Exploring the unmapped DNA and RNA reads in a songbird genome

Laine, Veronika N.; Gossmann, Toni I.; Oers, Kees van; Visser, Marcel E.; Groenen, M.A.M.

doi:10.1101/371963

Cited by 11 publications

(13 citation statements)

References 58 publications

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“…The extent to which extrinsic environmental conditions shape host-pathogen coevolution and contribute to the emergence of locally adapted populations are currently poorly understood. Here, we demonstrate how integrated use of complementary NGS approaches can provide novel insights on such complex associations [2,15,18,60]. By analysing both host-speci c and unmapped whole-eye RNA-seq reads, we discovered that perch individuals from humic and clear-water lakes differ in immune system related gene expression, and that this difference could be explained by contrasting diplostomid parasite pressure between the two habitats.…”

Section: Discussionmentioning

confidence: 87%

Humic-acid-driven escape from eye parasites revealed by RNA-seq and target-specific metabarcoding

Noreikienė

Ozerov²,

Ahmad³

et al. 2020

Preprint

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Background: Next generation sequencing (NGS) technologies are extensively used to dissect the molecular mechanisms of host-parasite interactions in human pathogens. However, ecological studies have yet to fully exploit the power of NGS as a rich source for formulating and testing new hypotheses. Methods: We studied Eurasian perch (Perca fluviatilis) and its eye parasite (Trematoda, Diplostomidae) communities in 14 lakes that differed in humic content in order to explore host-parasite-environment interactions. We hypothesised that high humic content along with low pH would decrease the abundance of the intermediate hosts (gastropods), thus limiting the occurrence of diplostomid parasites in humic lakes. This hypothesis was initially invoked by whole eye RNA-seq data analysis and subsequently tested using PCR-based detection and a novel targeted metabarcoding approach.Results: Whole eye transcriptome results revealed overexpression of immune-related genes and the presence of eye parasite sequences in RNA-seq data obtained from perch living in clear-water lakes. Both PCR-based and targeted-metabarcoding approach showed that perch from humic lakes were completely free from diplostomid parasites, while the prevalence of eye flukes in clear-water lakes that contain low amounts of humic substances was close to 100%, with the majority of NGS reads assigned to Tylodelphys clavata. Conclusions: High intraspecific diversity of T. clavata indicates that massively parallel sequencing of naturally pooled samples represents an efficient and powerful strategy for shedding light on cryptic diversity of eye parasites. Our results demonstrate that perch populations in clear-water lakes experience contrasting eye parasite pressure compared to those from humic lakes, which is reflected by prevalent differences in the expression of immune-related genes in the eye. This study highlights the utility of NGS to discover novel host-parasite-environment interactions and provide unprecedented power to characterize the molecular diversity of cryptic parasites.

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Section: Discussionmentioning

confidence: 87%

Humic-acid-driven escape from eye parasites revealed by RNA-seq and target-specific metabarcoding

Noreikienė

Ozerov²,

Ahmad³

et al. 2020

Preprint

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“…The map-then-assemble approach allows to perform individual assemblies after shared sequences are identified ( Figure 4C). The idea here is to map all the sequences upon a reference sequence, then to re-assemble per individual the unmapped data (12,42,56). An alternative way is to re-assemble through an iterative mode (39), where samples are mapped successively on a panreference, which is updated each turn by the newly assembled sequences.…”

Section: Methods For Pangenome Assemblymentioning

confidence: 99%

Plant Pangenome: Impacts on Phenotypes and Evolution

Tranchant‐Dubreuil¹,

Rouard²,

Sabot³

2019

Annual Plant Reviews Online

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HAL is a multidisciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L'archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d'enseignement et de recherche français ou étrangers, des laboratoires publics ou privés.

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“…We obtained sequencing data for coding genes from three bird species: great tit (Laine et al, 2016), zebra finch (Warren et al, 2010) and chicken (Hillier et al, 2004) - three of the best annotated and most studied bird genomes (Laine et al, 2018) currently available along with the high quality collared flycatcher genome (Ellegren et al, 2012; Kawakami et al, 2014) that was not considered here. An alignment pipeline was applied as described in Corcoran et al (2017) from which we extracted aligned 4-fold degenerate sites only, as GC-biased gene conversion is supposed to act in particular on these sites (Bolivar et al, 2016).…”

Section: Methodsmentioning

confidence: 99%

Evidence for strong fixation bias at 4-fold degenerate sites across genes in the great tit genome

Gossmann

Bockwoldt

Diringer

et al. 2018

Preprint

Self Cite

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3It is well established that GC content varies across the genome in many species and that 4 GC biased gene conversion, one form of meiotic recombination, is likely to contribute to this 5 heterogeneity. Bird genomes provide an extraordinary system to study the impact of GC biased 6 gene conversion owed to their specific genomic features. They are characterised by a high 7 karyotype conservation with substantial heterogeneity in chromosome sizes, with up to a dozen 8 large macrochromosomes and many smaller microchromosomes common across all bird species. 9 This heterogeneity in chromosome morphology is also reflected by other genomic features, such 10 as smaller chromosomes being gene denser, more compact and more GC rich relative to their 11 macrochromosomal counterparts -illustrating that the intensity of GC biased gene conversion 12 varies across the genome. Here we study whether it is possible to infer heterogeneity in GC biased 13 gene conversion rates across the genome using a recently published method that accounts for 14 GC biased gene conversion when estimating branch lengths in a phylogenetic context. To infer the 15 strength of GC biased gene conversion we contrast branch length estimates across the genome 16 both taking and not taking non-stationary GC composition into account. Using simulations we 17 show that this approach works well when GC fixation bias is strong and note that the number of 18 substitutions along a branch is consistently overestimated when GC biased gene conversion is 19 1 Gossmann et al. GC fixation bias in bird genomesnot accounted for. We use this predictable feature to infer the strength of GC dynamics across the 20 great tit genome by applying our new test statistic to data at 4-fold degenerate sites from three 21 bird species -great tit, zebra finch and chicken -three species that are among the best annotated 22 bird genomes to date. We show that using a simple one-dimensional binning we fail to capture a 23 signal of fixation bias as observed in our simulations. However, using a multidimensional binning 24 strategy, we find evidence for heterogeneity in the strength of fixation bias, including AT fixation 25 bias. This highlights the difficulties when combining sequence data across different regions in the 26 genome. 27

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Exploring the unmapped DNA and RNA reads in a songbird genome

Abstract: Background: A widely used approach in next-generation sequencing projects is the alignment of

Cited by 11 publications

References 58 publications

Humic-acid-driven escape from eye parasites revealed by RNA-seq and target-specific metabarcoding

Humic-acid-driven escape from eye parasites revealed by RNA-seq and target-specific metabarcoding

Plant Pangenome: Impacts on Phenotypes and Evolution

Evidence for strong fixation bias at 4-fold degenerate sites across genes in the great tit genome

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