Reduced Genome Size Research Articles

Identification of the pleiotropic function of TOUSLED kinase in tomato (Solanum lycopersicum L.) using a Cucumber mosaic virus-based vector

TOUSLED (TSL) is a nuclear serine/threonine kinase highly conserved in plants and animals, including humans. In Arabidopsis thaliana, TSL participates in leaf and flower morphogenesis, cell-cycle regulation, and maintenance of transcriptional gene silencing. To identify the functions of TSL in tomato, we conducted TSL gene silencing using a reassortant Gn-CMV vector. Two parts of the tomato TSL gene, the 3′ proximal and middle regions of the TSL ORF (termed tsl-4 and tsl-9), were amplified and cloned into the Y-R2A1 vector. Tomato plants inoculated with the Gn-tsl4 and Gn-tsl9 vectors showed pleiotropic effects, such as changes in leaf color, formation of thick stems, reduction of genome size, and extreme bud outgrowth. The mechanisms of bud outgrowth have been well studied in various plant species, but this is the first report of a function for TSL in bud outgrowth of tomato. In addition, our results showed that the reassortant Gn-CMV vector can be successfully applied for virus-induced gene silencing to study functional genomics in tomato.

When Less is More: Red Algae as Models for Studying Gene Loss and Genome Evolution in Eukaryotes

Genome evolution is usually viewed through the lens of growth in size and complexity over time, exemplified by plants and animals. In contrast, genome reduction is associated with a narrowing of ecological potential, such as in parasites and endosymbionts. But, can nuclear genome reduction also occur in, and potentially underpin a major radiation of free-living eukaryotes? An intriguing example of this phenomenon is provided by the red algae (Rhodophyta) that have lost many conserved pathways such as for flagellar motility, macroautophagy regulation, and phytochrome based light sensing. This anciently diverged, species-rich, and ecologically important algal lineage has undergone at least two rounds of large-scale genome reduction during its >1 billion-year evolutionary history. Here, using recent analyses of genome data, we review knowledge about the evolutionary trajectory of red algal nuclear and organelle gene inventories and plastid encoded autocatalytic introns. We compare and contrast Rhodophyta genome evolution to Viridiplantae (green algae and plants), both of which are members of the Archaeplastida, and highlight their divergent paths. We also discuss evidence for the speculative hypothesis that reduction in red algal plastid genome size through endosymbiotic gene transfer is counteracted by ongoing selection for compact nuclear genomes in red algae. Finally, we describe how the spliceosomal intron splicing apparatus provides an example of “evolution in action” in Rhodophyta and how the overall constraints on genome size in this lineage has left significant imprints on this key step in RNA maturation. Our review reveals the red algae to be an exciting, yet under-studied model that offers numerous novel insights as well as many unanswered questions that remain to be explored using modern genomic, genetic, and biochemical methods. The fact that a speciose lineage of free-living eukaryotes has spread throughout many aquatic habitats after having lost about 25% of its primordial gene inventory challenges us to elucidate the mechanisms underlying this remarkable feat.

Characterization of ML0314c of Mycobacterium leprae and deciphering its role in the immune response in leprosy patients

Mycobacterium leprae has a reduced genome size due to the reductive evolution over a long period of time. Lipid metabolism plays an important role in the life cycle and pathogenesis of this bacterium. In comparison to 26 lip genes (Lip A-Z) of M. tuberculosis, M. leprae retained only three orthologs indicating their importance in its life cycle. ML0314c (LipU) is one of them. It is conserved throughout the mycobacterium species. Bioinformatics analysis showed the presence of an α/β hydrolase fold and ‘GXSXG’ characteristic of the esterases/lipases. The gene was expressed in E. coli and purified to homogeneity. It showed preference towards short chain esters with pNP-acetate as the preferred substrate. The enzyme showed optimal activity at 45°C and pH8.0. ML0314c protein was stable between temperatures ranging from 20 to 60°C and pH5.0–8.0, i.e., relatively acidic and neutral conditions. The active site residues predicted bioinformatically were confirmed to be Ser168, Glu267, and His297 by site directed mutagenesis. E-serine, DEPC and Tetrahydrolipstatin (THL) completely inhibited the activity of ML0314c. The protein was localized in cell wall and extracellular medium. Several antigenic epitopes were predicted in ML0314c. Protein elicited strong humoral immune response in leprosy patients, whereas, a reduced immune response was observed in the relapsed cases. No humoral response was observed in treatment completed patients. Overexpression of ml0314c in the surrogate host M. smegmatis showed marked difference in the colony morphology and growth rate. In conclusion, ML0314c is a secretary carboxyl esterase that could modulate the immune response in leprosy patients.

