From tradition to innovation: conventional and deep learning frameworks in genome annotation

Briefings in Bioinformatics, Год журнала: 2024, Номер 25(3)

Опубликована: Март 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.

Язык: Английский

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Chromosome-scale genome assembly reveals how repeat elements shape non-coding RNA landscapes active during newt limb regeneration

Cell Genomics, Год журнала: 2025, Номер unknown, С. 100761 - 100761

Опубликована: Янв. 1, 2025

Язык: Английский

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The haplotype-resolved genome assembly of an ancient citrus variety provides insights into the domestication history and fruit trait formation of loose-skin mandarins

Genome biology, Год журнала: 2025, Номер 26(1)

Опубликована: Март 17, 2025

Loose-skin mandarins (LSMs) are among the oldest domesticated horticultural crops, yet their domestication history and genetic basis underlying formation of key selected traits remain unclear. We provide a chromosome-scale haplotype-resolved assembly for ancient Chinese citrus variety Nanfengmiju tangerine. Through integration 77 resequenced 114 published germplasm genomes, we categorize LSMs into 12 distinct groups based on population genomic analyses. infer that ancestors modern cultivated diverged from wild in Daoxian approximately 500,000 years ago, when they entered Yangtze Pearl River Basins. There, were four cultivation groups, forming cornerstone LSM cultivation. identify selective sweeps quantitative trait loci genes related to important fruit quality traits, including sweetness size. reveal co-selection sugar transporter metabolism associated with increased sweetness. Significant alterations auxin gibberellin signaling networks may contribute enlargement fruits. also comprehensive, high-spatiotemporal-resolution atlas allelic gene expression during development. detect 5890 allele pairs showing specific patterns significant increase variation levels. Our study provides valuable resources further revises origin LSMs, offering insights improvement plants.

Язык: Английский

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The brittle star genome illuminates the genetic basis of animal appendage regeneration

Nature Ecology & Evolution, Год журнала: 2024, Номер 8(8), С. 1505 - 1521

Опубликована: Июль 19, 2024

Species within nearly all extant animal lineages are capable of regenerating body parts. However, it remains unclear whether the gene expression programme controlling regeneration is evolutionarily conserved. Brittle stars a species-rich class echinoderms with outstanding regenerative abilities, but investigations into genetic bases in this group have been hindered by limited genomic resources. Here we report chromosome-scale genome assembly for brittle star Amphiura filiformis. We show that most rearranged among sequenced so far, featuring reorganized Hox cluster reminiscent rearrangements observed sea urchins. In addition, performed an extensive profiling during adult arm and identified sequential waves governing wound healing, proliferation differentiation. conducted comparative transcriptomic analyses other invertebrate vertebrate models appendage uncovered hundreds genes conserved dynamics, particularly proliferative phase regeneration. Our findings emphasize crucial importance to detect long-range conservation between vertebrates classical model systems.

Язык: Английский

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A high-quality, haplotype-phased genome reconstruction reveals unexpected haplotype diversity in a pearl oyster

DNA Research, Год журнала: 2022, Номер 29(6)

Опубликована: Сен. 12, 2022

Homologous chromosomes in the diploid genome are thought to contain equivalent genetic information, but this common concept has not been fully verified animal genomes with high heterozygosity. Here we report a near-complete, haplotype-phased, assembly of pearl oyster, Pinctada fucata, using hi-fidelity (HiFi) long reads and chromosome conformation capture data. This includes 14 pairs scaffolds (>38 Mb) corresponding (2n = 28). The accuracy assembly, as measured by an analysis k-mers, is estimated be 99.99997%. Moreover, haplotypes 95.2% 95.9%, respectively, complete single-copy BUSCO genes, demonstrating quality assembly. Transposons comprise 53.3% major contributor structural variations. Despite overall collinearity between haplotypes, one chromosomal contains megabase-scale non-syntenic regions, which necessarily have never detected resolved conventional haplotype-merged assemblies. These regions encode expanded gene families NACHT, DZIP3/hRUL138-like HEPN, immunoglobulin domains, multiplying immunity repertoire, hypothesize important for innate immune capability oysters. oyster provides insight into remarkable haplotype diversity animals.

Язык: Английский

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Near-gapless genome and transcriptome analyses provide insights into fruiting body development in Lentinula edodes

International Journal of Biological Macromolecules, Год журнала: 2024, Номер 263, С. 130610 - 130610

Опубликована: Март 5, 2024

Язык: Английский

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A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility

Genome Research, Год журнала: 2022, Номер 32(10), С. 1862 - 1875

Опубликована: Сен. 15, 2022

Despite insertions and deletions being the most common structural variants (SVs) found across genomes, not much is known about how these SVs vary within populations between closely related species, nor their significance in evolution. To address questions, we characterized evolution of indel using genome assemblies three

Язык: Английский

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A chromosome-level phased genome enabling allele-level studies in sweet orange: a case study on citrus Huanglongbing tolerance

Horticulture Research, Год журнала: 2022, Номер 10(1)

Опубликована: Ноя. 3, 2022

Sweet orange originated from the introgressive hybridizations of pummelo and mandarin resulting in a highly heterozygous genome. How alleles two species cooperate shaping sweet phenotypes under distinct circumstances is unknown. Here, we assembled chromosome-level phased diploid Valencia (DVS) genome with over 99.999% base accuracy 99.2% gene annotation BUSCO completeness. DVS enables allele-level studies for other hybrids between mandarin. We first configured an allele-aware transcriptomic profiling pipeline applied it to 740 transcriptomes. On average, 32.5% genes have significantly biased allelic expression Different cultivars, transgenic lineages, tissues, development stages, disease status all impacted expressions resulted diversified patterns orange, but particularly citrus Huanglongbing (HLB) shifted hundreds leaves calyx abscission zones. In addition, detected structural mutations HLB-tolerant mutant (T19) more sensitive (T78) through long-read sequencing. The irradiation-induced mostly involved double-strand breaks, while most spontaneous were transposon insertions. mutants, significant ratio alterations (≥1.5-fold) directly affected by those mutations. T19, located at translocated segment terminal upregulated, including

Язык: Английский

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DCiPatho: deep cross-fusion networks for genome scale identification of pathogens

Briefings in Bioinformatics, Год журнала: 2023, Номер 24(4)

Опубликована: Май 30, 2023

Abstract Pathogen detection from biological and environmental samples is important for global disease control. Despite advances in pathogen using deep learning, current algorithms have limitations processing long genomic sequences. Through the cross-fusion of cross, residual neural networks, we developed DCiPatho accurate based on integrated frequency features 3-to-7 k-mers. Compared with existing state-of-the-art algorithms, can be used to accurately identify distinct pathogenic bacteria infecting humans, animals plants. We evaluated both learned unlearned species genomics metagenomics datasets. an effective tool genomic-scale identification pathogens by integrating k-mers into networks. The source code publicly available at https://github.com/LorMeBioAI/DCiPatho.

Язык: Английский

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A nuclear genome assembly of an extinct flightless bird, the little bush moa

Science Advances, Год журнала: 2024, Номер 10(21)

Опубликована: Май 23, 2024

We present a draft genome of the little bush moa (

Язык: Английский

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