A Genetic Perspective on Cetacean Evolution

Cabrera, Andrea A.; Bérubé, Martine; Lopes, Xênia Moreira; Louis, Marie; Oosting, Tom; Rey‐Iglesia, Alba; Rivera-León, Vania E.; Székely, Dóra; Lorenzen, Eline D.

doi:10.1146/annurev-ecolsys-012021-105003

Cited by 14 publications

(10 citation statements)

References 127 publications

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“…Long interspersed nuclear elements (LINEs) were the most predominant TE subtype (34.23%) (Table S8). Phylogenomic analysis supported that the short‐finned pilot whale along with the long‐finned pilot whale is closely related to the melon‐headed whale ( Peponocephala electra ), consistent with a recent large‐scale phylogenetic analysis of cetaceans (Cabrera et al, 2021; Figure 1d). Taken together, we generated a genome assembly suitable for single‐nucleus transcriptome analyses.…”

Section: Resultssupporting

confidence: 85%

A genome and single‐nucleus cerebral cortex transcriptome atlas of the short‐finned pilot whale Globicephala macrorhynchus

Kang

Seim

et al. 2023

Molecular Ecology Resources

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Cetaceans (dolphins, whales, and porpoises) have large and anatomically sophisticated brains. To expand our understanding of the cellular makeup of cetacean brains and the similarities and divergence between the brains of cetaceans and terrestrial mammals, we report a short‐finned pilot whale (Globicephala macrorhynchus) single‐nucleus transcriptome atlas. To achieve this goal, we assembled a chromosome‐scale reference genome spanning 2.25 Gb on 22 chromosomes and profiled the gene expression of five major anatomical cortical regions of the short‐finned pilot whale by single‐nucleus RNA‐sequencing (snRNA‐seq). We identified six major cell lineages in the cerebral cortex (excitatory neurons, inhibitory neurons, oligodendrocytes, oligodendrocyte precursor cells, astrocytes, and endothelial cells), eight molecularly distinct subclusters of excitatory neurons, and four subclusters of inhibitory neurons. Finally, a comparison of snRNA‐seq data from the short‐finned pilot whale, human, and rhesus macaque revealed a broadly conserved cellular makeup of brain cell types. Our study provides genomic resources and molecular insights into cetacean brain evolution.

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Section: Resultssupporting

confidence: 85%

A genome and single‐nucleus cerebral cortex transcriptome atlas of the short‐finned pilot whale Globicephala macrorhynchus

Kang

Seim

et al. 2023

Molecular Ecology Resources

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“…Many genome-scale studies have considered the evolution of marine mammals. However, compared to cetaceans and pinnipeds 6,7 , the lack of high-quality genomes has limited insights into sirenians, the only fully aquatic mammals within Afrotheria. To better understand the evolution to aquatic life by sirenians, we generated and juxtaposed a chromosome-level genome and gene set of the dugong with other afrotherian mammals (including a manatee).…”

Section: Mainmentioning

confidence: 99%

“…However, compared to cetaceans and pinnipeds 6,7 , the lack of high-quality genomes has limited insights into sirenians, the only fully aquatic mammals within Afrotheria.…”

Section: Mainmentioning

confidence: 99%

Sirenian genomes illuminate the evolution of fully aquatic species within the mammalian superorder Afrotheria

Tian,

Zhang,

Kang

et al. 2023

Preprint

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Sirenians of the diverse superorder Afrotheria were the first mammals to retransition from land to water and are the sole herbivorous marine mammals, but little is known about the underlying genomic changes. Here, we generated a chromosome-level dugong (Dugong dugon) genome. A comparison of our assembly and a recent West Indian manatee genome with other afrotherian genomes revealed possible molecular solutions to aquatic life by sirenians, including a shift in daily activity patterns (circadian clock) and tolerance to a high-iodine plant diet mediated through changes in the iodide transporter NIS (SLC5A5) and its co-transporters. Functional in vitro assays confirmed that sirenian amino acid substitutions alter the properties of the circadian clock protein PER2 and NIS. Sirenians show evidence of convergent regression of integumentary system (skin and its appendages) genes with cetaceans, the only other fully aquatic mammal group. Our analysis also uncovered gene losses that may be maladaptive in a modern environment, including a candidate gene (KCNK18) for sirenian cold stress syndrome likely lost during their evolutionary shift in daily activity patterns. Finally, genomes from nine Australian locations and the functionally extinct Okinawan population confirm and date a genetic break on the Australian east coast and highlight the need for whole-genome resequencing data from small or isolated dugong populations worldwide for conservation and genetic management.

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“…Reference genome assemblies from nonmodel vertebrate species with assembled sex chromosomes are relatively scarce. Available mammalian genome assemblies with at least one sex chromosome (most commonly the X chromosome) include humans, several domesticates such as cat ( Felis catus ), cow ( Bos taurus ), dog ( Canis familiaris ), horse ( Equus caballus ), sheep ( Ovis aries ), and wild species such as blue whale ( Balaenoptera musculus ), bottlenose dolphin ( Tursiops truncatus ), greater horseshoe bat ( Rhinolophus ferrumequinum ), gorilla ( Gorilla gorilla ), meerkat ( Suricata suricatta ), orangutan ( Pongo pygmaeus ), and vaquita ( Phocoena sinus ) (Cabrera et al, 2021; de Flamingh et al, 2020). In the absence of a conspecific chromosome‐level assembly, alternative approaches can be used to identify scaffolds originating from sex chromosomes.…”

Section: Introductionmentioning

confidence: 99%

How low can you go? Introducing SeXY: sex identification from low‐quantity sequencing data despite lacking assembled sex chromosomes

Cabrera

Rey‐Iglesia

Louis

et al. 2022

Ecology and Evolution

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Accurate sex identification is crucial for elucidating the biology of a species. In the absence of directly observable sexual characteristics, sex identification of wild fauna can be challenging, if not impossible. Molecular sexing offers a powerful alternative to morphological sexing approaches. Here, we present SeXY, a novel sex-identification pipeline, for very low-coverage shotgun sequencing data from a single individual.SeXY was designed to utilize low-effort screening data for sex identification and does not require a conspecific sex-chromosome assembly as reference. We assess the accuracy of our pipeline to data quantity by downsampling sequencing data from 100,000 to 1000 mapped reads and to reference genome selection by mapping to a variety of reference genomes of various qualities and phylogenetic distance. We show that our method is 100% accurate when mapping to a high-quality (highly contiguous N50 > 30 Mb) conspecific genome, even down to 1000 mapped reads. For lower-quality reference assemblies (N50 < 30 Mb), our method is 100% accurate with 50,000 mapped reads, regardless of reference assembly quality or phylogenetic distance. The SeXY pipeline provides several advantages over previously implemented methods; SeXY (i) requires sequencing data from only a single individual, (ii) does not require assembled conspecific sex chromosomes, or even a conspecific reference assembly, (iii) takes into account variation in coverage across the genome, and (iv) is accurate with only 1000 mapped reads in many cases.

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A Genetic Perspective on Cetacean Evolution

Cited by 14 publications

References 127 publications

A genome and single‐nucleus cerebral cortex transcriptome atlas of the short‐finned pilot whale Globicephala macrorhynchus

A genome and single‐nucleus cerebral cortex transcriptome atlas of the short‐finned pilot whale Globicephala macrorhynchus

Sirenian genomes illuminate the evolution of fully aquatic species within the mammalian superorder Afrotheria

How low can you go? Introducing SeXY: sex identification from low‐quantity sequencing data despite lacking assembled sex chromosomes

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