Abstract
Genome duplication and repeat multiplication contribute to genome evolution in plants. Our previous work identified a recent allotetraploidization event and five high-copy LTR retrotransposon (LTR-RT) families PgDel, PgTat, PgAthila, PgTork, and PgOryco in Panax ginseng. Here, using whole-genome sequences, we quantified major repeats in five Panax species and investigated their role in genome evolution. The diploids P. japonicus, P. vietnamensis, and P. notoginseng and the tetraploids P. ginseng and P. quinquefolius were analyzed alongside their relative Aralia elata. These species possess 0.8–4.9 Gb haploid genomes. The PgDel, PgTat, PgAthila, and PgTork LTR-RT superfamilies accounted for 39–52% of the Panax species genomes and 17% of the A. elata genome. PgDel included six subfamily members, each with a distinct genome distribution. In particular, the PgDel1 subfamily occupied 23–35% of the Panax genomes and accounted for much of their genome size variation. PgDel1 occupied 22.6% (0.8 Gb of 3.6 Gb) and 34.5% (1.7 Gb of 4.9 Gb) of the P. ginseng and P. quinquefolius genomes, respectively. Our findings indicate that the P. quinquefolius genome may have expanded due to rapid PgDel1 amplification over the last million years as a result of environmental adaptation following migration from Asia to North America.
Highlights
Nuclear genome sizes in flowering plants are diverse, and can vary over 2,400-fold, ranging from 63 Mb in Genlisea margaretae to 149 Genome number size (Gb) in Paris japonica[1]
We determined the amount of each repeat by calculating its genomic proportion (GP) in each Whole genome sequence (WGS), via quantification of homologous nucleotides in each WGS based on repeat masking using RepeatMasker[28]
We estimated the prevalence of each repeat by determining GP using various WGS data sets, based on the calculation of masked homologous sequence in WGS reads by RepeatMasker[28]
Summary
Nuclear genome sizes in flowering plants are diverse, and can vary over 2,400-fold, ranging from 63 Mb in Genlisea margaretae to 149 Gb in Paris japonica[1]. The family Araliaceae is composed of approximately 55 genera and 1,500 species, which include many valuable medicinal and ornamental plants[14] Within this family, the genus Panax contains economically important medicinal plants including the diploids P. japonicus, P. vietnamensis, and P. notoginseng (2n = 2x = 24), and the tetraploids P. quinquefolius and P. ginseng (2n = 4x = 48). The genus Panax contains economically important medicinal plants including the diploids P. japonicus, P. vietnamensis, and P. notoginseng (2n = 2x = 24), and the tetraploids P. quinquefolius and P. ginseng (2n = 4x = 48) These five species are perennial and absolute shade plants that have been used for medicinal purposes in Asia and North America because of their beneficial effects on human health[15]. Our comparative analysis revealed dynamic impacts of these major repeats on genome size variation, speciation, and evolution in the Panax genus
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