Evolutionary analysis of the Moringa oleifera genome reveals a recent burst of plastid to nucleus gene duplications

Abstract

It is necessary to identify suitable alternative crops to ensure the nutritional demands of a growing global population. The genome of Moringa oleifera, a fast-growing drought-tolerant orphan crop with highly valuable agronomical, nutritional and pharmaceutical properties, has recently been reported. We model here gene family evolution in Moringa as compared with ten other flowering plant species. Despite the reduced number of genes in the compact Moringa genome, 101 gene families, grouping 957 genes, were found as significantly expanded. Expanded families were highly enriched for chloroplastidic and photosynthetic functions. Indeed, almost half of the genes belonging to Moringa expanded families grouped with their Arabidopsis thaliana plastid encoded orthologs. Microsynteny analysis together with modeling the distribution of synonymous substitutions rates, supported most plastid duplicated genes originated recently through a burst of simultaneous insertions of large regions of plastid DNA into the nuclear genome. These, together with abundant short insertions of plastid DNA, contributed to the occurrence of massive amounts of plastid DNA in the Moringa nuclear genome, representing 4.71%, the largest reported so far. Our study provides key genetic resources for future breeding programs and highlights the potential of plastid DNA to impact the structure and function of nuclear genes and genomes.

Chromosome‐scale assembly of the Moringa oleifera Lam. genome uncovers polyploid history and evolution of secondary metabolism pathways through tandem duplication

“…In terms of structural gene annotation, a combination of three strategies (ab initio prediction, protein homology, and RNA‐seq‐based evidence) and manual curation resulted in 22,714 protein‐coding genes, 93.1% of which (21,143 genes) are supported by transcriptome data together with isoforms from Iso‐seq in this new moringa assembly (AOCC v2), a number substantially higher than that of the previous one (AOCC v1), which represented approximately 77.9% of its estimated genome size and was annotated with a total of 18,451 genes (Chang et al., 2019; Ojeda‐Lopez et al., 2020). On average, predicted protein‐coding genes are 3,340 bp long and contain 5.5 exons, values that are slightly higher than that observed in the previous assembly of the moringa genome (Chang et al., 2019; Ojeda‐Lopez et al., 2020) (Table 2). Five libraries of RNA‐seq data from different moringa tissues were downloaded from the NCBI Short Read Sequence Archive (Supplemental Table S1) and aligned to the new moringa genome assembly (Pasha et al., 2020).…”

“…We found at least 11 glucosinolate‐related orthogroups including tandemly arranged genes in moringa. Two notable examples are formed by orthogroup HOG0000577, annotated as myrosinases, and orthogroup HOG0009822 annotated as encoding for GDSL‐type esterases/lipases, both of which were found to be specifically expanded in moringa and in agreement with what had been previously observed (Ojeda‐Lopez et al., 2020). Glucosinolates are relatively stable in nature and have no biological activity.…”

A chromosome-level assembly of the “Cascade” hop (Humulus lupulus) genome uncovers signatures of molecular evolution and improves time of divergence estimates for the Cannabaceae family

“…ICL penalizes clusters that overlap excessively and tends to prefer clusters with well-delineated separation (Biernacki et al , 2000). Our approach is adapted from previously described methods (Lang et al , 2018; Li et al , 2018; Shingate et al , 2020; Mabry et al , 2020; Ojeda-López et al , 2020).…”

A genome resource for Acacia, Australia’s largest plant genus

“…Here, we provide a bioinformatic method to determine and investigate the source of NUMPTs in genome assemblies. Accurate identification of NUMTs and NUPTs is important for genome assemblies, and for understanding their role during evolution [76,77].…”