The Prediction and Validation of Small CDSs Expand the Gene Repertoire of the Smallest Known Eukaryotic Genomes

AbstractEukaryotic genomes are known to have garnered innovations from both archaeal and bacterial domains but the sequence of events that led to the complex gene repertoire of eukaryotes is largely unresolved. Here, through the enrichment of hydrothermal vent microorganisms, we recovered two circularized genomes of Heimdallarchaeum species that belong to an Asgard archaea clade phylogenetically closest to eukaryotes. These genomes reveal diverse mobile elements, including an integrative viral genome that bidirectionally replicates in a circular form and aloposons, transposons that encode the 5,000 amino acid-sized proteins Otus and Ephialtes. Heimdallaechaeal mobile elements have garnered various genes from bacteria and bacteriophages, likely playing a role in shuffling functions across domains. The number of archaea- and bacteria-related genes follow strikingly different scaling laws in Asgard archaea, exhibiting a genome size-dependent ratio and a functional division resembling the bacteria- and archaea-derived gene repertoire across eukaryotes. Bacterial gene import has thus likely been a continuous process unaltered by eukaryogenesis and scaled up through genome expansion. Our data further highlight the importance of viewing eukaryogenesis in a pan-Asgard context, which led to the proposal of a conceptual framework, that is, the Heimdall nucleation–decentralized innovation–hierarchical import model that accounts for the emergence of eukaryotic complexity.

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Genomic and transcriptomic insights into the cytochrome P450 monooxygenase gene repertoire in the rice pest brown planthopper,Nilaparvata lugens

10.1603/ice.2016.108969 ◽

2016 ◽

Author(s):

Yanyuan Bao

Keyword(s):

Cytochrome P450 ◽

Brown Planthopper ◽

Nilaparvata Lugens ◽

Cytochrome P450 Monooxygenase ◽

Gene Repertoire ◽

P450 Monooxygenase ◽

Monooxygenase Gene ◽

Rice Pest

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Faculty Opinions recommendation of Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1088364.541962 ◽

2007 ◽

Author(s):

Billie J Swalla

Keyword(s):

Genomic Organization ◽

Sea Anemone ◽

Gene Repertoire

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Arylamine N-Acetyltransferases in Prokaryotic and Eukaryotic Genomes: A Survey of Public Databases

Current Drug Metabolism ◽

10.2174/138920008785821729 ◽

2008 ◽

Vol 9 (7) ◽

pp. 628-660 ◽

Cited By ~ 21

Author(s):

Eirini Vagena ◽

Giannoulis Fakis ◽

Sotiria Boukouvala

Keyword(s):

Eukaryotic Genomes

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The tepary bean genome provides insight into evolution and domestication under heat stress

Nature Communications ◽

10.1038/s41467-021-22858-x ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Samira Mafi Moghaddam ◽

Atena Oladzad ◽

Chushin Koh ◽

Larissa Ramsay ◽

John P. Hart ◽

...

Keyword(s):

Heat Stress ◽

Common Bean ◽

Sonoran Desert ◽

Climate Adaptation ◽

Human Consumption ◽

Disease Resistance Gene ◽

Gene Repertoire ◽

Tepary Bean ◽

Hot Environments ◽

Insight Into

AbstractTepary bean (Phaseolus acutifolis A. Gray), native to the Sonoran Desert, is highly adapted to heat and drought. It is a sister species of common bean (Phaseolus vulgaris L.), the most important legume protein source for direct human consumption, and whose production is threatened by climate change. Here, we report on the tepary genome including exploration of possible mechanisms for resilience to moderate heat stress and a reduced disease resistance gene repertoire, consistent with adaptation to arid and hot environments. Extensive collinearity and shared gene content among these Phaseolus species will facilitate engineering climate adaptation in common bean, a key food security crop, and accelerate tepary bean improvement.

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Analysis of the chromosomal clustering of Fusarium-responsive wheat genes uncovers new players in the defence against head blight disease

Scientific Reports ◽

10.1038/s41598-021-86362-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Alexandre Perochon ◽

Harriet R. Benbow ◽

Katarzyna Ślęczka-Brady ◽

Keshav B. Malla ◽

Fiona M. Doohan

Keyword(s):

Map Kinases ◽

Gene Families ◽

Gene Clusters ◽

Head Blight ◽

Orphan Gene ◽

Metabolic Genes ◽

Eukaryotic Gene ◽

Blight Disease ◽

Genomic Regions ◽

Eukaryotic Genomes

AbstractThere is increasing evidence that some functionally related, co-expressed genes cluster within eukaryotic genomes. We present a novel pipeline that delineates such eukaryotic gene clusters. Using this tool for bread wheat, we uncovered 44 clusters of genes that are responsive to the fungal pathogen Fusarium graminearum. As expected, these Fusarium-responsive gene clusters (FRGCs) included metabolic gene clusters, many of which are associated with disease resistance, but hitherto not described for wheat. However, the majority of the FRGCs are non-metabolic, many of which contain clusters of paralogues, including those implicated in plant disease responses, such as glutathione transferases, MAP kinases, and germin-like proteins. 20 of the FRGCs encode nonhomologous, non-metabolic genes (including defence-related genes). One of these clusters includes the characterised Fusarium resistance orphan gene, TaFROG. Eight of the FRGCs map within 6 FHB resistance loci. One small QTL on chromosome 7D (4.7 Mb) encodes eight Fusarium-responsive genes, five of which are within a FRGC. This study provides a new tool to identify genomic regions enriched in genes responsive to specific traits of interest and applied herein it highlighted gene families, genetic loci and biological pathways of importance in the response of wheat to disease.

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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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Islands of complex DNA are widespread in Drosophila centric heterochromatin.

Genetics ◽

10.1093/genetics/141.1.283 ◽

1995 ◽

Vol 141 (1) ◽

pp. 283-303

Author(s):

M H Le ◽

D Duricka ◽

G H Karpen

Keyword(s):

Dna Sequences ◽

Structure And Function ◽

Southern Analysis ◽

Cloning And Sequencing ◽

Pulsed Field ◽

Drosophila Heterochromatin ◽

And Function ◽

Heterochromatin Structure ◽

Derivatives Of ◽

Eukaryotic Genomes

Abstract Heterochromatin is a ubiquitous yet poorly understood component of multicellular eukaryotic genomes. Major gaps exist in our knowledge of the nature and overall organization of DNA sequences present in heterochromatin. We have investigated the molecular structure of the 1 Mb of centric heterochromatin in the Drosophila minichromosome Dp1187. A genetic screen of irradiated minichromosomes yielded rearranged derivatives of Dp1187 whose structures were determined by pulsed-field Southern analysis and PCR. Three Dp1187 deletion derivatives and an inversion had one breakpoint in the euchromatin and one in the heterochromatin, providing direct molecular access to previously inaccessible parts of the heterochromatin. End-probed pulsed-field restriction mapping revealed the presence of at least three "islands" of complex DNA, Tahiti, Moorea, and Bora Bora, constituting approximately one half of the Dp1187 heterochromatin. Pulsed-field Southern analysis demonstrated that Drosophila heterochromatin in general is composed of alternating blocks of complex DNA and simple satellite DNA. Cloning and sequencing of a small part of one island, Tahiti, demonstrated the presence of a retroposon. The implications of these findings to heterochromatin structure and function are discussed.

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