Abstract:
:Cyanobacteria are dominant primary producers of various ecosystems and they colonize marine as well as freshwater and terrestrial habitats. On the basis of their oxygenic photosynthesis they are known to synthesize a high number of secondary metabolites, which makes them promising for biotechnological applications. State-of-the-art sequencing and analytical techniques and the availability of several axenic strains offer new opportunities for the understanding of the hidden metabolic potential of cyanobacteria beyond those of single model organisms. Here, we report comprehensive genomic and metabolic analyses of five non-marine cyanobacteria, that is, Nostoc sp. DSM 107007, Anabaena variabilis DSM 107003, Calothrix desertica DSM 106972, Chroococcidiopsis cubana DSM 107010, Chlorogloeopsis sp. PCC 6912, and the reference strain Synechocystis sp. PCC 6803. Five strains that are prevalently belonging to the order Nostocales represent the phylogenetic depth of clade B1, a morphologically highly diverse sister lineage of clade B2 that includes strain PCC 6803. Genome sequencing, light and scanning electron microscopy revealed the characteristics and axenicity of the analyzed strains. Phylogenetic comparisons showed the limits of the 16S rRNA gene for the classification of cyanobacteria, but documented the applicability of a multilocus sequence alignment analysis based on 43 conserved protein markers. The analysis of metabolites of the core carbon metabolism showed parts of highly conserved metabolic pathways as well as lineage specific pathways such as the glyoxylate shunt, which was acquired by cyanobacteria at least twice via horizontal gene transfer. Major metabolic changes were observed when we compared alterations between day and night samples. Furthermore, our results showed metabolic potential of cyanobacteria beyond Synechocystis sp. PCC 6803 as model organism and may encourage the cyanobacterial community to broaden their research to related organisms with higher metabolic activity in the desired pathways.
journal_name
Genome Biol Evoljournal_title
Genome biology and evolutionauthors
Will SE,Henke P,Boedeker C,Huang S,Brinkmann H,Rohde M,Jarek M,Friedl T,Seufert S,Schumacher M,Overmann J,Neumann-Schaal M,Petersen Jdoi
10.1093/gbe/evy275subject
Has Abstractpub_date
2019-01-01 00:00:00pages
270-294issue
1issn
1759-6653pii
5258472journal_volume
11pub_type
杂志文章abstract::The phylum Apicomplexa is a quintessentially parasitic lineage, whose members infect a broad range of animals. One exception to this may be the apicomplexan genus Nephromyces, which has been described as having a mutualistic relationship with its host. Here we analyze transcriptome data from Nephromyces and its parasi...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy251
更新日期:2019-01-01 00:00:00
abstract::The Asian honey bee (Apis dorsata) is distinct from its more widely distributed cousin Apis mellifera by a few key characteristics. Most prominently, A. dorsata, nest in the open by forming a colony clustered around the honeycomb, whereas A. mellifera nest in concealed cavities. Additionally, the worker and reproducti...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz277
更新日期:2020-01-01 00:00:00
abstract::Polyadenylation is a step of mRNA processing which is crucial for its expression and stability. The major polyadenylation signal (PAS) represents a nucleotide hexamer that adheres to the AATAAA consensus sequence. Over a half of human genes have multiple cleavage and polyadenylation sites, resulting in a great diversi...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw137
更新日期:2016-07-02 00:00:00
abstract::Arbuscular mycorrhizal fungi (AMF) represent an ecologically important and evolutionarily intriguing group of symbionts of land plants, currently thought to have propagated clonally for over 500 Myr. AMF produce multinucleate spores and may exchange nuclei through anastomosis, but meiosis has never been observed in th...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evr089
更新日期:2011-01-01 00:00:00
abstract::Plasma membrane NADPH oxidases (NOXs) are key producers of reactive oxygen species under both normal and stress conditions in plants and they form functional subfamilies. Studies of these subfamilies indicated that they show considerable evolutionary selection. We performed a comparative genomic analysis that identifi...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw035
更新日期:2016-02-23 00:00:00
abstract::Gene duplication is the primary source of new genes, but the mechanisms underlying the functional divergence and retention of duplicate genes are not well understood. Because eukaryotic proteins are localized to subcellular structures and localization can be altered by a single amino acid replacement, it was recently ...
