Mitochondrial genomes of two parasitic Cuscuta species lack clear evidence of horizontal gene transfer and retain unusually fragmented ccmFC genes

Abstract Background The intimate association between parasitic plants and their hosts favours the exchange of genetic material, potentially leading to horizontal gene transfer (HGT) between plants. With the recent publication of several parasitic plant nuclear genomes, there has been considerable focus on such non-sexual exchange of genes. To enhance the picture on HGT events in a widely distributed parasitic genus, Cuscuta (dodders), we assembled and analyzed the organellar genomes of two recently sequenced species, C. australis and C. campestris, making this the first account of complete mitochondrial genomes (mitogenomes) for this genus. Results The mitogenomes are 265,696 and 275,898 bp in length and contain a typical set of mitochondrial genes, with 10 missing or pseudogenized genes often lost from angiosperm mitogenomes. Each mitogenome also possesses a structurally unusual ccmFC gene, which exhibits splitting of one exon and a shift to trans-splicing of its intron. Based on phylogenetic analysis of mitochondrial genes from across angiosperms and similarity-based searches, there is little to no indication of HGT into the Cuscuta mitogenomes. A few candidate regions for plastome-to-mitogenome transfer were identified, with one suggestive of possible HGT. Conclusions The lack of HGT is surprising given examples from the nuclear genomes, and may be due in part to the relatively small size of the Cuscuta mitogenomes, limiting the capacity to integrate foreign sequences.

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Mitochondrial genomes of two parasitic Cuscuta species show little evidence of horizontal gene transfer and retain unusually fragmented ccmFC genes

10.1101/2021.04.15.439983 ◽

2021 ◽

Author(s):

Benjamin M. Anderson ◽

Kirsten Krause ◽

Gitte Petersen

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Genetic Material ◽

Mitochondrial Genes ◽

Mitochondrial Genomes ◽

Sexual Exchange ◽

Intimate Association ◽

Nuclear Genomes ◽

Candidate Regions ◽

Complete Mitochondrial Genomes

Background: The intimate association between parasitic plants and their hosts favours the exchange of genetic material, potentially leading to horizontal gene transfer (HGT) between plants. With the recent publication of several parasitic plant nuclear genomes, there has been considerable focus on such non-sexual exchange of genes. To enhance the picture on HGT events in a widely distributed parasitic genus, Cuscuta (dodders), we assembled and analyzed the organellar genomes of two recently sequenced species, C. australis and C. campestris, making this the first account of complete mitochondrial genomes (mitogenomes) for this genus. Results: The mitogenomes are 265,696 and 275,898 bp in length and contain a typical set of mitochondrial genes, with ten missing or pseudogenized genes often lost from angiosperm mitogenomes. Each mitogenome also possesses a structurally unusual ccmFC gene, which exhibits splitting of one exon and a shift to trans-splicing of its intron. Based on phylogenetic analysis of mitochondrial genes from across angiosperms and similarity-based searches, there is little to no indication of HGT into the Cuscuta mitogenomes. A few candidate regions for plastome-to-mitogenome transfer were identified, with one suggestive of possible HGT. Conclusions: The lack of HGT is surprising given examples from the nuclear genomes, and may be due in part to the relatively small size of our Cuscuta mitogenomes, limiting the capacity to integrate foreign sequences.

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Involvement of plastid, mitochondrial and nuclear genomes in plant-to-plant horizontal gene transfer

Acta Societatis Botanicorum Poloniae ◽

10.5586/asbp.2014.041 ◽

2014 ◽

Vol 83 (4) ◽

pp. 317-323 ◽

Cited By ~ 18

Author(s):

