Biology subjects

Preick, M.

Publications and source records attributed to Preick, M..

5 recordsLinked to original sources

bioRxiv2026

Ancient DNA reveals early use of melons in China's Song Dynasty

Melon (Cucumis melo L.) domestication is thought to have occurred independently once in Northeast Africa and twice in India, but archaeobotanical seed remains point to a possible additional domestication in China. Because Cucumis seeds are difficult to diagnose morphologically, genomic data from archaeological material are needed to evaluate these scenarios and reconstruct ancient melon traits. We sequenced two Song Dynasty melon seeds from Shuomen Gugang (China), recovering 4.6x and 1.7x nuclear genome coverage. Nuclear and chloroplast analyses place both seeds within cultivated C. melo from China, supporting introduction from the broader Asian domestication pool rather than independent Chinese domestication. To assess whether these seeds carried traits associated with sweet dessert melons, we examined loci underlying fruit phenotypes. Neither seed carried alleles for orange flesh; one harbored an allele linked to yellow/orange peel, the other possessed alleles associated with green flesh and reduced acidity. Since wild melons are monoecious, the presence of the derived andromonoecy allele in one seed, associated with rounder fruit shape, suggests early selection on fruit morphology. Together, these findings indicate that Song Dynasty melons were likely consumed as fresh or culinary fruits rather than as sweet dessert melons. Their flesh coloration resonates with Song-period aesthetic sensibilities, exemplified by jade-green celadon ceramics frequently crafted in melon-shaped forms. By anchoring East Asian archaeobotanical remains within modern melon genomic variation, this study provides a temporal framework for melon dispersal into China and shows how ancient genomics can illuminate past crop use.

evolutionary biology↗

bioRxiv2023

Efficient hybrid strategies for assembling the plastome, mitochondriome, and large nuclear genome of diploid Ranunculus cassubicifolius (Ranunculaceae)

Currently, it is still a challenge - in terms of laboratory effort and cost, as well as assembly quality - to unravel the sequence of large and complex genomes from non-model plants. This often hampers the study of evolutionarily intricate species groups. The species-rich genus Ranunculus (Ranunculaceae) is an angiosperm model system for the study of polyploidy, apomixis, reticulate evolution, and biogeography. However, neither mitochondrial, nor high-quality nuclear genome sequences are available. This limits phylogenomic, functional, and taxonomic analyses thus far. Here, we tested Illumina short-read, Oxford Nanopore Technology (ONT) or PacBio/HiFi long-read, and hybrid-read assembly strategies. We used the diploid progenitor species R. cassubicifolius (R. auricomus complex), and selected the best assemblies in terms of completeness, contiguity, and quality scores. We first assembled the plastome (156 kbp, 85 genes) and mitogenome (1.18 Mbp, 40 genes) sequences using Illumina and Illumina-PacBio-hybrid strategies, respectively. We also present an updated plastome and the first mitogenome phylogeny of Ranunculaceae, including studies of gene loss (e.g., infA, ycf15, or rps) with evolutionary implications. For the nuclear genome, we favored a PacBio-based assembly three-times polished with filtered reads and subsequently scaffolded into 8 pseudochromosomes by chromatin conformation data (Hi-C) as the representative sequence. We obtained a haploid genome sequence with 2.69 Gbp, 94.5% complete BUSCO embryophyta_odb10 genes found, and 31,322 annotated genes. The genomic information presented here will improve phylogenomic analyses in this species complex, and will enable advanced functional, evolutionary, and biogeographic analyses for the genus and beyond Ranunculaceae in the future. Significance StatementThe genus Ranunculus is a model system in flowering plants for polyploidy, apomixis, evolution, and biogeography research. We present the first nuclear and mitochondrial genome sequence, and the plastid evolution of Ranunculaceae. Using Illumina, ONT, and PacBio data, we developed an efficient assembly strategy that can be applied to other non-model plants. Results presented here are useful for improving population genomic and phylogenomic analyses, and enable better functional analyses at species, genus and family level.

genomics↗

bioRxiv2021

Genome assembly of the tayra (Eira barbara, Mustelidae) and comparative genomic analysis reveal adaptive genetic variation in the subfamily Guloninae