Surviving a Genome Collision: Genomic Signatures of Allopolyploidization in the Recent Crop Species Brassica napus.

Polyploidization has played a major role in crop plant evolution, leading to advantageous traits that have been selected by humans. Here, we describe restructuring patterns in the genome of L., a recent allopolyploid species. Widespread segmental deletions, duplications, and homeologous chromosome exchanges were identified in diverse genome sequences from 32 natural and 20 synthetic accessions, indicating that homeologous exchanges are a major driver of postpolyploidization genome diversification. Breakpoints of genomic rearrangements are rich in microsatellite sequences that are known to interact with the meiotic recombination machinery. In both synthetic and natural , a subgenome bias was observed toward exchanges replacing larger chromosome segments from the C-subgenome by their smaller, homeologous A-subgenome segments, driving postpolyploidization genome size reduction. Selection in natural favored segmental deletions involving genes associated with immunity, reproduction, and adaptation. Deletions affecting mismatch repair system genes, which are assumed to control homeologous recombination, were also found to be under selection. Structural exchanges between homeologous subgenomes appear to be a major source of novel genetic diversity in de novo allopolyploids. Documenting the consequences of genomic collision by genomic resequencing gives insights into the adaptive processes accompanying allopolyploidization.

Residence time, native range size, and genome size predict naturalization among angiosperms introduced to Australia.

Although critical to progress in understanding (i) if, and (ii) at what rate, introduced plants will naturalize and potentially become invasive, establishing causal links between traits and invasion success is complicated by data gaps, phylogenetic nonindependence of species, the inability to control for differences between species in residence time and propagule pressure, and covariance among traits. Here, we focus on statistical relationships between genomic factors, life history traits, native range size, and naturalization status of angiosperms introduced to Australia. In a series of analyses, we alternately investigate the role of phylogeny, incorporate introduction history, and use graphical models to explore the network of conditional probabilities linking traits and introduction history to naturalization status. Applying this ensemble of methods to the largest publicly available data set on plant introductions and their fates, we found that, overall, residence time and native range size best predicted probability of naturalization. Yet, importantly, probability of naturalization consistently increased as genome size decreased, even when the effects of shared ancestry and residence time in Australia were accounted for, and that this pattern was stronger in species without a history of cultivation, but present across annual–biennials, and herbaceous and woody perennials. Thus, despite introduction biases and indirect effects of traits via introduction history, across analyses, reduced genome size was nevertheless consistently associated with a tendency to naturalize.

Non-Mendelian assortment of homologous autosomes of different sizes in males is the ancestral state in the Caenorhabditis lineage

Organismal genome sizes vary by six orders of magnitude and appear positively correlated with organismal size and complexity. Neutral models have been proposed to explain the broad patterns of genome size variation based on organism population sizes. In the Caenorhabditis genus, hermaphrodite genomes are smaller than those of gonochoristic species. One possible driving force for this genome size difference could be non-random chromosome segregation. In Caenorhabditis elegans, chromosome assortment is non-independent and violates Mendel’s second law. In males, the shorter homologue of a heterozygous autosome pair preferentially co-segregates with the X chromosome while the longer one preferentially co-segregates with the nullo-X (O) chromosome in a process we call “skew”. Since hermaphrodites preferentially receive the shorter chromosomes and can start populations independently, their genome size would be predicted to decrease over evolutionary time. If skew is an important driver for genome size reduction in hermaphroditic Caenorhabditis species, then it should be present in all congeneric species. In this study, we tested this hypothesis and found that skew is present in all eight examined species. Our results suggest that skew is likely the ancestral state in this genus. More speculatively, skew may drive genome size patterns in hermaphroditic species in other nematodes.

Convergent adaptive evolution in marginal environments: unloading transposable elements as a common strategy among mangrove genomes.

