Comparative genome analyses highlight transposon-mediated genome expansion shapes the evolutionary architecture of 3D genomic folding in cotton

Abstract Transposable element (TE) amplification has been recognized as a driving force mediating genome size expansion and evolution, but the effect on shaping of 3D genomic architecture remains largely unknown in plants. Here, we report three reference-grade cotton genome assemblies of Gossypium rotundifolium (K2), G. arboreum (A2) and G. raimondii (D5) using Oxford Nanopore sequencing technology. Comparative genome analyses document the details of lineage-specific TE amplification contributing to three-fold change of genome size (K2, 2.44 Gb; A2, 1.62 Gb; D5, 750.19 Mb), and indicate a relatively conserved gene content and synteny relationship among genomes. We found that approximately 17% of syntenic genes exhibit chromatin status switching of A/B compartment, and active TE amplification increases the proportion of A compartment in gene regions in K2 and A2 relative to D5. We also found that only 42% of topologically associating domain (TAD) boundaries were conserved by comparing three genomes, and abundant TE amplification was linked to the organization of lineage-specific TADs. This study sheds light on the regulatory role of transposon-mediated genome expansion in the evolution of higher-order chromatin structure in plants.

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DNA transposon expansion is associated with genome size increase in mudminnows

10.1101/2021.06.07.447207 ◽

2021 ◽

Author(s):

Robert Lehmann ◽

Ales Kovarik ◽

Konrad Ocalewicz ◽

Lech Kirtiklis ◽

Andrea Zuccolo ◽

...

Keyword(s):

Genome Size ◽

North American ◽

Size Increase ◽

Dna Transposon ◽

Whole Genome Duplications ◽

Genome Expansion ◽

Genome Duplications ◽

Robertsonian Rearrangements ◽

Eukaryotic Organisms ◽

Genome Assemblies

Genome sizes of eukaryotic organisms vary substantially, with whole genome duplications (WGD) and transposable element expansion acting as main drivers for rapid genome size increase. The two North American mudminnows, Umbra limi and U. pygmaea, feature genomes about twice the size of their sister lineage Esocidae (e.g., pikes and pickerels). However, it is unknown whether all Umbra species share this genome expansion and which causal mechanisms drive this expansion. Using flow cytometry, we find that the genome of the European mudminnow is expanded similarly to both North American species, ranging between 4.5-5.4 pg per diploid nucleus. Observed blocks of interstitially located telomeric repeats in Umbra limi suggest frequent Robertsonian rearrangements in its history. Comparative analyses of transcriptome and genome assemblies show that the genome expansion in Umbra is driven by extensive DNA transposon expansion without WGD. Furthermore, we find a substantial ongoing expansion of repeat sequences in the Alaska blackfish Dallia pectoralis, the closest relative to the family Umbridae, which might mark the beginning of a similar genome expansion. Our study suggests that the genome expansion in mudminnows, driven mainly by transposon expansion, but not WGD, occurred before the separation into the American and European lineage.

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Comparative genome analyses highlight transposon-mediated genome expansion shapes the evolutionary architecture of 3D genomic folding in cotton

10.21203/rs.3.rs-93594/v2 ◽

2020 ◽

Keyword(s):

Comparative Genome ◽

Genome Expansion ◽

Genome Analyses

Abstract The authors have requested that this preprint be withdrawn due to erroneous posting.

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Faculty Opinions recommendation of Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis.

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

10.3410/f.1007665.123659 ◽

2002 ◽

Author(s):

Marie-Angele Grandbastien

Keyword(s):

Genome Size ◽

Size Reduction ◽

Illegitimate Recombination ◽

Genome Expansion

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Gut Microbiota and Antipsychotics Induced Metabolic Alteration

Global Clinical and Translational Research ◽

10.36316/gcatr.01.0020 ◽

2019 ◽

pp. 131-143

Author(s):

Dong-Yu Kan ◽

Su-Juan Li ◽

Chen-Chen Liu ◽

Ren-Rong Wu

Keyword(s):

Gut Microbiota ◽

Body Weight Gain ◽

Neuropsychiatric Disorders ◽

Elevated Risk ◽

Metabolic Disturbance ◽

Metabolic Dysfunction ◽

Sequencing Technology ◽

Severe Mental Disorder ◽

Metabolic Alteration

Schizophrenia is a chronic and severe mental disorder with antipsychotics as primary medications, but the antipsychotic-induced metabolic side effects may contribute to the elevated risk of overall morbidity and mortality in patients with psych-iatric diseases. With the development in sequencing technology and bioinformatics, dysbiosis has been shown to contribute to body weight gain and metabolic dysfunction. However, the role of gut microbiota in the antipsychotic-induced metabolic alteration remains unknown. In this paper, we reviewed the recent studies of the gut microbiota with psychiatric disorders and antipsychotic-induced metabolic dysfunction. Patients with neuropsychiatric disorders may have a different composi-tion of gut microbiota compared with healthy controls. In addition, it seems that the use of antipsychotics is concurrently associated with both altered composition of gut microbiota and metabolic disturbance. Further study is needed to address the role of gut microbiota in the development of neuropsychiatric disorders and antipsychotic-induced metabolic disturbance, to develop novel therapeutics for both neuropsychiatric disorders and metabolic dysfunction.

