Genome of Plant Maca ( Lepidium meyenii ) Illuminates Genomic Basis for High-Altitude Adaptation in the Central Andes

Abstract

Maca (Lepidium meyenii Walp, 2n = 8x = 64), belonging to the Brassicaceae family, is an economic plant cultivated in the central Andes sierra in Peru (4000-4500 m). Considering that the rapid uplift of the central Andes occurred 5-10 million years ago (Ma), an evolutionary question arises regarding how plants such as maca acquire high-altitude adaptation within a short geological period. Here, we report the high-quality genome assembly of maca, in which two closely spaced maca-specific whole-genome duplications (WGDs; ∼6.7 Ma) were identified. Comparative genomic analysis between maca and closely related Brassicaceae species revealed expansions of maca genes and gene families involved in abiotic stress response, hormone signaling pathway, and secondary metabolite biosynthesis via WGDs. The retention and subsequent functional divergence of many duplicated genes may account for the morphological and physiological changes (i.e., small leaf shape and self-fertility) in maca in a high-altitude environment. In addition, some duplicated maca genes were identified with functions in morphological adaptation (i.e., LEAF CURLING RESPONSIVENESS) and abiotic stress response (i.e., GLYCINE-RICH RNA-BINDING PROTEINS and DNA-DAMAGE-REPAIR/TOLERATION 2) under positive selection. Collectively, the maca genome provides useful information to understand the important roles of WGDs in the high-altitude adaptation of plants in the Andes.

Genomic basis of parallel adaptation varies with divergence inArabidopsisand its relatives

“…To address our hypothesis at deeper phylogenetic scales, we performed a meta-analysis of gene-and function-level parallelism by complementing our data with gene candidate lists from six genome-wide studies of alpine adaptation from the Brassicaceae family [36][37][38][39][40][41] (species diverging 0.5 -18 millions of years ago 48,49 , Supplementary Tables 8, 9). We found significant parallelism both at the level of candidate genes (overlaps between 19 % of species pairs were significant, all within the Arabidopsis genus, p < 0.05, Fisher's exact test, Fig.…”

“…Arabidopsis halleri subsp. gemmifera from Japan 41 , aly: Arabidopsis lyrata from Northern Europe 39 , ath: Arabidopsis thaliana from Alps 38 , chi: Crucihimalaya himalaica 36 , lme: Lepidium meyenii 40 .…”

“…We gathered lists of gene candidates from all available studies focused on alpine adaptation in Brassicaceae [36][37][38][39][40][41] , i.e., adaptation towards treeless high-elevation habitats addressed by studies of whole genome sequence data ( Supplementary Table 8). We unified (merged) the gene candidate lists if multiple altitudinal gradients were screened within a species (except for A. halleri from Europe and Japan which were kept as separate units due to extraordinarily high spatial and genetic divergence of these two lineages) 61 .…”

“…Here, we aimed to test this hypothesis and investigate whether allele reuse is a major mechanism. We used replicated instances of adaptation to a challenging alpine environment, spanning a range of divergence from populations to tribes within the plant family Brassicaceae [36][37][38][39][40][41] (Fig. 1a).…”

Identification and characterization of microRNAs and their targets in high-altitude stress-adaptive plant maca (Lepidium meyenii Walp)

“…With the recent draft genome sequence available (http://www. herbal-genome.cn/) (Zhang et al 2016), it is important to exploit this information for better understanding the physiological processes in maca.…”