Novel subpopulations in date palm (Phoenix dactylifera) identified by population-wide organellar genome sequencing

Abstract

Background The date palm is one of the oldest cultivated fruit trees. The tree can withstand high temperatures and low water and the fruit can be stored dry offering nutrition across the year. The first region of cultivation is believed to be near modern day Iraq, however, where and if the date palm was domesticated is still a topic of debate. Recent studies of chloroplast and genomic DNA revealed two major subpopulations of cultivars centered in both the Eastern range of date palm cultivation including Arabian Peninsula, Iraq and parts of South Asia, and the Western range, including North Africa. Results To better understand the origins of date palm cultivation we sequenced and analyzed over 200 mitochondrial and chloroplast genomes from a geographically diverse set of date palms. Here we show that, based on mitochondrial and chloroplast genome-wide genotyping data, the most common cultivated date palms contain 4 haplotypes that appear associated with geographical region of cultivar origin. Conclusions These data suggest at least 3 and possibly 4 original maternal contributions to the current date palm population and doubles the original number. One new haplotype was found mainly in Tunisia, Algeria and Egypt and the second in Iraq, Iran and Oman. We propose that earliest date palm cultivation occurred independently in at least 3 distinct locations. This discovery will further inform understanding of the history and origins of cultivated date palm. Electronic supplementary material The online version of this article (10.1186/s12864-019-5834-7) contains supplementary material, which is available to authorized users.

Archaeogenomics of a ~2,100-year-old Egyptian leaf provides a new timestamp on date palm domestication

“…Comparisons of our plastid and nuclear topologies and population structure analysis conducted on two reference genomes representing contrasting levels of contiguity and completeness provide robust evidence for the genomic affiliation of the Saqqara leaf with modern North African P. dactylifera populations, as well as the occurrence of ancient gene flow between P. dactylifera, P. theophrasti, and P. sylvestris. The clustering of P. sylvestris with selected North African date palm cultivars in plastid phylogenies has been previously reported by several studies (Pintaud et al 2013;Chaluvadi et al, 2019;Flowers et al, 2019;Mohamoud et al, 2019), thus opening the question of whether gene flow or ancestral polymorphisms are responsible for such patterns (Flowers et al, 2019). Phoenix dactylifera and P. sylvestris overlap their distribution ranges in north western India and Pakistan, they are interfertile and known to produce fertile hybrids (Newton et al, 2013), suggesting that gene flow between both species is plausible.…”

“…In particular, one major haplotype (NA1, see Fig. 2 in Mohamoud et al, 2019) reported for North Africa is thought to be highly divergent from the remaining three haplotypes and is shared with P. sylvestris (Mohamoud et al, 2019). The trace of gene flow between the Saqqara leaf and P. sylvestris detected by our introgression analyses suggests that the recurrent clustering patterns of individuals from both species in plastid phylogenies could be derived from one or several chloroplast-capture processes mediated by hybridisation.…”

“…Recently, extensive sequencing of over 200 organellar genomes of P. dactylifera revealed that date palm cultivars contain four haplotypes that are tightly linked to the geographical origin of the cultivar (Mohamoud et al, 2019), but the time of their diversification is largely unknown. In particular, one major haplotype (NA1, see Fig.…”

Evidence of Recombination Suppression Blocks on the Y Chromosome of Date Palm (Phoenix dactylifera)

“…While our goal in the previous study was to identify conservation of sex determination genes across the genus, this study aims to identify the broadest regions of divergence between the sex chromosomes in the date palm species alone. Our previous study took advantage of male/female genome comparisons across the genus, while this study utilized the unique resource of male/female genome comparisons within a single (Western) date palm subpopulation (Mathew et al, 2015;Mohamoud et al, 2019). In so doing, we hope to provide a resource to begin understanding the process and breadth of divergence between X and Y chromosomes of date palm.…”

Chloroplast phylogenomics and the dynamic evolution of Santalum (Santalaceae)

“…Phylogenetic analyses based on whole chloroplast genome sequences have been widely used at different taxonomic levels [14][15][16]. Chloroplast genome data also provide effective genetic markers to resolve complex evolutionary histories [17,18]. Also, a comparison of chloroplast sequences can help understand the evolutionary patterns of plants.…”