu ◽

Pina M. Fratamico ◽

Christopher H. Sommers ◽

Luca Rotundo ◽

...

Keyword(s):

Listeria Monocytogenes ◽

Stress Responses ◽

Draft Genome ◽

Foodborne Pathogen ◽

Whole Genome ◽

Genome Sequences ◽

Content Type

Listeria monocytogenes is an important foodborne pathogen that causes listeriosis. Here, we report the draft genome sequences of seven L. monocytogenes strains isolated from food, environmental, and clinical sources.

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The genome and transcriptome of the Phalaenopsis yield insights into floral organ development and flowering regulation

10.7287/peerj.preprints.1707v1 ◽

2016 ◽

Cited By ~ 1

Author(s):

Jian-Zhi Huang ◽

Chih-Peng Lin ◽

Ting-Chi Cheng ◽

Ya-Wen Huang ◽

Yi-Jung Tsai ◽

...

Keyword(s):

Economic Value ◽

Draft Genome ◽

Floral Organ ◽

Cool Temperature ◽

Organ Development ◽

Nucleotide Polymorphisms ◽

Protein Coding ◽

Draft Genome Assembly ◽

Genome Data ◽

Expression Of Genes

Phalaenopsis orchid is an important potted flower with high economic value around the world. We report the 3.1 Gb draft genome assembly of an important winter flowering Phalaenopsis ‘KHM190’ cultivar. We generated 89.5 Gb RNA-seq and 113 million sRNA-seq reads to use these data to identify 41,153 protein-coding genes and 188 miRNA families. We also generated a draft genome for Phalaenopsis pulcherrima ‘B8802’, a summer flowering species, via resequencing. Comparison of genome data between the two Phalaenopsis cultivars allowed the identification of 691,532 single-nucleotide polymorphisms. In this study, we reveal the key role of PhAGL6b in the regulation of flower organ development involves alternative splicing. We also show gibberellin pathways that regulate the expression of genes control flowering time during the stage in reproductive phase change induced by cool temperature. Our work should contribute a valuable resource for the flowering control, flower architecture development, and breeding of the Phalaenopsis orchids.

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'Candidatus Phytoplasma sacchari’, a novel taxon - associated with Sugarcane Grassy Shoot (SCGS) disease

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004591 ◽

2020 ◽

Author(s):

Kiran Kirdat ◽

Bhavesh Tiwarekar ◽

Vipool Thorat ◽

Shivaji Sathe ◽

Yogesh Shouche ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Gene ◽

Indian Subcontinent ◽

Phylogenetic Analyses ◽

Draft Genome ◽

Housekeeping Genes ◽

Rrna Gene ◽

Genome Sequences ◽

Phytoplasma Strain ◽

White Leaf

Sugarcane Grassy Shoot (SCGS) disease is known to be related to Rice Yellow Dwarf (RYD) phytoplasmas (16SrXI-B group) which are found predominantly in sugarcane growing areas of the Indian subcontinent and South-East Asia. The 16S rRNA gene sequences of SCGS phytoplasma strains belonging to the 16SrXI-B group share 98.07 % similarity with ‘Ca. Phytoplasma cynodontis’ strain BGWL-C1 followed by 97.65 % similarity with ‘Ca. P. oryzae’ strain RYD-J. Being placed distinctly away from both the phylogenetically related species, the taxonomic identity of SCGS phytoplasma is unclear and confusing. We attempted to resolve the phylogenetic positions of SCGS phytoplasma based on the phylogenetic analysis of 16S rRNA gene (>1500 bp), nine housekeeping genes (>3500 aa), core genome phylogeny (>10 000 aa) and OGRI values. The draft genome sequences of SCGS phytoplasma (strain SCGS) and Bermuda Grass White leaf (BGWL) phytoplasma (strain LW01), closely related to ‘Ca. P. cynodontis’, were obtained. The SCGS genome was comprised of 29 scaffolds corresponding to 505 173 bp while LW01 assembly contained 21 scaffolds corresponding to 483 935 bp with the fold coverages over 330× and completeness over 90 % for both the genomes. The G+C content of SCGS was 19.86 % while that of LW01 was 20.46 %. The orthoANI values for the strain SCGS against strains LW01 was 79.42 %, and dDDH values were 22. Overall analysis reveals that SCGS phytoplasma forms a distant clade in RYD group of phytoplasmas. Based on phylogenetic analyses and OGRI values obtained from the genome sequences, a novel taxon ‘Candidatus Phytoplasma sacchari’ is proposed.

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Whole-Genome Sequences of Seven Listeria monocytogenes Strains from Different Stages of a Poultry Meat Production Chain

Microbiology Resource Announcements ◽

10.1128/mra.00088-19 ◽

2019 ◽

Vol 8 (11) ◽

Cited By ~ 2

Author(s):

Victoria López-Alonso ◽

Sagrario Ortiz ◽

Joaquín V. Martínez-Suárez

Keyword(s):

Listeria Monocytogenes ◽

Draft Genome ◽

Poultry Meat ◽

Meat Production ◽

Whole Genome ◽

Genome Sequences ◽

Production Chain ◽

Content Type ◽

Three Stages

Here, we present the draft genome sequences of seven Listeria monocytogenes strains isolated during three independent studies carried out in three stages of a poultry meat production chain. The genome sequences of these strains obtained from different stages can help to understand the possible transmission of L. monocytogenes.

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