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Abstract Diatoms, a major group of microalgae, play a critical role in global carbon cycling and primary production. Despite their ecological significance, comprehensive genomic resources for diatoms are limited. To address this, we have annotated previously unannotated genome assemblies of 49 diatom species. Genome assemblies were obtained from NCBI Datasets and processed for repeat elements using RepeatModeler2 and RepeatMasker. For gene prediction, BRAKER2 was employed in the absence of transcriptomic data, while BRAKER3 was utilised when transcriptome short read data were available from the Sequence Read Archive. The quality of genome assemblies and predicted protein sets was evaluated using BUSCO, ensuring high-quality genomic resources. Functional annotation was performed using EnTAP, providing insights into the biological roles of the predicted proteins. Our study enhances the genomic toolkit available for diatoms, facilitating future research in diatom biology, ecology, and evolution. 

Abstract The first chromosome-scale reference genome of the rare narrow-endemic African moss Physcomitrellopsis africana (P. africana) is presented here. Assembled from 73 × Oxford Nanopore Technologies (ONT) long reads and 163 × Beijing Genomics Institute (BGI)-seq short reads, the 414 Mb reference comprises 26 chromosomes and 22,925 protein-coding genes [Benchmarking Universal Single-Copy Ortholog (BUSCO) scores: C:94.8% (D:13.9%)]. This genome holds 2 genes that withstood rigorous filtration of microbial contaminants, have no homolog in other land plants, and are thus interpreted as resulting from 2 unique horizontal gene transfers (HGTs) from microbes. Further, P. africana shares 176 of the 273 published HGT candidates identified in Physcomitrium patens (P. patens), but lacks 98 of these, highlighting that perhaps as many as 91 genes were acquired in P. patens in the last 40 million years following its divergence from its common ancestor with P. africana. These observations suggest rather continuous gene gains via HGT followed by potential losses during the diversification of the Funariaceae. Our findings showcase both dynamic flux in plant HGTs over evolutionarily “short” timescales, alongside enduring impacts of successful integrations, like those still functionally maintained in extant P. africana. Furthermore, this study describes the informatic processes employed to distinguish contaminants from candidate HGT events. 

Abstract Human activity changes multiple factors in the environment, which can have positive or negative synergistic effects on organisms. However, few studies have explored the causal effects of multiple anthropogenic factors, such as urbanization and invasive species, on animals and the mechanisms that mediate these interactions. This study examines the influence of urbanization on the detrimental effect of invasive avian vampire flies (Philornis downsi) on endemic Darwin's finches in the Galápagos Islands. We experimentally manipulated nest fly abundance in urban and non‐urban locations and then characterized nestling health, fledging success, diet, and gene expression patterns related to host defense. Fledging success of non‐parasitized nestlings from urban (79%) and non‐urban (75%) nests did not differ significantly. However, parasitized, non‐urban nestlings lost more blood, and fewer nestlings survived (8%) compared to urban nestlings (50%). Stable isotopic values (δ¹⁵N) from urban nestling feces were higher than those from non‐urban nestlings, suggesting that urban nestlings are consuming more protein. δ¹⁵N values correlated negatively with parasite abundance, which suggests that diet might influence host defenses (e.g., tolerance and resistance). Parasitized, urban nestlings differentially expressed genes within pathways associated with red blood cell production (tolerance) and pro‐inflammatory response (innate immunological resistance), compared to parasitized, non‐urban nestlings. In contrast, parasitized non‐urban nestlings differentially expressed genes within pathways associated with immunoglobulin production (adaptive immunological resistance). Our results suggest that urban nestlings are investing more in pro‐inflammatory responses to resist parasites but also recovering more blood cells to tolerate blood loss. Although non‐urban nestlings are mounting an adaptive immune response, it is likely a last effort by the immune system rather than an effective defense against avian vampire flies since few nestlings survived.