Identification of tandem repeat families from long-read sequences of Humulus lupulus

Abstract

Hop (Humulus lupulus L.) is known for its use as a bittering agent in beer and has a rich history of cultivation, beginning in Europe and now spanning the globe. There are five wild varieties worldwide, which may have been introgressed with cultivated varieties. As a dioecious species, its obligate outcrossing, non-Mendelian inheritance, and genomic structural variability have confounded directed breeding efforts. Consequently, understanding the hop genome represents a considerable challenge, requiring additional resources. In order to facilitate investigations into the transmission genetics of hop, we report here a tandem repeat discovery pipeline developed using k-mer filtering and dot plot analysis of PacBio long-read sequences from the hop cultivar Apollo. From this we identified 17 new and distinct tandem repeat sequence families, which represent candidates for FISH probe development. For two of these candidates, HuluTR120 and HuluTR225, we produced oligonucleotide FISH probes from conserved regions of and demonstrated their utility by staining meiotic chromosomes from wild hop, var. neomexicanus to address, for example, questions about hop transmission genetics. Collectively, these tandem repeat sequence families represent new resources suitable for development of additional cytogenomic tools for hop research.

Hop (Humulus lupulus L.) extract reverts glycaemic imbalance and cognitive impairment in an animal model of obesity

“…That family includes the Humulus genus, of which the most studied species are Humulus lupulus L. 40 Humulus lupulus L. is a climbing plant that has a perennial, intertwined, dioecious biological cycle, found in the northern hemisphere in temperate zones commonly. 41,42 In, the inflorescences of the female plant give rise to "cones" (strobilus) that can secrete lupulin (resin) from glands. 40 The lupulin glands of hop flowers secrete powder rich in metabolites that can be classified into bitter acids (resinous), essential oils, and polyphenols.…”

Concerted and Independent Evolution of Control Regions 1 and 2 of Water Monitor Lizards (Varanus salvator macromaculatus) and Different Phylogenetic Informative Markers

“…Variable number of tandem repeats (VNTRs) have been reported to exist only at the 3′ end of both CRs [ 19 , 20 ]. Tandem repeat sequences, including the motif, length of repeats, and copy number in the CR region, were investigated using the Tandem Repeats Finder 4.09 program [ 21 ].…”

Novel Centromeric and Subtelomeric Repetitive DNA Sequences for Karyotyping the Bambara Groundnut (<b><i>Vigna subterranea</i></b> L. Verdc.)

“…Probes were detected on the chromosomes with streptavidin-conjugated Alexa Fluor 488 (Invitrogen) and rhodamine-conjugated anti-digoxigenin (Roche) antibodies. To detect telomeric sequences, a TAMRA-labeled probe was used [Easterling et al, 2020]. Chromosomes were counterstained with 4′,6-diamidino-2-phenylindole (DAPI).…”