A Draft Genome of the Ginger Species Alpinia nigra and New Insights into the Genetic Basis of Flexistyly

Abstract

Angiosperms possess various strategies to ensure reproductive success, such as stylar polymorphisms that encourage outcrossing. Here, we investigate the genetic basis of one such dimorphism that combines both temporal and spatial separation of sexual function, termed flexistyly. It is a floral strategy characterised by the presence of two morphs that differ in the timing of stylar movement. We performed a de novo assembly of the genome of Alpinia nigra using high-depth genomic sequencing. We then used Pool-seq to identify candidate regions for flexistyly based on allele frequency or coverage differences between pools of anaflexistylous and cataflexistylous morphs. The final genome assembly size was 2 Gb, and showed no evidence of recent polyploidy. The Pool-seq did not reveal large regions with high FST values, suggesting large structural chromosomal polymorphisms are unlikely to underlie differences between morphs. Similarly, no region had a 1:2 mapping depth ratio which would be indicative of hemizygosity. We propose that flexistyly is governed by a small genomic region that might be difficult to detect with Pool-seq, or a complex genomic region that proved difficult to assemble. Our genome will be a valuable resource for future studies of gingers, and provides the first steps towards characterising this complex floral phenotype.

Multi-omics Comparison among Populations of Three Plant Sources of Amomi Fructus

“…The length of 24 pseudochromosomes was from 151,371,763 (chr_01) to 66,131,911 bp (chr_24) (Figure 1B and Table S1). The genome size of WVV was almost the same as the published WVV genome size (2.80 Gb) 17 and 1.4~2.9 times larger than that of other Zingiberaceae species [41][42][43][44] . The average GC content of WVV genome was 40.73% (Table 1).…”

The genomic and bulked segregant analysis of Curcuma alismatifolia revealed its diverse bract pigmentation

“…Currently, only three genomes from Zingiberaceae have been published, including Alpinia nigra (Ranavat et al 2021 ), Z. officinale (Cheng et al 2021b ; Li et al 2021 ), and C. longa (Chakraborty et al 2021 ), of which C. longa is only a draft genome. Here, we present the chromosome-scale assembly of C. alismatifolia , the first genome in Curcuma .…”

Highly Contiguous Plant Genome Assembly and Transcriptional Regulation

“…Currently, numerous species have seen completed molecular markers, gene mining and cloning, and the functional identification of important agronomic traits, marking the onset of the post-genome era. However, research on Zingiberaceae is still in its nascent stages, with only a few genomes having been sequenced, including those of Amomum tsao-ko (Li et al, 2022), Zingiber officinale (Cheng et al, 2021b;Li et al, 2021a), Wurfbainia villosa , Curcuma alismatifolia (Liao et al, 2022), Curcuma longa (Chakraborty et al, 2021), and Alpinia nigra (Ranavat et al, 2021). It is worth noting that the genomes of Curcuma longa and Alpinia nigra are only a sketch, meaning that the whole-genome information of genus Alpinia has yet to be revealed or reported.…”