Several clades of mangrove trees independently invade the interface between land and sea at the margin of woody plant distribution. As phenotypic convergence among mangroves is common, the possibility of convergent adaptation in their genomes is quite intriguing. To study this molecular convergence, we sequenced multiple mangrove genomes. In this study, we focused on the evolution of transposable elements (TEs) in relation to the genome size evolution. TEs, generally considered genomic parasites, are the most common components of woody plant genomes. Analyzing the long terminal repeat-retrotransposon (LTR-RT) type of TE, we estimated their death rates by counting solo-LTRs and truncated elements. We found that all lineages of mangroves massively and convergently reduce TE loads in comparison to their nonmangrove relatives; as a consequence, genome size reduction happens independently in all six mangrove lineages; TE load reduction in mangroves can be attributed to the paucity of young elements; the rarity of young LTR-RTs is a consequence of fewer births rather than access death. In conclusion, mangrove genomes employ a convergent strategy of TE load reduction by suppressing element origination in their independent adaptation to a new environment.

Insect-bacteria parallel evolution in multiple-co-obligate-aphid association: a case in Lachninae (Hemiptera: Aphididae)

Parallel phylogenies between aphid and its obligate symbiont Buchnera are hot topics which always focused on aphid lower taxonomic levels. Symbionts in the subfamily Lachninae are special. Buchnera in many lachnine species has undergone functional and genome size reduction that was replaced by other co-obligate symbionts. In this study, we constructed the phylogenetic relationships of Lachninae with a combined dataset of five genes sequenced from Buchnera to estimate the effects of a dual symbiotic system in the aphid-Buchnera cospeciation association. The phylogeny of Buchnera in Lachninae was well-resolved in the combined dataset. Each of the genera formed strongly supported monophyletic groups, with the exception of the genus Cinara. The phylogeny based on sequences from Buchnera was divided into five tribes according to the clades of the Lachninae hosts tree, with the phylogenies of Buchnera and Lachninae being generally congruent. These results first provided evidence of parallel evolution at the aphid subfamily level comprehensively and supported the view that topological congruence between the phylogenies of Buchnera and Lachninae would not be interfered with the other co-obligate symbionts, such as Sarretia, in aphid-entosymbiont association. These results also provided new insight in understanding host-plant coevolution in lachnine lineages.

Genome Reduction for Niche Association in Campylobacter Hepaticus, A Cause of Spotty Liver Disease in Poultry.

The term “spotty liver disease” (SLD) has been used since the late 1990s for a condition seen in the UK and Australia that primarily affects free range laying hens around peak lay, causing acute mortality and a fall in egg production. A novel thermophilic SLD-associated Campylobacter was reported in the United Kingdom (UK) in 2015. Subsequently, similar isolates occurring in Australia were formally described as a new species, Campylobacter hepaticus. We describe the comparative genomics of 10 C. hepaticus isolates recovered from 5 geographically distinct poultry holdings in the UK between 2010 and 2012. Hierarchical gene-by-gene analyses of the study isolates and representatives of 24 known Campylobacter species indicated that C. hepaticus is most closely related to the major pathogens Campylobacter jejuni and Campylobacter coli. We observed low levels of within-farm variation, even between isolates collected over almost 3 years. With respect to C. hepaticus genome features, we noted that the study isolates had a ~140 Kb reduction in genome size, ~144 fewer genes, and a lower GC content compared to C. jejuni. The most notable reduction was in the subsystem containing genes for iron acquisition and metabolism, supported by reduced growth of C. hepaticus in an iron depletion assay. Genome reduction is common among many pathogens and in C. hepaticus has likely been driven at least in part by specialization following the occupation of a new niche, the chicken liver.

Coordinated Changes in Mutation and Growth Rates Induced by Genome Reduction.

