Title: Genome sequences of bacteria associated with the diatom Cyclotella cryptica strain CCMP332
ABSTRACT We report draft genomes of two bacterial strains in the genera Hyphobacterium and Reichenbachiella , which are associated with the diatom Cyclotella cryptica strain CCMP332. Genomes from these strains were 2,691,501 bp and 3,325,829 bp, respectively, and will be useful for understanding interactions between diatoms and bacteria. more »« less
ABSTRACT The genus Saccharibacter is currently understudied, with only one described species, Saccharibacter floricola , isolated from a flower. In an effort to better understand the microbes that come in contact with native bee pollinators, we isolated and sequenced four additional strains of Saccharibacter from native bees in the genera Melissodes and Anthophora . These genomes range in size from 2,104,494 to 2,316,791 bp (mean, 2,246,664 bp) and contain between 1,860 and 2,167 (mean, 2,060) protein-coding genes.
Garcia, Alejandro; Katada, Althea C.; Serrano, Alyssa; Gonzalez-Karlsson, Adrea; Carrillo, Angel; Castellanos, Angelica; Mendez-Gomez, Azucena; Flores, Carlos J.; Limon, Christopher; Lopez, Cynthia; et al
(, Microbiology Resource Announcements)
Stajich, Jason E.
(Ed.)
ABSTRACT Here, we present the complete chloroplast genomes of Quercus × morehus , Q. wislizeni , and Q. kelloggii from California. The genomes are 161,119 to 161,130 bp and encode 132 genes. Quercus × morehus and Q. wislizeni are identical in sequence but differ from Q. kelloggii by three indels and eight SNPs.
Yacoub, Mark N; Stajich, Jason E
(, Genome Biology and Evolution)
Giraud, Tatiana
(Ed.)
Abstract The Global Panzootic Lineage (GPL) of Batrachochytrium dendrobatidis (Bd) has been described as a main driver of amphibian extinctions. Pathogen studies have benefited from three Bd-GPL strain genomes, but identifying the genetic and molecular features that distinguish the B. dendrobatidis lineages requires additional high-quality genomes from diverse lineages. We sequenced and assembled genomes with Oxford Nanopore Technologies to produce assemblies of three Bd-BRAZIL isolates and one nonpathogen outgroup species Polyrhizophydium stewartii. The Bd-BRAZIL assembly sizes ranged between 22.0 and 26.1 Mb with 8,495 to 8,620 predicted protein-coding genes. We sought to categorize the pangenome of the species by identifying homologous genes across the sampled genomes as either being core and present in all strains, or accessory and shared among strains in a lineage, an analysis that has not yet been conducted on B. dendrobatidis and its lineages. We identified a core genome consisting of 6,278 gene families, and an accessory genome of 202 Bd-BRAZIL and 172 Bd-GPL specific gene families. We discovered copy number differences in pathogenicity gene families: M36 Peptidases, Crinkler Necrosis genes, Aspartyl Peptidases, Carbohydrate-Binding Module-18 genes, and S41 Proteases, between Bd-BRAZIL and Bd-GPL strains. Comparison of B. dendrobatidis and two closely related saprophytic species identified differences in protein sequence and domain counts for M36 and CBM18 families respectively. Our pangenome analysis of lineage-specific gene content led us to explore how the selection of the reference genome affects recovery of RNAseq transcripts when comparing different strains. We tested the hypothesis that genomic variation among Bd-GPL and Bd-BRAZIL lineages can impact transcript count data by comparing results with our new Bd-BRAZIL genomes as the reference genomes. Our analysis examines the genomic variation between strains in Bd-BRAZIL and Bd-GPL and offers insights into the application of these high-quality reference genomes resources for future studies.
Osborne, Megan J; Barela_Hudgell, Megan A; Caeiro-Dias, Guilherme; Turner, Thomas F
(, Mitochondrial DNA Part B)
Macrhybopsis tetranema and Oncorhynchus gilae are fish species endemic to the Southwestern United States. We present the complete mitochondrial genomes for these species. Each genome consisted of 13 protein-coding genes, two ribosomal (rRNA) genes, 22 transfer RNA (tRNA) genes, and the control region (D-loop). Mitogenome lengths were 16,916 base pairs (bp) for M. tetranema, and 16,976 bp for O. gilae. The GC content was 41% for M. tetranema and 46% for O. gilae. The relationships of M. tetranema and O. gilae were consistent with previous phylogenetic analyses.
