Frontiers in metabolic reconstruction and modeling of plant genomes

AbstractWe identified and characterized the pseudogene complements of five plant species: four dicots (Arabidopsis thaliana, Vitis vinifera, Populus trichocarpa and Phaseolus vulgaris) and one monocot (Oryza sativa). Retroposition was considered of modest importance for pseudogene formation in all investigated species except V. vinifera, which showed an unusually high number of retro-pseudogenes in non coding genic regions. By using a pipeline for the classification of sequence duplicates in plant genomes, we compared the relative importance of whole genome, tandem, proximal, transposed and dispersed duplication modes in the pseudo and functional gene complements. Pseudogenes showed higher tendencies than functional genes to genomic dispersion. Dispersed pseudogenes were prevalently fragmented and showed high sequence divergence at flanking regions. On the contrary, those deriving from whole genome duplication were proportionally less than expected based on observations on functional loci and showed higher levels of flanking sequence conservation than dispersed pseudogenes. Pseudogenes deriving from tandem and proximal duplications were in excess compared to functional loci, probably reflecting the high evolutionary rate associated with these duplication modes in plant genomes. These data are compatible with high rates of sequence turnover at neutral sites and double strand break repairs mediated duplication mechanisms.

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Tc8, a Tourist-like Transposon in Caenorhabditis elegans

Genetics ◽

10.1093/genetics/158.3.1081 ◽

2001 ◽

Vol 158 (3) ◽

pp. 1081-1088 ◽

Cited By ~ 2

Author(s):

Quang Hien Le ◽

Kime Turcotte ◽

Thomas Bureau

Keyword(s):

Caenorhabditis Elegans ◽

Expressed Sequence Tags ◽

Large Family ◽

Insertion Sequences ◽

Normal Plant ◽

Nematode Caenorhabditis Elegans ◽

Plant Genomes ◽

Plant Genes ◽

Expressed Sequence ◽

Eukaryotic Genomes

Abstract Members of the Tourist family of miniature inverted-repeat transposable elements (MITEs) are very abundant among a wide variety of plants, are frequently found associated with normal plant genes, and thus are thought to be important players in the organization and evolution of plant genomes. In Arabidopsis, the recent discovery of a Tourist member harboring a putative transposase has shed new light on the mobility and evolution of MITEs. Here, we analyze a family of Tourist transposons endogenous to the genome of the nematode Caenorhabditis elegans (Bristol N2). One member of this large family is 7568 bp in length, harbors an ORF similar to the putative Tourist transposase from Arabidopsis, and is related to the IS5 family of bacterial insertion sequences (IS). Using database searches, we found expressed sequence tags (ESTs) similar to the putative Tourist transposases in plants, insects, and vertebrates. Taken together, our data suggest that Tourist-like and IS5-like transposons form a superfamily of potentially active elements ubiquitous to prokaryotic and eukaryotic genomes.

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A comprehensive annotation dataset of intact LTR retrotransposons of 300 plant genomes

Scientific Data ◽

10.1038/s41597-021-00968-x ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Shan-Shan Zhou ◽

Xue-Mei Yan ◽

Kai-Fu Zhang ◽

Hui Liu ◽

Jie Xu ◽

...

Keyword(s):

Evolutionary Dynamics ◽

Age Determination ◽

Genome Plasticity ◽

Ltr Retrotransposons ◽

Functional Variation ◽

Plant Genomes ◽

Sequencing Technologies ◽

Plant Groups ◽

Functional Implications ◽

Classification Information

AbstractLTR retrotransposons (LTR-RTs) are ubiquitous and represent the dominant repeat element in plant genomes, playing important roles in functional variation, genome plasticity and evolution. With the advent of new sequencing technologies, a growing number of whole-genome sequences have been made publicly available, making it possible to carry out systematic analyses of LTR-RTs. However, a comprehensive and unified annotation of LTR-RTs in plant groups is still lacking. Here, we constructed a plant intact LTR-RTs dataset, which is designed to classify and annotate intact LTR-RTs with a standardized procedure. The dataset currently comprises a total of 2,593,685 intact LTR-RTs from genomes of 300 plant species representing 93 families of 46 orders. The dataset is accompanied by sequence, diverse structural and functional annotation, age determination and classification information associated with the LTR-RTs. This dataset will contribute valuable resources for investigating the evolutionary dynamics and functional implications of LTR-RTs in plant genomes.