Maria Virginia Sanchez-Puerta

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Plant Mitochondria ◽

Genetic Material ◽

Single Copy ◽

Convincing Evidence ◽

Cell Contact ◽

Plant Mtdna ◽

Nuclear Genomes ◽

Foreign Genes

This review focuses on plant-to-plant horizontal gene transfer (HGT) involving the three DNA-containing cellular compartments. It highlights the great incidence of HGT in the mitochondrial genome (mtDNA) of angiosperms, the increasing number of examples in plant nuclear genomes, and the lack of any convincing evidence for HGT in the well-studied plastid genome of land plants. Most of the foreign mitochondrial genes are non-functional, generally found as pseudogenes in the recipient plant mtDNA that maintains its functional native genes. The few exceptions involve chimeric HGT, in which foreign and native copies recombine leading to a functional and single copy of the gene. Maintenance of foreign genes in plant mitochondria is probably the result of genetic drift, but a possible evolutionary advantage may be conferred through the generation of genetic diversity by gene conversion between native and foreign copies. Conversely, a few cases of nuclear HGT in plants involve functional transfers of novel genes that resulted in adaptive evolution. Direct cell-to-cell contact between plants (e.g. host-parasite relationships or natural grafting) facilitate the exchange of genetic material, in which HGT has been reported for both nuclear and mitochondrial genomes, and in the form of genomic DNA, instead of RNA. A thorough review of the literature indicates that HGT in mitochondrial and nuclear genomes of angiosperms is much more frequent than previously expected and that the evolutionary impact and mechanisms underlying plant-to-plant HGT remain to be uncovered.

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Complete Plastid and Mitochondrial Genomes of Aeginetia indica Reveal Intracellular Gene Transfer (IGT), Horizontal Gene Transfer (HGT), and Cytoplasmic Male Sterility (CMS)

International Journal of Molecular Sciences ◽

10.3390/ijms22116143 ◽

2021 ◽

Vol 22 (11) ◽

pp. 6143

Author(s):

Kyoung-Su Choi ◽

Seonjoo Park

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Chloroplast Genome ◽

Mitochondrial Genes ◽

Rrna Genes ◽

Mitochondrial Genomes ◽

Reading Frame ◽

Chloroplast Genomes ◽

Intracellular Gene Transfer ◽

Atpi Gene

Orobanchaceae have become a model group for studies on the evolution of parasitic flowering plants, and Aeginetia indica, a holoparasitic plant, is a member of this family. In this study, we assembled the complete chloroplast and mitochondrial genomes of A. indica. The chloroplast and mitochondrial genomes were 56,381 bp and 401,628 bp long, respectively. The chloroplast genome of A. indica shows massive plastid genes and the loss of one IR (inverted repeat). A comparison of the A. indica chloroplast genome sequence with that of a previous study demonstrated that the two chloroplast genomes encode a similar number of proteins (except atpH) but differ greatly in length. The A. indica mitochondrial genome has 53 genes, including 35 protein-coding genes (34 native mitochondrial genes and one chloroplast gene), 15 tRNA (11 native mitochondrial genes and four chloroplast genes) genes, and three rRNA genes. Evidence for intracellular gene transfer (IGT) and horizontal gene transfer (HGT) was obtained for plastid and mitochondrial genomes. ψndhB and ψcemA in the A. indica mitogenome were transferred from the plastid genome of A. indica. The atpH gene in the plastid of A. indica was transferred from another plastid angiosperm plastid and the atpI gene in mitogenome A. indica was transferred from a host plant like Miscanthus siensis. Cox2 (orf43) encodes proteins containing a membrane domain, making ORF (Open Reading Frame) the most likely candidate gene for CMS development in A. indica.

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Detecting Horizontal Gene Transfer by Mapping Sequencing Reads Across Species Boundaries

10.1101/039495 ◽

2016 ◽

Author(s):

