The Asian lotus (Nelumbo nucifera) pan-plastome: diversity and divergence in a living fossil grown for seed, rhizome, and aesthetics

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Abstract
The Asian lotus (Nelumbo nucifera) has a history of cultivation in Asia dating back over 3,000 years where it has been an important food crop producing edible rhizomes and seeds as well as flowers of great aesthetic and cultural value. Here, we de novo assembled the plastomes of 316 lotus accessions including five North American lotus (N. lutea) and 311 Asian lotus (N. nucifera) to construct a pan-plastome genome map, and investigate the phylogeography and genetic diversity among the only two extant species within this living fossil lineage. A total of 113 unique genes were annotated and plastome sizes varied between 163,457 and 163,672 bp with only minor differences in each of the four major genomic units. The most abundant nucleotide differences among plastomes were single nucleotide variants followed by insertions/deletions and block substitutions mainly found in intergenic spacer regions of the large single copy portion of the plastome. Seven well-supported genetic clusters were resolved using multiple different population structure analyses. The different lotus types (flower, seed, rhizome, or wild) were disproportionally assigned to multiple different genetic clusters. This pattern indicates that the domestication of Asian lotus involved multiple genetic origins and possible matrilineal introgression. Geographic mapping of accessions also revealed that genetic diversity is unevenly distributed with eastern China possessing the highest genetic diversity and regions such as Yunnan, Indonesian, and Thailand possessing unique haplotypes. These results provide an important maternal history of Nelumbo and necessary groundwork for future studies on intergenomic gene transfer, cytonuclear incompatibility, and conservation genetics.

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