scholarly journals Evolution of photosynthetic prokaryotes: a maximum-likelihood mapping approach

2003 ◽  
Vol 358 (1429) ◽  
pp. 223-230 ◽  
Author(s):  
Jason Raymond ◽  
Olga Zhaxybayeva ◽  
J. Peter Gogarten ◽  
Robert E. Blankenship
Keyword(s):  
Maximum Likelihood ◽  
Phylogenetic Signal ◽  
Molecular Genetic ◽  
Whole Genome ◽  
Photosynthetic Organisms ◽  
Genome Data ◽  
Genetic Techniques ◽  
Genome Analyses ◽  
Maximum Likelihood Mapping ◽  
Evolution Of Photosynthesis

Reconstructing the early evolution of photosynthesis has been guided in part by the geological record, but the complexity and great antiquity of these early events require molecular genetic techniques as the primary tools of inference. Recent genome sequencing efforts have made whole genome data available from representatives of each of the five phyla of bacteria with photosynthetic members, allowing extensive phylogenetic comparisons of these organisms. Here, we have undertaken whole genome comparisons using maximum likelihood to compare 527 unique sets of orthologous genes from all five photosynthetic phyla. Substantiating recent whole genome analyses of other prokaryotes, our results indicate that horizontal gene transfer (HGT) has played a significant part in the evolution of these organisms, resulting in genomes with mosaic evolutionary histories. A small plurality phylogenetic signal was observed, which may be a core of remnant genes not subject to HGT, or may result from a propensity for gene exchange between two or more of the photosynthetic organisms compared.

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

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.

scholarly journals Complex population structure of the Atlantic puffin revealed by whole genome analyses

2020 ◽  
Author(s):  
Oliver Kersten ◽  
Bastiaan Star ◽  
Deborah M. Leigh ◽  
Tycho Anker-Nilssen ◽  
Hallvard Strøm ◽  
...  
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Isolation By Distance ◽  
Spatial Scales ◽  
Secondary Contact ◽  
Whole Genome ◽  
Genome Data ◽  
Complex Population ◽  
Genome Analyses ◽  
Atlantic Puffin

AbstractThe factors underlying gene flow and genomic population structure in vagile seabirds are notoriously difficult to understand due to their complex ecology with diverse dispersal barriers and extensive periods at sea. Yet, such understanding is vital for conservation management of seabirds that are globally declining at alarming rates. Here, we elucidate the population structure of the Atlantic puffin (Fratercula arctica) by assembling its reference genome and analyzing genome-wide resequencing data of 72 individuals from 12 colonies. We identify four large, genetically distinct clusters, observe isolation-by-distance between colonies within these clusters, and obtain evidence for a secondary contact zone. These observations disagree with the current taxonomy, and show that a complex set of contemporary biotic factors impede gene flow over different spatial scales. Our results highlight the power of whole genome data to reveal unexpected population structure in vagile marine seabirds and its value for seabird taxonomy, evolution and conservation.

scholarly journals Molecular genetic survey of 16 kindreds with hereditary antithrombin III deficiency

Blood ◽  
1987 ◽  
Vol 70 (5) ◽  
pp. 1273-1278
Author(s):  
SC Bock ◽  
EV Prochownik
Keyword(s):  
Southern Blotting ◽  
Nucleotide Substitution ◽  
Antithrombin Iii ◽  
Molecular Genetic ◽  
Biologically Active ◽  
Whole Genome ◽  
Antithrombin Iii Deficiency ◽  
Genetic Techniques ◽  
Genetic Survey ◽  
Gene Status

Molecular genetic techniques were utilized to examine antithrombin III (ATIII) gene status in 16 independently ascertained kindreds with hereditary ATIII deficiency. In one of these families antithrombin III deficiency is caused by hemizygosity of the ATIII locus. In the remaining 15 kindreds, two copies of the ATIII gene are present and appear to be grossly normal at the level of whole genome Southern blotting, suggesting that small deletions, insertions or limited nucleotide substitution(s) in the antithrombin III gene, or “trans- acting” defects at other loci involved in the processing, modification, and secretion of biologically active ATIII are responsible for the observed anticoagulant disorders.