journal_title:Genome biology and evolution
pub_type: 信件
doi:10.1093/gbe/evp021
更新日期:2009-07-22 00:00:00
abstract::Amoebae have been considered as a genetic "melting pot" for its symbionts, facilitating genetic exchanges of the bacteria that co-inhabit the same host. To test the "melting pot" hypothesis, we analyzed six genomes of amoeba endosymbionts within Rickettsiales, four of which belong to Holosporaceae family and two to Ca...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx246
更新日期:2017-11-01 00:00:00
abstract::The Bateson-Dobzhansky-Muller (BDM) model of reproductive isolation by genetic incompatibility is a widely accepted model of speciation. Because of the exceptionally rich biological information about the budding yeast Saccharomyces cerevisiae, the identification of BDM incompatibilities in yeast would greatly deepen o...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evt091
更新日期:2013-01-01 00:00:00
abstract::Chagas disease was described by Carlos Chagas, who first identified the parasite Trypanosoma cruzi from a 2-year-old girl called Berenice. Many T. cruzi sequencing projects based on short reads have demonstrated that genome assembly and downstream comparative analyses are extremely challenging in this species, given t...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz129
更新日期:2019-07-01 00:00:00
abstract::piRNA clusters are thought to repress transposable element (TE) activity in mammals and invertebrates. Here, we show that a simple population genetics model reveals a constraint on the size of piRNA clusters: The total size of the piRNA clusters of an organism must exceed 0.2% of a genome to repress TE invasions. More...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evaa064
更新日期:2020-05-01 00:00:00
abstract::Genomic structural variants (SVs) are distributed nonrandomly across the human genome. The "hotspots" of SVs have been implicated in evolutionary innovations, as well as medical conditions. However, the evolutionary and biomedical features of these hotspots remain incompletely understood. Here, we analyzed data from 2...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz058
更新日期:2019-04-01 00:00:00
abstract::Nuclear-encoded pentatricopeptide repeat (PPR) proteins are site-specific factors for C-to-U RNA editing in plant organelles coevolving with their targets. Losing an editing target by C-to-T conversion allows for eventual loss of its editing factor, as recently confirmed for editing factors CLB19, CRR28, and RARE1 tar...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz032
更新日期:2019-03-01 00:00:00
abstract::The large repABC plasmids of the order Rhizobiales with Class I quorum-regulated conjugative transfer systems often define the nature of the bacterium that harbors them. These otherwise diverse plasmids contain a core of highly conserved genes for replication and conjugation raising the question of their evolutionary ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv227
更新日期:2015-11-19 00:00:00
abstract::Plants and fungi display a broad range of interactions in natural and agricultural ecosystems ranging from symbiosis to parasitism. These ecological interactions result in coevolution between genes belonging to different partners. A well-understood example is secreted fungal effector proteins and their host targets, w...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy023
更新日期:2018-02-01 00:00:00
abstract::Analysis of more than 150 Clostridium botulinum Group II type E genomes identified a small fraction (6%) where neurotoxin-encoding genes were located on plasmids. Seven closely related (134-144 kb) neurotoxigenic plasmids of subtypes E1, E3, and E10 were characterized; all carried genes associated with plasmid mobilit...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evw017
更新日期:2016-03-02 00:00:00
abstract::Sex determination evolves rapidly, often because of turnover of the genes at the top of the pathway. The house fly, Musca domestica, has a multifactorial sex determination system, allowing us to identify the selective forces responsible for the evolutionary turnover of sex determination in action. There is a male dete...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv128
更新日期:2015-07-02 00:00:00
abstract::DNA methylation and chromatin states play key roles in development and disease. However, the extent of recent evolutionary divergence in the human epigenome and the influential factors that have shaped it are poorly understood. To determine the links between genome sequence and human epigenome evolution, we examined t...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evu142
更新日期:2014-06-24 00:00:00
abstract::The nearly neutral theory, which proposes that most mutations are deleterious or close to neutral, predicts that the ratio of nonsynonymous over synonymous substitution rates (dN/dS), and potentially also the ratio of radical over conservative amino acid replacement rates (Kr/Kc), are negatively correlated with effect...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evt083
