HiFiAdapterFilt, a memory efficient read processing pipeline, prevents occurrence of adapter sequence in PacBio HiFi reads and their negative impacts on genome assembly

Sim, Sheina B.; Corpuz, Renée L.; Simmonds, Tyler J.; Geib, Scott M.

doi:10.1186/s12864-022-08375-1

Cited by 139 publications

(78 citation statements)

References 25 publications

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“…To generate this assembly, we removed remnant adapter sequences from the PacBio HiFi dataset using HiFiAdapterFilt [Version 1.0] ( Sim 2021 ) and assembled the initial set of contigs with the filtered PacBio reads using HiFiasm [Version 0.13-r308] ( Cheng et al 2021 ) (see Table 1 for assembly pipeline and relevant software). Next, we identified sequences corresponding to haplotypic duplications and contig overlaps on the primary assembly with purge_dups [Version 1.0.1] ( Guan et al 2020 ) and transferred them to the alternate assembly.…”

Section: Methodsmentioning

confidence: 99%

Reference Genome Assembly of the Big Berry Manzanita (Arctostaphylos glauca)

Huang

Escalona

Morrison

et al. 2021

Journal of Heredity

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Arctostaphylos (Ericaceae) species, commonly known as manzanitas, are an invaluable fire-adapted chaparral clade in the California Floristic Province (CFP), a world biodiversity hotspot on the west coast of North America. This diverse woody genus includes many rare and/or endangered taxa, and the genus plays essential ecological roles in native ecosystems. Despite their importance in conservation management, and the many ecological and evolutionary studies that have focused on manzanitas, virtually no research has been conducted on the genomics of any manzanita species. Here, we report the first genome assembly of a manzanita species, the widespread Arctostaphylos glauca. Consistent with the genomics strategy of the California Conservation Genomics project, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 271 scaffolds spanning 547Mb, close to the genome size estimated by flow cytometry. This assembly, with a scaffold N50 of 31Mb and BUSCO complete score of 98.2%, will be used as a reference genome for understanding the genetic diversity and the basis of adaptations of both common and rare and endangered manzanita species.

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Section: Methodsmentioning

confidence: 99%

Reference Genome Assembly of the Big Berry Manzanita (Arctostaphylos glauca)

Huang

Escalona

Morrison

et al. 2021

Journal of Heredity

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“…The SMRTcell (SMRT Cell 8M) was sequenced for 30 hours. The obtained raw reads were processed with the ccs tool v.6.2.0 (RRID:SCR_021174) to generate circular consensus sequences, and further filtered for remaining adapter sequences using HiFiAdapterFilt v. 2.0.0 (Sim et al 2022).…”

Section: Methodsmentioning

confidence: 99%

Genome assembly of the acoel flatworm Symsagittifera roscoffensis, a model for research on photosymbiosis

Martinez

Ustyantsev

Biryukov

et al. 2022

Preprint

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Symsagittifera roscoffensis is a well-known member of the order Acoela that lives in symbiosis with the algae Tetraselmis convolutae during its adult stage. Its natural habitat is the eastern coast of the Atlantic, where at specific locations thousands of individuals can be found lying in large pools on the surface of sand at low tide and in the sandy interstitial web at high tide. As a member of the Acoela it has been used as a proxy for early bilaterian animals; however, its phylogenetic position remains debated. In order to understand the basic structural characteristics of the acoel genome, we sequenced and assembled the genome of aposymbiotic S. roscoffensis. The size of S. roscoffensis genome was measured to be in range 910 - 940 Mb. Sequencing of the genome was performed using PacBio Hi-Fi technology. Hi-C and RNA-seq data were also generated to scaffold and annotate the genome. The resulting assembly is 1.1 Gb large (covering 118% of the estimated genome size) and highly continuous, with N50 scaffold size of 1.04 Mb. The repetitive fraction of the genome is 61%, of which 85% (half of the genome) are LTR retrotransposons. Genome-guided transcriptome assembly identified 34,493 genes, of which 29,351 are protein coding (BUSCO score 97.6%), and 30.2% of genes are spliced leader (SL) trans-spliced. The completeness of this genome suggests that it can be used extensively to characterize gene families and conduct accurate phylogenomic reconstructions.

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“…Adapter-contaminated HiFi reads were filtered from the circular consensus sequencing (CCS) dataset using HiFiAdapterFilt v2.0 (Sim et al, 2022). Filtered CCS reads were assembled into a contig assembly using HiFiASM v0.16.1-r375 (Cheng et al 2021) with no modifications to the default parameters.…”

Section: Methodsmentioning

confidence: 99%

Whole-genome resequencing data support a single introduction of the invasive white pine sawfly, Diprion similis

Davis

Sim

Geib

et al. 2022

Preprint

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Biological introductions are unintended "natural experiments" that provide unique insights into evolutionary processes. Invasive phytophagous insects are of particular interest to evolutionary biologists studying adaptation, as introductions often require rapid adaptation to novel host plants. However, adaptive potential of invasive populations may be limited by reduced genetic diversity—a problem known as the "genetic paradox of invasions". One potential solution to this paradox is if there are multiple invasive waves that bolster genetic variation in invasive populations. Evaluating this hypothesis requires characterizing genetic variation and population structure in the introduced range. To this end, we assemble a reference genome and describe patterns of genetic variation in the introduced white pine sawfly, Diprion similis. This species was introduced to North America in 1914, where it has undergone a rapid host shift to the thin-needled eastern white pine (Pinus strobus), making it an ideal invasion system for studying adaptation to novel environments. To evaluate evidence of multiple introductions, we generated whole-genome resequencing data for 64 D. similis females sampled across the North American range. Both model-based and model-free clustering analyses supported a single population for North American D. similis. Within this population, we found evidence of isolation-by-distance and a pattern of declining heterozygosity with distance from the hypothesized introduction site. Together, these results support a single-introduction event. We consider implications of these findings for the genetic paradox of invasion and discuss priorities for future research in D. similis, a promising model system for invasion biology.

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HiFiAdapterFilt, a memory efficient read processing pipeline, prevents occurrence of adapter sequence in PacBio HiFi reads and their negative impacts on genome assembly

Cited by 139 publications

References 25 publications

Reference Genome Assembly of the Big Berry Manzanita (Arctostaphylos glauca)

Reference Genome Assembly of the Big Berry Manzanita (Arctostaphylos glauca)

Genome assembly of the acoel flatworm Symsagittifera roscoffensis, a model for research on photosymbiosis

Whole-genome resequencing data support a single introduction of the invasive white pine sawfly, Diprion similis

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