The native mussel Mytilus chilensis genome reveals adaptative molecular signatures facing the marine environment.

Gallardo-Escarate, C.; Valenzuela-Munoz, V.; Nunez-Acuna, G.; Valenzuela-Miranda, D.; Tapia, F.; Yevenes, M.; Gajardo, G.; Toro, J. E.; Oyarzun, P. A.; Arriagada, G.; novoa, b.; Figueras, A.; Roberts, S.; Gerdol, M.

doi:10.1101/2022.09.06.506863

bioRxiv · 10.1101/2022.09.06.506863

The native mussel Mytilus chilensis genome reveals adaptative molecular signatures facing the marine environment.

Gallardo-Escarate, C.·Valenzuela-Munoz, V.·Nunez-Acuna, G.·Valenzuela-Miranda, D.·Tapia, F.·Yevenes, M.·Gajardo, G.·Toro, J. E.·Oyarzun, P. A.·Arriagada, G.·novoa, b.·Figueras, A.·Roberts, S.·Gerdol, M.

View original source ↗Export metadata ↓

Abstract

The blue mussel Mytilus chilensis is a key socioeconomic species inhabiting the southern coast of Chile. This endemic marine mussel supports a booming aquaculture industry, which entirely relies on artificially collected seeds from natural beds that are translocated to a diverse physical-chemical ocean conditions for farming. Furthermore, mussel production is threatened by a broad range of microorganisms, pollution, and environmental stressors that eventually impact its survival and growth. Herein, understanding the genomic basis of the local adaption is pivotal to developing sustainable shellfish aquaculture. We present a high-quality reference genome of M. chilensis, which is the first chromosome-level genome for a Mytilidae member in South America. The assembled genome size was 1.93 Gb, with a contig N50 of 134 Mb. Through Hi-C proximity ligation, 11,868 contigs were clustered, ordered, and assembled into 14 chromosomes in congruence with the karyological evidence. The M. chilensis genome comprises 34,530 genes and 4,795 non-coding RNAs. A total of 57% of the genome contains repetitive sequences with predominancy of LTR-retrotransposons and unknown elements. Comparative genome analysis was conducted among M. chilensis and M. coruscus, revealing genic rearrangements distributed into the whole genome. Notably, Steamer-like elements associated with horizontal transmissible cancer were explored in reference genomes, suggesting putative phylogenetic relationships at the chromosome level in Bivalvia. Genome expression analysis was also conducted, showing putative genomic differences between two ecologically different mussel populations. Collectively, the evidence suggests that local genome adaptation can be analyzed to develop sustainable mussel production. The genome of M. chilensis provides pivotal molecular knowledge for the Mytilus complex evolution and will help to understand how climate change can impact mussel biology.

Explore related subjects

genomics Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Gallardo-Escarate, C., Valenzuela-Munoz, V., Nunez-Acuna, G., Valenzuela-Miranda, D., Tapia, F., Yevenes, M., Gajardo, G., Toro, J. E., Oyarzun, P. A., Arriagada, G., novoa, b., Figueras, A., Roberts, S., Gerdol, M.. 2022-09-07. The native mussel Mytilus chilensis genome reveals adaptative molecular signatures facing the marine environment.. https://doi.org/10.1101/2022.09.06.506863

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

RNA isoform-resolved multiplexed sequencing with bioorthogonal barcoding

RNA isoform dysregulation drives disease pathogenesis and is the target of FDA-approved splice-switching therapeutics. However, multiplexed sequencing methods discard splice junction information because only 3' termini are barcoded and counted. Here, we repurpose acylation and click chemistries to conjugate bioorthogonal barcodes (bobcodes) directly onto multiple internal positions along cellular RNAs. Bobcoded RNAs from multiple samples are pooled for multiplexed cDNA synthesis, during which reverse transcriptase switches from each RNA template onto its tethered bobcode with greater than 99% accuracy in species mixing experiments. Bobcode attachment intervals set cDNA insert sizes without a library fragmentation step, and priming with poly(dT) or random hexamers selects between 3'-end counting and full-length isoform capture. A bioorthogonal barcode-sequencing (BOB-seq v0.1) drug screen identifies transcriptome-wide on- and off-target RNA splicing effects and outperforms existing multiplexing RNA sequencing methods in workflow simplicity, sample-to-sample variability, and barcoding accuracy. Bobcodes add isoform resolution to scalable multiplexed RNA sequencing.

genomics↗

bioRxiv2026

Integrative Nanopore and Illumina sequencing reveals age-associated tRNA modification and CCA-tail dynamics in yeast

Aging is characterized by a progressive loss of proteostasis. Transfer RNAs (tRNAs) are essential regulators of translation, yet their dynamics during aging remain poorly understood due to challenges in sequencing highly modified RNAs. Here we present a benchmarked Nanopore direct RNA sequencing (RNA004 chemistry) resource that profiles the Saccharomyces cerevisiae tRNAome during replicative aging at single-molecule resolution. Using in vitro transcribed tRNA controls, we establish modification detection thresholds and validate key findings with orthogonal Illumina sequencing. While overall tRNA abundance remains largely stable, our resource reveals age-associated terminal A cleavage at the 3' CCA tail of mature tRNAs, targeted T-loop and anticodon modification changes, and single-molecule evidence of modification co-occurrence. This dataset provides a resource for exploring tRNA regulation, translation fidelity, and longevity.

genomics↗

bioRxiv2026

A hydrogen-producing mitochondrion in an anaerobic eukaryotrophic rhizarian

Diverse eukaryotes thrive under low oxygen conditions, in part through highly modified mitochondrion-related organelles (MROs) that use alternate metabolic pathways to support ATP production and cofactor recycling. Anaerobic lifestyles have evolved repeatedly across the eukaryotic tree of life, each providing an independent opportunity to understand how eukaryotes adapt to life in low oxygen conditions. Here, we use single-cell transcriptomics to reconstruct the MRO metabolism of PCE SSF, a benthic eukaryotrophic flagellate and the first cultivated representative of Novel Clade 12 (NC12; Rhizaria), an independently anaerobic rhizarian lineage. PCE SSF possesses an anaerobic hydrogen-producing mitochondrion capable of hydrogenosome-type substrate-level phosphorylation. It also retains a nearly complete but likely branched tricarboxylic acid pathway that lacks citrate synthase and malate dehydrogenase. The function of citrate synthase may instead be fulfilled by the typically cytosolic ATP citrate lyase, previously reported in this context only in the anaerobic cercozoan, Brevimastigomonas motovehiculus. Unlike B. motovehiculus, however, PCE SSF retains only Complex II and the NuoE/NuoF subunits of the electron transport chain and lacks a mitochondrial genome. Together, these features indicate an atypical and reduced mitochondrial metabolism, highlighting the diversity of evolutionary solutions to anaerobic energy metabolism in eukaryotes.

genomics↗