ABSTRACTGenome size is determined during evolution, but it can also be altered by genetic engineering in laboratories. The systematic characterization of reduced genomes provides valuable insights into the cellular properties that are quantitatively described by the global parameters related to the dynamics of growth and mutation. In the present study, we analyzed a small collection of W3110 Escherichia coli derivatives containing either the wild-type genome or reduced genomes of various lengths to examine whether the mutation rate, a global parameter representing genomic plasticity, was affected by genome reduction. We found that the mutation rates of these cells increased with genome reduction. The correlation between genome length and mutation rate, which has been reported for the evolution of bacteria, was also identified, intriguingly, for genome reduction. Gene function enrichment analysis indicated that the deletion of many of the genes encoding membrane and transport proteins play a role in the mutation rate changes mediated by genome reduction. Furthermore, the increase in the mutation rate with genome reduction was highly associated with a decrease in the growth rate in a nutrition-dependent manner; thus, poorer media showed a larger change that was of higher significance. This negative correlation was strongly supported by experimental evidence that the serial transfer of the reduced genome improved the growth rate and reduced the mutation rate to a large extent. Taken together, the global parameters corresponding to the genome, growth, and mutation showed a coordinated relationship, which might be an essential working principle for balancing the cellular dynamics appropriate to the environment.

The metabolic potential of the single cell genomes obtained from the Challenger Deep, Mariana Trench within the candidate superphylum Parcubacteria (OD1).

Candidate phyla (CP) are broad phylogenetic clusters of organisms that lack cultured representatives. Included in this fraction is the candidate Parcubacteria superphylum. Specific characteristics that have been ascribed to the Parcubacteria include reduced genome size, limited metabolic potential and exclusive reliance on fermentation for energy acquisition. The study of new environmental niches, such as the marine versus terrestrial subsurface, often expands the understanding of the genetic potential of taxonomic groups. For this reason, we analyzed 12 Parcubacteria single amplified genomes (SAGs) from sediment samples collected within the Challenger Deep of the Mariana Trench, obtained during the Deepsea Challenge (DSC) Expedition. Many of these SAGs are closely related to environmental sequences obtained from deep-sea environments based on 16S rRNA gene similarity and BLAST matches to predicted proteins. DSC SAGs encode features not previously identified in Parcubacteria obtained from other habitats. These include adaptation to oxidative stress, polysaccharide modification and genes associated with respiratory nitrate reduction. The DSC SAGs are also distinguished by relative greater abundance of genes for nucleotide and amino acid biosynthesis, repair of alkylated DNA and the synthesis of mechanosensitive ion channels. These results present an expanded view of the Parcubacteria, among members residing in an ultra-deep hadal environment.

The Evolution of Bacterial Genome Architecture.

The genome architecture of bacteria and eukaryotes evolves in opposite directions when subject to genetic drift, a difference that can be ascribed to the fact that bacteria exhibit a mutational bias that deletes superfluous sequences, whereas eukaryotes are biased toward large insertions. Expansion of eukaryotic genomes occurs through the addition of non-functional sequences, such as repetitive sequences and transposable elements, whereas variation in bacterial genome size is largely due to the acquisition and loss of functional accessory genes. These properties create the situation in which eukaryotes with very similar numbers of genes can have vastly different genome sizes, while in bacteria, gene number scales linearly with genome size. Some bacterial genomes, however, particularly those of species that undergo bottlenecks due to recent association with hosts, accumulate pseudogenes and mobile elements, conferring them a low gene content relative to their genome size. These non-functional sequences are gradually eroded and eliminated after long-term association with hosts, with the result that obligate symbionts have the smallest genomes of any cellular organism. The architecture of bacterial genomes is shaped by complex and diverse processes, but for most bacterial species, genome size is governed by a non-adaptive process, i.e., genetic drift coupled with a mutational bias toward deletions. Thus, bacteria with small effective population sizes typically have the smallest genomes. Some marine bacteria counter this near-universal trend: despite having immense population sizes, selection, not drift, acts to reduce genome size in response to metabolic constraints in their nutrient-limited environment.

Mitochondrial genome evolution in Alismatales: Size reduction and extensive loss of ribosomal protein genes.

The order Alismatales is a hotspot for evolution of plant mitochondrial genomes characterized by remarkable differences in genome size, substitution rates, RNA editing, retrotranscription, gene loss and intron loss. Here we have sequenced the complete mitogenomes of Zostera marina and Stratiotes aloides, which together with previously sequenced mitogenomes from Butomus and Spirodela, provide new evolutionary evidence of genome size reduction, gene loss and transfer to the nucleus. The Zostera mitogenome includes a large portion of DNA transferred from the plastome, yet it is the smallest known mitogenome from a non-parasitic plant. Using a broad sample of the Alismatales, the evolutionary history of ribosomal protein gene loss is analyzed. In Zostera almost all ribosomal protein genes are lost from the mitogenome, but only some can be found in the nucleus.

