Repeat-rich regions cause false positive detection of NUMTs: a case study in amphibians using an improved cane toad reference genome

Genome Biology and Evolution, Journal Year: 2024, Volume and Issue: 16(11)

Published: Nov. 1, 2024

Abstract Mitochondrial DNA (mtDNA) has been widely used in genetics research for decades. Contamination from nuclear of mitochondrial origin (NUMTs) can confound studies phylogenetic relationships and mtDNA heteroplasmy. Homology searches with are to detect NUMTs the genome. Nevertheless, false-positive detection is common when handling repeat-rich sequences, while fragmented genomes might result missing true NUMTs. In this study, we investigated different NUMT methods how quality genome assembly affects them. We presented an improved (aRhiMar1.3) invasive cane toad (Rhinella marina) additional long-read Nanopore 10× linked-read sequencing. The final was 3.47 Gb length 91.3% tetrapod universal single-copy orthologs (n = 5,310), indicating gene-containing regions were well assembled. 3 complementary (NUMTFinder, dinumt, PALMER) study landscape All yielded consistent results, showing very few Furthermore, expanded analyses other amphibians confirmed a weak relationship between size number present Amphibians repeat-rich, show that found highly repetitive prone inflation using homology-based without filters. Together, provides exemplar robustly identify complex confounding effects on concern.

Language: Английский

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Genomic Insights Into Genetic Basis of Evolutionary Conservatism and Innovation in Frogs

Integrative Zoology, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 11, 2024

Examining closely related species evolving in similar environments offers valuable insights into the mechanisms driving phylogenetic conservatism and evolutionary lability. This can elucidate intricate relationship between inheritance environmental factors. Nonetheless, precise genomic dynamics molecular underpinnings of this process remain enigmatic. study explores adaptation exhibited by two high-altitude frog species: Nanorana parkeri N. pleskei. We assembled a high-quality genome for Tibetan pleskei compared it to genomes their lowland relatives. Our findings reveal that these diverged approximately 16.6 million years ago, pointing possible ancestral colonization high-elevation habitats. Following colonization, significant adaptive evolution occurred both coding non-coding regions lineage. led notable phenotypic alterations, as evidenced reduced body size. Also, due purifying selection, most features persisted descendant species, indicating strong element conservatism. However, evolved novel adaptations exacerbated challenges Tibet Plateau, mainly hypoxia response. Furthermore, our analysis underscores critical role regulatory variations evolution. Notably, hub genes networks, such EGLN3, accumulated more they were transmitted from ancestors descendants. In sum, sheds light on profound lasting impact genetic heritage species'

Language: Английский

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Multi-omics analysis reveals the evolution, function, and regulatory mechanisms of SPF pheromones in Anurans

Communications Biology, Journal Year: 2024, Volume and Issue: 7(1)

Published: Dec. 20, 2024

Pheromones play a pivotal role in chemical communication across various taxa, with protein-based pheromones being particularly significant amphibian courtship and reproduction. In this study, we investigate the Emei music frog (Nidirana daunchina), which utilizes both acoustic signals for communication. Base on de novo assembled genome of male frog, identify substantial expansion four pheromone-related gene families associated Notably, six members two-domain three-finger protein (2D-TFP) family, belonging to sodefrin precursor-like factor (SPF) pheromone system, exhibited high specific expression post-axillary glands during breeding season. Structural evolutionary analyses confirm presence SPF system amphibians, classifiable into distinct classes (two within urodeles two anurans). We propose complete regulatory network governing secretion via hypothalamic-pituitary-testicular-breeding gland axis, suggest testosterone synthesis as pathway. Behavioral experiments further reveal previously unknown female-attractant anurans. Overall, these findings not only highlight underestimated diversity function anurans, but also provide important insights evolution vertebrates. Multi-omics techniques facilitate comprehensive understanding mechanisms Anurans, shedding lights multi-modal

Language: Английский

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Genome assembly of the dyeing poison frog provides insights into the dynamics of transposable element and genome-size evolution

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

Published: Nov. 7, 2023

Abstract Genome size varies greatly across the tree of life and transposable elements are an important contributor to this variation. Among vertebrates, amphibians display greatest variation in genome size, making them ideal models explore causes consequences However, high-quality assemblies for have, until recently, been rare. Here, we generate a assembly dyeing poison frog, Dendrobates tinctorius . We compare publicly-available frog genomes find evidence both large-scale conserved synteny widespread rearrangements between lineages. Comparing orthologs annotated these revealed strong correlation gene size. To cause gene-size variation, quantified location relative features that accumulation introns has played role evolution D. , while estimates insertion times suggest many events recent species-specific. Finally, show diversity abundance can complicate genotyping efforts rely on repetitive as sequence anchors. Our results have clearly large Future studies needed fully understand dynamics element optimise primer or bait design cost-effective population-level species with large, genomes. Significance Amphibians more than any other vertebrate lineage. Complexities associated frequently hamper population genetic studies. Here use long-read HiFi sequences 6.3 Gbp leverage comparative genomics de novo annotations quantify aspects driven by elements. provide support dynamic play driving “genomic gigantism” amphibians. also how be leveraged cost-efficient using limited input material.

Language: Английский

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