Kathrin Trappe ◽

Tobias Marschall ◽

Bernhard Y. Renard

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Phylogenetic Trees ◽

Genetic Material ◽

Real Data ◽

A Genome ◽

Split Read ◽

Candidate Regions ◽

Next Generation Sequencing Ngs ◽

Ngs Data

AbstractHorizontal gene transfer (HGT) is a fundamental mechanism that enables organisms such as bacteria to directly transfer genetic material between distant species. This way, bacteria can acquire new traits such as antibiotic resistance or pathogenic toxins. Current bioinfor-matics approaches focus on the detection of past HGT events by exploring phylogenetic trees or genome composition inconsistencies. However, this normally requires the availability of finished and fully annotated genomes and of sufficiently large deviations that allow detection. Thus, these techniques are not widely applicable. Especially in an outbreak scenario where new HGT mediated pathogens emerge, there is need for fast and precise HGT detection. Next-generation sequencing (NGS) technologies can facilitate swift analysis of unknown pathogens but, to the best of our knowledge, so far no approach uses NGS data directly to detect HGTs.We present Daisy, a novel mapping-based tool for HGT detection directly from NGS data. Daisy determines HGT boundaries with split-read mapping and evaluates candidate regions relying on read pair and coverage information. Daisy can successfully detect HGT regions with base pair resolution in both simulated and real data, and outperforms alternative approaches using a genome assembly of the reads. We see our approach as a powerful complement for a comprehensive analysis of HGT in the context of NGS data. Daisy is freely available fromhttp://github.com/ktrappe/daisy.

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Horizontal Gene Transfer Involving Chloroplasts

International Journal of Molecular Sciences ◽

10.3390/ijms22094484 ◽

2021 ◽

Vol 22 (9) ◽

pp. 4484

Author(s):

Ewa Filip ◽

Lidia Skuza

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Driving Force ◽

Genetic Material ◽

Adaptive Significance ◽

Chloroplast Genomes ◽

Organelle Genomes ◽

Number Of Genes ◽

Cellular Compartments

Horizontal gene transfer (HGT)- is defined as the acquisition of genetic material from another organism. However, recent findings indicate a possible role of HGT in the acquisition of traits with adaptive significance, suggesting that HGT is an important driving force in the evolution of eukaryotes as well as prokaryotes. It has been noted that, in eukaryotes, HGT is more prevalent than originally thought. Mitochondria and chloroplasts lost a large number of genes after their respective endosymbiotic events occurred. Even after this major content loss, organelle genomes still continue to lose their own genes. Many of these are subsequently acquired by intracellular gene transfer from the original plastid. The aim of our review was to elucidate the role of chloroplasts in the transfer of genes. This review also explores gene transfer involving mitochondrial and nuclear genomes, though recent studies indicate that chloroplast genomes are far more active in HGT as compared to these other two DNA-containing cellular compartments.

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Mitochondrial genome of the nonphotosynthetic mycoheterotrophic plant Hypopitys monotropa, its structure, gene expression and RNA editing

PeerJ ◽

10.7717/peerj.9309 ◽

2020 ◽

Vol 8 ◽

pp. e9309

Author(s):

Viktoria Yu Shtratnikova ◽

Mikhail I. Schelkunov ◽

Aleksey A. Penin ◽

Maria D. Logacheva

Keyword(s):

Mitochondrial Genome ◽

Rna Editing ◽

Transcriptome Sequencing ◽

Unique Feature ◽

Genetic Material ◽

Mitochondrial Genes ◽

Vaccinium Macrocarpon ◽

Mitochondrial Genomes ◽

Plastid Genomes ◽

Trans Splicing

Heterotrophic plants—plants that have lost the ability to photosynthesize—are characterized by a number of changes at all levels of organization. Heterotrophic plants are divided into two large categories—parasitic and mycoheterotrophic (MHT). The question of to what extent such changes are similar in these two categories is still open. The plastid genomes of nonphotosynthetic plants are well characterized, and they exhibit similar patterns of reduction in the two groups. In contrast, little is known about the mitochondrial genomes of MHT plants. We report the structure of the mitochondrial genome of Hypopitys monotropa, a MHT member of Ericaceae, and the expression of its genes. In contrast to its highly reduced plastid genome, the mitochondrial genome of H. monotropa is larger than that of its photosynthetic relative Vaccinium macrocarpon, and its complete size is ~810 Kb. We observed an unusually long repeat-rich structure of the genome that suggests the existence of linear fragments. Despite this unique feature, the gene content of the H. monotropa mitogenome is typical of flowering plants. No acceleration of substitution rates is observed in mitochondrial genes, in contrast to previous observations in parasitic non-photosynthetic plants. Transcriptome sequencing revealed the trans-splicing of several genes and RNA editing in 33 of 38 genes. Notably, we did not find any traces of horizontal gene transfer from fungi, in contrast to plant parasites, which extensively integrate genetic material from their hosts.

