scholarly journals Plastid Genomes from Diverse Glaucophyte Genera Reveal a Largely Conserved Gene Content and Limited Architectural Diversity

2018 ◽  
Vol 11 (1) ◽  
pp. 174-188 ◽  
Author(s):  
Francisco Figueroa-Martinez ◽  
Christopher Jackson ◽  
Adrian Reyes-Prieto
Keyword(s):  
Gene Content ◽  
Plastid Genomes ◽  
Conserved Gene

scholarly journals Rhopalocnemis phalloides has one of the most reduced and mutated plastid genomes known

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7500 ◽  
Author(s):  
Mikhail I. Schelkunov ◽  
Maxim S. Nuraliev ◽  
Maria D. Logacheva
Keyword(s):  
Plant Species ◽  
Mutation Rate ◽  
Plastid Genome ◽  
Gene Content ◽  
High Mutation Rate ◽  
Base Pairs ◽  
Plastid Genomes ◽  
The Family

Although most plant species are photosynthetic, several hundred species have lost the ability to photosynthesize and instead obtain nutrients via various types of heterotrophic feeding. Their plastid genomes markedly differ from the plastid genomes of photosynthetic plants. In this work, we describe the sequenced plastid genome of the heterotrophic plant Rhopalocnemis phalloides, which belongs to the family Balanophoraceae and feeds by parasitizing other plants. The genome is highly reduced (18,622 base pairs vs. approximately 150 kbp in autotrophic plants) and possesses an extraordinarily high AT content, 86.8%, which is inferior only to AT contents of plastid genomes of Balanophora, a genus from the same family. The gene content of this genome is quite typical of heterotrophic plants, with all of the genes related to photosynthesis having been lost. The remaining genes are notably distorted by a high mutation rate and the aforementioned AT content. The high AT content has led to sequence convergence between some of the remaining genes and their homologs from AT-rich plastid genomes of protists. Overall, the plastid genome of R. phalloides is one of the most unusual plastid genomes known.

scholarly journals Rampant Nuclear Transfer and Substitutions of Plastid Genes in Passiflora

2020 ◽  
Vol 12 (8) ◽  
pp. 1313-1329 ◽  
Author(s):  
Bikash Shrestha ◽  
Lawrence E Gilbert ◽  
Tracey A Ruhlman ◽  
Robert K Jansen
Keyword(s):  
Nuclear Transfer ◽  
Protein Complexes ◽  
Nuclear Gene ◽  
Transit Peptide ◽  
Purifying Selection ◽  
Rna Recognition Motif ◽  
Rna Recognition ◽  
Plastid Genomes ◽  
Type Gene ◽  
Conserved Gene

Abstract Gene losses in plastid genomes (plastomes) are often accompanied by functional transfer to the nucleus or substitution of an alternative nuclear-encoded gene. Despite the highly conserved gene content in plastomes of photosynthetic land plants, recent gene loss events have been documented in several disparate angiosperm clades. Among these lineages, Passiflora lacks several essential ribosomal genes, rps7, rps16, rpl20, rpl22, and rpl32, the two largest plastid genes, ycf1 and ycf2, and has a highly divergent rpoA. Comparative transcriptome analyses were performed to determine the fate of the missing genes in Passiflora. Putative functional transfers of rps7, rpl22, and rpl32 to nucleus were detected, with the nuclear transfer of rps7, representing a novel event in angiosperms. Plastid-encoded rps7 was transferred into the intron of a nuclear-encoded plastid-targeted thioredoxin m-type gene, acquiring its plastid transit peptide (TP). Plastid rpl20 likely experienced a novel substitution by a duplicated, nuclear-encoded mitochondrial-targeted rpl20 that has a similar gene structure. Additionally, among rosids, evidence for a third independent transfer of rpl22 in Passiflora was detected that gained a TP from a nuclear gene containing an organelle RNA recognition motif. Nuclear transcripts representing rpoA, ycf1, and ycf2 were not detected. Further analyses suggest that the divergent rpoA remains functional and that the gene is under positive or purifying selection in different clades. Comparative analyses indicate that alternative translocon and motor protein complexes may have substituted for the loss of ycf1 and ycf2 in Passiflora.

scholarly journals The Jekyll and Hyde Symbiont: Could Wolbachia Be a Nutritional Mutualist?

