Characterization of the house sparrow (<i><scp>P</scp>asser domesticus</i>) transcriptome: a resource for molecular ecology and immunogenetics

Ekblom, Robert; Wennekes, Paul Louis; Horsburgh, Gavin J.; Burke, Terry

doi:10.1111/1755-0998.12213

Cited by 15 publications

(21 citation statements)

References 86 publications

(171 reference statements)

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“…Ekblom et al 2014;Koglin et al 2017;Peterson et al 2012;Richardson et al 2017;Santure et al 2011;Srivastava et al 2012) (Box 1), sometimes in combination with the genome analyses of the same species (e.g. Chung et al 2015;Mueller et al 2015).…”

Section: Characterisation Of Transcriptomesmentioning

confidence: 99%

“…For House Sparrow Passer domesticus, a transcriptomic approach yielded 327 gene-linked microsatellites, thereby providing important genomic tools for future molecular ecology studies in this species (Ekblom et al 2014).…”

Section: Genetic Marker Discoverymentioning

confidence: 99%

“…SNPs are abundant in the genome and can be found especially in non-coding but also in coding regions, and are hence valuable markers for many types of research questions or to see whether genetic variants are associated with a certain trait or disease. SNPs have been discovered using transcriptomics in many avian species (Balakrishnan et al 2013;Ekblom and Wang 2017;Ekblom et al 2014;Hagen et al 2013;Kaiser et al 2017;Lundberg et al 2013;Ramstad et al 2016;Santure et al 2011;Srivastava 2011;Srivastava et al 2012;Vijayakumar et al 2014;Zhang et al 2014b) (Box 3). Whole body transcriptomics was used to find candidate loci explaining the divergence between two subspecies of songbirds with several phenotypically different characteristics inhabiting either the mainland or islands of Alaska (Srivastava 2011).…”

Section: Genetic Marker Discoverymentioning

confidence: 99%

“…Further, the collection of samples from wild individuals usually requires special licences and the agreement of an ethical committee. Several studies have compared the transcriptomic profile between whole blood and other tissues during the immune response (Désert et al 2016;Ekblom et al 2014;Sandford et al 2012), showing the utility of RNA from blood for disease ecology studies. Blood has further been successfully used to study sex chromosome evolution in two rare kiwi species, Apteryx owenii and Apteryx rowi, showing that this tissue can be used as a source of RNA for transcriptomic studies in protected birds (Ramstad et al 2016).…”

Section: Tissuesmentioning

confidence: 99%

“…If the goal of the study is to make a reference transcriptome then aiming for longer sequences might be the appropriate choice, as this will facilitate the de novo assembly. For this reason, many avian studies have used the now deprecated Roche 454 sequencing technology where sequence lengths can be several hundreds of nucleotides long (Ekblom et al 2014;Peterson et al 2012). However, if a good reference genome or transcriptome is already available for the target species or a closely related one then shorter sequences (as generated by Illumina sequencers) might be sufficient-and much cheaper.…”

Section: Sequencing Depth and Read Lengthmentioning

confidence: 99%

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Avian transcriptomics: opportunities and challenges

Jax

Kraus

2018

J Ornithol

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Recent developments in next-generation sequencing technologies have greatly facilitated the study of whole transcriptomes in model and non-model species. Studying the transcriptome and how it changes across a variety of biological conditions has had major implications for our understanding of how the genome is regulated in different contexts, and how to interpret adaptations and the phenotype of an organism. The aim of this review is to highlight the potential of these new technologies for the study of avian transcriptomics, and to summarise how transcriptomics has been applied in ornithology. A total of 81 peer-reviewed scientific articles that used transcriptomics to answer questions within a broad range of study areas in birds are used as examples throughout the review. We further provide a quick guide to highlight the most important points which need to be take into account when planning a transcriptomic study in birds, and discuss how researchers with little background in molecular biology can avoid potential pitfalls. Suggestions for further reading are supplied throughout. We also discuss possible future developments in the technology platforms used for ribonucleic acid sequencing. By summarising how these novel technologies can be used to answer questions that have long been asked by ornithologists, we hope to bridge the gap between traditional ornithology and genomics, and to stimulate more interdisciplinary research.

