Publications
Embedded Files
Haplotype-resolved chromosome-level genome assemblies of four Diamesa species reveal the genetic basis of cold tolerance and high-altitude adaptations in arctic chironomids
Martin SLF., La Torre R., Danneels B., Tooming-Klunderud A., Skage M., Kollias S., Tørresen OK., Anbaran MF., Stur E., Jakobsen KS., Martin MD., Ekrem T.
Gigascience (2025), giaf160
doi: 10.1093/gigascience/giaf160
Arctic and alpine insects face extreme cold and hypoxic conditions, yet the genomic basis of their adaptation remains poorly understood. Here, we present the first haplotype-resolved, chromosome-level genomes for four cold-adapted Diamesa midge species, assembled using PacBio HiFi and Hi-C data. Phylogenomic analyses reveal introgression among species and place Diamesinae as sister to most Chironomidae. Comparative genomics across Diptera show extensive gene family contractions related to oxygen transport and metabolism, alongside expansions in histone, immune, and glucose dehydrogenase gene families linked to cold stress tolerance. These results suggest genome condensation and lineage-specific gene family shifts underpin adaptation to extreme cold environments.
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Sedimentary ancient DNA metagenomic analysis provides new insights into farming in central Norway from the Bronze Age to late Medieval period
La Torre R., Kosel P., Bieker VC., Westergaard KB., Mykkeltvedt JL., Yildrim KL., Seiler M., Philippsen B., Macphail RI., Cannell RJS., Halvorsen LS., Lorentzen AB., Sauvage R., Martin MD., Breivik HM., Martin SLF.
bioRxiv (2025)
doi: 10.1101/2025.06.19.660509
Sedimentary ancient DNA (sedaDNA) offers a powerful approach to reconstruct past biodiversity and environmental change, yet its application to human-driven landscape dynamics remains limited. Here, we use a sedaDNA metagenomic framework to examine land use and environmental change at the Torgårdsletta archaeological site in central Norway from the Bronze Age to the Medieval period. Stratified sediments reveal temporal shifts in plant, animal, and microbial communities associated with land clearance, cultivation, and animal husbandry. Periods of climatic stress, including the AD 536–540 volcanic event, coincide with marked declines in biological diversity and landscape reorganization. These results highlight sedaDNA as a valuable complement to traditional proxies for high-resolution reconstructions of past human–environment interactions.
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Lima megacity's influence on aquatic microbial communities in the Rimac River: Dominance over spatial and seasonal variations
Samaniego T., La Torre R., Orjeda G., Ramirez JL.
Microbial Ecology, 88(1), 57 (2025)
doi: 10.1007/s00248-025-02558-5
The Rímac River, which supplies nearly 80% of Lima’s water, faces severe pollution from domestic, industrial, and mining effluents. Using 16S rRNA metabarcoding, we characterized bacterial communities along the river across seasons and altitudinal zones. Results revealed marked spatial differences: the Metropolitan zone showed reduced microbial diversity and increased pathogenic taxa, while seasonal effects were minor. Betaproteobacteria dominated most samples, and Aliarcobacter cryaerophilus, a fecal contamination indicator, was prevalent downstream. These findings underscore the strong influence of human activity on riverine microbiota and the need for molecular monitoring to guide effective water management in the Rímac watershed.
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A chromosome-level genome assembly of the Peruvian Algarrobo (Neltuma pallida) provides insights on its adaptation to its unique ecological niche
La Torre R., Hamilton JP., Saucedo-Bazalar M., Caycho E., Vaillancourt B., Wood JC., Ramirez M., Buell CR., Orjeda G.
G3: Genes, Genomes, Genetics, 15.2 (2025), jkae283
doi: 10.1093/g3journal/jkae283
The dry forests of northern Peru are dominated by Neltuma pallida, a leguminous tree adapted to arid tropical environments but now threatened in its native range. To support conservation and study its adaptive traits, we generated a high-quality chromosome-scale reference genome (403.7 Mb; 14 pseudochromosomes; N50 = 26.2 Mb; GC = 34.3%). The assembly showed 99.2% complete BUSCOs and 51.2% repetitive content, mainly long terminal repeats. We annotated 22,409 protein-coding genes forming 24,607 gene models. Comparative analyses revealed rapid evolution in gene families related to disease resistance, transcription factors, and signaling. This genome provides a key resource for understanding adaptation in dry ecosystems.
Assembly, annotation and analysis of the chloroplast genome of the Algarrobo tree Neltuma pallida (subfamily: Caesalpinioideae)
Caycho E., La Torre R., Orjeda G.
BMC Plant Biology, 23.1 (2023): 570
doi: 10.1186/s12870-023-04581-5
Neltuma pallida is a key tree of Peru’s Equatorial Dry Forest, vital for both people and ecosystems but currently threatened and understudied genetically. We assembled and analyzed its chloroplast genome (162,381 bp), which displays the typical quadripartite structure and 35.97% GC content. A total of 132 genes were annotated, including 19 duplicates and 22 with introns. Over 800 repetitive elements were identified, notably 142 SSR markers. Phylogenetic analyses grouped N. pallida with other Neltuma species and Prosopis cineraria, revealing high sequence similarity. These genomic resources offer valuable tools for diversity assessment and conservation of N. pallida.
