Conserved keratin gene clusters in ancient fish: An evolutionary seed for terrestrial adaptation

Kimura, Yûki; Nikaido, Masato

doi:10.1016/j.ygeno.2020.11.008

Cited by 7 publications

(19 citation statements)

References 52 publications

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“…Therefore, WGD is unlikely to have made a significant impact on the expansion of V2R s during vertebrate evolution. Recent study on the keratin multigene family also revealed no apparent link between the gene expansion and WGD 40 . In multigene families such as chemoreceptor genes and keratin genes, tandem duplication, not WGD, may be the main driving force to increase copy number.…”

Section: Discussionmentioning

confidence: 99%

Remarkable diversity of vomeronasal type 2 receptor (OlfC) genes of basal ray-finned fish and its evolutionary trajectory in jawed vertebrates

Zhang

Sakuma

Kuraku

et al. 2022

Sci Rep

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The vomeronasal type 2 receptor (V2R, also called OlfC) multigene family is found in a broad range of jawed vertebrates from cartilaginous fish to tetrapods. V2Rs encode receptors for food-related amino acids in teleost fish, whereas for peptide pheromones in mammals. In addition, V2Rs of teleost fish are phylogenetically distinct from those of tetrapods, implying a drastic change in the V2R repertoire during terrestrial adaptation. To understand the process of diversification of V2Rs in vertebrates from “fish-type” to “tetrapod-type”, we conducted an exhaustive search for V2Rs in cartilaginous fish (chimeras, sharks, and skates) and basal ray-finned fish (reedfish, sterlet, and spotted gar), and compared them with those of teleost, coelacanth, and tetrapods. Phylogenetic and synteny analyses on 1897 V2Rs revealed that basal ray-finned fish possess unexpectedly higher number of V2Rs compared with cartilaginous fish, implying that V2R gene repertoires expanded in the common ancestor of Osteichthyes. Furthermore, reedfish and sterlet possessed various V2Rs that belonged to both “fish-type” and “tetrapod-type”, suggesting that the common ancestor of Osteichthyes possess “tetrapod-type” V2Rs although they inhabited underwater environments. Thus, the unexpected diversity of V2Rs in basal ray-finned fish may provide insight into how the olfaction of osteichthyan ancestors adapt from water to land.

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Section: Discussionmentioning

confidence: 99%

Remarkable diversity of vomeronasal type 2 receptor (OlfC) genes of basal ray-finned fish and its evolutionary trajectory in jawed vertebrates

Zhang

Sakuma

Kuraku

et al. 2022

Sci Rep

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“…These data suggest that the clade containing the KRT18 (type I) and the KRT80 and KRT8 (type II) proteins is least divergent from the ancient IntFil protein lamin, and most closely resembles precursors for the other members of the keratin group. Localization of the majority of IntFil proteins from earlier Phyla, Classes or Orders (i.e., Cnidaria , Arthropoda , Cephalochordata , Hyperoartia , Chrondrichthyes , Actinopterygii , Coelacanthimorpha and Dipnoi ) closest to the ancient protein lamin, and closest to the KRT18, KRT80, and KRT8 clade strengthens the hypothesis that these three keratins were likely the first keratins to form the embryonic epithelium in the Animalia Kingdom [ 47 , 48 ].…”

Section: Main Textmentioning

confidence: 66%

Update of the keratin gene family: evolution, tissue-specific expression patterns, and relevance to clinical disorders