2019 ◽  
Vol 202 (4) ◽  
Author(s):  
Irene L. G. Newton ◽  
Danny W. Rice
Keyword(s):  
Large Scale ◽  
Gene Content ◽  
Scale Analysis ◽  
Content Type ◽  
Wolbachia Pipientis ◽  
Beneficial Role ◽  
Intracellular Symbiont ◽  
Large Scale Analysis ◽  
Conserved Gene

ABSTRACT The most common intracellular symbiont on the planet—Wolbachia pipientis—is infamous largely for the reproductive manipulations induced in its host. However, more recent evidence suggests that this bacterium may also serve as a nutritional mutualist in certain host backgrounds and for certain metabolites. We performed a large-scale analysis of conserved gene content across all sequenced Wolbachia genomes to infer potential nutrients made by these symbionts. We review and critically evaluate the prior research supporting a beneficial role for Wolbachia and suggest future experiments to test hypotheses of metabolic provisioning.

scholarly journals Recent advances in understanding mitochondrial genome diversity

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 270 ◽  
Author(s):  
Rafael Zardoya
Keyword(s):  
Mitochondrial Genome ◽  
High Throughput Sequencing ◽  
Gene Content ◽  
Mitochondrial Genomes ◽  
Genetic Codes ◽  
Evolutionary Trajectories ◽  
Gene Structures ◽  
Mitochondrial Genome Diversity ◽  
Conserved Gene ◽  
Self Splicing

Ever since its discovery, the double-stranded DNA contained in the mitochondria of eukaryotes has fascinated researchers because of its bacterial endosymbiotic origin, crucial role in encoding subunits of the respiratory complexes, compact nature, and specific inheritance mechanisms. In the last few years, high-throughput sequencing techniques have accelerated the sequencing of mitochondrial genomes (mitogenomes) and uncovered the great diversity of organizations, gene contents, and modes of replication and transcription found in living eukaryotes. Some early divergent lineages of unicellular eukaryotes retain certain synteny and gene content resembling those observed in the genomes of alphaproteobacteria (the inferred closest living group of mitochondria), whereas others adapted to anaerobic environments have drastically reduced or even lost the mitogenome. In the three main multicellular lineages of eukaryotes, mitogenomes have pursued diverse evolutionary trajectories in which different types of molecules (circular versus linear and single versus multipartite), gene structures (with or without self-splicing introns), gene contents, gene orders, genetic codes, and transfer RNA editing mechanisms have been selected. Whereas animals have evolved a rather compact mitochondrial genome between 11 and 50 Kb in length with a highly conserved gene content in bilaterians, plants exhibit large mitochondrial genomes of 66 Kb to 11.3 Mb with large intergenic repetitions prone to recombination, and fungal mitogenomes have intermediate sizes of 12 to 236 Kb.

scholarly journals Tight association of genome rearrangements with gene expression in conifer plastomes

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Chung-Shien Wu ◽  
Edi Sudianto ◽  
Shu-Miaw Chaw
Keyword(s):  
Gene Expression ◽  
Gene Order ◽  
Genomic Rearrangements ◽  
First Line ◽  
Conifer Species ◽  
Antisense Transcripts ◽  
Plastid Genomes ◽  
Rnaseq Data ◽  
Tight Association ◽  
Conserved Gene

Abstract Background Our understanding of plastid transcriptomes is limited to a few model plants whose plastid genomes (plastomes) have a highly conserved gene order. Consequently, little is known about how gene expression changes in response to genomic rearrangements in plastids. This is particularly important in the highly rearranged conifer plastomes. Results We sequenced and reported the plastomes and plastid transcriptomes of six conifer species, representing all six extant families. Strand-specific RNAseq data show a nearly full transcription of both plastomic strands and detect C-to-U RNA-editing sites at both sense and antisense transcripts. We demonstrate that the expression of plastid coding genes is strongly functionally dependent among conifer species. However, the strength of this association declines as the number of plastomic rearrangements increases. This finding indicates that plastomic rearrangement influences gene expression. Conclusions Our data provide the first line of evidence that plastomic rearrangements not only complicate the plastomic architecture but also drive the dynamics of plastid transcriptomes in conifers.