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

2021 ◽  
Vol 43 (3) ◽  
pp. 2048-2058
Author(s):  
Chenghao Jia ◽  
Tianyan Yang ◽  
Takashi Yanagimoto ◽  
Tianxiang Gao
Keyword(s):  
Phylogenetic Analyses ◽  
Complete Mitochondrial Genome ◽  
Economic Value ◽  
Draft Genome ◽  
Whole Genome ◽  
Genome Sequences ◽  
Genome Data ◽  
Genome Survey ◽  
Genome Wide ◽  
Genome Analyses

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.

scholarly journals Hypervirulent Klebsiella pneumoniae of Lineage ST66-K2 Caused Tonsillopharyngitis in a German Patient

2021 ◽  
Vol 9 (1) ◽  
pp. 133
Author(s):  
Kathleen Klaper ◽  
Sebastian Wendt ◽  
Christoph Lübbert ◽  
Norman Lippmann ◽  
Yvonne Pfeifer ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Snp Analysis ◽  
Whole Genome ◽  
Single Nucleotide ◽  
German Patient ◽  
Genome Data ◽  
Genome Analyses ◽  
Clinical Awareness

Hypervirulent Klebsiella pneumoniae (hvKp) is a novel pathotype that has been rarely described in Europe. This study characterizes a hvKp isolate that caused a community-acquired infection. The hypermucoviscous Klebsiella pneumoniae (K. pneumoniae) strain 18-0005 was obtained from a German patient with tonsillopharyngitis in 2017. Antibiotic susceptibility testing was performed and the genome was sequenced by Illumina and Nanopore technology. Whole genome data were analyzed by conducting core genome multilocus sequence typing (cgMLST) and single nucleotide polymorphism (SNP) analysis. Virulence genes were predicted by applying Kleborate. Phenotypic and whole genome analyses revealed a high similarity of the study isolate 18-0005 to the recently reported antibiotic-susceptible hvKp isolate SB5881 from France and the “ancestral” strain Kp52.145; both were assigned to the ST66-K2 lineage. Comparative genomic analysis of the three plasmids showed that the 18-0005 plasmid II differs from SB5881 plasmid II by an additional 3 kb integrated fragment of plasmid I. Our findings demonstrate the genetic flexibility of hvKp and the occurrence of a strain of the clonal group CG66-K2 in Germany. Hence, it emphasizes the need to improve clinical awareness and infection monitoring of hvKp.

scholarly journals Molecular genetic survey of 16 kindreds with hereditary antithrombin III deficiency

Blood ◽  
1987 ◽  
Vol 70 (5) ◽  
pp. 1273-1278 ◽  
Author(s):  
SC Bock ◽  
EV Prochownik
Keyword(s):  
Southern Blotting ◽  
Nucleotide Substitution ◽  
Antithrombin Iii ◽  
Molecular Genetic ◽  
Biologically Active ◽  
Whole Genome ◽  
Antithrombin Iii Deficiency ◽  
Genetic Techniques ◽  
Genetic Survey ◽  
Gene Status

Abstract Molecular genetic techniques were utilized to examine antithrombin III (ATIII) gene status in 16 independently ascertained kindreds with hereditary ATIII deficiency. In one of these families antithrombin III deficiency is caused by hemizygosity of the ATIII locus. In the remaining 15 kindreds, two copies of the ATIII gene are present and appear to be grossly normal at the level of whole genome Southern blotting, suggesting that small deletions, insertions or limited nucleotide substitution(s) in the antithrombin III gene, or “trans- acting” defects at other loci involved in the processing, modification, and secretion of biologically active ATIII are responsible for the observed anticoagulant disorders.

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