Origins and evolution of extreme life span in Pacific Ocean rockfishes

Kolora, Sree Rohit Raj; Owens, Gregory L.; Vazquez, Juan Manuel; Stubbs, Alexander L.; Chatla, Kamalakar; Jainese, Conner; Seeto, Katelin; McCrea, Merit; Sandel, Michael J.; Vianna, Juliana A.; Maslenikov, Katherine P.; Bachtrog, Doris; Orr, James W.; Love, Milton S.; Sudmant, Peter H.

doi:10.1126/science.abg5332

Cited by 97 publications

(80 citation statements)

References 79 publications

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“…In agreement with our findings, other authors reported that high levels of the AKT1 isoform could be related with the loss of BRCA1 expression and HR inhibition in breast cancer models, suggesting that a similar mechanism could be possible in HGSOC [ 23 , 24 ]. Furthermore, AKT1 has been identified as an age-associated gene in different non-human species, thanks to its ability to stimulate the insulin/IGF1 pathway and inhibit DNA repair mechanisms [ 25 , 26 ].…”

Section: Discussionmentioning

confidence: 99%

AKT Isoforms Interplay in High-Grade Serous Ovarian Cancer Prognosis and Characterization

Azzalini

Tierno

Bartoletti

et al. 2022

Cancers

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High-grade serous ovarian cancer (HGSOC) is among the deadliest gynecological malignancies. The acquired resistance to platinum-based therapies and the intrinsic heterogeneity of the disease contribute to the low survival rate. To improve patients’ outcomes, new combinatorial approaches able to target different tumor vulnerabilities and enhance the efficacy of the current therapies are required. AKT inhibitors are promising antineoplastic agents able to act in synergy with PARP inhibitors, but the spectrum of patients who can benefit from this combination is unclear, since the role of the three different isoforms of AKT is still unknown. Here, we study the expression of AKT isoforms on a retrospective cohort of archive tissue by RT-droplet digital PCR (ddPCR) analyzing their association with the clinicopathological features of patients. Based on AKT1/AKT2 and AKT1/AKT3 ratios, we define four AKT classes which were related to patients’ survival, tumor morphology and BRCA1 expression. Moreover, our results show that high AKT3 expression levels were frequently associated with tumors having classic features, a low number of mitoses and the presence of psammoma bodies. Overall, our study obtains new insights on AKT isoforms and their associations with the clinicopathological features of HGSOC patients. These evidences could help to better define the subsets of patients who can benefit from AKT and PARP inhibitors therapy in future clinical trials.

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Section: Discussionmentioning

confidence: 99%

AKT Isoforms Interplay in High-Grade Serous Ovarian Cancer Prognosis and Characterization

Azzalini

Tierno

Bartoletti

et al. 2022

Cancers

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“…Furthermore, Kolora et al (2021) found an expansion in the immune modulatory butyrophilin gene family in long-lived rockfishes compared to short-lived rockfishes. A similar number of genes in most immune pathways (60%, 12 in 20 pathways, Table S10) were detected both in the three short-lived fish species (T. fasciatus, N.…”

Section: Expansion and Contraction Of The Roughskin Sculpin Genomementioning

confidence: 95%

“…The lifespans of vertebrates are highly variable, which range from a few weeks to several hundred years in nature (Kolora et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

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A high‐quality chromosome‐level genome of the endangered roughskin sculpin provides insights into its evolution and adaptation

Xue

Xing

Liu

2022

Molecular Ecology Resources

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The cottids (Cottidae) are a taxonomically diverse and ecologically important component of many marine and freshwater ecosystems. Despite recent breakthroughs in long-read sequencing, high quality genomic resources are still limited for studies of ecological and evolutionary processes in cottids. Here, we generated a high-quality, chromosome-scale genome assembly (521.26 Mb) of the catadromous roughskin sculpin (Trachidermus fasciatus Heckel) with a contig N50 of 2.93 Mb and a scaffold N50 of 24.06 Mb. Approximately 21.97% of the genome was composed of repetitive elements. A total of 21,872 protein-coding genes were predicted, of which 19,900 genes (90.98%) were functionally annotated. Phylogenetic analysis supported the validity of Scorpaenoidei and Cottioidei as two suborders of the Perciformes. Chromosomescale collinearity analyses identified four chromosome fusions leading to the reduction of chromosome number in T. fasciatus. Gene families related to cell apoptosis and cell death were expanded and those related to immune system were contracted, suggesting that these gene families might be relevant to a host of phenotypic differences between T. fasciatus and other teleosts. Gene families associated with osmoregulation were also expanded, which might be associated with its catadromous life history. A total of 50 aging-associated genes were found to be under positive selection, which might be associated with the short lifespan of T. fasciatus. The high-quality genome assembly and annotation will promote researches into the evolution of catadromous life history and short lifespan for T. fasciatus and facilitate comparative genomic studies of cottids in the near future.

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“…Recent advances in sequencing technologies along with falling sequencing costs have made it increasingly feasible to sequence and assemble reference genomes for non-model species (Feng et al, 2020; Kolora et al, 2021; Hotaling et al, 2021; Formenti et al, 2022; Rhie et al, 2021). Non-model reference genomes can then be used to assemble short reads from reduced-representation or whole genome sequencing into shared loci across individuals, and an increasing number of studies use a reference genome of a focal study taxon for assembly.…”

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confidence: 99%

Reference genome choice and filtering thresholds jointly influence phylogenomic analyses

Rick

Brock

Lewanski

et al. 2022

Preprint

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Molecular phylogenies are a cornerstone of modern comparative biology and are commonly employed to investigate a range of biological phenomena, such as diversification rates, patterns in trait evolution, biogeography, and community assembly. Recent work has demonstrated that significant biases may be introduced into downstream phylogenetic analyses from processing genomic data; however, it remains unclear whether there are interactions among bioinformatic parameters or biases introduced through the choice of reference genome for sequence alignment and variant-calling. We address these knowledge gaps by employing a combination of simulated and empirical data sets to investigate to what extent the choice of reference genome in upstream bioinformatic processing of genomic data influences phylogenetic inference, as well as the way that reference genome choice interacts with bioinformatic filtering choices. We demonstrate that more stringent minor allele filters bias inferred trees away from the true species tree topology, and that these biased trees tend to be more imbalanced and have a higher center of gravity than the true trees. We find greatest topological accuracy when filtering sites for minor allele count > 3--4 in our 51-taxa data sets, while tree center of gravity was closest to the true value when filtering for sites with minor allele count > 1-2. In contrast, filtering for missing data increased accuracy in the inferred topologies; however, this effect was small in comparison to the effect of minor allele filters and may be undesirable due to a subsequent mutation spectrum distortion. The bias introduced by these filters differs based on the reference genome used in short read alignment, indicating that choosing a reference genome for alignment is an important bioinformatic decision with implications for downstream analyses. These results demonstrate that care needs to be taken when choosing parameters for assembling and filtering large genomic data sets from short read data.

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Origins and evolution of extreme life span in Pacific Ocean rockfishes

Cited by 97 publications

References 79 publications

AKT Isoforms Interplay in High-Grade Serous Ovarian Cancer Prognosis and Characterization

AKT Isoforms Interplay in High-Grade Serous Ovarian Cancer Prognosis and Characterization

A high‐quality chromosome‐level genome of the endangered roughskin sculpin provides insights into its evolution and adaptation

Reference genome choice and filtering thresholds jointly influence phylogenomic analyses

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