Steenwyk, Jacob L; Balamurugan, Charu; Raja, Huzefa A; Gonçalves, Carla; Li, Ningxiao; Martin, Frank; Berman, Judith; Oberlies, Nicholas H; Gibbons, John G; Goldman, Gustavo H; et al
(, Microbiology Spectrum)
Alanio, Alexandre
(Ed.)
ABSTRACT Modern taxonomic classification is often based on phylogenetic analyses of a few molecular markers, although single-gene studies are still common. Here, we leverage genome-scale molecular phylogenetics (phylogenomics) of species and populations to reconstruct evolutionary relationships in a dense data set of 710 fungal genomes from the biomedically and technologically important genusAspergillus. To do so, we generated a novel set of 1,362 high-quality molecular markers specific forAspergillusand provided profile Hidden Markov Models for each, facilitating their use by others. Examining the resulting phylogeny helped resolve ongoing taxonomic controversies, identified new ones, and revealed extensive strain misidentification (7.59% of strains were previously misidentified), underscoring the importance of population-level sampling in species classification. These findings were corroborated using the current standard, taxonomically informative loci. These findings suggest that phylogenomics of species and populations can facilitate accurate taxonomic classifications and reconstructions of the Tree of Life.IMPORTANCEIdentification of fungal species relies on the use of molecular markers. Advances in genomic technologies have made it possible to sequence the genome of any fungal strain, making it possible to use genomic data for the accurate assignment of strains to fungal species (and for the discovery of new ones). We examined the usefulness and current limitations of genomic data using a large data set of 710 publicly available genomes from multiple strains and species of the biomedically, agriculturally, and industrially important genusAspergillus. Our evolutionary genomic analyses revealed that nearly 8% of publicly availableAspergillusgenomes are misidentified. Our work highlights the usefulness of genomic data for fungal systematic biology and suggests that systematic genome sequencing of multiple strains, including reference strains (e.g., type strains), of fungal species will be required to reduce misidentification errors in public databases.
Gargas, Cory B., Roberts, Wade R., and Alverson, Andrew J. Genome sequences of bacteria associated with the diatom Cyclotella cryptica strain CCMP332. Retrieved from https://par.nsf.gov/biblio/10231023. Microbiology Resource Announcements 9.46 Web. doi:10.1128/MRA.01030-20.
Gargas, Cory B., Roberts, Wade R., & Alverson, Andrew J. Genome sequences of bacteria associated with the diatom Cyclotella cryptica strain CCMP332. Microbiology Resource Announcements, 9 (46). Retrieved from https://par.nsf.gov/biblio/10231023. https://doi.org/10.1128/MRA.01030-20
Gargas, Cory B., Roberts, Wade R., and Alverson, Andrew J.
"Genome sequences of bacteria associated with the diatom Cyclotella cryptica strain CCMP332". Microbiology Resource Announcements 9 (46). Country unknown/Code not available: ASM Journals. https://doi.org/10.1128/MRA.01030-20.https://par.nsf.gov/biblio/10231023.
@article{osti_10231023,
place = {Country unknown/Code not available},
title = {Genome sequences of bacteria associated with the diatom Cyclotella cryptica strain CCMP332},
url = {https://par.nsf.gov/biblio/10231023},
DOI = {10.1128/MRA.01030-20},
abstractNote = {ABSTRACT We report draft genomes of two bacterial strains in the genera Hyphobacterium and Reichenbachiella , which are associated with the diatom Cyclotella cryptica strain CCMP332. Genomes from these strains were 2,691,501 bp and 3,325,829 bp, respectively, and will be useful for understanding interactions between diatoms and bacteria.},
journal = {Microbiology Resource Announcements},
volume = {9},
number = {46},
publisher = {ASM Journals},
author = {Gargas, Cory B. and Roberts, Wade R. and Alverson, Andrew J.},
editor = {Maresca, Julia A}
}
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