Selection signatures and population dynamics of transposable elements in Lima bean DOI Creative Commons
Daniela Lozano‐Arce,

Tatiana García,

Laura González

et al.

Research Square (Research Square), Journal Year: 2023, Volume and Issue: unknown

Published: Jan. 4, 2023

Abstract The domestication process in Lima bean ( Phaseolus lunatus L. ) involves at least two independent events, within the Mesoamerican and Andean gene pools. Both processes produced similar phenotypic changes landraces, making an excellent model to understand convergent evolution. Despite recent research efforts, mechanisms of adaptation followed by landraces are largely unknown. genes related these adaptations can be selected identification selective sweeps Most previous genetic analyses have relied on Single Nucleotide Polymorphism (SNP) loci ignored transposable elements (TEs) which a major source variation plant genomes. current availability high-throughput sequencing technologies enables collection whole-genome resequencing (WGS) data approach intraspecies population dynamics TEs. present collected WGS from 60 wild domesticated accessions generate most complete characterization developed date SNP genome. We generated updated annotation 223,780 Furthermore, we identified variable TEs affected sweeps. Combining three different approaches, were predicted set candidate genes. A small percentage under selection (1.6%) shared among pools, suggesting that avenues both Up 25% with previously reported common also detected bean. built catalog 39,459 presence-absence (PAV). fact 75% located close shows their potential affect functions structure inferred was consistent obtained markers, TE demographic history its adaptive processes, particular during domestication.

Language: Английский

The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars DOI Creative Commons
Jarkko Salojärvi,

Aditi Rambani,

Zhe Yu

et al.

Nature Genetics, Journal Year: 2024, Volume and Issue: 56(4), P. 721 - 731

Published: April 1, 2024

Abstract Coffea arabica , an allotetraploid hybrid of eugenioides and canephora is the source approximately 60% coffee products worldwide, its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies a di-haploid C. accession modern representatives diploid progenitors, . The three species exhibit largely conserved genome structures between parents descendant subgenomes, with no obvious global subgenome dominance. find evidence for founding polyploidy event 350,000–610,000 years ago, followed by pre-domestication bottlenecks, resulting in narrow genetic variation. A split wild cultivar progenitors occurred ~30.5 thousand period migration two populations. Analysis varieties, including lines historically introgressed highlights their breeding histories loci that may contribute to pathogen resistance, laying groundwork future genomics-based

Language: Английский

Citations

39
Artificial intelligence in plant breeding DOI Creative Commons
Muhammad Amjad Farooq, Shang Gao, Muhammad Adeel Hassan

et al.

Trends in Genetics, Journal Year: 2024, Volume and Issue: 40(10), P. 891 - 908

Published: Aug. 7, 2024

Harnessing cutting-edge technologies to enhance crop productivity is a pivotal goal in modern plant breeding. Artificial intelligence (AI) renowned for its prowess big data analysis and pattern recognition, revolutionizing numerous scientific domains including We explore the wider potential of AI tools various facets breeding, collection, unlocking genetic diversity within genebanks, bridging genotype–phenotype gap facilitate This will enable development cultivars tailored projected future environments. Moreover, also hold promise refining traits by improving precision gene-editing systems predicting effects gene variants on phenotypes. Leveraging AI-enabled breeding can augment efficiency programs holds optimizing cropping at grassroots level. entails identifying optimal inter-cropping crop-rotation models agricultural sustainability field.

Language: Английский

Citations

31
The genome awakens: transposon-mediated gene regulation DOI
Ileana Tossolini, Regina Mencia, A. Arce

et al.

Trends in Plant Science, Journal Year: 2025, Volume and Issue: unknown

Published: March 1, 2025

Language: Английский

Citations

3
From tradition to innovation: conventional and deep learning frameworks in genome annotation DOI Creative Commons

Zhaojia Chen,

Noor ul Ain, Qian Zhao

et al.

