The Plasticity of Genome Architecture

Farré, Marta; Ruiz‐Herrera, Aurora

doi:10.3390/genes11121413

Cited by 2 publications

(2 citation statements)

References 26 publications

(28 reference statements)

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“…The rapid development of sequencing tools in the last 20 years has allowed interrogation of coding and noncoding sequence evolution [ 1 – 6 ], gene regulation [ 7 – 15 ], protein-genome interactions [ 16 – 19 ], and many other processes [ 20 – 22 ]. Although the initial focus of genomics was on a few model organisms, nontraditional rodents have proved particularly useful subjects because of their diverse phenotypes and the ease with which tools developed for model rodents can be applied to them.…”

Section: Introductionmentioning

confidence: 99%

De novo assembly and annotation of the singing mouse genome

Smith,

Frazel,

Khodadadi-Jamayran

et al. 2023

BMC Genomics

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Background Developing genomic resources for a diverse range of species is an important step towards understanding the mechanisms underlying complex traits. Specifically, organisms that exhibit unique and accessible phenotypes-of-interest allow researchers to address questions that may be ill-suited to traditional model organisms. We sequenced the genome and transcriptome of Alston’s singing mouse (Scotinomys teguina), an emerging model for social cognition and vocal communication. In addition to producing advertisement songs used for mate attraction and male-male competition, these rodents are diurnal, live at high-altitudes, and are obligate insectivores, providing opportunities to explore diverse physiological, ecological, and evolutionary questions. Results Using PromethION, Illumina, and PacBio sequencing, we produced an annotated genome and transcriptome, which were validated using gene expression and functional enrichment analyses. To assess the usefulness of our assemblies, we performed single nuclei sequencing on cells of the orofacial motor cortex, a brain region implicated in song coordination, identifying 12 cell types. Conclusions These resources will provide the opportunity to identify the molecular basis of complex traits in singing mice as well as to contribute data that can be used for large-scale comparative analyses.

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Section: Introductionmentioning

confidence: 99%

De novo assembly and annotation of the singing mouse genome

Smith,

Frazel,

Khodadadi-Jamayran

et al. 2023

BMC Genomics

View full text Add to dashboard Cite

show abstract

“…The rapid development of sequencing tools in the last 20 years has allowed interrogation of coding and noncoding sequence evolution (1)(2)(3)(4)(5)(6), gene regulation (7)(8)(9)(10)(11)(12)(13)(14)(15), protein-genome interactions (16)(17)(18)(19), and many other processes (20)(21)(22). Although initial focus was on a few model organisms, genomic sequencing and analysis has become increasingly feasible for nontraditional species.…”

Section: Introductionmentioning

confidence: 99%

De novo assembly and annotation of the singing mouse genome

Smith

Frazel

Khodadadi‐Jamayran

et al. 2022

Preprint

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Background: Developing genomic resources for a diverse range of species is an important step towards understanding the mechanisms underlying complex traits. Specifically, organisms that exhibit unique, accessible phenotypes-of-interests, allow researchers to address questions that may be ill-suited to traditional model organisms. We sequenced the genome and transcriptome of Alston's singing mouse (Scotinomys teguina), an emerging model for social cognition and vocal communication. In addition to producing advertisement songs used for mate attraction and male-male competition, these rodents are diurnal, live at high-altitudes, and are obligate insectivores, providing opportunities to explore diverse physiological, ecological, and evolutionary questions. Results: Using PromethION, Illumina, and PacBio sequencing, we produced an annotated genome and transcriptome, which were validated using gene expression and functional enrichment analyses. To assess the usefulness of our assemblies, we performed single nuclei sequencing on cells of the orofacial motor cortex, a brain region implicated in song coordination, identifying 12 cell types. Conclusions: These resources will provide the opportunity to identify the molecular basis of complex traits in singing mice as well as to contribute data that can be used for large-scale comparative analyses.

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The Plasticity of Genome Architecture

Abstract: Understanding the origin of species and their adaptability to new environments is one of the main questions in biology [...]

Cited by 2 publications

References 26 publications

De novo assembly and annotation of the singing mouse genome

De novo assembly and annotation of the singing mouse genome

De novo assembly and annotation of the singing mouse genome

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