Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline

Genome biology, Journal Year: 2019, Volume and Issue: 20(1)

Published: Dec. 16, 2019

Abstract Background Sequencing technology and assembly algorithms have matured to the point that high-quality de novo is possible for large, repetitive genomes. Current assemblies traverse transposable elements (TEs) provide an opportunity comprehensive annotation of TEs. Numerous methods exist each class TEs, but their relative performances not been systematically compared. Moreover, a pipeline needed produce non-redundant library TEs species lacking this resource generate whole-genome TE annotations. Results We benchmark existing programs based on carefully curated rice evaluate performance annotating long terminal repeat (LTR) retrotransposons, inverted (TIR) transposons, short TIR transposons known as miniature (MITEs), Helitrons. Performance metrics include sensitivity, specificity, accuracy, precision, FDR, F 1 . Using most robust programs, we create called Extensive de-novo Annotator (EDTA) produces filtered structurally intact fragmented elements. EDTA also deconvolutes nested insertions frequently found in highly genomic regions. other model with libraries (maize Drosophila), shown be across both plant animal species. Conclusions The benchmarking results developed here will greatly facilitate eukaryotic These annotations promote much more in-depth understanding diversity evolution at intra- inter-species levels. open-source freely available: https://github.com/oushujun/EDTA

Language: Английский

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De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

Science, Journal Year: 2021, Volume and Issue: 373(6555), P. 655 - 662

Published: Aug. 5, 2021

We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as founders maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. results demonstrate ancient tetraploid character continues to degrade by fractionation present day. Excellent contiguity over repeat arrays complete annotation centromeres revealed additional variation major cytological landmarks. show combining structural single-nucleotide polymorphisms can improve power quantitative studies. also document at level DNA methylation unmethylated regions are enriched cis-regulatory elements contribute phenotypic variation.

Language: Английский

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F1000Research

F1000Research, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 19, 2025

The Madagascar periwinkle, Catharanthus roseus, belongs to the Apocynaceae family.This medicinal plant, endemic Madagascar, produces many important drugs including monoterpene indole alkaloids (MIA) vincristine and vinblastine used treat cancer worldwide.Here, we provide a new version of C. roseus genome sequence obtained through combination Oxford Nanopore Technologies long-reads Illumina short-reads.This more contiguous assembly consists 173 scaffolds with total length 581.128Mb an N50 12.241 Mb.Using publicly available RNAseq data, 21,061 protein coding genes were predicted functionally annotated.A 42.87% was annotated as transposable elements, most them being long-terminal repeats.Together increasing access MIA-producing plant genomes, this updated should ease evolutionary studies leading better understanding MIA biosynthetic pathway evolution.

Language: Английский

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Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations

Cell, Journal Year: 2021, Volume and Issue: 184(13), P. 3542 - 3558.e16

Published: May 28, 2021

Language: Английский

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A super pan-genomic landscape of rice

Cell Research, Journal Year: 2022, Volume and Issue: 32(10), P. 878 - 896

Published: July 12, 2022

Pan-genomes from large natural populations can capture genetic diversity and reveal genomic complexity. Using de novo long-read assembly, we generated a graph-based super pan-genome of rice consisting 251-accession panel comprising both cultivated wild species Asian African rice. Our reveals extensive structural variations (SVs) gene presence/absence variations. Additionally, our enables the accurate identification nucleotide-binding leucine-rich repeat genes characterization their inter- intraspecific diversity. Moreover, uncovered grain weight-associated SVs which specify traits by affecting expression nearby genes. We characterized variants associated with submergence tolerance, seed shattering plant architecture found independent selection for common set that drove adaptation domestication in This facilitates pinpointing lineage-specific haplotypes trait-associated provides insights into evolutionary events have shaped various species.

Language: Английский

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Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance

Nature Genetics, Journal Year: 2024, Volume and Issue: 56(4), P. 710 - 720

Published: March 15, 2024

Abstract Polyploidy (genome duplication) is a pivotal force in evolution. However, the interactions between parental genomes polyploid nucleus, frequently involving subgenome dominance, are poorly understood. Here we showcase analyses of bamboo system (Poaceae: Bambusoideae) comprising series lineages from diploid (herbaceous) to tetraploid and hexaploid (woody), with 11 chromosome-level de novo genome assemblies 476 transcriptome samples. We find that woody subgenomes exhibit stunning karyotype stability, parallel dominance two clades gradual shift clade. Allopolyploidization have shaped evolution tree-like lignified culms, rapid growth synchronous flowering characteristic bamboos as large grasses. Our work provides insights into remarkable system, including its dependence on genomic context ability switch which dominant over evolutionary time.