Genomic epidemiology of a national outbreak of post-surgical Mycobacterium abscessus wound infections in Brazil.

An epidemic of post-surgical wound infections, caused by a non-tuberculous mycobacterium, has been on-going in Brazil. It has been unclear whether one or multiple lineages are responsible and whether their wide geographical distribution across Brazil is due to spread from a single point source or is the result of human-mediated transmission. 188 isolates, collected from nine Brazilian states, were whole genome sequenced and analysed using phylogenetic and comparative genomic approaches. The isolates from Brazil formed a single clade, which was estimated to have emerged in 2003. We observed temporal and geographic structure within the lineage that enabled us to infer the movement of sub-lineages across Brazil. The genome size of the Brazilian lineage was reduced relative to most strains in the three subspecies of Mycobacterium abscessus and contained a novel plasmid, pMAB02, in addition to the previously described pMAB01 plasmid. One lineage, which emerged just prior to the initial outbreak, is responsible for the epidemic of post-surgical wound infections in Brazil. Phylogenetic analysis indicates that multiple transmission events led to its spread. The presence of a novel plasmid and the reduced genome size suggest that the lineage has undergone adaptation to the surgical niche.

Who lives in a fungus? The diversity, origins and functions of fungal endobacteria living in Mucoromycota

Bacterial interactions with plants and animals have been examined for many years; differently, only with the new millennium the study of bacterial-fungal interactions blossomed, becoming a new field of microbiology with relevance to microbial ecology, human health and biotechnology. Bacteria and fungi interact at different levels and bacterial endosymbionts, which dwell inside fungal cells, provide the most intimate example. Bacterial endosymbionts mostly occur in fungi of the phylum Mucoromycota and include Betaproteobacteria (Burkhoderia-related) and Mollicutes (Mycoplasma-related). Based on phylogenomics and estimations of divergence time, we hypothesized two different scenarios for the origin of these interactions (early vs late bacterial invasion). Sequencing of the genomes of fungal endobacteria revealed a significant reduction in genome size, particularly in endosymbionts of Glomeromycotina, as expected by their uncultivability and host dependency. Similar to endobacteria of insects, the endobacteria of fungi show a range of behaviours from mutualism to antagonism. Emerging results suggest that some benefits given by the endobacteria to their plant-associated fungal host may propagate to the interacting plant, giving rise to a three-level inter-domain interaction.

Comparative genomics reveals contraction in olfactory receptor genes in bats

Gene loss and gain during genome evolution are thought to play important roles in adaptive phenotypic diversification. Among mammals, bats possess the smallest genomes and have evolved the unique abilities of powered flight and laryngeal echolocation. To investigate whether gene family evolution has contributed to the genome downsizing and phenotypic diversification in this group, we performed comparative evolutionary analyses of complete proteome data for eight bat species, including echolocating and non-echolocating forms, together with the proteomes of 12 other laurasiatherian mammals. Our analyses revealed extensive gene loss in the most recent ancestor of bats, and also of carnivores (both >1,000 genes), although this gene contraction did not appear to correlate with the reduction in genome size in bats. Comparisons of highly dynamic families suggested that expansion and contraction affected genes with similar functions (immunity, response to stimulus) in all laurasiatherian lineages. However, the magnitude and direction of these changes varied greatly among groups. In particular, our results showed contraction of the Olfactory Receptor (OR) gene repertoire in the last common ancestor of all bats, as well as that of the echolocating species studied. In contrast, non-echolocating fruit bats showed evidence of expansion in ORs, supporting a “trade-off” between sensory modalities.

Limited mitogenomic degradation in response to a parasitic lifestyle in Orobanchaceae.

