Molecular Biology Reports, Год журнала: 2024, Номер 51(1)
Опубликована: Янв. 18, 2024
Язык: Английский
Genes, Год журнала: 2023, Номер 14(10), С. 1905 - 1905
Опубликована: Окт. 4, 2023
Alopecurus myosuroides (blackgrass) is a problematic weed of Western European winter wheat, and its success largely due to widespread multiple-herbicide resistance. Previous analysis F2 seed families derived from two distinct blackgrass populations exhibiting equivalent non-target site resistance (NTSR) phenotypes shows polygenic evolves standing genetic variation. Using CIDER-seq pipeline, we show that herbicide-resistant (HR) herbicide-sensitive (HS) F3 plants these as well the parent they were carry extra-chromosomal circular DNA (eccDNA). We identify similarities differences in coding structures within between resistant sensitive populations. Although numbers size detected eccDNAs varied populations, comparisons HR HS identified shared unique content, predicted genes, functional protein domains. These include genes related herbicide detoxification such Cytochrome P450s, ATP-binding cassette transporters, glutathione transferases including AmGSTF1. eccDNA content was mapped A. reference genome, revealing genomic regions at distal end chromosome 5 near center chromosomes 1 7 with high number gene density. Mapping 15 known QTL showed sequences matched twelve, four matching sequences; only one region contained sequences. findings establish that, like other pernicious weeds, has contain homologs chromosomal may contribute heterogeneity evolutionary innovation rapidly adapt abiotic stresses, treatment.
Язык: Английский
Процитировано
3
Plants, Год журнала: 2022, Номер 11(24), С. 3579 - 3579
Опубликована: Дек. 19, 2022
Transposable elements (TEs) contribute not only to genome diversity but also transcriptome in plants. To unravel the sources of LTR retrotransposon (RTE) transcripts sunflower, we exploited a recently developed transposon activation method ('TEgenesis') along with long-read cDNA Nanopore sequencing. This approach allows for identification 56 RTE from different genomic loci including full-length and non-autonomous RTEs. Using mobilome analysis, provided new set expressed transpositional active sunflower RTEs future studies. Among them, Ty3/Gypsy called SUNTY3 exhibited ongoing transposition activity, as detected by eccDNA analysis. We showed that contains diverse encoding single protein, previously described TR-GAG (terminal repeat GAG domain) well categories, TR-RT-RH, TR-RH, TR-INT-RT. Our results demonstrate 40% RTE-related (nonLTR-RTEs) lack their sequences resemble conventional eucaryotic genes proteins unknown functions. It was evident based on phylogenetic analysis three nonLTR-RTEs encode (HadGAG1-3) fused host protein. These HadGAG have homologs found other plant species, potentially indicating domestication. Ultimately, retrotranscriptome originated transcription RTEs, gene-like transcripts, those domesticated proteins.
Язык: Английский
Процитировано
4
Опубликована: Сен. 20, 2023
Alopecurus myosuroides (blackgrass) is a problematic weed of Western European winter wheat and its success largely due to widespread multiple-herbicide resistance. Previous analysis F2 seed families derived from two distinct blackgrass populations exhibiting equivalent non-target site resistance (NTSR) phenotypes shows polygenic evolves standing genetic variation. Using CIDER-seq pipeline we show that herbicide resistant (HR) sensitive (HS) F3 plants these as well the parent they were carry extra-chromosomal circular DNA (eccDNA). We identify similarities differences in coding structures within between populations. Although numbers size detected eccDNAs varied populations, comparisons HR HS identified shared unique content, predicted genes, functional protein domains. These include genes related detoxification such Cytochrome P450s, ATP-binding cassette transporters glutathione transferases including AmGSTF1. eccDNA content was mapped reference genome, revealing genomic regions at distal end chromosome 5 near center 1 7 with high number gene density. Mapping 15 known herbicide-resistant QTL showed sequences match 12 four QLT matching one region only contained sequences. findings establish like other pernicious weeds, has contain homologs chromosomal may contribute heterogeneity evolutionary innovation rapidly adapt abiotic stresses treatment.
Язык: Английский
Процитировано
1
bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown
Опубликована: Окт. 30, 2023
Abstract Background Despite the many cheap and fast ways to generate genomic data, good exact genome assembly is still a problem, with especially repeats being vastly underrepresented often misassembled. As short reads in low coverage are already sufficient represent repeat landscape of any given genome, read cluster algorithms were brought forward that provide identification classification. But how can trustworthy, reliable representative full-length consensuses be derived from unassembled genomes? Results Here, we combine methods derive these robust consensuses. We test several use cases, such as (1) consensus building clustered non-model genomes, (2) genome-wide amplification setups, (3) specific repeat-centred questions, linked vs. unlinked arrangement ribosomal genes. In all our use-cases, representative. To evaluate overall performance, compare high-fidelity RepeatExplorer2-derived contigs check, if they real transposable elements found long reads. Our results demonstrate it possible useful, trustworthy by combination an automatable way. Conclusion anticipate workflow opens way towards more efficient less manual characterization annotation, benefitting studies, but those organisms.
Язык: Английский
Процитировано
1
Molecular Biology Reports, Год журнала: 2024, Номер 51(1)
Опубликована: Янв. 18, 2024
Язык: Английский
Процитировано
0