Evolutionary genomics: the fruits of genomic approaches applied to evolutionary biology

Sands, Timothy R.

doi:10.1186/s13059-018-1615-x

Cited by 5 publications

(3 citation statements)

References 16 publications

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“…We downloaded the list of putative miRNA targets from mirdb.org (miRDB v6.0, source miRBase 22) ( Chen and Wang, 2020 ; Liu and Wang, 2019 ). RefSeq IDs were converted to entrez IDs using the biomaRt package.…”

Section: Methodsmentioning

confidence: 99%

Proteomic analysis of young and old mouse hematopoietic stem cells and their progenitors reveals post-transcriptional regulation in stem cells

Zaro

Noh

Mascetti

et al. 2020

eLife

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The balance of hematopoietic stem cell (HSC) self-renewal and differentiation is critical for a healthy blood supply; imbalances underlie hematological diseases. The importance of HSCs and their progenitors have led to their extensive characterization at genomic and transcriptomic levels. However, the proteomics of hematopoiesis remains incompletely understood. Here we report a proteomics resource from mass spectrometry of mouse young adult and old adult mouse HSCs, multipotent progenitors and oligopotent progenitors; 12 cell types in total. We validated differential protein levels, including confirmation that Dnmt3a protein levels are undetected in young adult mouse HSCs until forced into cycle. Additionally, through integrating proteomics and RNA-sequencing datasets, we identified a subset of genes with apparent post-transcriptional repression in young adult mouse HSCs. In summary, we report proteomic coverage of young and old mouse HSCs and progenitors, with broader implications for understanding mechanisms for stem cell maintenance, niche interactions and fate determination.

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Section: Methodsmentioning

confidence: 99%

Proteomic analysis of young and old mouse hematopoietic stem cells and their progenitors reveals post-transcriptional regulation in stem cells

Zaro

Noh

Mascetti

et al. 2020

eLife

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“…We used plyranges (v. 1.6.5; Lee et al. 2019 ) to identify genetic variants overlapping with gene regions.…”

Section: Methodsmentioning

confidence: 99%

Few Fixed Variants between Trophic Specialist Pupfish Species Reveal CandidateCis-Regulatory Alleles Underlying Rapid Craniofacial Divergence

McGirr

Martin

2020

Molecular Biology and Evolution

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Investigating closely related species that rapidly evolved divergent feeding morphology is a powerful approach to identify genetic variation underlying variation in complex traits. This can also lead to the discovery of novel candidate genes influencing natural and clinical variation in human craniofacial phenotypes. We combined whole-genome resequencing of 258 individuals with 50 transcriptomes to identify candidate cis-acting genetic variation underlying rapidly evolving craniofacial phenotypes within an adaptive radiation of Cyprinodon pupfishes. This radiation consists of a dietary generalist species and two derived trophic niche specialists – a molluscivore and a scale-eating species. Despite extensive morphological divergence, these species only diverged 10 kya and produce fertile hybrids in the laboratory. Out of 9.3 million genome-wide SNPs and 80,012 structural variants, we found very few alleles fixed between species – only 157 SNPs and 87 deletions. Comparing gene expression across 38 purebred F1 offspring sampled at three early developmental stages, we identified 17 fixed variants within 10 kilobases of 12 genes that were highly differentially expressed between species. By measuring allele-specific expression in F1 hybrids from multiple crosses, we found that the majority of expression divergence between species was explained by trans-regulatory mechanisms. We also found strong evidence for two cis-regulatory alleles affecting expression divergence of two genes with putative effects on skeletal development (dync2li1 and pycr3). These results suggest that SNPs and structural variants contribute to the evolution of novel traits and highlight the utility of the San Salvador Island pupfish system as an evolutionary model for craniofacial development.

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“…Genome sequences have been used widely for species identification with high accuracy and have been useful to many research areas in the biotechnological (Costessi et al, 2018), environmental (Vandenkoornhuyse et al, 2010), evolutionary (Bruger and Marx, 2018;Sands, 2019), and clinical sciences (Balloux et al, 2018). With the rapid technological development of genome sequencing, more and more organisms have been sequenced across all kingdoms (Galagan et al, 2005;Land et al, 2015;Houldcroft et al, 2017;Chen et al, 2019;Rexroad et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

KITSUNE: A Tool for Identifying Empirically Optimal K-mer Length for Alignment-Free Phylogenomic Analysis

Pornputtapong

Acheampong

Patumcharoenpol

et al. 2020

Front. Bioeng. Biotechnol.

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Genomic DNA is the best "unique identifier" for organisms. Alignment-free phylogenomic analysis, simple, fast, and efficient method to compare genome sequences, relies on looking at the distribution of small DNA sequence of a particular length, referred to as k-mer. The k-mer approach has been explored as a basis for sequence analysis applications, including assembly, phylogenetic tree inference, and classification. Although this approach is not novel, selecting the appropriate k-mer length to obtain the optimal resolution is rather arbitrary. However, it is a very important parameter for achieving the appropriate resolution for genome/sequence distances to infer biologically meaningful phylogenetic relationships. Thus, there is a need for a systematic approach to identify the appropriate k-mer from whole-genome sequences. We present K-mer-length Iterative Selection for UNbiased Ecophylogenomics (KITSUNE), a tool for assessing the empirically optimal k-mer length of any given set of genomes of interest for phylogenomic analysis via a three-step approach based on (1) cumulative relative entropy (CRE), (2) average number of common features (ACF), and (3) observed common features (OCF). Using KITSUNE, we demonstrated the feasibility and reliability of these measurements to obtain empirically optimal k-mer lengths of 11, 17, and ∼34 from large genome datasets of viruses, bacteria, and fungi, respectively. Moreover, we demonstrated a feature of KITSUNE for accurate species identification for the two de novo assembled bacterial genomes derived from error-prone long-reads sequences, and for a published yeast genome. In addition, KITSUNE was used to identify the shortest species-specific k-mer accurately identifying viruses. KITSUNE is freely available at https://github.com/natapol/kitsune.

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Evolutionary genomics: the fruits of genomic approaches applied to evolutionary biology

Cited by 5 publications

References 16 publications

Proteomic analysis of young and old mouse hematopoietic stem cells and their progenitors reveals post-transcriptional regulation in stem cells

Proteomic analysis of young and old mouse hematopoietic stem cells and their progenitors reveals post-transcriptional regulation in stem cells

Few Fixed Variants between Trophic Specialist Pupfish Species Reveal CandidateCis-Regulatory Alleles Underlying Rapid Craniofacial Divergence

KITSUNE: A Tool for Identifying Empirically Optimal K-mer Length for Alignment-Free Phylogenomic Analysis

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