Rapid amplification of four retrotransposon families promoted speciation and genome size expansion in the genus Panax

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.

Genome and evolution of the shade‐requiring medicinal herb Panax ginseng

“…Tetraploids P. ginseng and P. quinquefolius formed~2.59 MYA (Figure 2a). Five uniquely enriched LTR-RT families (PgDel, PgTat, PgAthila, PgTork and PgSire;Choi et al, 2014;Jang et al, 2017;Lee et al, 2017a) occupy >50% of the genome. PgDel LTR-RTs largely account for genome size variation among seven Panax species (Figure 2b,e).…”

Comparative analysis of DNA repeats and identification of novel Fesreba centromeric element in fescues and ryegrasses

“…This observation indicates a burst of Athila LTR element linked with Lolium speciation. It is known, that activation and integration of transposable elements may occur, e.g., due to environment change, lead to a rapid burst in a species-specific manner [45,46,56] and impact the evolution and speciation [45,57]. In some species, rapid increase of lineage-specific retroelements can also result in significant genome upsizing [23,[57][58][59], which was not observed in fescues and ryegrasses included in our study.…”

Characterization of Chromosome-Specific Microsatellite Repeats and Telomere Repeats Based on Low Coverage Whole Genome Sequence Reads in Panax ginseng

“…Recently, our studies revealed the evolution of major repeats in Panax genus Lee et al 2017). We also provided distribution pattern of these major repeats and established chromosome identification system using these repeats .…”