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Trasposon Mediated Horizontal Gene Transfer (T-HGT) of Circulating Tumor DNA Reshapes MM Clonal Architecture

Blood ◽

10.1182/blood-2019-126699 ◽

2019 ◽

Vol 134 (Supplement_1) ◽

pp. 3065-3065

Author(s):

Munevver Cinar ◽

Steven Flygare ◽

Marina Mosunjac ◽

Ganji Nagaraju ◽

Dongkyoo Park ◽

...

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Drug Sensitivity ◽

Genetic Material ◽

Host Cells ◽

Response To Treatment ◽

Hierarchical Architecture ◽

Tumor Evolution ◽

Sequencing Analysis

Spatial genetic heterogeneity is a characteristic phenomenon that influences multiple myeloma's (MM) phenotype and drug sensitivity (Rasche L. et al and Bolli N et al.). Hence, the branch model of tumor evolution is not sufficient to explain the disorganized architecture observed in MM. In this study, we investigated whether MM ctDNA horizontal gene transfer (HGT) affect tumor genetic architecture and drug sensitivity, resembling what is seen in prokaryotes, and elucidated the mechanisms involved in the mobilization of genetic material from one cell to another. We identified that plasma from patients with MM transmits drug sensitivity or resistance to cells in culture. This transmission of drug sensitivity is mediated by ctDNA transfer of oncogenes to a host cell. Importantly, in vitro and in vivo demonstrated that ctDNA mainly targets cells resembling the cell of origin (tropism). Karyotype spreads and whole genome sequencing demonstrated that once patients ctDNA encounters host cells, it migrates into the nucleus where it ultimately integrates into the cell's genome. Integration to the genome was confirmed to be targeted to myeloma cells. Further sequencing analysis of multiple MM samples identified ctDNA tropism and integration is dependent on the 5' and 3' end presence of transposable elements (TE), particularly of the MIR and ALUsq family. These results were further validated by TE mediated delivery of GFP into MM cells in vitro and HSVTK in tumors of mouse xenografts. In conclusion, this data indicates for the first time that TE mediates MM ctDNA HGT into homologous tumor cells shaping the hierarchical architecture of tumor clones and affecting tumor response to treatment. Therapeutically, this unique quality of ctDNA can be exploited for targeted gene therapeutic approaches in MM and potentially other cancers. Disclosures Bernal-Mizrachi: Kodikas Therapeutic Solutions, Inc: Equity Ownership; TAKEDA: Research Funding; Winship Cancer Institute: Employment, Patents & Royalties.

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CryoEM structure of the type IVa pilus secretin required for natural competence in Vibrio cholerae

Nature Communications ◽

10.1038/s41467-020-18866-y ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Sara J. Weaver ◽

Davi R. Ortega ◽

Matthew H. Sazinsky ◽

Triana N. Dalia ◽

Ankur B. Dalia ◽

...

Keyword(s):

Antibiotic Resistance ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Vibrio Cholerae ◽

Natural Transformation ◽

Domain Architecture ◽

Genetic Material ◽

Surface Binding ◽

Exogenous Dna ◽

Insight Into

Abstract Natural transformation is the process by which bacteria take up genetic material from their environment and integrate it into their genome by homologous recombination. It represents one mode of horizontal gene transfer and contributes to the spread of traits like antibiotic resistance. In Vibrio cholerae, a type IVa pilus (T4aP) is thought to facilitate natural transformation by extending from the cell surface, binding to exogenous DNA, and retracting to thread this DNA through the outer membrane secretin, PilQ. Here, we use a functional tagged allele of VcPilQ purified from native V. cholerae cells to determine the cryoEM structure of the VcPilQ secretin in amphipol to ~2.7 Å. We use bioinformatics to examine the domain architecture and gene neighborhood of T4aP secretins in Proteobacteria in comparison with VcPilQ. This structure highlights differences in the architecture of the T4aP secretin from the type II and type III secretion system secretins. Based on our cryoEM structure, we design a series of mutants to reversibly regulate VcPilQ gate dynamics. These experiments support the idea of VcPilQ as a potential druggable target and provide insight into the channel that DNA likely traverses to promote the spread of antibiotic resistance via horizontal gene transfer by natural transformation.

