Haplotype-resolved genome assembly and allele- specific gene expression in cultivated ginger

Ginger(Zingiber officinale)is one of the most valued spice plants worldwide;it is prized for its culinary and folk medicinal applications and is therefore of high economic and cultural importance.Here,we present a haplotype-resolved,chromosome-scale assembly for diploid ginger anchored to 11 pseudochromosome pairs with a total length of 3.1 Gb.Remarkable structural variation was identified between haplotypes,and two inversions larger than 15Mb on chromosome 4 may be associated with ginger infertility.We performed a comprehensive,spatiotemporal,genome-wide analysis of allelic expression patterns,revealing that most alleles are coordinately expressed.The alleles that exhibited the largest differences in expression showed closer proximity to transposable elements,greater coding sequence divergence,more relaxed selection pressure,and more transcription factor binding site differences.We also predicted the transcription factors potentially regulating 6-gingerol biosynthesis.Our allele-aware assembly provides a powerful platform for future functional genomics,molecular breeding,and genome editing in ginger.

Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome

Polyploidization plays a key role in plant evolution,but the forces driving the fate of homoeologs in polyploid genomes,i.e.,paralogs resulting from a whole-genome duplication(WGD)event,remain to be elucidated.Here,we present a chromosome-scale genome assembly of tetraploid scarlet sage(Salvia splendens),one of the most diverse ornamental plants.We found evidence for three WGD events following an older WGD event shared by most eudicots(theγevent).A comprehensive,spatiotemporal,genome-wide analysis of homoeologs from the most recent WGD unveiled expression asymmetries,which could be associated with genomic rearrangements,transposable element proximity discrepancies,coding sequence variation,selection pressure,and transcription factor binding site differences.The observed differences between homoeologs may reflect the first step toward sub-and/or neofunctionalization.This assembly provides a powerful tool for understanding WGD and gene and genome evolution and is useful in developing functional genomics and genetic engineering strategies for scarlet sage and other Lamiaceae species.

“Winter Is Coming” : How did Polyploid Plants Survive?

Cold and dark periods have descended on Earth several times in geological history. One such period characterized the Cretaceous-Paleogene (K-Pg) boundary, following a meteor impact near Chicxulub in Mexico, about 66 million years ago, which caused dust, sulfate aerosols, and soot particles to be ejected into the atmosphere. This in turn led to a so-called “impact winter,” inhibiting photosynthesis and causing a global collapse of terrestrial and marine food webs, leading to the extinction of 60%–70% of plants and animals ( Alvarez et al., 1980 ). Different from animals that might still be able to find shelter and detritus food in a harsh environment, plants are sessile and require (lots of) light for photosynthesis. How did they survive in a time of prolonged darkness and decreasing temperatures ( Vellekoop et al., 2016 )?