Language: Английский

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Rapid and dynamic evolution of a giant Y chromosome in Silene latifolia

Science, Journal Year: 2025, Volume and Issue: 387(6734), P. 637 - 643

Published: Feb. 6, 2025

Some plants have massive sex-linked regions. To test hypotheses about their evolution, we sequenced the genome of Silene latifolia , in which giant heteromorphic sex chromosomes were first discovered 1923. It has long been known that Y chromosome consists mainly a male-specific region does not recombine with X and carries sex-determining genes other male functions. However, only whole assembly can candidate be validated experimentally locations determined related to suppression recombination. We describe genomic changes as ancestral evolved into current XY pair, testing ideas evolution large nonrecombining regions mechanisms created present recombination pattern.

Language: Английский

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Mapping regulatory variants controlling gene expression in drought response and tolerance in maize

Genome biology, Journal Year: 2020, Volume and Issue: 21(1)

Published: July 6, 2020

Abstract Background Gene expression is a key determinant of cellular response. Natural variation in gene bridges genetic to phenotypic alteration. Identification the regulatory variants controlling response drought, major environmental threat crop production worldwide, great value for drought-tolerant identification. Results A total 627 RNA-seq analyses are performed 224 maize accessions which represent wide diversity under three water regimes; 73,573 eQTLs detected about 30,000 expressing genes with high-density genome-wide single nucleotide polymorphisms, reflecting comprehensive and dynamic architecture drought. The constitutively or drought-dynamically unraveled. Focusing on resolved encoding transcription factors, drought-responsive network hierarchy factors their target built. Moreover, 97 prioritized associate drought tolerance due variations through Mendelian randomization analysis. One candidate genes, Abscisic acid 8′-hydroxylase , verified play negative role plant tolerance. Conclusions This study unravels effects dynamics allows us better understand distal proximal plasticity. drought-associated may serve as direct targets functional investigation allelic mining.

Language: Английский

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DeepTE: a computational method for de novo classification of transposons with convolutional neural network

Bioinformatics, Journal Year: 2020, Volume and Issue: 36(15), P. 4269 - 4275

Published: May 12, 2020

Abstract Motivation Transposable elements (TEs) classification is an essential step to decode their roles in genome evolution. With a large number of genomes from non-model species becoming available, accurate and efficient TE has emerged as new challenge genomic sequence analysis. Results We developed novel tool, DeepTE, which classifies unknown TEs using convolutional neural networks (CNNs). DeepTE transferred sequences into input vectors based on k-mer counts. A tree structured process was used where eight models were trained classify super families orders. also detected domains inside correct false classification. An additional model distinguish between non-TEs plants. Given unclassified different species, can seven orders, include 15, 24 16 plants, metazoans fungi, respectively. In several benchmarking tests, outperformed other existing tools for conclusion, successfully leverages CNN classification, be precisely newly sequenced eukaryotic genomes. Availability implementation accessible at https://github.com/LiLabAtVT/DeepTE. Supplementary information data are available Bioinformatics online.

Language: Английский

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Transposable elements contribute to dynamic genome content in maize

The Plant Journal, Journal Year: 2019, Volume and Issue: 100(5), P. 1052 - 1065

Published: Aug. 5, 2019

Transposable elements (TEs) are ubiquitous components of eukaryotic genomes and can create variation in genome organization content. Most maize composed TEs. We developed an approach to define shared variable TE insertions across assemblies applied this method four (B73, W22, Mo17 PH207) with uniform structural annotations Among these we identified approximately 400 000 TEs that polymorphic, encompassing 1.6 Gb sequence. These polymorphic include a combination recent transposition events as well deletions older There examples within each the superfamilies they found distributed genome, including regions ancestry among individuals. many or near genes. In addition, there 2380 gene B73 located TEs, providing evidence for role contributing substantial differences annotated content genotypes. highly our survey temperate genomes, highlighting major contribution driving OPEN RESEARCH BADGES: This article has earned Open Data Badge making publicly available digitally-shareable data necessary reproduce reported results. The is at https://github.com/SNAnderson/maizeTE_variation; https://mcstitzer.github.io/maize_TEs.

Language: Английский

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