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Effect of the environment on horizontal gene transfer between bacteria and archaea

PeerJ ◽

10.7717/peerj.3865 ◽

2017 ◽

Vol 5 ◽

pp. e3865 ◽

Cited By ~ 23

Author(s):

Clara A. Fuchsman ◽

Roy Eric Collins ◽

Gabrielle Rocap ◽

William J. Brazelton

Keyword(s):

High Temperature ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Genome Size ◽

Thermophilic Bacteria ◽

Genetic Material ◽

Strongly Correlated ◽

Temperature Conditions ◽

Large Numbers ◽

Reciprocal Blast

BackgroundHorizontal gene transfer, the transfer and incorporation of genetic material between different species of organisms, has an important but poorly quantified role in the adaptation of microbes to their environment. Previous work has shown that genome size and the number of horizontally transferred genes are strongly correlated. Here we consider how genome size confuses the quantification of horizontal gene transfer because the number of genes an organism accumulates over time depends on its evolutionary history and ecological context (e.g., the nutrient regime for which it is adapted).ResultsWe investigated horizontal gene transfer between archaea and bacteria by first counting reciprocal BLAST hits among 448 bacterial and 57 archaeal genomes to find shared genes. Then we used the DarkHorse algorithm, a probability-based, lineage-weighted method (Podell & Gaasterland, 2007), to identify potential horizontally transferred genes among these shared genes. By removing the effect of genome size in the bacteria, we have identified bacteria with unusually large numbers of shared genes with archaea for their genome size. Interestingly, archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share unusually large numbers of genes. However, high salt was not found to significantly affect the numbers of shared genes. Numbers of shared (genome size-corrected, reciprocal BLAST hits) and transferred genes (identified by DarkHorse) were strongly correlated. Thus archaea and bacteria that live in anaerobic and/or high temperature conditions are more likely to share horizontally transferred genes. These horizontally transferred genes are over-represented by genes involved in energy conversion as well as the transport and metabolism of inorganic ions and amino acids.ConclusionsAnaerobic and thermophilic bacteria share unusually large numbers of genes with archaea. This is mainly due to horizontal gene transfer of genes from the archaea to the bacteria.In general, these transfers are from archaea that live in similar oxygen and temperature conditions as the bacteria that receive the genes. Potential hotspots of horizontal gene transfer between archaea and bacteria include hot springs, marine sediments, and oil wells. Cold spots for horizontal transfer included dilute, aerobic, mesophilic environments such as marine and freshwater surface waters.

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Variability in Assembly of Degradation Operons for Naphthalene and its derivative, Carbaryl, Suggests Mobilization through Horizontal Gene Transfer

Genes ◽

10.3390/genes10080569 ◽

2019 ◽

Vol 10 (8) ◽

pp. 569 ◽

Cited By ~ 7

Author(s):

Phale ◽

Shah ◽

Malhotra

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Food Web ◽

Microbial Communities ◽

Metabolic Pathways ◽

Anthropogenic Activities ◽

Genetic Material ◽

Genomic Islands ◽

Biochemical Pathways ◽

Integrative Conjugative Elements

In the biosphere, the largest biological laboratory, increased anthropogenic activities have led microbes to evolve and adapt to the changes occurring in the environment. Compounds, specifically xenobiotics, released due to such activities persist in nature and undergo bio-magnification in the food web. Some of these compounds act as potent endocrine disrupters, mutagens or carcinogens, and therefore their removal from the environment is essential. Due to their persistence, microbial communities have evolved to metabolize them partially or completely. Diverse biochemical pathways have evolved or been assembled by exchange of genetic material (horizontal gene transfer) through various mobile genetic elements like conjugative and non-conjugative plasmids, transposons, phages and prophages, genomic islands and integrative conjugative elements. These elements provide an unlimited opportunity for genetic material to be exchanged across various genera, thus accelerating the evolution of a new xenobiotic degrading phenotype. In this article, we illustrate examples of the assembly of metabolic pathways involved in the degradation of naphthalene and its derivative, Carbaryl, which are speculated to have evolved or adapted through the above-mentioned processes.

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