Biology subjects

Fuentes, N.

Publications and source records attributed to Fuentes, N..

4 recordsLinked to original sources

bioRxiv2023

First whole genome sequence and assembly of the Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps), a critically endangered species, using Oxford Nanopore Technologies

The Ecuadorian brown-headed spider monkey (Ateles fusciceps fusciceps) is currently considered one of the most endangered primates in the world and is classified as critically endangered (IUCN). It faces multiple threats, the most significant one being habitat loss due to deforestation in western Ecuador. Genomic tools are key for the management of endangered species, but this requires a reference genome which until now was unavailable for A. f. fusciceps. The present study reports the first whole genome sequence and assembly of A. f. fusciceps generated using Oxford Nanopore long reads. DNA was extracted from a subadult male and libraries were prepared for sequencing following the Ligation Sequencing Kit SQK-LSK112 workflow. Sequencing was performed using a MinION Mk1C sequencer. The sequencing reads were processed to generate a genome assembly. Two different assemblers were used to obtain draft genomes using raw reads, of which the Flye assembly was found to be superior. The final assembly has a total length of 2.63 Gb and contains 3,861 contigs, with an N50 of 7,560,531 bp. The assembly was analyzed for annotation completeness based on primate ortholog prediction using a high-resolution database, and was found to be 84.3% complete, with a low number of duplicated genes indicating a precise assembly. The annotation of the assembly predicted 31,417 protein-coding genes, comparable to other mammal assemblies. A reference genome for this critically endangered species will allow researchers to gain insight into the genetics of its populations and thus aid conservation and management efforts of this vulnerable species.

genomics↗

bioRxiv2023

Machine-guided design of synthetic cell type-specific cis-regulatory elements

Cis-regulatory elements (CREs) control gene expression, orchestrating tissue identity, developmental timing, and stimulus responses, which collectively define the thousands of unique cell types in the body. While there is great potential for strategically incorporating CREs in therapeutic or biotechnology applications that require tissue specificity, there is no guarantee that an optimal CRE for an intended purpose has arisen naturally through evolution. Here, we present a platform to engineer and validate synthetic CREs capable of driving gene expression with programmed cell type specificity. We leverage innovations in deep neural network modeling of CRE activity across three cell types, efficient in silico optimization, and massively parallel reporter assays (MPRAs) to design and empirically test thousands of CREs. Through in vitro and in vivo validation, we show that synthetic sequences outperform natural sequences from the human genome in driving cell type-specific expression. Synthetic sequences leverage unique sequence syntax to promote activity in the on-target cell type and simultaneously reduce activity in off-target cells. Together, we provide a generalizable framework to prospectively engineer CREs and demonstrate the required literacy to write regulatory code that is fit-for-purpose in vivo across vertebrates.

synthetic biology↗

bioRxiv2022

Machine learning improves global models of plant diversity

Despite the paramount role of plant diversity for ecosystem functioning, biogeochemical cycles, and human welfare, knowledge of its global distribution is incomplete, hampering basic research and biodiversity conservation. Here, we used machine learning (random forests, extreme gradient boosting, neural networks) and conventional statistical methods (generalised linear models, generalised additive models) to model species richness and phylogenetic richness of vascular plants worldwide based on 830 regional plant inventories including c. 300,000 species and predictors of past and present environmental conditions. Machine learning showed an outstanding performance, explaining up to 80.9% of species richness and 83.3% of phylogenetic richness. Current climate and environmental heterogeneity emerged as the primary drivers, while past environmental conditions left only small but detectable imprints on plant diversity. Finally, we combined predictions from multiple modelling techniques (ensemble predictions) to reveal global patterns and centres of plant diversity at multiple resolutions down to 7,774 km2. Our predictive maps provide the most accurate estimates of global plant diversity available to date at grain sizes relevant for conservation and macroecology.

ecology↗

bioRxiv2020

Planktonic diatom assemblage seasonal diversity used to assess environmental health in a coastal wetland of southern Chile

Although planktonic diatoms are one of the most abundant taxonomic groups in coastal wetlands, their assemblages have not been used to determine the environmental health of these ecosystems. Studies of ecosystem environmental health have been based on other taxonomic groups; we propose that diatom genera diversity represents a viable alternative for this purpose. Thus, our aim was to determine the alpha and beta diversities of the planktonic diatom assemblage present in Caulin Bay, Chiloe Island (41{degrees} 49S; 73{degrees} 38O), southern Chile, during the austral winter and spring of the years 2012 and 2014. Inasmuch Caulin Bay is an important site for aquatic bird observation and conservation, hunting is prohibited on a national scale and, internationally, the site has been declared an Important Bird and Biodiversity Area (IBA). Our results indicate different diversities between sampling stations, but not between the years studied. In total, we recorded 53 diatom genera, of which the most abundant were Coscinodiscus (21.99%) and Cocconeis (16.23%). The study area presented high genera diversity (i.e., H(log2) >3.74) and beta diversity indicated that Caulin presents a low level of heterogeneity and is a low genera replacement environment. Consequently, we infer that Caulin Bay is productive and environmentally stable ecosystem. This leads us to conclude that diatom diversity determination is a viable alternative to establish aquatic ecosystem environmental health and we recommend that future conservation strategies be established for Caulin Bay. RESUMENSi bien las diatomeas planctonicas son uno de los grupos taxonomicos mas abundantes de los humedales costeros, sus ensambles no se han utilizado para determinar el estado ambiental de estos ecosistemas. Aunque se han realizado estudios de la salud ambiental de un ecosistema utilizando otros grupos taxonomicos, nosotros proponemos que la diversidad de generos de diatomeas representa una alternativa viable. Por lo tanto, el objetivo de este estudio fue determinar las diversidades alfa y beta del ensamble de diatomeas planctonicas presentes en la Bahia de Caulin, Isla de Chiloe (41 {degrees} 49S; 73 {degrees} 38O), sur de Chile, durante las temporadas de invierno y primavera austral de los anos 2012 y 2014. Bahia Caulin es un sitio importante para la observacion y conservacion de aves acuaticas por lo que a nivel nacional se ha prohibido la caza y a nivel internacional fue decretada un Area Importante para la Conservacion de Aves, AICA. Los resultados de este estudio indicaron diferencias en las diversidades entre las estaciones de muestreo, pero no entre los anos estudiados. En total, se identificaron 53 generos de diatomeas; los mas abundantes fueron Coscinodiscus (21,99%) y Cocconeis (16,23%). El area de estudio presento una alta diversidad de generos (i.e., H(log2) >3.74) y la diversidad beta indico que Caulin presento bajo nivel de heterogeneidad y es un entorno con bajo reemplazo de generos. Asi, inferimos que Bahia Caulin es un ecosistema productivo y ambientalmente estable, por lo cual concluimos que la determinacion de las diversidades de diatomeas es una alternativa para establecer la salud ambiental de los ecosistemas acuaticos y recomendamos establecer futuras estrategias de conservacion para Bahia Caulin. PALABRAS CLAVE: diatomeas, diversidades ecologicas, plancton, humedales costeros, desembocadura

ecology↗