The genome of the cold-adapted diatom Fragilariopsis cylindrus is characterized by highly diverged haplotypes that intersperse its homozygous genome. Here, we describe how a combination of PacBio DNA and Illumina RNA sequencing can be used to resolve this complex genomic landscape locally into the highly diverged haplotypes, and how to map various environmentally controlled transcripts onto individual haplotypes. We assembled PacBio sequence data with the FALCON assembler and created a haplotype resolved annotation of the assembly using annotations of a Sanger sequenced F. cylindrus genome. RNA-seq datasets from six different growth conditions were used to resolve allele-specifc gene expression in F. cylindrus. This approach enables to study differential expression of alleles in a complex genomic landscape and provides a useful tool to study how diverged haplotypes in diploid organisms are used for adaptation and evolution to highly variable environments.
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http://dx.doi.org/10.1038/sdata.2017.149 | DOI Listing |
Plants (Basel)
January 2025
Faculty of Forestry, University of Sarajevo, Zmaja od Bosne 8, 71 000 Sarajevo, Bosnia and Herzegovina.
Polyploidy is a powerful mechanism driving genetic, physiological, and phenotypic changes among cytotypes of the same species across both large and small geographic scales. These changes can significantly shape population structure and increase the evolutionary and adaptation potential of cytotypes. , an edaphic steno-endemic species with a narrow distribution in the Balkan Peninsula, serves as an intriguing case study.
View Article and Find Full Text PDFSci Adv
January 2025
Institute of Zoology, University of Cologne, Cologne, Germany.
Some unique asexual species persist over time and contradict the consensus that sex is a prerequisite for long-term evolutionary survival. How they escape the dead-end fate remains enigmatic. Here, we generated a haplotype-resolved genome assembly on the basis of a single individual and collected genomic data from worldwide populations of the parthenogenetic diploid oribatid mite to identify signatures of persistence without sex.
View Article and Find Full Text PDFFront Plant Sci
January 2025
Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
Background: The genus is endemic to China and belongs to the Apiaceae family, which is widely distributed in the Himalaya-Hengduan Mountains (HHM) region. However, its morphology, phylogeny, phylogeography, taxonomy, and evolutionary history were not investigated due to insufficient sampling and lack of population sampling and plastome data. Additionally, we found that was not similar to members but resembled species in morphology, indicating that the taxonomic position of needs to be re-evaluated.
View Article and Find Full Text PDFInt J Parasitol Parasites Wildl
April 2025
Department of Medical Parasitology & Mycology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.
is a parasite prevalent in the temperate regions of the vast Palearctic realm, including Iran. In this study, we investigated infection in road-killed animals and carcasses in northern and northeastern Iran by artificial digestion. We assessed species identification and intraspecific genetic diversity using the markers 5S ribosomal DNA intergenic spacer (5S rDNA), internal transcribed spacer I (ITS1), and cytochrome oxidase subunit I ().
View Article and Find Full Text PDFActa Trop
January 2025
Department of Public Health and Health Promotion, College of Allied Health Sciences, Suan Sunandha Rajabhat University, Samut Songkhram 75000, Thailand. Electronic address:
Mansonia dives is recognized as a vector for brugian filariasis in Thailand. A recent study analyzing the cytochrome c oxidase subunit I (COI) gene revealed two distinct clades within the Ma. dives population in Thailand.
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