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Survey of lichenized-fungi DNA barcodes in King George Island (Antarctica): An aid to species discovery
La Torre R., Ramos D., Mejia M., Neyra E., Loarte E., Orjeda G.
Journal of Fungi (2023)
doi: 10.3390/jof9050552
DNA barcoding is effective for identifying lichenized fungi where existing diversity is well-represented in databases and taxonomy is robust. However, its use is limited in understudied regions like Antarctica, where genetic diversity is poorly characterized. This exploratory study surveyed lichenized fungi on King George Island using a fungal barcode marker for initial identification. Samples were collected near Admiralty Bay. Most were identified up to the species or genus level with high confidence. Morphological evaluation of samples with novel barcodes led to the identification of unknown Austrolecia, Buellia, and Lecidea species. These results contribute to better representing Antarctic lichen diversity in nucleotide databases and offer a valuable approach for exploratory taxonomic surveys in other understudied regions
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Presentations
Oral
I Peruvian Colloquium of Archaeometry (2025). "Assessment of the potential of archaeogenomics for studying our past biodiversity and human impact". La Torre R., Chauca G., Bieker VC., Kosel P., Martin S., Arce S., Rivas-Chamorro M., Orjeda G., Beresford-Jones D., Martin MD.
Science week - Science with the North, UNF, Piura, Peru (2025). "Advances in the genomics of algarrobo (Neltuma pallida): Generating evidence to understand its diversity". La Torre R. [PDF-ESP]
VI International Congress of the Peruvian Society of Bioinformatics and Computational Biology, Lima, Peru (2025). "Generating evidence to understand the Algarrobo (Neltuma pallida) decline: Omic sciences and bioinformatics at the service of conservation". La Torre R., Orjeda G. [PDF]
XV Meeting of the Latinoamerican Group of Lichenology, Argentina (2022). "Standardization of a methodology for DNA extraction and amplification of lichenized fungi from King George Island, Antarctica". La Torre R., Mejia M., Loarte E., Cotera C., Neyra E., Orjeda G. [PDF-ESP]
XV Meeting of the Latinoamerican Group of Lichenology, Argentina (2022). "Evaluation of the identification of lichenized fungi in King George Island, Antarctica, using DNA barcoding". La Torre R., Mejia M., Loarte E., Cotera C., Neyra E., Orjeda G. [PDF-ESP]
I National Congress of Life Sciences and XXVII Scientific Meeting ICBAR, Lima, Peru (2020). "Detection of viral RNA sequences in transcriptomes of three Prosopis species (Fabaceae) submitted to NCBI". La Torre R., Rivera A., Lozano R., Orjeda G.
Poster
VI International Congress of the Peruvian Society of Bioinformatics and Computational Biology, Lima, Peru (2025). "Genomic effects of the Nazca on the huarango (Neltuma limensis) woodlands: Paleogenomics and population genomics for unveiling past biodiversity". La Torre R., Bieker VC., Rivas-Chamorro M., Saldana C., Arbizu CI., Chauca G., Kosel P., Martin SL., Arce S., Beresford-Jones D., Orjeda G., Martin MD. [PDF-ESP]
VI International Congress of the Peruvian Society of Bioinformatics and Computational Biology, Lima, Peru (2025). "Generating evidence to understand the Algarrobo (Neltuma pallida) decline: Omic sciences and bioinformatics at the service of conservation". La Torre R., Hamilton JP., Caycho E., Saucedo-Bazalar M., Vaillancourt B., Wood JC., Suarez R., Collins S., Ramirez M., Mayta K., Naupari K., Buell CR., Orjeda G.
Ecological Integration Symposium, College Station, USA (2020). "Effect of wasp parasitism on the bacterial densities in the Spiroplasma-Drosophila melanogaster symbiosis". La Torre R., Mateos M. [PDF-Abstracts]
IV International Scientific Symposium of Biosciences, Lima, Peru (2019). "In silico identification of Exon-Primmed Intron-Crossing markers in the Pomacea genus". La Torre R., Solis M., Silvestre T., Ore D.
XXII International Congress of Genetics, Parana, Brazil (2018). "Family-based association study between variants rs914458 and rs941798 (PTPN1 gene) with diabetes mellitus type 2". La Torre R., Torres D., Padilla C., Garcia-Quispes W., Calderon J., Paredes M. [PDF]
III International Scientific Symposium of Biosciences, Lima, Peru (2017). "Primer design of conserved microsatellite markers from Expressed Sequence Tags of taxon Gekkota". La Torre R., Velasquez A., Ojanama B., Justino S., Ccama S., Toledo G., Ore D. [PDF-ESP]
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