scholarly journals Conservation of Microstructure between a Sequenced Region of the Genome of Rice and Multiple Segments of the Genome of Arabidopsis thaliana

2001 ◽  
Vol 11 (7) ◽  
pp. 1167-1174
Author(s):  
Klaus Mayer ◽  
George Murphy ◽  
Renato Tarchini ◽  
Rolf Wambutt ◽  
Guido Volckaert ◽  
...  
Keyword(s):  
Sequence Data ◽  
Rice Genome ◽  
Rice Chromosome ◽  
Gene Content ◽  
Chromosome 2 ◽  
Chromosome 4 ◽  
Orthologous Genes ◽  
Protein Coding ◽  
Duplication Events ◽  
Conserved Gene

The nucleotide sequence was determined for a 340-kb segment of rice chromosome 2, revealing 56 putative protein-coding genes. This represents a density of one gene per 6.1 kb, which is higher than was reported for a previously sequenced segment of the rice genome. Sixteen of the putative genes were supported by matches to ESTs. The predicted products of 29 of the putative genes showed similarity to known proteins, and a further 17 genes showed similarity only to predicted or hypothetical proteins identified in genome sequence data. The region contains a few transposable elements: one retrotransposon, and one transposon. The segment of the rice genome studied had previously been identified as representing a part of rice chromosome 2 that may be homologous to a segment of Arabidopsis chromosome 4. We confirmed the conservation of gene content and order between the two genome segments. In addition, we identified a further four segments of the Arabidopsis genome that contain conserved gene content and order. In total, 22 of the 56 genes identified in the rice genome segment were represented in this set of Arabidopsis genome segments, with at least five genes present, in conserved order, in each segment. These data are consistent with the hypothesis that theArabidopsis genome has undergone multiple duplication events. Our results demonstrate that conservation of the genome microstructure can be identified even between monocot and dicot species. However, the frequent occurrence of duplication, and subsequent microstructure divergence, within plant genomes may necessitate the integration of subsets of genes present in multiple redundant segments to deduce evolutionary relationships and identify orthologous genes.

scholarly journals Many nonuniversal archaeal ribosomal proteins are found in conserved gene clusters

Archaea ◽  
2009 ◽  
Vol 2 (4) ◽  
pp. 241-251 ◽  
Author(s):  
Jiachen Wang ◽  
Indrani Dasgupta ◽  
George E. Fox
Keyword(s):  
Protein Synthesis ◽  
Ribosomal Proteins ◽  
Gene Clusters ◽  
Cellular Systems ◽  
Gene Content ◽  
Genomic Context ◽  
Gene Encoding ◽  
Cellular Processes ◽  
Conserved Gene

The genomic associations of the archaeal ribosomal proteins, (r-proteins), were examined in detail. The archaeal versions of the universal r-protein genes are typically in clusters similar or identical and to those found in bacteria. Of the 35 nonuniversal archaeal r-protein genes examined, the gene encoding L18e was found to be associated with the conservedL13cluster, whereas the genes for S4e, L32e and L19e were found in the archaeal version of thespcoperon. Eleven nonuniversal protein genes were not associated with any common genomic context. Of the remaining 19 protein genes, 17 were convincingly assigned to one of 10 previously unrecognized gene clusters. Examination of the gene content of these clusters revealed multiple associations with genes involved in the initiation of protein synthesis, transcription or other cellular processes. The lack of such associations in the universal clusters suggests that initially the ribosome evolved largely independently of other processes. More recently it likely has evolved in concert with other cellular systems. It was also verified that a second copy of the gene encoding L7ae found in some bacteria is actually a homolog of the gene encoding L30e and should be annotated as such.

scholarly journals Genome Sequences of Three Agrobacterium Biovars Help Elucidate the Evolution of Multichromosome Genomes in Bacteria