更新日期:2013-01-01 00:00:00
abstract::Plant genomes encode many lineage-specific, unique transcription factors. Expansion of such gene families has been previously found to coincide with the evolution of morphological complexity, although comparative analyses have been hampered by severe sampling bias. Here, we make use of the recently increased availabil...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evx258
更新日期:2017-12-01 00:00:00
abstract::Protein metabolism is one of the most costly processes in the cell and is therefore expected to be under the effective control of natural selection. We stimulated yeast strains to overexpress each single gene product to approximately 1% of the total protein content. Consistent with previous reports, we found that exce...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evt154
更新日期:2013-01-01 00:00:00
abstract::Dinoflagellates are a group of unicellular protists with immense ecological and evolutionary significance and cell biological diversity. Of the photosynthetic dinoflagellates, the majority possess a plastid containing the pigment peridinin, whereas some lineages have replaced this plastid by serial endosymbiosis with ...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy057
更新日期:2018-04-01 00:00:00
abstract::Lateral gene transfer (LGT) is an important factor contributing to the evolution of prokaryotic genomes. The Aquificae are a hyperthermophilic bacterial group whose genes show affiliations to many other lineages, including the hyperthermophilic Thermotogae, the Proteobacteria, and the Archaea. Previous phylogenomic an...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evt195
更新日期:2013-01-01 00:00:00
abstract::Balancing selection maintains advantageous diversity in populations through various mechanisms. Although extensively explored from a theoretical perspective, an empirical understanding of its prevalence and targets lags behind our knowledge of positive selection. Here, we describe the Non-central Deviation (NCD), a si...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy054
更新日期:2018-03-01 00:00:00
abstract::Parasitoid wasps are among the most speciose animals, yet have relatively few available genomic resources. We report a draft genome assembly of the wasp Diachasma alloeum (Hymenoptera: Braconidae), a host-specific parasitoid of the apple maggot fly Rhagoletis pomonella (Diptera: Tephritidae), and a developing model fo...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz205
更新日期:2019-10-01 00:00:00
abstract::The question on the patterns and limits of reduction of plastid genomes in nonphotosynthetic plants and the reasons of their conservation is one of the intriguing topics in plant genome evolution. Here, we report sequencing and analysis of plastid genome in nonphotosynthetic orchids Epipogium aphyllum and Epipogium ro...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv019
更新日期:2015-01-28 00:00:00
abstract::The availability of spontaneously occurring genetic variants is an important driving force of biological evolution. Largely thanks to experimental investigations by microbial geneticists, we know today that several different molecular mechanisms contribute to the overall genetic variations. These mechanisms can be ass...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evr035
更新日期:2011-01-01 00:00:00
abstract::Allopolyploidization plays an important role in speciation, and some natural or synthetic allopolyploid fishes have been extensively applied to aquaculture. Although genetic and epigenetic inheritance and variation associated with plant allopolyploids have been well documented, the relative research in allopolyploid a...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy165
更新日期:2018-09-01 00:00:00
abstract::Because natural selection is likely to act on multiple genes underlying a given phenotypic trait, we study here the potential effect of ongoing and past selection on the genetic diversity of human biological pathways. We first show that genes included in gene sets are generally under stronger selective constraints tha...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evv083
更新日期:2015-05-13 00:00:00
abstract::We sequenced genomes of five parasite species in family Orobanchaceae to explore the evolutionary role of horizontal gene transfer in plants. Orobanche minor and Aeginetia indica are obligate parasites with no photosynthetic activity, whereas the other three (Pedicularis keiskei, Phtheirospermum japonicum, and Melampy...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evy219
更新日期:2018-12-01 00:00:00
abstract::Amoebiasis is the third-most common cause of mortality worldwide from a parasitic disease. Although the primary etiological agent of amoebiasis is the obligate human parasite Entamoeba histolytica, other members of the genus Entamoeba can infect humans and may be pathogenic. Here, we present the first annotated refere...
journal_title:Genome biology and evolution
pub_type: 杂志文章
doi:10.1093/gbe/evz009
更新日期:2019-03-01 00:00:00