Briefings in Bioinformatics, Journal Year: 2024, Volume and Issue: 25(3)

Published: March 27, 2024

Following the milestone success of Human Genome Project, 'Encyclopedia DNA Elements (ENCODE)' initiative was launched in 2003 to unearth information about numerous functional elements within genome. This endeavor coincided with emergence novel technologies, accompanied by provision vast amounts whole-genome sequences, high-throughput data such as ChIP-Seq and RNA-Seq. Extracting biologically meaningful from this massive dataset has become a critical aspect many recent studies, particularly annotating predicting functions unknown genes. The core idea behind genome annotation is identify genes various sequence infer their biological functions. Traditional wet-lab experimental methods still rely on extensive efforts for verification. However, early bioinformatics algorithms software primarily employed shallow learning techniques; thus, ability characterize features limited. With widespread adoption RNA-Seq technology, scientists community began harness potential machine deep approaches gene structure prediction annotation. In context, we reviewed both conventional contemporary frameworks, highlighted perspectives challenges arising during underscoring dynamic nature evolving scientific landscape.

Language: Английский

Citations

11
DANTE and DANTE_LTR: lineage-centric annotation pipelines for long terminal repeat retrotransposons in plant genomes DOI Creative Commons
Petr Novák,

Nina Hoštáková,

Pavel Neumann

et al.

NAR Genomics and Bioinformatics, Journal Year: 2024, Volume and Issue: 6(3)

Published: July 2, 2024

Long terminal repeat (LTR) retrotransposons constitute a predominant class of repetitive DNA elements in most plant genomes. With the increasing number sequenced genomes, there is an ongoing demand for computational tools facilitating efficient annotation and classification LTR genome assemblies. Herein, we introduce DANTE, pipeline Domain-based ANnotation Transposable Elements, designed sensitive detection these via their conserved protein domain sequences. The identified domains are subsequently inputted into DANTE_LTR to annotate complete element sequences by detecting structural features, such as LTRs, adjacent genomic regions. Leveraging allows precise phylogenetic lineages, offering more granular compared with coarser conventional superfamily-based methods. efficiency accuracy this approach were evidenced 93 Results benchmarked against several established pipelines, showing that capable identifying significantly intact retrotransposons. DANTE provided user-friendly Galaxy accessible public server (https://repeatexplorer-elixir.cerit-sc.cz), installable on local instances from tool shed or executable command line.

Language: Английский

Citations

6
De novo genome assembly of white clover (Trifolium repens L.) reveals the role of copy number variation in rapid environmental adaptation DOI Creative Commons
Wen‐Hsi Kuo, Sara J. Wright,

Linda L. Small

et al.

BMC Biology, Journal Year: 2024, Volume and Issue: 22(1)

Published: Aug. 7, 2024

White clover (Trifolium repens) is a globally important perennial forage legume. This species also serves as an eco-evolutionary model system for studying within-species chemical defense variation; it features well-studied polymorphism cyanogenesis (HCN release following tissue damage), with higher frequencies of cyanogenic plants favored in warmer locations worldwide. Using newly generated haplotype-resolved genome and two other long-read assemblies, we tested the hypothesis that copy number variants (CNVs) at genes play role ability white to rapidly adapt local environments. We examined questions on subgenome evolution this recently evolved allotetraploid chromosomal rearrangements broader IRLC legume clade.

Language: Английский

Citations

4
TEclass2: Classification of transposable elements using Transformers DOI Creative Commons

Lucas Bickmann,

Matías Rodríguez, Xiaoyi Jiang

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Oct. 16, 2023

Abstract Motivation Transposable elements (TEs) are interspersed repetitive sequences that major constituents of most eukaryotic genomes and crucial for genome evolution. Despite the existence multiple tools their classification annotation, none them can achieve completely reliable results making it a challenge genomic studies. In this work, we introduce TEclass2, new software uses deep learning approach based upon linear Transformer architecture with k-mer to-kenizer further adaptations to handle DNA sequences. This has an easy configuration allows training models on datasets TE providing metrics evaluation results. Results work shows successful adaptation Transformers from consensus sequences, these lay foundation novel methodologies in bioinformatics. We provide tool custom data web page interface pre-trained dataset curated non-curated libraries allowing fast simple TEs. Availability https://bioinformatics.uni-muenster.de/tools/teclass2/index.pl Contact [email protected] Supplementary information available at Bioinformatics online.

