Despite their suitability for studying evolution, many conifer species have large and repetitive giga-genomes (16-31 Gbp) that create hurdles to producing high coverage SNP data sets that capture diversity from across the entirety of the genome. Due in part to multiple ancient whole genome duplication events, gene family expansion and subsequent evolution within Pinaceae, false diversity from the misalignment of paralog copies creates further challenges in accurately and reproducibly inferring evolutionary history from sequence data. Here, we leverage the cost-saving benefits of pool-seq and exome-capture to discover SNPs in two conifer species, Douglas-fir (Pseudotsuga menziesii var. menziesii (Mirb.) Franco, Pinaceae) and jack pine (Pinus banksiana Lamb., Pinaceae). We show, using minimal baseline filtering, that allele frequencies estimated from pooled individuals show a strong, positive correlation with those estimated by sequencing the same population as individuals (r > .948), on par with such comparisons made in model organisms. Further, we highlight the utility of haploid megagametophyte tissue for identifying sites that are probably due to misaligned paralogs. Together with additional minor filtering, we show that it is possible to remove many of the loci with large frequency estimate discrepancies between individual and pooled sequencing approaches, improving the correlation further (r > .973). Our work addresses bioinformatic challenges in non-model organisms with large and complex genomes, highlights the use of megagametophyte tissue for the identification of paralogous artefacts, and suggests the combination of pool-seq and exome capture to be robust for further evolutionary hypothesis testing in these systems.
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http://dx.doi.org/10.1111/1755-0998.13474 | DOI Listing |
BMC Med Genomics
January 2025
The Affiliated Hospital of Yunnan University (The Second People's Hospital of Yunnan Province), Kunming, Yunnan Province, China.
Purpose: To explore possible pathogenic genes for concomitant exotropia using whole-exome sequencing.
Methods: In this study, 47 individuals from 10 concomitant exotropia (including intermittent exotropia and constant exotropia) pedigrees were enrolled. Whole-exome sequencing was used to screen mutational profiles in 25 affected individuals and 10 unaffected individuals.
Mov Disord Clin Pract
January 2025
Department of Neurology, All India Institute of Medical Sciences, New Delhi, India.
Sci Rep
January 2025
Laboratory for Regenerative Biology, National Institute for Basic Biology, Okazaki, Aichi, Japan.
Analysis of genome-scale evolution has been difficult in large, endangered animals because opportunities to collect high-quality genetic samples are limited. There is a need for novel field-friendly, cost-effective genetic techniques. This study conducted an exome-wide analysis of a total of 42 chimpanzees (Pan troglodytes) across six African regions, providing insights into population discrimination techniques.
View Article and Find Full Text PDFCommun Med (Lond)
December 2024
National Clinical Research Center for Ocular Diseases, Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
Background: High myopia (HM), characterized by a severe myopic refractive error, stands as a leading cause of visual impairment and blindness globally. HM is a multifactorial ocular disease that presents high genetic heterogeneity. Employing a genetic risk score (GRS) is useful for capturing genetic susceptibility to HM.
View Article and Find Full Text PDFZhonghua Er Bi Yan Hou Tou Jing Wai Ke Za Zhi
December 2024
Medical Genetics Center, Gansu Provincial Maternity and Child-care Hospital, Gansu Provincial Central Hospital, Lanzhou730050, China Gansu Provincial Clinical Research Center for Birth Defects and Rare Diseases, Lanzhou730050, China.
To investigate the clinical and genetic characteristics of nonsyndromic sensorineural hearing loss caused by biallelic variation. A child with hearing impairment who was diagnosed at Gansu Provincial Maternal and Child Health Hospital on May 2022 and was selected as the research object. Peripheral blood of the child and her parents was collected, genomic DNA was extracted.
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