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Chromosomal assembly of the nuclear genome of the endosymbiont-bearing trypanosomatid Angomonas deanei

G3 Genes|Genome|Genetics ◽

10.1093/g3journal/jkaa018 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

John W Davey ◽

Carolina M C Catta-Preta ◽

Sally James ◽

Sarah Forrester ◽

Maria Cristina M Motta ◽

...

Keyword(s):

Chromosome Number ◽

Noncoding Rnas ◽

Nuclear Genome ◽

Supernumerary Chromosome ◽

Ribosomal Rnas ◽

Protein Coding ◽

Transfer Rnas ◽

Protein Coding Genes ◽

Oxford Nanopore ◽

Genome Assemblies

Abstract Angomonas deanei is an endosymbiont-bearing trypanosomatid with several highly fragmented genome assemblies and unknown chromosome number. We present an assembly of the A. deanei nuclear genome based on Oxford Nanopore sequence that resolves into 29 complete or close-to-complete chromosomes. The assembly has several previously unknown special features; it has a supernumerary chromosome, a chromosome with a 340-kb inversion, and there is a translocation between two chromosomes. We also present an updated annotation of the chromosomal genome with 10,365 protein-coding genes, 59 transfer RNAs, 26 ribosomal RNAs, and 62 noncoding RNAs.

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A comparative genome‐wide analysis of the ABC transporter gene family among three Gossypium species and the evidence for a role of some GhABCs in fiber development and response to stresses

Crop Science ◽

10.1002/csc2.20525 ◽

2021 ◽

Author(s):

Baolu Cui ◽

Yan Li ◽

Yanjie Zhang

Keyword(s):

Gene Family ◽

Abc Transporter ◽

Fiber Development ◽

Transporter Gene ◽

Comparative Genome ◽

Genome Wide Analysis ◽

Gossypium Species ◽

Genome Wide

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Hapo-G, haplotype-aware polishing of genome assemblies with accurate reads

NAR Genomics and Bioinformatics ◽

10.1093/nargab/lqab034 ◽

2021 ◽

Vol 3 (2) ◽

Author(s):

Jean-Marc Aury ◽

Benjamin Istace

Keyword(s):

Single Molecule ◽

Direct Consequence ◽

High Quality ◽

Sequencing Errors ◽

Coding Regions ◽

Sequencing Technologies ◽

Long Reads ◽

Oxford Nanopore ◽

Long Read ◽

Genome Assemblies

Abstract Single-molecule sequencing technologies have recently been commercialized by Pacific Biosciences and Oxford Nanopore with the promise of sequencing long DNA fragments (kilobases to megabases order) and then, using efficient algorithms, provide high quality assemblies in terms of contiguity and completeness of repetitive regions. However, the error rate of long-read technologies is higher than that of short-read technologies. This has a direct consequence on the base quality of genome assemblies, particularly in coding regions where sequencing errors can disrupt the coding frame of genes. In the case of diploid genomes, the consensus of a given gene can be a mixture between the two haplotypes and can lead to premature stop codons. Several methods have been developed to polish genome assemblies using short reads and generally, they inspect the nucleotide one by one, and provide a correction for each nucleotide of the input assembly. As a result, these algorithms are not able to properly process diploid genomes and they typically switch from one haplotype to another. Herein we proposed Hapo-G (Haplotype-Aware Polishing Of Genomes), a new algorithm capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes.

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Adaptation, Ecology, and Evolution of the Halophilic Stromatolite ArchaeonHalococcus hamelinensisInferred through Genome Analyses

Archaea ◽

10.1155/2015/241608 ◽

2015 ◽

Vol 2015 ◽

pp. 1-11 ◽

Cited By ~ 10

Author(s):

Reema K. Gudhka ◽

Brett A. Neilan ◽

Brendan P. Burns

Keyword(s):

Unknown Function ◽

Energy Production ◽

Extreme Environment ◽

Evolutionary Significance ◽

Base Pairs ◽

Protein Coding ◽

Inorganic Ion ◽

Damage Repair ◽

Genome Analyses

Halococcus hamelinensiswas the first archaeon isolated from stromatolites. These geomicrobial ecosystems are thought to be some of the earliest known on Earth, yet, despite their evolutionary significance, the role of Archaea in these systems is still not well understood. Detailed here is the genome sequencing and analysis of an archaeon isolated from stromatolites. The genome ofH. hamelinensisconsisted of 3,133,046 base pairs with an average G+C content of 60.08% and contained 3,150 predicted coding sequences or ORFs, 2,196 (68.67%) of which were protein-coding genes with functional assignments and 954 (29.83%) of which were of unknown function. Codon usage of theH. hamelinensisgenome was consistent with a highly acidic proteome, a major adaptive mechanism towards high salinity. Amino acid transport and metabolism, inorganic ion transport and metabolism, energy production and conversion, ribosomal structure, and unknown function COG genes were overrepresented. The genome ofH. hamelinensisalso revealed characteristics reflecting its survival in its extreme environment, including putative genes/pathways involved in osmoprotection, oxidative stress response, and UV damage repair. Finally, genome analyses indicated the presence of putative transposases as well as positive matches of genes ofH. hamelinensisagainst various genomes of Bacteria, Archaea, and viruses, suggesting the potential for horizontal gene transfer.

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