Thompson²,

Fisk

et al. 2022

Hum Genomics

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Intermediate filament (IntFil) genes arose during early metazoan evolution, to provide mechanical support for plasma membranes contacting/interacting with other cells and the extracellular matrix. Keratin genes comprise the largest subset of IntFil genes. Whereas the first keratin gene appeared in sponge, and three genes in arthropods, more rapid increases in keratin genes occurred in lungfish and amphibian genomes, concomitant with land animal-sea animal divergence (~ 440 to 410 million years ago). Human, mouse and zebrafish genomes contain 18, 17 and 24 non-keratin IntFil genes, respectively. Human has 27 of 28 type I “acidic” keratin genes clustered at chromosome (Chr) 17q21.2, and all 26 type II “basic” keratin genes clustered at Chr 12q13.13. Mouse has 27 of 28 type I keratin genes clustered on Chr 11, and all 26 type II clustered on Chr 15. Zebrafish has 18 type I keratin genes scattered on five chromosomes, and 3 type II keratin genes on two chromosomes. Types I and II keratin clusters—reflecting evolutionary blooms of keratin genes along one chromosomal segment—are found in all land animal genomes examined, but not fishes; such rapid gene expansions likely reflect sudden requirements for many novel paralogous proteins having divergent functions to enhance species survival following sea-to-land transition. Using data from the Genotype-Tissue Expression (GTEx) project, tissue-specific keratin expression throughout the human body was reconstructed. Clustering of gene expression patterns revealed similarities in tissue-specific expression patterns for previously described “keratin pairs” (i.e., KRT1/KRT10, KRT8/KRT18, KRT5/KRT14, KRT6/KRT16 and KRT6/KRT17 proteins). The ClinVar database currently lists 26 human disease-causing variants within the various domains of keratin proteins.

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“…In our data set, we observed the presence of the keratin8 and keratin1 8 pair. This keratin pair is shared among all vertebrates ( Kimura and Nikaido 2021 ) and resembles most closely the ancestral precursor of all other keratins ( Krushna Padhi et al . 2006 ), In mammals, keratin5 typically pairs with keratin14 , while keratin15 does not require pairing and serves as a marker for epidermal stem cells, often coexpressed with keratin5 / keratin14 ( Bose et al .…”

Section: Resultsmentioning

confidence: 99%

Transcriptomic landscape of Atlantic salmon (Salmo salar L.) skin

Sveen,

Robinson,

Krasnov

et al. 2023

G3: Genes, Genomes, Genetics

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In this study, we present the first spatial transcriptomic atlas of Atlantic salmon skin using the Visium Spatial Gene Expression protocol. We utilized frozen skin tissue from four distinct sites, namely the operculum, pectoral and caudal fins, and scaly skin at the flank of the fish close to the lateral line, obtained from two Atlantic salmon (150 g). High quality frozen tissue sections were obtained by embedding tissue in O.C.T media prior to freezing and sectioning. Further, we generated libraries and spatial transcriptomic maps, achieving a minimum of 80 million reads per sample with mapping efficiencies ranging from 79.3% to 89.4%. Our analysis revealed the detection of over 80.000 transcripts and nearly 30.000 genes in each sample. Among the tissue types observed in the skin, the epithelial tissues exhibited the highest number of transcripts (UMI-counts), followed by muscle tissue, loose and fibrous connective tissue, and bone. Notably, the widest nodes in the transcriptome network were shared among the epithelial clusters, while dermal tissues showed less consistency, which is likely attributable to the presence of multiple cell types at different body locations. Additionally, we identified collagen type 1 as the most prominent gene family in the skin, while keratins were found to be abundant in the epithelial tissue. Furthermore, we successfully identified gene markers specific to epithelial tissue, bone, and mesenchyme. To validate their expression patterns, we conducted a meta-analysis of the microarray database, which confirmed high expression levels of these markers in mucosal organs, skin, gills, and the olfactory rosette.

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Conserved keratin gene clusters in ancient fish: An evolutionary seed for terrestrial adaptation

Cited by 7 publications

References 52 publications

Remarkable diversity of vomeronasal type 2 receptor (OlfC) genes of basal ray-finned fish and its evolutionary trajectory in jawed vertebrates

Remarkable diversity of vomeronasal type 2 receptor (OlfC) genes of basal ray-finned fish and its evolutionary trajectory in jawed vertebrates

Update of the keratin gene family: evolution, tissue-specific expression patterns, and relevance to clinical disorders

Transcriptomic landscape of Atlantic salmon (Salmo salar L.) skin

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