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Section: Characterisation Of Transcriptomesmentioning

confidence: 99%

Section: Genetic Marker Discoverymentioning

confidence: 99%

Section: Genetic Marker Discoverymentioning

confidence: 99%

Section: Tissuesmentioning

confidence: 99%

Section: Sequencing Depth and Read Lengthmentioning

confidence: 99%

See 3 more Smart Citations

Avian transcriptomics: opportunities and challenges

Jax

Kraus

2018

J Ornithol

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Mature sperm small-RNA profile in the sparrow: implications for transgenerational effects of age on fitness

Matsushima

Brink

Schroeder

et al. 2019

Environmental Epigenetics

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Mammalian sperm RNA has recently received a lot of interest due to its involvement in epigenetic germline inheritance. Studies of epigenetic germline inheritance have shown that environmental exposures can induce effects in the offspring without altering the DNA sequence of germ cells. Most mechanistic studies were conducted in laboratory rodents and C.elegans while observational studies confirm the phenotypic phenomenon in wild populations of humans and other species including birds. Prominently, paternal age in house sparrows affects offspring fitness, yet the mechanism is unknown. This study provides a first reference of house sparrow sperm small RNA as an attempt to uncover their role in the transmission of the effects of paternal age on the offspring. In this small-scale pilot, we found no statistically significant differences between miRNA and tRNA fragments in aged and prime sparrow sperm. These results indicate a role of other epigenetic information carriers, such as distinct RNA classes, RNA modifications, DNA methylation and retained histones, and a clear necessity of future studies in wild populations.

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Effects of Plastic Ingestion on Blood Chemistry, Gene Expression and Body Condition in Wedge-Tailed Shearwaters (Ardenna Pacifica)

Mejia

Termignoni-García

Edwards

et al. 2022

Preprint

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Plastic pollution is a global threat and affects almost every marine ecosystem. The amount of plastic in the ocean has increased substantially over the past decade, posing a mounting threat to biodiversity. Seabirds, typically top predators in marine food chains, have been negatively affected by plastic pollution. Here we focused on documenting the sublethal effects of plastic in Wedge-tailed Shearwaters (Ardenna pacifica, WTSH) on the island of Maui, Hawaii. Through analyses of blood chemistry, gene expression, morphometrics and stomach contents, we documented the effects of plastic ingestion on adult WTHS from 3 established colonies. We detected a negative relationship between body weight and the presence of plastic in regurgitated stomach contents. Genes associated with metabolic, biosynthetic pathways, inflammatory responses and ribosome function were upregulated in lighter birds. Birds that had ingested plastic tended to be lighter in weight, in comparison to birds that did not have plastic and tended to weight more. Furthermore, there were 43 genes differentiating males and females that did not have plastic compared to only 11 genes differentiating males and females that had ingested plastic. There was also a marginal negative relationship between lighter birds and blood urea nitrogen levels. We also hope that the morphometric measurements, blood parameters and gene expression data we collected contributes to a database that will be used for future studies on understanding anthropogenic effects on seabird body condition.

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Characterization of the house sparrow (Passer domesticus) transcriptome: a resource for molecular ecology and immunogenetics

Abstract: Characterization of the house sparrow (Passer domesticus) transcriptome: a resource for molecular ecology and immunogenetics. were specifically chosen to obtain a diverse representation of expressed genes and to Molecular Ecology Resources

Cited by 15 publications

References 86 publications

Avian transcriptomics: opportunities and challenges

Avian transcriptomics: opportunities and challenges

Mature sperm small-RNA profile in the sparrow: implications for transgenerational effects of age on fitness

Effects of Plastic Ingestion on Blood Chemistry, Gene Expression and Body Condition in Wedge-Tailed Shearwaters (Ardenna Pacifica)

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