Species of the mustelid subfamily Guloninae inhabit diverse habitats on multiple continents, and occupy a variety of ecological niches. They differ in feeding ecologies, reproductive strategies and morphological adaptations. To identify candidate loci associated with adaptations to their respective environments, we generated a de novo assembly of the tayra (Eira barbara), the earliest diverging species in the subfamily, and compared this with the genomes available for the wolverine (Gulo gulo) and the sable (Martes zibellina). Our comparative genomic analyses included searching for signs of positive selection, examining changes in gene family sizes, as well as searching for species-specific structural variants (SVs). Among candidate loci associated with phenotypic traits, we observed many related to diet, body condition and reproduction. For example, for the tayra, which has an atypical gulonine reproductive strategy of aseasonal breeding, we observe species-specific changes in many pregnancy-related genes. For the wolverine, a circumpolar hypercarnivore that must cope with seasonal food scarcity, we observed many changes in genes associated with diet and body condition. All types of genomic variation examined contributed substantially to the identification of candidate loci. This strongly argues for consideration of variation other than single nucleotide polymorphisms in comparative genomics studies aiming to identify loci of adaptive significance.

evolutionary biology↗

bioRxiv2020

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

O_LIThe date palm (Phoenix dactylifera) has been a cornerstone of Middle Eastern and North African agriculture for millennia. It is presumed that date palms were first domesticated in the Persian Gulf and subsequently introduced into North Africa, where their evolution in the latter region appears to have been influenced by gene flow from the wild relative P. theophrasti, which is restricted to Crete and Turkey. However, the timing of gene flow from P. theophrasti to P. dactylifera remains unknown due to the limited archaeobotanical evidence of P. theophrasti and their exclusion from population genomic studies. C_LIO_LIWe addressed this issue by investigating the relatedness and ancestry of a ~2,100-year-old P. dactylifera leaf from Saqqara (Egypt), combining genome sequencing of this ancient specimen with a broad sample of date palm cultivars and closely related species. C_LIO_LIThe ancient Saqqara date palm shares close genetic ancestry with North African date palm populations. We find clear genomic admixture between the Saqqara date palm, P. theophrasti and the closest known relative P. sylvestris. C_LIO_LIOur study highlights that gene flow from P. theophrasti and P. sylvestris to North African date palms had already occurred at least ~2,100 years ago, providing a minimum timestamp for hybridisation between species. C_LI

evolutionary biology↗

bioRxiv2019

A 3500-year-old leaf from a Pharaonic tomb reveals that New Kingdom Egyptians were cultivating domesticated watermelon

Domestication of the watermelon (Citrullus lanatus) has alternatively been placed in South Africa, the Nile valley, or more recently West Africa, with the oldest archeological evidence coming from Libya and Egypt. The geographic origin and domestication of watermelons has therefore remained unclear. Using extensive nuclear and plastid genomic data from a 3,560-year-old Citrullus leaf from a mummys sarcophagus and skimmed genomes for representatives of the seven extant species of Citrullus, we show that modern cultivars and the ancient plant uniquely share mutations in a lycopene metabolism gene (LYCB) affecting pulp color and a stop codon in a transcription factor regulating bitter cucurbitacin compounds. This implies that the plant we sequenced had red-fleshed and sweet fruits and that New Kingdom Egyptians were cultivating domesticated watermelons. The genomic data also identify extant Sudanese watermelons with white, sweet pulp as the closest relatives of domesticated watermelons.\n\nSignificance statementWith some 197.8 million tons in 2017, watermelon, Citrullus lanatus, is among the Worlds most important crops, yet its area of origin and domestication have remained unclear, with competing hypotheses favoring South Africa, West Africa, Central Africa, or the Nile valley. We generated extensive nuclear and plastid genomic data from a 3500-year-old leaf from a Pharaonic sarcophagus and performed genome skimming for representatives of all other Citrullus species to compare key genes involved in fruit bitterness and color. White-fleshed, non-bitter melons from southern Sudan are the closest relatives of domesticated watermelon, and the ancient genome shares unique alleles with a red-fleshed, non-bitter domesticated form (but no wild forms), implying that 18th Dynasty Egyptians were cultivating domesticated watermelon by 3500 years ago.

evolutionary biology↗