Biology subjects

Audi, L.

Publications and source records attributed to Audi, L..

3 recordsLinked to original sources

bioRxiv2023

Phylogenetically diverse wild plant species use common biochemical strategies to thrive in the Atacama Desert

The best ideotypes are under mounting pressure due to increased aridity in many parts of the world. Understanding the conserved molecular mechanisms that evolve in wild plant species adapted to harsh environments is crucial in developing new strategies for sustainable agriculture. Yet our knowledge of such mechanisms in wild species is scant, particularly in extreme environments. We performed metabolic pathway reconstruction using transcriptome information from 32 Atacama plant species and phylogenetically related plant species that do not live in Atacama (Sister species). We analyzed pathway and reaction enrichment to understand the biochemical commonalities and differences of wild Atacama plant species. To gain insights into the mechanisms that ensure plant survival, we compared expressed gene isoform numbers and gene expression patterns between the annotated biochemical reactions from 32 Atacama and Sister species. We found significant biochemical convergences in primary and secondary metabolism characterized by reactions enriched in at least 50% of the Atacama species across major plant phylogenetic lineages. Analysis of the annotation indicated potential advantages against drought, salinity, high solar irradiance, and nitrogen starvation. These findings suggest that the adaptation in the Atacama Desert may result in part from shared genetic legacies governing the expression of key metabolic pathways to face harsh environmental conditions. Enriched reactions corresponded to ubiquitous compounds common to extreme and agronomic species and were congruent with our previous metabolomic analyses in these Atacama species. Hence, genes underlying these adaptive traits offer promising candidates for improving abiotic stress resilience in crop species.

plant biology↗

bioRxiv2022

Amis Pacilo and Yami Cipoho are not the same as the Pacific breadfruit starch crop--Target enrichment phylogenomics of a long-misidentified Artocarpus species sheds light on the northward Austronesian migration from the Philippines to Taiwan

Breadfruit is a common tree species in Taiwan. In the indigenous Austronesian Amis culture of eastern Taiwan, breadfruit is known as Pacilo, and its fruits are consumed as food. On Lanyu (Botel Tobago) where the indigenous Yami people live, breadfruit is called Cipoho and used for constructing houses and plank-boats. Elsewhere in Taiwan, breadfruit is also a common ornamental tree. As an essential component of traditional Yami culture, Cipoho has long been assumed to have been transported from the Batanes Island of the Philippines to Lanyu. As such, it represents a commensal species that potentially can be used to test the hypothesis of the northward Austronesian migration into Taiwan. However, recent phylogenomic studies using target enrichment show that Taiwanese breadfruit might not be the same as the Pacific breadfruit (Artocarpus altilis) that was domesticated in Oceania and widely cultivated throughout the tropics. To resolve persistent misidentification of this culturally and economically important tree species of Taiwan, we sampled 36 trees of Taiwanese Artocarpus and used the Moraceae probe set to enrich 529 nuclear genes. Along with 28 archived Artocarpus sequence datasets (representing a dozen taxa from all subgenera), phylogenomic analyses showed that all Taiwanese breadfruit samples, together with a cultivated ornamental tree from Hawaii, form a fully supported clade within the A. treculianus complex, which is composed only of endemic Philippine species. Morphologically, the Taiwanese breadfruit matches the characters of A. treculianus. Within the Taiwanese samples of A. treculianus, Amis samples form a fully supported clade derived from within the paraphyletic grade composed of Yami samples, suggesting a Lanyu origin. Results of our target enrichment phylogenomics are consistent with the scenario that Cipoho was transported northward from the Philippines to Lanyu by Yami ancestors, though the possibility that A. treculianus is native to Lanyu cannot be ruled out completely.

plant biology↗

bioRxiv2020

Phylogenomics of Brosimum Sw. (Moraceae) and allied genera, including a revised subgeneric system

We present a phylogenomic study of Brosimum and the allied genera Trymatococcus and Helianthostylis, with near-complete taxon sampling. Distributed from Mexico and the Greater Antilles to the Amazon, this clade contains the underutilized crop ramon (bread nut) (Brosimum alicastrum) as well as other species valued for timber or medicinal uses. Target enrichment for 333 genes produced a well-resolved phylogenetic tree and showed that Trymatoccocus and Helianthostylis are nested within Brosimum. We present a revised subgeneric classification of Brosimum based on phylogenetic and morphological considerations, including the reduction of Trymatococcus and Helianthostylis to subgenera. The monophyletic subgenera can be diagnosed based on stipule, pistillode, and cotyledon synapomorphies. Divergence date estimates suggest a Miocene origin for Brosimum, and ancestral area reconstruction indicated that all four subgenera originated and initially diversified in Amazonia before dispersing into other parts of South and Central America. ResumenPresentamos un estudio filogenomico del genero Brosimum y sus aliados, Trymatococcus y Helianthostylis, y que incluye practicamente todas las especies descritas. Su distribucion va desde Mexico y las Antillas Mayores hasta el Amazonas y comprende especies como el ramon (B. alicastrum), un cultivo infrautilizado, y otras especies empleadas como madera o en medicina. La secuenciacion masiva dirigida de 333 marcadores nucleares de copia unica permitio la reconstruccion de una filogenia bien resuelta, en la que se demuestra que Trymatococcus y Helianthostylis estan anidados en Brosimum. Presentamos, por lo tanto, una clasificacion revisada a nivel de especies, teniendo en cuenta los resultados moleculares y las caracteristicas morfologicas, y donde Trymatococcus y Helianthostylis pasan a ser subgeneros de Brosimum. Estos subgeneros monofileticos pueden ser identificados por caracteres de las estipulas y de los pistilodios.

plant biology↗