2009 ◽  
Vol 191 (8) ◽  
pp. 2501-2511 ◽  
Author(s):  
Steven C. Slater ◽  
Barry S. Goldman ◽  
Brad Goodner ◽  
João C. Setubal ◽  
Stephen K. Farrand ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Biochemical Properties ◽  
Gene Content ◽  
Bacterial Genomes ◽  
Associated Bacteria ◽  
Narrow Host Range ◽  
Chromosome Architecture ◽  
The Family ◽  
Chromosome Formation ◽  
Conserved Gene

ABSTRACT The family Rhizobiaceae contains plant-associated bacteria with critical roles in ecology and agriculture. Within this family, many Rhizobium and Sinorhizobium strains are nitrogen-fixing plant mutualists, while many strains designated as Agrobacterium are plant pathogens. These contrasting lifestyles are primarily dependent on the transmissible plasmids each strain harbors. Members of the Rhizobiaceae also have diverse genome architectures that include single chromosomes, multiple chromosomes, and plasmids of various sizes. Agrobacterium strains have been divided into three biovars, based on physiological and biochemical properties. The genome of a biovar I strain, A. tumefaciens C58, has been previously sequenced. In this study, the genomes of the biovar II strain A. radiobacter K84, a commercially available biological control strain that inhibits certain pathogenic agrobacteria, and the biovar III strain A. vitis S4, a narrow-host-range strain that infects grapes and invokes a hypersensitive response on nonhost plants, were fully sequenced and annotated. Comparison with other sequenced members of the Alphaproteobacteria provides new data on the evolution of multipartite bacterial genomes. Primary chromosomes show extensive conservation of both gene content and order. In contrast, secondary chromosomes share smaller percentages of genes, and conserved gene order is restricted to short blocks. We propose that secondary chromosomes originated from an ancestral plasmid to which genes have been transferred from a progenitor primary chromosome. Similar patterns are observed in select Beta- and Gammaproteobacteria species. Together, these results define the evolution of chromosome architecture and gene content among the Rhizobiaceae and support a generalized mechanism for second-chromosome formation among bacteria.

scholarly journals Conserved and specific genomic features of endogenous polydnaviruses revealed by whole genome sequencing of two ichneumonid wasps

2019 ◽  
Author(s):  
Fabrice Legeai ◽  
Bernardo F. Santos ◽  
Stéphanie Robin ◽  
Anthony Bretaudeau ◽  
Rebecca B. Dikow ◽  
...  
Keyword(s):  
Particle Production ◽  
Biological Properties ◽  
Gene Content ◽  
Wasp Species ◽  
Virulence Proteins ◽  
Endogenous Viruses ◽  
Genomic Environment ◽  
Hyposoter Didymator ◽  
Conserved Gene ◽  
Genomic Regions

AbstractPolydnaviruses (PDVs) are mutualistic endogenous viruses associated with some lineages of parasitoid wasps that allow successful development of the wasps within their hosts. PDVs include two taxa resulting from independent virus acquisitions in braconid (bracoviruses) and ichneumonid wasps (ichnoviruses). PDV genomes are fully incorporated into the wasp genomes and comprise (1) virulence genes located on proviral segments that are packaged into the viral particle, and (2) genes involved in the production of the viral particles, which are not encapsidated. Whereas the genomic organization of bracoviruses within the wasp genome is relatively well known, the architecture of endogenous ichnoviruses remains poorly understood. We sequenced the genome of two ichnovirus-carrying wasp species, Hyposoter didymator and Campoletis sonorensis. Complete assemblies with long scaffold sizes allowed identification of the integrated ichnovirus, highlighting an extreme dispersion within the wasp genomes of the viral loci, i.e. isolated proviral segments and clusters of replication genes. Comparing the two wasp species, proviral segments harbor distinct gene content and variable genomic environment, whereas viral machinery clusters show conserved gene content and order, and can be inserted in collinear wasp genomic regions. This distinct architecture is consistent with the biological properties of the two viral elements: proviral segments producing virulence proteins allowing parasitism success are fine-tuned to the host physiology, while an ancestral viral architecture was likely maintained for the genes involved in virus particle production. Finding a distinct genomic architecture of ichnoviruses and bracoviruses highlights different evolutionary trajectories leading to virus domestication in the two wasp lineages.

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