Alex Copeland

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Papers by Alex Copeland

Automatic Outlier Detection for Genome Assembly Quality Assessment

2013 IEEE 9th International Conference on e-Science, 2013

ABSTRACT In this work we describe a method to automatically detect errors in de novo assembled ge... more ABSTRACT In this work we describe a method to automatically detect errors in de novo assembled genomes. The method extends a Bayesian assembly quality evaluation framework, ALE, which computes the likelihood of an assembly given a set of unassembled data. Starting from ALE output, this method applies outlier detection algorithms to identify the precise locations of assembly errors. We show results from a microbial genome with manually curated assembly errors. Our method detects all deletions, 82.3% of insertions, and 88.8% of single base substitutions. It was also able to detect an inversion error that spans more than 400 bases.

Complete genome sequence of Mesorhizobium opportunistum type strain WSM2075(T.)

by Alex Copeland, Chris Detter, Uma Meenakshi, Ron Yates, and Wayne Reeve

Standards in genomic sciences, Jan 20, 2013

Mesorhizobium opportunistum strain WSM2075(T) was isolated in Western Australia in 2000 from root... more Mesorhizobium opportunistum strain WSM2075(T) was isolated in Western Australia in 2000 from root nodules of the pasture legume Biserrula pelecinus that had been inoculated with M. ciceri bv. biserrulae WSM1271. WSM2075(T) is an aerobic, motile, Gram negative, non-spore-forming rod that has gained the ability to nodulate B. pelecinus but is completely ineffective in N2 fixation with this host. This report reveals that the genome of M. opportunistum strain WSM2075(T) contains a chromosome of size 6,884,444 bp, encoding 6,685 protein-coding genes and 62 RNA-only encoding genes. The genome contains no plasmids, but does harbor a 455.7 kb genomic island from Mesorhizobium ciceri bv. biserrulae WSM1271 that has been integrated into a phenylalanine-tRNA gene.

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Permanent draft genome sequence of Comamonas testosteroni KF-1

Standards in Genomic Sciences, 2013

Comamonas testosteroni KF-1 is a model organism for the elucidation of the novel biochemical degr... more Comamonas testosteroni KF-1 is a model organism for the elucidation of the novel biochemical degradation pathways for xenobiotic 4-sulfophenylcarboxylates (SPC) formed during biodegradation of synthetic 4-sulfophenylalkane surfactants (linear alkylbenzenesulfonates, LAS) by bacterial communities. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 6,026,527 bp long chromosome (one sequencing gap) exhibits an average G+C content of 61.79% and is predicted to encode 5,492 protein-coding genes and 114 RNA genes.

format_quoteStrain KF-1's chromosome (6.03 Mb) is larger than other published C. testosteroni strains, indicating possible enhanced capabilities.format_quote

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Complete genome sequence of Haliangium ochraceum type strain (SMP-2)

by Alex Copeland, Chris Daum, Krishnaveni Palaniappan, Tijana Del Rio, Jan-fang Cheng, and Amy Chen

Standards in genomic sciences, 2010

Haliangium ochraceum Fudou et al. 2002 is the type species of the genus Haliangium in the myxococ... more Haliangium ochraceum Fudou et al. 2002 is the type species of the genus Haliangium in the myxococcal family 'Haliangiaceae'. Members of the genus Haliangium are the first halophilic myxobacterial taxa described. The cells of the species follow a multicellular lifestyle in highly organized biofilms, called swarms, they decompose bacterial and yeast cells as most myxobacteria do. The fruiting bodies contain particularly small coccoid myxospores. H. ochraceum encodes the first actin homologue identified in a bacterial genome. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the myxococcal suborder Nannocystineae, and the 9,446,314 bp long single replicon genome with its 6,898 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

format_quoteThe genome of H. ochraceum is 9,446,314 bp with 6,951 genes, showing a high proportion of predicted functional roles.format_quote

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Complete genome sequence of Thermobispora bispora type strain (R51)

Standards in genomic sciences, 2010

Thermobispora bispora (Henssen 1957) Wang et al. 1996 is the type species of the genus Thermobisp... more Thermobispora bispora (Henssen 1957) Wang et al. 1996 is the type species of the genus Thermobispora. This genus is of great interest because it is strictly thermophilic and because it has been shown for several of its members that the genome contains substantially distinct (6.4% sequence difference) and transcriptionally active 16S rRNA genes. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the second completed genome sequence of a member from the suborder Streptosporangineae and the first genome sequence of a member of the genus Thermobispora. The 4,189,976 bp long genome with its 3,596 protein-coding and 63 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

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Complete genome sequence of Archaeoglobus profundus type strain (AV18)

by Yun-juan Chang and Alex Copeland

Standards in genomic sciences, 2010

Archaeoglobus profundus (Burggraf et al. 1990) is a hyperthermophilic archaeon in the euryarchaea... more Archaeoglobus profundus (Burggraf et al. 1990) is a hyperthermophilic archaeon in the euryarchaeal class Archaeoglobi, which is currently represented by the single family Archaeoglobaceae, containing six validly named species and two strains ascribed to the genus 'Geoglobus' which is taxonomically challenged as the corresponding type species has no validly published name. All members were isolated from marine hydrothermal habitats and are obligate anaerobes. Here we describe the features of the organism, together with the complete genome sequence and annotation. This is the second completed genome sequence of a member of the class Archaeoglobi. The 1,563,423 bp genome with its 1,858 protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

