MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads

BMC Bioinformatics, Journal Year: 2023, Volume and Issue: 24(1)

Published: July 18, 2023

Abstract Background PacBio high fidelity (HiFi) sequencing reads are both long (15–20 kb) and highly accurate (> Q20). Because of these properties, they have revolutionised genome assembly leading to more contiguous genomes. In eukaryotes the mitochondrial is sequenced alongside nuclear often at very coverage. A dedicated tool for using HiFi still missing. Results MitoHiFi was developed within Darwin Tree Life Project assemble genomes from generated target species. The input either raw or assembled contigs, outputs a sequence fasta file along with annotation protein RNA genes. Variants arising heteroplasmy independently, insertions sequences identified not used in organellar assembly. has been 374 (368 Metazoa 6 Fungi species) Project, Vertebrate Genomes Aquatic Symbiosis Genome Project. Inspection 60 species that already reference public databases showed widespread presence previously unreported repeats. Conclusions able wide phylogenetic range taxa Pacbio data. written python freely available on GitHub ( https://github.com/marcelauliano/MitoHiFi ). its dependencies as Docker container (ghcr.io/marcelauliano/mitohifi:master).

Language: Английский

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MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio High Fidelity reads

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Dec. 23, 2022

Abstract Background PacBio high fidelity (HiFi) sequencing reads are both long (15-20 kb) and highly accurate (>Q20). Because of these properties, they have revolutionised genome assembly leading to more contiguous genomes. In eukaryotes the mitochondrial is sequenced alongside nuclear often at very coverage. A dedicated tool for using HiFi still missing. Results MitoHiFi was developed within Darwin Tree Life Project assemble genomes from generated target species. The input either raw or assembled contigs, outputs a sequence fasta file along with annotation protein RNA genes. Variants arising heteroplasmy independently, insertions sequences identified not used in organellar assembly. has been 374 (369 12 phyla 39 orders Metazoa 6 species Fungi) Project, Vertebrate Genomes Aquatic Symbiosis Genome Project. Inspection 60 that already reference public databases showed widespread presence previously unreported repeats. Conclusions able wide phylogenetic range taxa Pacbio data. written python freely available on github ( https://github.com/marcelauliano/MitoHiFi ). its dependencies as singularity image (ghcr.io/marcelauliano/mitohifi:master).

Language: Английский

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Phylogenetic relationships and divergence times of Odonata inferred from mitochondrial genome

iScience, Journal Year: 2025, Volume and Issue: 28(2), P. 111806 - 111806

Published: Jan. 11, 2025

Understanding the origin and evolutionary history of Odonata are crucial, as they represent central members first winged lineages. Here, we assembled largest mitogenome dataset to date, comprising 143 mitogenomes representing three suborders, 18 families, which 53 were newly sequenced. Phylogenetic inferences demonstrate that is a powerful tool for resolving lower-level divergence within Odonata, it falls short in addressing higher-level relationships like suborder, superfamily, interfamily classifications. The was reconstructed by incorporating 11 fossil records, estimating occurred Jurassic, with Cretaceous emerging critical period initial radiation main Furthermore, employed calibration strategies from various studies calibrate our analyses, enabling investigation mito-nuclear discordance patterns time inferences. Our results revealed significant differences estimates inferred solely mitochondrial or nuclear data particularly pronounced when using older upper bounds values fossils.

Language: Английский

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Island songbirds as windows into evolution in small populations

Current Biology, Journal Year: 2021, Volume and Issue: 31(6), P. 1303 - 1310.e4

Published: Jan. 20, 2021

Language: Английский

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Fourteen New, Endemic Species of Shrew (Genus Crocidura) from Sulawesi Reveal a Spectacular Island Radiation

Bulletin of the American Museum of Natural History, Journal Year: 2021, Volume and Issue: 454(1)

Published: Dec. 14, 2021

After nearly a decade of field inventories in which we preserved voucher specimens the small terrestrial mammals Sulawesi, combined qualitative and quantitative analyses morphological traits with molecular phylogenetics to better understand diversity shrews (Soricidae: Crocidura) on island. We examined morphology 1368 obtained extensive data from many them, including mitochondrial DNA sequences 851 specimens, up five nuclear exons 657 thousands ultraconserved elements 90 specimens. By iteratively testing species limits using distinct character datasets appropriate taxon sampling, found clear, mostly consistent evidence for existence 21 only seven were previously recognized. divide these into morphogroups, provide emended diagnoses named species, describe 14 new species. The Long-Tailed Group contains Crocidura caudipilosa, C. elongata, microelongata, quasielongata, species; Rhoditis rhoditis, pseudorhoditis, australis, pallida, Small-Bodied lea, levicula, baletei, mediocris, parva, tenebrosa, Thick-Tailed brevicauda, caudicrassa, Ordinary musseri, nigripes, normalis, ordinaria, solita, Documenting endemic reveals local radiation (20 are members an clade) elevational gradients played prominent role either promoting speciation, or at minimum, fostering cooccurrence phenotypically similar As now understood, species-level Sulawesi is three times known any other insular shrew fauna. This study highlights fact that if wish true extent biodiversity Earth, large-scale, vouchered organismal followed thorough examinations genetic, morphological, geographic sorely needed montane tropical regions, even purportedly well-studied groups such as mammals.