In parasitic plants, the reduction in plastid genome (plastome) size and content is driven predominantly by the loss of photosynthetic genes. The first completed mitochondrial genomes (mitogenomes) from parasitic mistletoes also exhibit significant degradation, but the generality of this observation for other parasitic plants is unclear. We sequenced the complete mitogenome and plastome of the hemiparasite Castilleja paramensis (Orobanchaceae) and compared them with additional holoparasitic, hemiparasitic and nonparasitic species from Orobanchaceae. Comparative mitogenomic analysis revealed minimal gene loss among the seven Orobanchaceae species, indicating the retention of typical mitochondrial function among Orobanchaceae species. Phylogenetic analysis demonstrated that the mobile cox1 intron was acquired vertically from a nonparasitic ancestor, arguing against a role for Orobanchaceae parasites in the horizontal acquisition or distribution of this intron. The C. paramensis plastome has retained nearly all genes except for the recent pseudogenization of four subunits of the NAD(P)H dehydrogenase complex, indicating a very early stage of plastome degradation. These results lend support to the notion that loss of ndh gene function is the first step of plastome degradation in the transition to a parasitic lifestyle.

Genome size variation and evolution in Dipterocarpaceae

Background: Dipterocarpaceae is a pantropical tree family that plays an important role in our understanding of the ecology of Asian tropical rain forests. However, genome sizes for members of the Dipterocarpaceae are still poorly known.Aims: To report the genome size of 115 dipterocarp species and examine the variation and evolution of genome size in this family.Methods: Genome size was estimated using flow cytometry. Both the rpoB and trnL intron were sequenced to uncover the evolution of genome size within a phylogenetic framework.Results: The 1C genome size varied between 0.267 and 0.705 pg in Shorea hemsleyana and Shorea ovalis, respectively, a 2.64-fold variation across the family. Most dipterocarps are characterised by very small genomes with a mean 1C value of 0.416 pg (sd = 0.075) and five polyploids are recorded. The ancestral genome size for dipterocarps was reconstructed as 1Cx = 0.481 pg (95% CI = 0.433–0.534).Conclusions: Genome size variation in dipterocarps was characterised by very small values with a narrow range. Overall, genome size reduction from the ancestral state is a general trend in Dipterocarpaceae.

Dissecting genome reduction and trait loss in insect endosymbionts.

Symbiosis has played a major role in eukaryotic evolution beyond the origin of the eukaryotic cell. Thus, organisms across the tree of life are associated with diverse microbial partners, conferring to the host new adaptive traits that enable it to explore new niches. This is the case for insects thriving on unbalanced diets, which harbor mutualistic intracellular microorganisms, mostly bacteria that supply them with the required nutrients. As a consequence of the lifestyle change, from free-living to host-associated mutualist, a bacterium undergoes many structural and metabolic changes, of which genome shrinkage is the most dramatic. The trend toward genome size reduction in endosymbiotic bacteria is associated with large-scale gene loss, reflecting the lack of an effective selection mechanism to maintain genes that are rendered superfluous by the constant and rich environment provided by the host. This genome-reduction syndrome is so strong that it has generated the smallest bacterial genomes found to date, whose gene contents are so limited that their status as cellular entities is questionable. The recent availability of data on several endosymbiotic bacteria is enabling us to form a comprehensive picture of the genome-reduction process and the phenotypic consequences for the dwindling symbiont.

A novel roseobacter phage possesses features of podoviruses, siphoviruses, prophages and gene transfer agents.

Bacteria in the Roseobacter lineage have been studied extensively due to their significant biogeochemical roles in the marine ecosystem. However, our knowledge on bacteriophage which infects the Roseobacter clade is still very limited. Here, we report a new bacteriophage, phage DSS3Φ8, which infects marine roseobacter Ruegeria pomeroyi DSS-3. DSS3Φ8 is a lytic siphovirus. Genomic analysis showed that DSS3Φ8 is most closely related to a group of siphoviruses, CbK-like phages, which infect freshwater bacterium Caulobacter crescentus. DSS3Φ8 contains a smaller capsid and has a reduced genome size (146 kb) compared to the CbK-like phages (205–279 kb). DSS3Φ8 contains the DNA polymerase gene which is closely related to T7-like podoviruses. DSS3Φ8 also contains the integrase and repressor genes, indicating its potential to involve in lysogenic cycle. In addition, four GTA (gene transfer agent) genes were identified in the DSS3Φ8 genome. Genomic analysis suggests that DSS3Φ8 is a highly mosaic phage that inherits the genetic features from siphoviruses, podoviruses, prophages and GTAs. This is the first report of CbK-like phages infecting marine bacteria. We believe phage isolation is still a powerful tool that can lead to discovery of new phages and help interpret the overwhelming unknown sequences in the viral metagenomics.