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Non-contiguous finished genome sequence and contextual data of the filamentous soil bacterium Ktedonobacter racemifer type strain (SOSP1-21)

by Yun-juan Chang and Alex Copeland

Standards in genomic sciences, Jan 15, 2011

Ktedonobacter racemifer corrig. Cavaletti et al. 2007 is the type species of the genus Ktedonobac... more Ktedonobacter racemifer corrig. Cavaletti et al. 2007 is the type species of the genus Ktedonobacter, which in turn is the type genus of the family Ktedonobacteraceae, the type family of the order Ktedonobacterales within the class Ktedonobacteria in the phylum 'Chloroflexi'. Although K. racemifer shares some morphological features with the actinobacteria, it is of special interest because it was the first cultivated representative of a deep branching unclassified lineage of otherwise uncultivated environmental phylotypes tentatively located within the phylum 'Chloroflexi'. The aerobic, filamentous, non-motile, spore-forming Gram-positive heterotroph was isolated from soil in Italy. The 13,661,586 bp long non-contiguous finished genome consists of ten contigs and is the first reported genome sequence from a member of the class Ktedonobacteria. With its 11,453 protein-coding and 87 RNA genes, it is the largest prokaryotic genome reported so far. It comprises a large n...

format_quoteThe genome consists of ten contiguous fragments and houses 11,540 genes, with 61.2% of protein-coding genes assigned a putative function.format_quote

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Draft genome sequences of 10 strains of the genus exiguobacterium

Genome announcements, 2014

High-quality draft genome sequences were determined for 10 Exiguobacterium strains in order to pr... more High-quality draft genome sequences were determined for 10 Exiguobacterium strains in order to provide insight into their evolutionary strategies for speciation and environmental adaptation. The selected genomes include psychrotrophic and thermophilic species from a range of habitats, which will allow for a comparison of metabolic pathways and stress response genes.

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Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575)

by Yun-juan Chang and Alex Copeland

Standards in genomic sciences, 2009

Desulfotomaculum acetoxidans Widdel and Pfennig 1977 was one of the first sulfate-reducing bacter... more Desulfotomaculum acetoxidans Widdel and Pfennig 1977 was one of the first sulfate-reducing bacteria known to grow with acetate as sole energy and carbon source. It is able to oxidize substrates completely to carbon dioxide with sulfate as the electron acceptor, which is reduced to hydrogen sulfide. All available data about this species are based on strain 5575(T), isolated from piggery waste in Germany. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a Desulfotomaculum species with validly published name. The 4,545,624 bp long single replicon genome with its 4370 protein-coding and 100 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

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Complete genome sequence of Rhizobium leguminosarum bv. trifolii strain WSM1325, an effective microsymbiont of annual Mediterranean clovers

by Alex Copeland, Lambert Bräu, Ron Yates, Julie Ardley, and Wayne Reeve

Standards in Genomic Sciences, 2010

Rhizobium leguminosarum bv trifolii is the effective nitrogen fixing microsymbiont of a diverse r... more Rhizobium leguminosarum bv trifolii is the effective nitrogen fixing microsymbiont of a diverse range of annual and perennial Trifolium (clover) species. Strain WSM2304 is an aerobic, motile, non-spore forming, Gram-negative rod, isolated from Trifolium polymorphum in Uruguay in 1998. This microsymbiont predominated in the perennial grasslands of Glencoe Research Station, in Uruguay, to competitively nodulate its host, and fix atmospheric nitrogen. Here we describe the basic features of WSM2304, together with the complete genome sequence, and annotation. This is the first completed genome sequence for a nitrogen fixing microsymbiont of a clover species from the American center of origin. We reveal that its genome size is 6,872,702 bp encoding 6,643 protein-coding genes and 62 RNA only encoding genes. This multipartite genome was found to contain 5 distinct replicons; a chromosome of size 4,537,948 bp and four circular plasmids of size 1,266,105 bp, 501,946 bp, 308,747 bp and 257,956 bp.

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Complete genome sequence of the Medicago microsymbiont Ensifer (Sinorhizobium) medicae strain WSM419

by Alex Copeland, Alla Lapidus, Wayne Reeve, Lambert Bräu, and Stephanie Malfatti

Standards in Genomic Sciences, 2010

Ensifer (Sinorhizobium) medicae is an effective nitrogen fixing microsymbiont of a diverse range ... more Ensifer (Sinorhizobium) medicae is an effective nitrogen fixing microsymbiont of a diverse range of annual Medicago (medic) species. Strain WSM419 is an aerobic, motile, non-spore forming, Gram-negative rod isolated from a M. murex root nodule collected in Sardinia, Italy in 1981. WSM419 was manufactured commercially in Australia as an inoculant for annual medics during 1985 to 1993 due to its nitrogen fixation, saprophytic competence and acid tolerance properties. Here we describe the basic features of this organism, together with the complete genome sequence, and annotation. This is the first report of a complete genome sequence for a microsymbiont of the group of annual medic species adapted to acid soils. We reveal that its genome size is 6,817,576 bp encoding 6,518 protein-coding genes and 81 RNA only encoding genes. The genome contains a chromosome of size 3,781,904 bp and 3 plasmids of size 1,570,951 bp, 1,245,408 bp and 219,313 bp. The smallest plasmid is a feature unique to this medic microsymbiont. Editorial note -Readers are advised that in Opinion 84 the Judicial Commission of the International Committee on Systematics of Prokaryotes ruled that the genus name Ensifer Casida 1982 has priority over Sinorhizobium Chen et al. 1988 and the names are synonyms [1]. It was further concluded that the transfer of members of the genus Sinorhizobium to the genus Ensifer, as proposed by Young [2] would not cause confusion.

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Complete genome sequence of Thauera aminoaromatica strain MZ1T

by Jennifer DeBruyn, Alex Copeland, Eileen Dalin, and