Language: Английский

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A near-complete and time-calibrated phylogeny of the Old World flycatchers, robins and chats (Aves, Muscicapidae)

Molecular Phylogenetics and Evolution, Journal Year: 2022, Volume and Issue: 178, P. 107646 - 107646

Published: Oct. 17, 2022

The Old World flycatchers, robins and chats (Aves, Muscicapidae) are a diverse songbird family with over three hundred species. Despite continuous efforts the past two decades, there is still no comprehensive well-resolved species-level phylogeny for Muscicapidae. Here we present supermatrix that includes all 50 currently recognized genera ca. 92% of species, built using data from up to 15 mitochondrial 13 nuclear loci. In addition assembling nucleotide sequences available in public databases, also extracted genome assemblies raw sequencing reads GenBank included few unpublished sequences. Our analyses resolved phylogenetic position several previously unsampled taxa, example, Grand Comoro Flycatcher Humblotia flavirostris, Collared Palm Thrush Cichladusa arquata, Taiwan Whistling-Thrush Myophonus insularis, etc. We provide taxonomic recommendations exhibit paraphyly or polyphyly. results suggest Muscicapidae diverged Turdidae (thrushes allies) early Miocene, most recent common ancestors four subfamilies (Muscicapinae, Niltavinae, Cossyphinae Saxicolinae) arose around middle Miocene.

Language: Английский

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Mito-nuclear discordance within Anthozoa, with notes on unique properties of their mitochondrial genomes

Scientific Reports, Journal Year: 2023, Volume and Issue: 13(1)

Published: May 8, 2023

Whole mitochondrial genomes are often used in phylogenetic reconstruction. However, discordant patterns species relationships between and nuclear phylogenies commonly observed. Within Anthozoa (Phylum Cnidaria), (mt)-nuclear discordance has not yet been examined using a large comparable dataset. Here, we data obtained from target-capture enrichment sequencing to assemble annotate mt reconstruct for comparisons inferred hundreds of loci the same samples. The datasets comprised 108 hexacorals 94 octocorals representing all orders > 50% extant families. Results indicated rampant at every taxonomic level. This is attributable substitution saturation, but rather likely caused by introgressive hybridization unique properties genomes, including slow rates evolution driven strong purifying selection rate variation. Strong across caution their use analyses that rely on assumptions neutrality. Furthermore, were noted, genome rearrangements presence nad5 introns. Specifically, note homing endonuclease ceriantharians. dataset further demonstrates utility off-target reads generated assembly adds growing knowledge anthozoan evolution.

Language: Английский

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The genome sequence of the giant clam, Tridacna gigas (Linnaeus, 1758)

Wellcome Open Research, Journal Year: 2024, Volume and Issue: 9, P. 145 - 145

Published: March 19, 2024

We present a chromosomal-level genome assembly from an individual Tridacna gigas (the giant clam; Mollusca; Bivalvia; Veneroida; Cardiidae). The sequence is 1,175.9 megabases in span. Most of the scaffolded into 17 chromosomal pseudomolecules. mitochondrial has also been assembled and 25.34 kilobases length. Gene annotation this on Ensembl identified 18,177 protein coding genes.

Language: Английский

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GeneMiner: A tool for extracting phylogenetic markers from next‐generation sequencing data

Molecular Ecology Resources, Journal Year: 2024, Volume and Issue: 24(3)

Published: Jan. 10, 2024

Abstract The advancement of next‐generation sequencing (NGS) technologies has been revolutionary for the field evolutionary biology. This technology led to an abundance available genomes and transcriptomes researchers mine. Specifically, can mine various types molecular markers that are vital phylogenetic, ecological studies. Numerous tools have developed extract these from NGS data. However, due insufficient number well‐annotated reference non‐model organisms, it remains challenging obtain accurately efficiently. Here, we present GeneMiner, improved expanded version our previous tool, Easy353. GeneMiner combines reference‐guided de Bruijn graph assembly with seed self‐discovery greedy extension. Additionally, includes a verification step using parameter‐bootstrap method reduce pitfalls associated relatively distant reference. Our results, both experimental simulation data, showed acquire phylogenetic plants transcriptomic, genomic other is designed be user‐friendly, fast memory‐efficient. Further, compatible Linux, Windows macOS. All source codes publicly on GitHub ( https://github.com/sculab/GeneMine r) Gitee https://gitee.com/sculab/GeneMiner ) easy accessibility transparency.

Language: Английский

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Skimming genomes for systematics and DNA barcodes of corals

Ecology and Evolution, Journal Year: 2024, Volume and Issue: 14(5)

Published: May 1, 2024

Numerous genomic methods developed over the past two decades have enabled discovery and extraction of orthologous loci to help resolve phylogenetic relationships across various taxa scales. Genome skimming (or low-coverage genome sequencing) is a promising method not only extract high-copy but also 100s 1000s phylogenetically informative nuclear (e.g., ultraconserved elements [UCEs] exons) from contemporary museum samples. The subphylum Anthozoa, including important ecosystem engineers stony corals, black anemones, octocorals) in marine environment, critical need resolution thus might benefit genome-skimming approach. We conducted on 242 anthozoan corals collected 1886 2022. Using existing target-capture baitsets, we bioinformatically obtained UCEs exons data incorporated them with previously published studies. mean number UCE exon extracted was 1837 ± 662 SD for octocorals 1379 476 hexacorals. Phylogenetic were well resolved within each class. A 1422 720 historical specimens, 1253 recovered oldest specimen 1886. partial whole mitogenomes rRNA genes >95% Bioinformatically pulling UCEs, exons, mitochondrial genomes, viable low-cost option This approach can be used review support taxonomic revisions reconstruct evolutionary histories, type specimens.

Language: Английский

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