Genus-wide sequencing supports a two-locus model for sex-determination in Phoenix

Torres, María Fernanda; Mathew, Lisa S.; Ahmed, Ikhlak; Al-Azwani, Iman K.; Krueger, Robert R.; Rivera, Diego; Mohamoud, Yasmin Ali; Clark, Andrew G.; Suhre, Karsten; Malek, Joel A.

doi:10.1038/s41467-018-06375-y

Cited by 90 publications

(69 citation statements)

References 46 publications

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“…We found associations (p<10 -10 ) with sucrose on 34 contigs, the strongest association at p=5x10 -16 and a genomics inflation of lambda=1.28. These contigs were matched to the oil palm reference using MUMmer (Marçais et al 2018 (Torres et al 2018). The Khalas reference sequence was noted to include sequence missing in the Deglet Nour reference and so all genomes were aligned to the Khalas contig and diploid coverage normalized to 1 for analysis of copy number changes in the region.…”

Section: Genotype Association With Sucrosementioning

confidence: 99%

Deletion of beta-fructofuranosidase (invertase) genes is associated with sucrose content in Date Palm fruit

Malek

Mathew

et al. 2019

Preprint

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The fruit of date palm trees are an important part of the diet for a large portion of the Middle East and North Africa. The fruit is consumed both fresh and dry and can be stored dry for extended periods of time. Date fruits vary significantly across hundreds of cultivars identified in the main regions of cultivation. Most dried date fruit are low in sucrose but high in glucose and fructose. However, high sucrose content is a distinctive feature of some date fruit and affects flavor as well as texture and water retention. To identify the genes controlling high sucrose content we analyzed date fruit metabolomics for association with genotype data from 121 date fruits. We found significant association of dried date sucrose content and a genomic region that contains 3 tandem copies of the betafructofuranosidase (invertase) gene in the reference Khalas genome, a low sucrose fruit. High sucrose cultivars including the popular Deglet Noor had a homozygous deletion of two of the 3 copies of the invertase gene. We show the deletion allele is derived when compared to the ancestral allele that retains the all copies of the gene in 3 other species of Phoenix. The fact that 2 of the 3 tandem invertase copies are associated with dry fruit sucrose content will assist in better understanding the distinct roles of multiple date palm invertases in plant physiology. Identification of the recessive alleles associated with end-point sucrose content in date fruit may be used in selective breeding in the future. Date palm, sucrose, invertaseDate palm invertase deletion

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Section: Genotype Association With Sucrosementioning

confidence: 99%

Deletion of beta-fructofuranosidase (invertase) genes is associated with sucrose content in Date Palm fruit

Malek

Mathew

et al. 2019

Preprint

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“…These databases provide many additional avenues for functional exploration of the genome including Gene Ontology (GO) terms and analysis of genes in the context of biochemical pathways. Although only a female cultivar has been de novo assembled, the full-length sequencing of male-specific sequences from a single male individual using PacBio and 10X Genomics technologies was recently published [ 34 ]. This provides an assembly of the Phoenix sex-determination region and is therefore valuable for studies of the male specific sequences.…”

Section: High-throughput Sequencing Of Date Palmsmentioning

confidence: 99%

Genomic Insights into Date Palm Origins

Gros-Balthazard

Hazzouri

Flowers

2018

Genes

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With the development of next-generation sequencing technology, the amount of date palm (Phoenix dactylifera L.) genomic data has grown rapidly and yielded new insights into this species and its origins. Here, we review advances in understanding of the evolutionary history of the date palm, with a particular emphasis on what has been learned from the analysis of genomic data. We first record current genomic resources available for date palm including genome assemblies and resequencing data. We discuss new insights into its domestication and diversification history based on these improved genomic resources. We further report recent discoveries such as the existence of wild ancestral populations in remote locations of Oman and high differentiation between African and Middle Eastern populations. While genomic data are consistent with the view that domestication took place in the Gulf region, they suggest that the process was more complex involving multiple gene pools and possibly a secondary domestication. Many questions remain unanswered, especially regarding the genetic architecture of domestication and diversification. We provide a road map to future studies that will further clarify the domestication history of this iconic crop.

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“…This suggests that these species inherited a highly degenerate Y chromosome from their common ancestor, well before the origin of the P. parae male morphs. Short sequences representing all the possible substrings of length k that are contained in a genome are referred to as k-mers, and k-mer comparisons between male and female genomes has been used to identify Y chromosome sequence (Y-mers) in a wide range of organisms [32][33][34] , including guppies 35 and P. picta 21 . We first compared all males, representing all five morphs, to all females.…”

Section: The P Parae Y Chromosome Is Highly Diverged From the X And mentioning

confidence: 99%

“…picta 21 These morph-mers reveal two insights: (1) at a gross level they provide a sense of how much Y sequence is shared within versus across morphs and (2) mapping these morphmers to the respective de novo genomes allows us to identify regions of morph specific sequence 34,35,77,78 . To find these regions of morph specific sequence we first mapped the corresponding set of 31bp morph-mers to each of the 22 de novo male genomes (pseudohap style of Supernova output) using bowtie2 73 allowing for no mismatches, gaps, or trimming.…”

Section: Identifying Morph Specific Sequence By K-mersmentioning

confidence: 99%

Extreme Y chromosome polymorphism corresponds to five male reproductive morphs

Sandkam

Almeida

Darolti

et al. 2020

Preprint

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Sex chromosomes form once recombination is halted between the X and Y chromosomes. This loss of recombination quickly depletes Y chromosomes of functional content and genetic variation, which is thought to severely limit their potential to generate adaptive diversity. We examined Y diversity in Poecilia parae, where males occur as one of five discrete morphs, all of which shoal together in natural populations where morph frequency has been stable for over 50 years. Each morph utilizes different complex reproductive strategies, and differ dramatically from each other in color, body size, and mating behavior. Remarkably, morph phenotype is passed perfectly from father to son, indicating there are five Y haplotypes segregating in the species, each of which encodes the complex male morph characteristics. Using linked-read sequencing on multiple P. parae females and males of all five morphs from natural populations, we found that the genetic architecture of the male morphs evolved on the Y chromosome long after recombination suppression had occurred with the X. Comparing Y chromosomes between each of the morphs revealed that although the Ys of the three minor morphs that differ predominantly in color are highly similar, there are substantial amounts of unique genetic material and divergence between the Ys of the three major morphs that differ in reproductive strategy, body size and mating behavior. Taken together, our results reveal the extraordinary ability of evolution to overcome the constraints of recombination loss to generate extreme diversity resulting in five discrete Y chromosomes that control complex reproductive strategies.

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Genus-wide sequencing supports a two-locus model for sex-determination in Phoenix

Cited by 90 publications

References 46 publications

Deletion of beta-fructofuranosidase (invertase) genes is associated with sucrose content in Date Palm fruit

Deletion of beta-fructofuranosidase (invertase) genes is associated with sucrose content in Date Palm fruit

Genomic Insights into Date Palm Origins

Extreme Y chromosome polymorphism corresponds to five male reproductive morphs

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