Language: Английский

Citations

7
BERTE: High-precision hierarchical classification of transposable elements by a transfer learning method with BERT pre-trained model and convolutional neural network DOI Creative Commons
Yiqi Chen, Yang Qi,

Yingfu Wu

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 31, 2024

Abstract Transposable Elements (TEs) are abundant repeat sequences found in living organisms. They play a pivotal role biological evolution and gene regulation intimately linked to human diseases. Existing TE classification tools can classify classes, orders, superfamilies concurrently, but they often struggle effectively extract sequence features. This limitation frequently results subpar results, especially hierarchical classification. To tackle this problem, we introduced BERTE, tool for BERTE encoded into distinctive features that consisted of both attentional cumulative k-mer frequency information. By leveraging the multi-head self-attention mechanism pre-trained BERT model, transformed Additionally, calculated multiple vectors concatenate them form Following feature extraction, parallel Convolutional Neural Network (CNN) model was employed as an efficient classifier, capitalizing on its capability high-dimensional transformation. We evaluated BERTE’s performance filtered datasets collected from 12 eukaryotic databases. Experimental demonstrated could improve F1-score at different levels by up 21% compared current state-of-the-art methods. Furthermore, indicated not only better characterize also CNN more than other popular deep learning classifiers. In general, classifies with greater precision. is available https://github.com/yiqichen-2000/BERTE .

Language: Английский

Citations

2
Efficient homology‐based annotation of transposable elements using minimizers DOI Creative Commons
Laura González, Daniela Lozano‐Arce,

Juan Pablo Londoño

et al.

Applications in Plant Sciences, Journal Year: 2023, Volume and Issue: 11(4)

Published: May 11, 2023

Transposable elements (TEs) make up more than half of the genomes complex plant species and can modulate expression neighboring genes, producing significant variability agronomically relevant traits. The availability long-read sequencing technologies allows building genome assemblies for with large genomes. Unfortunately, TE annotation currently represents a bottleneck in assemblies.

Language: Английский

Citations

5
Look4LTRs: a Long terminal repeat retrotransposon detection tool capable of cross species studies and discovering recently nested repeats DOI Creative Commons

Anthony B. Garza,

Emmanuelle Lerat, Hani Z. Girgis

et al.

Mobile DNA, Journal Year: 2024, Volume and Issue: 15(1)

Published: April 16, 2024

Plant genomes include large numbers of transposable elements. One particular type these elements is flanked by two Long Terminal Repeats (LTRs) and can translocate using RNA. Such are known as LTR-retrotransposons; they the most abundant transposons in plant genomes. They have many important functions involving gene regulation rise new genes pseudo response to severe stress. Additionally, LTR-retrotransposons several applications biotechnology. Due abundance importance LTR-retrotransposons, multiple computational tools been developed for their detection. However, none take advantages availability related genomes; process one chromosome at a time. Further, recently nested (multiple same family inserted into each other) cannot be annotated accurately - or all currently available tools. Motivated overcome limitations, we built Look4LTRs, which annotate simultaneously discover The methodology Look4LTRs depends on techniques imported from signal-processing field, graph algorithms, machine learning with minimal use alignment algorithms. Four were used developing eight evaluating it contrast three fastest while maintaining better comparable F1 scores (the harmonic average recall precision) those obtained other Our results demonstrate added benefit annotating ability Expert human manual examination six not included ground truth revealed that belong families likely families. With respect examining out five confirmed valid its speed, accuracy, novel features represents true advancement annotation opening door studies focused understanding plants.

Language: Английский

Citations

1