intansv: an R package for integrative analysis of structural variations

Lee, Jia; Liu, Na; Huang, Fangfang; Zhou, Zhengfu; He, Xin; Li, Haoran; Wang, Zhizhan; Yao, Wen

doi:10.7717/peerj.8867

Cited by 6 publications

(4 citation statements)

References 25 publications

(35 reference statements)

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“…CNVs calls were filtered as follows: length greater than 1 kb, P-value (first e-value) < 0.01, q0 < 50%, and pN < 50%. The R package intansv v1.12.0 [ 94 ] was used to find correspondence between the identified CNVs and the genes in the potato genome. For this purpose, the CNVpytor output files were converted to the format required for input by removing the last two columns (pN and dG).…”

Section: Methodsmentioning

confidence: 99%

Analysis of Genome Structure and Its Variations in Potato Cultivars Grown in Russia

Karetnikov

Vasiliev

Toshchakov

et al. 2023

IJMS

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Solanum tuberosum L. (common potato) is one of the most important crops produced almost all over the world. Genomic sequences of potato opens the way for studying the molecular variations related to diversification. We performed a reconstruction of genomic sequences for 15 tetraploid potato cultivars grown in Russia using short reads. Protein-coding genes were identified; conserved and variable parts of pan-genome and the repertoire of the NBS-LRR genes were characterized. For comparison, we used additional genomic sequences for twelve South American potato accessions, performed analysis of genetic diversity, and identified the copy number variations (CNVs) in two these groups of potato. Genomes of Russian potato cultivars were more homogeneous by CNV characteristics and have smaller maximum deletion size in comparison with South American ones. Genes with different CNV occurrences in two these groups of potato accessions were identified. We revealed genes of immune/abiotic stress response, transport and five genes related to tuberization and photoperiod control among them. Four genes related to tuberization and photoperiod were investigated in potatoes previously (phytochrome A among them). A novel gene, homologous to the poly(ADP-ribose) glycohydrolase (PARG) of Arabidopsis, was identified that may be involved in circadian rhythm control and contribute to the acclimatization processes of Russian potato cultivars.

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Section: Methodsmentioning

confidence: 99%

Analysis of Genome Structure and Its Variations in Potato Cultivars Grown in Russia

Karetnikov

Vasiliev

Toshchakov

et al. 2023

IJMS

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“…Samples were individually called by DELLY and merged into a single vcf file using BCFtools merge 24 . The vcf was read into R using intansv 29 and VariantAnnotation 30 packages. Regions were filtered for length (90 – 20,000 bp) and at least two supporting reads.…”

Section: Methodsmentioning

confidence: 99%

Spatiotemporal variations in retrovirus-host interactions among Darwin’s finches

Hill

Lillie

Pettersson

et al. 2022

Preprint

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Endogenous retroviruses (ERVs) are inherited remnants of past retroviruses that colonized host germline over millions of years, providing a sampling of retroviral diversity across time. The utility of ERVs as markers of host genome evolution is augmented by their ability to reveal historic retrovirus-host interactions, given that ERVs are examples of active retroviruses at the time of germline invasion. Here, we utilize the strength of Darwin's finches, a system synonymous with evolutionary studies, for investigating ERV history, revealing recent retrovirus-host interactions in natural populations. By mapping ERV variation across all species of Darwin's finches and comparing with outgroup species, we highlight geographical and historical patterns of retrovirus-host occurrence, utilizing the system as a natural model for evaluating the extent and timing of retroviral activity in hosts undergoing adaptive radiation and colonization of new environments. We found shared ERVs among all samples indicating retrovirus-host associations pre-dating host speciation, as well as considerable ERV variation across populations of the entire Darwin's finches' radiation. Unexpected ERV variation in finch species on different islands suggest historical changes in gene flow and selection. Non-random distribution of ERVs along and between chromosomes, as well as across finch species, suggests association between ERV accumulation and the rapid speciation of Darwin's finches.

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“…The seven WGS samples had on average 311,500 SV calls (range 310,900–311,900), of which on average 1915 (range 1855–1949) had been called by at least two different callers. SV calls across all samples were combined using the R package intanSV (Jia et al 2020 ) by merging the calls that had been made in at least two samples with a reciprocal coordinate overlap larger than 10%. There were a total of 26,799 overlapped calls, 22,954 deletions, 3105 duplications, and 740 inversions.…”

Section: Methodsmentioning

confidence: 99%

Whole-genome sequencing identifies functional noncoding variation in SEMA3C that cosegregates with dyslexia in a multigenerational family

et al. 2021

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Dyslexia is a common heritable developmental disorder involving impaired reading abilities. Its genetic underpinnings are thought to be complex and heterogeneous, involving common and rare genetic variation. Multigenerational families segregating apparent monogenic forms of language-related disorders can provide useful entrypoints into biological pathways. In the present study, we performed a genome-wide linkage scan in a three-generational family in which dyslexia affects 14 of its 30 members and seems to be transmitted with an autosomal dominant pattern of inheritance. We identified a locus on chromosome 7q21.11 which cosegregated with dyslexia status, with the exception of two cases of phenocopy (LOD = 2.83). Whole-genome sequencing of key individuals enabled the assessment of coding and noncoding variation in the family. Two rare single-nucleotide variants (rs144517871 and rs143835534) within the first intron of the SEMA3C gene cosegregated with the 7q21.11 risk haplotype. In silico characterization of these two variants predicted effects on gene regulation, which we functionally validated for rs144517871 in human cell lines using luciferase reporter assays. SEMA3C encodes a secreted protein that acts as a guidance cue in several processes, including cortical neuronal migration and cellular polarization. We hypothesize that these intronic variants could have a cis-regulatory effect on SEMA3C expression, making a contribution to dyslexia susceptibility in this family.

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intansv: an R package for integrative analysis of structural variations

Cited by 6 publications

References 25 publications

Analysis of Genome Structure and Its Variations in Potato Cultivars Grown in Russia

Analysis of Genome Structure and Its Variations in Potato Cultivars Grown in Russia

Spatiotemporal variations in retrovirus-host interactions among Darwin’s finches

Whole-genome sequencing identifies functional noncoding variation in SEMA3C that cosegregates with dyslexia in a multigenerational family

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