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Metagenome-assembled genomes infer potential microbial metabolism in alkaline sulphidic tailings

Environmental Microbiome ◽

10.1186/s40793-021-00380-3 ◽

2021 ◽

Vol 16 (1) ◽

Author(s):

Wenjun Li ◽

Xiaofang Li

Keyword(s):

Community Structure ◽

Mine Tailings ◽

Fluorescent In Situ Hybridization ◽

High Throughput Sequencing ◽

Microbial Consortia ◽

Metabolic Reconstruction ◽

Metal Release ◽

Community Members ◽

Oxidative Stresses

Abstract Background Mine tailings are hostile environment. It has been well documented that several microbes can inhabit such environment, and metagenomic reconstruction has successfully pinpointed their activities and community structure in acidic tailings environments. We still know little about the microbial metabolic capacities of alkaline sulphidic environment where microbial processes are critically important for the revegetation. Microbial communities therein may not only provide soil functions, but also ameliorate the environment stresses for plants’ survival. Results In this study, we detected a considerable amount of viable bacterial and archaeal cells using fluorescent in situ hybridization in alkaline sulphidic tailings from Mt Isa, Queensland. By taking advantage of high-throughput sequencing and up-to-date metagenomic binning technology, we reconstructed the microbial community structure and potential coupled iron and nitrogen metabolism pathways in the tailings. Assembly of 10 metagenome-assembled genomes (MAGs), with 5 nearly complete, was achieved. From this, detailed insights into the community metabolic capabilities was derived. Dominant microbial species were seen to possess powerful resistance systems for osmotic, metal and oxidative stresses. Additionally, these community members had metabolic capabilities for sulphide oxidation, for causing increased salinity and metal release, and for leading to N depletion. Conclusions Here our results show that a considerable amount of microbial cells inhabit the mine tailings, who possess a variety of genes for stress response. Metabolic reconstruction infers that the microbial consortia may actively accelerate the sulphide weathering and N depletion therein.

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Genome-Wide Metabolic Reconstruction of the Synthesis of Polyhydroxyalkanoates from Sugars and Fatty Acids by Burkholderia Sensu Lato Species

Microorganisms ◽

10.3390/microorganisms9061290 ◽

2021 ◽

Vol 9 (6) ◽

pp. 1290

Author(s):

Natalia Alvarez-Santullano ◽

Pamela Villegas ◽

Mario Sepúlveda Mardones ◽

Roberto E. Durán ◽

Raúl Donoso ◽

...

Keyword(s):

Fatty Acids ◽

De Novo ◽

Reducing Power ◽

Pentose Phosphate ◽

Fine Tuning ◽

Metabolic Reconstruction ◽

Phylogenetic Groups ◽

Outlier Group ◽

Pha Genes ◽

High Level

Burkholderia sensu lato (s.l.) species have a versatile metabolism. The aims of this review are the genomic reconstruction of the metabolic pathways involved in the synthesis of polyhydroxyalkanoates (PHAs) by Burkholderia s.l. genera, and the characterization of the PHA synthases and the pha genes organization. The reports of the PHA synthesis from different substrates by Burkholderia s.l. strains were reviewed. Genome-guided metabolic reconstruction involving the conversion of sugars and fatty acids into PHAs by 37 Burkholderia s.l. species was performed. Sugars are metabolized via the Entner–Doudoroff (ED), pentose-phosphate (PP), and lower Embden–Meyerhoff–Parnas (EMP) pathways, which produce reducing power through NAD(P)H synthesis and PHA precursors. Fatty acid substrates are metabolized via β-oxidation and de novo synthesis of fatty acids into PHAs. The analysis of 194 Burkholderia s.l. genomes revealed that all strains have the phaC, phaA, and phaB genes for PHA synthesis, wherein the phaC gene is generally present in ≥2 copies. PHA synthases were classified into four phylogenetic groups belonging to class I II and III PHA synthases and one outlier group. The reconstruction of PHAs synthesis revealed a high level of gene redundancy probably reflecting complex regulatory layers that provide fine tuning according to diverse substrates and physiological conditions.

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