Loss of a gluconeogenic muscle enzyme contributed to adaptive metabolic traits in hummingbirds

Osipova, Ekaterina; Barsacchi, Rico; Brown, Tom; Sadanandan, Keren R.; Gaede, Andrea H.; Monte, Amanda; Jarrells, Julia; Moebius, Claudia; Pippel, Martin; Altshuler, Douglas L.; Winkler, Sylke; Bickle, Marc; Baldwin, Maude W.; Hiller, Michael

doi:10.1126/science.abn7050

Cited by 16 publications

(11 citation statements)

References 70 publications

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“…2). This result is consistent with other studies in which a reduction in gene copy number in cetaceans and other groups is associated with evolutionary innovations (Feng et al 2014; Nery et al 2014; Sun et al 2017; Huelsmann et al 2019; Helsen et al 2020a; McGowen et al 2020; Cabrera et al 2021; Randall et al 2022; Zheng et al 2022; Osipova et al 2023; Pinto et al 2023). We annotated, on average, 192.56 ion channels in the genomes of the species included in our taxonomic sampling, representing 0.96% of the protein-coding genes (Fig.…”

Section: Resultssupporting

confidence: 93%

Evolution of ion channels in cetaceans: A natural experiment in the Tree of life

Uribe

Nery

Zavala

et al. 2023

Preprint

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Cetaceans could be seen as a natural experiment within the tree of life in which a mammalian lineage changed from terrestrial to aquatic habitats. This shift involved extensive phenotypic modifications representing an opportunity to explore the genetic bases of phenotypic diversity. Furthermore, the availability of whole genome sequences in representative species of all main cetacean groups means that we are in a golden age for this type of study. Ion channels are a crucial component of the cellular machinery for the proper physiological functioning of all living species. This study aims to explore the evolution of ion channels during the evolutionary history of cetaceans. To do so, we created a bioinformatic pipeline to annotate the repertoire of ion channels in the genome of the species included in our sampling. Our main results show that cetaceans have fewer ion channels than non-cetacean mammals and that the signal of positive selection was found in ion channels related to heart, locomotion, and hearing phenotypes. Interestingly the NaV1.5 ion channel of most toothed whales (odontocetes) seems to be sensitive to TTX, similar to NaV1.7, given the presence of tyrosine, instead of cysteine, in a specific position of the ion channel. Finally, the gene turnover rate of the cetacean crown group is more than two times faster than non-cetacean mammals.

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Section: Resultssupporting

confidence: 93%

Evolution of ion channels in cetaceans: A natural experiment in the Tree of life

Uribe

Nery

Zavala

et al. 2023

Preprint

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“…67 These annotations identified many genes with variants that either result in a gain of STOP codon or cause a frameshift, which could lead to the loss of function (LoF). As exemplified in a recent work, 68 strains harboring these variants can be explored to investigate the function of these genes. Further, a near-complete catalog of strain-specific alleles and functional prediction is a stable source of potential candidate variants for interpreting genetic mapping results.…”

Section: Discussionmentioning

confidence: 99%

A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats

Jong¹,

Pan²,

Rastas³

et al. 2023

Preprint

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For over a decade, a large research community has relied on a flawed reference assembly of the genome ofRattus norvegicusknown as Rnor_6.0. The seventh assembly of the rat reference genome4mRatBN7.2, based on the inbred Brown Norway rat, corrects numerous misplaced segments, reduces base-level errors by approximately 9-fold, and increases contiguity by 290-fold, despite some remaining regions of potential misassembly. Gene annotations are now more complete, significantly improving the mapping precision of genomic, transcriptomic, and proteomics data sets. SimpleLiftOverfrom Rnor_6.0 to mRatBN7.2 misses ∼12% of variants. To facilitate the transition to mRatBN7.2, we performed a joint analysis of 163 whole genomes representing 120 strains/substrains. We defined 20.0 million sequence variations, of which 18.7 thousand are predicted to potentially impact the function of 6,677 genes. Phylogenetic analysis confirmed historical records and prior results and refined the ancestral relationship of these strains. Sixteen million polymorphisms segregate in the widely studied heterogeneous stock rat population, and 11313 million variants segregate collectively in the HXB/BXH and FXLE/LEXF strain families. Some inbred strains differ by only 132 M variants, and closely related substrains segregate by even fewer variants. We generated a new rat genetic map based on data from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites.

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“…A101030-ARI) following the Arima documents (User Guide for Animal Tissues, Part Number A160162 v00). 1×10 6 nuclei from each species was crosslinked and went into lysis step. The crosslinked gDNA was digested with a cocktail of four restriction enzymes.…”

Section: Methodsmentioning

confidence: 99%

“…For example, single nucleotide changes in coding gene sequences duplicate the goldfish tail fin 1 or cause nose loss in humans 2 ; changes in gene regulatory regions are associated with profound evolutionary body plan changes 3,4 , e.g. limb loss in snakes 5 , and gene loss is emerging as important mechanism in trait evolution 6,7 . On the other hand, the rapidly increasing number of sequenced genomes indicates that genome structure may also be evolutionarily constrained.…”

Section: Introductionmentioning

confidence: 99%

A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence

Ivankovic,

Brand,

Pandolfini

et al. 2023

Preprint

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The planarianSchmidtea mediterraneacan regenerate its entire body from small tissue fragments and is studied as regeneration model species. The assembly and functional analysis of planarian genomes has proven challenging due its high A/T content (70% A/T), repetitive nature, and limited transferability of routine laboratory protocols due to their divergent biochemistry. Only few and often fragmented genome assemblies are currently available, and open challenges include the provision of well-annotated chromosome-scale reference assemblies of the model species and other planarians for a comparative genome evolution perspective. Here we report a haplotype-phased, chromosome-scale genome assembly and high-quality gene annotations of the sexual S2 strain ofS. mediterraneaand provide putative regulatory region annotations via optimized ATAC-seq and ChIP-seq protocols. To additionally leverage sequence conservation for regulatory element annotations, we generated chromosome-scale genome assemblies and chromatin accessibility data for the three closest relatives ofS. mediterranea:S. polychroa,S. nova, andS. lugubris. We find substantial divergence in protein-coding sequences and regulatory regions, yet reveal remarkable conservation in ChIP-mark bearing open chromatin regions identified as promoters and enhancers inS. mediterranea. The resulting high-confidence set of evolutionary conserved enhancers and promoters provides a valuable resource for the analysis of gene regulatory circuits and their evolution within the taxon. In addition, our four chromosome-scale genome assemblies provide a first comparative perspective on planarian genome evolution. Our analyses reveal frequent retrotransposon-associated chromosomal inversions and inter-chromosomal translocations that lead to a degradation of synteny across the genus. Interestingly, we further find independent and near-complete losses of the ancestral metazoan synteny acrossSchmidteaand two other flatworm groups, indicating that platyhelminth genomes largely evolve without syntenic constraints. Our work provides valuable genome resources for the planarian research community and sets a foundation for the comparative genomics of planarians. We reveal a contrast between the fast structural evolution of planarian genomes and the conservation of their regulatory elements, suggesting a unique genome evolution in flatworms where gene positioning may not be essential.

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Loss of a gluconeogenic muscle enzyme contributed to adaptive metabolic traits in hummingbirds

Cited by 16 publications

References 70 publications

Evolution of ion channels in cetaceans: A natural experiment in the Tree of life

Evolution of ion channels in cetaceans: A natural experiment in the Tree of life

A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats

A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence

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