Biology subjects

Botigue, L. R.

Publications and source records attributed to Botigue, L. R..

3 recordsLinked to original sources

bioRxiv2023

Wild emmer contribution in wheat domestication and adaptation to new environments

Wheat is a staple crop, and its production is heavily threatened by climate change and soil erosion. Breeding programmes commonly rely on the wild progenitor, wild emmer wheat, Triticum turgidum subsp. dicoccoides, to find markers associated with traits conferring higher resistance to biotic and abiotic stresses, albeit how its genetic diversity contributed into domestication and adaptation to agricultural systems has never been studied. We explore the population structure and the influence of wild emmer populations from both the Northern and Southern Levant during the domestication process. Additionally, we examine their potential contribution to facilitating the adaptation and dispersal of domestic landraces to new environments. We quantify the genomic proportion of wild Southern Levant ancestry in two different domestic germplasms, including landraces from Europe, Africa and Asia. We obtain direct evidence that as much as 26% of the genome has Southern Levant ancestry in the population from Europe, and up to 40% in the population from Africa and Asia. We also estimate the time since admixture of the two wild populations to produce the domestic forms, obtaining two dates, one matching the domestication in Southwest Asia (ca 9500 BP) and the other matching the dispersal towards Africa (ca 6500 BP). We also inquire about the possible adaptive role of wild emmer from the Southern Levant into domestication and dispersal and find an overrepresentation of genes associated with resistance to biotic stress and drought. Overall, our work provides more information on the origins of domestic wheat and highlights the potential of modern domestic landraces of emmer wheat in the study of the genetic basis of resilience. Modeling wheat genome evolution under different demographic scenarios is needed to confirm the observed signals of positive selection and facilitate the use of emmer landraces in future wheat breeding programmes.

genomics↗

bioRxiv2021

A Comprehensive Phylogenomic Platform for Exploring the Angiosperm Tree of Life

The tree of life is the fundamental biological roadmap for navigating the evolution and properties of life on Earth, and yet remains largely unknown. Even angiosperms (flowering plants) are fraught with data gaps, despite their critical role in sustaining terrestrial life. Today, high-throughput sequencing promises to significantly deepen our understanding of evolutionary relationships. Here, we describe a comprehensive phylogenomic platform for exploring the angiosperm tree of life, comprising a set of open tools and data based on the 353 nuclear genes targeted by the universal Angiosperms353 sequence capture probes. This paper (i) documents our methods, (ii) describes our first data release and (iii) presents a novel open data portal, the Kew Tree of Life Explorer (https://treeoflife.kew.org). We aim to generate novel target sequence capture data for all genera of flowering plants, exploiting natural history collections such as herbarium specimens, and augment it with mined public data. Our first data release, described here, is the most extensive nuclear phylogenomic dataset for angiosperms to date, comprising 3,099 samples validated by DNA barcode and phylogenetic tests, representing all 64 orders, 404 families (96%) and 2,333 genera (17%). Using the multi-species coalescent, we inferred a "first pass" angiosperm tree of life from the data, which totalled 824,878 sequences, 489,086,049 base pairs, and 532,260 alignment columns. The tree is strongly supported and highly congruent with existing taxonomy, while challenging numerous hypothesized relationships among orders and placing many genera for the first time. The validated dataset, species tree and all intermediates are openly accessible via the Kew Tree of Life Explorer. This major milestone towards a complete tree of life for all flowering plant species opens doors to a highly integrated future for angiosperm phylogenomics through the systematic sequencing of standardised nuclear markers. Our approach has the potential to serve as a much-needed bridge between the growing movement to sequence the genomes of all life on Earth and the vast phylogenomic potential of the worlds natural history collections.

evolutionary biology↗

bioRxiv2018

A Universal Probe Set for Targeted Sequencing of 353 Nuclear Genes from Any Flowering Plant Designed Using k-medoids Clustering

Sequencing of target-enriched libraries is an efficient and cost-effective method for obtaining DNA sequence data from hundreds of nuclear loci for phylogeny reconstruction. Much of the cost associated with developing targeted sequencing approaches is preliminary data needed for identifying orthologous loci for probe design. In plants, identifying orthologous loci has proven difficult due to a large number of whole-genome duplication events, especially in the angiosperms (flowering plants). We used multiple sequence alignments from over 600 angiosperms for 353 putatively single-copy protein-coding genes to design a set of targeted sequencing probes for phylogenetic studies of any angiosperm lineage. To maximize the phylogenetic potential of the probes while minimizing the cost of production, we introduce a k-medoids clustering approach to identify the minimum number of sequences necessary to represent each coding sequence in the final probe set. Using this method, five to 15 representative sequences were selected per orthologous locus, representing the sequence diversity of angiosperms more efficiently than if probes were designed using available sequenced genomes alone. To test our approximately 80,000 probes, we hybridized libraries from 42 species spanning all higher-order lineages of angiosperms, with a focus on taxa not present in the sequence alignments used to design the probes. Out of a possible 353 coding sequences, we recovered an average of 283 per species and at least 100 in all species. Differences among taxa in sequence recovery could not be explained by relatedness to the representative taxa selected for probe design, suggesting that there is no phylogenetic bias in the probe set. Our probe set, which targeted 260 kbp of coding sequence, achieved a median recovery of 137 kbp per taxon in coding regions, a maximum recovery of 250 kbp, and an additional median of 212 kbp per taxon in flanking non-coding regions across all species. These results suggest that the Angiosperms353 probe set described here is effective for any group of flowering plants and would be useful for phylogenetic studies from the species level to higher-order lineages, including all angiosperms.

evolutionary biology↗