Gene duplication and the uniqueness of vertebrate genomes circa 1970–1999

doi:10.1006/scdb.1999.0332

Seminars in Cell & Developmental Biology

Volume 10, Issue 5, October 1999, Pages 517-522

https://doi.org/10.1006/scdb.1999.0332 Get rights and content

Abstract

In this article I review research undertaken over the past 30 years into the role that gene duplication played in shaping vertebrate genomes. I discuss early karyotype studies that pointed to a relative stability of mammalian and avian genomes, the discovery and possible evolutionary significance of enormous genomes in urodele amphibians and lungfish, genome compaction in certain specialised bony fish, evidence for two rounds of total genome doubling in early vertebrate evolution, and the fate of duplicated genes in polyploid fish.

References (16)

LG Lundin
Evolution of the vertebrate genome as reflected in paralogous chromosomal regions in man and the house mouse
Genomics
(1993)
J Spring
Vertebrate evolution by interspecific hybridization: Are we polyploid?
FEBS Lett
(1997)
S Ohno
Sex Chromosomes and Sex-linked Genes.
(1967)
S Ohno
Evolution by Gene Duplication.
(1970)
S Ohno
So much junk DNA in our genome,
M Vialli
La quantita di ADN per nucles negli eriticiti di latimeria
R C Inst Lumb Cl Sc Mat Nat
(1957)
R Hinegardner
Evolution of cellular DNA contents in teleost fishes
Am Nat
(1968)

There are more references available in the full text version of this article.

Cited by (279)

Timing neurogenesis: a clock or an algorithm?
2024, Current Opinion in Genetics and Development
Immunomodulatory role of vasoactive intestinal peptide and ghrelin in Oncorhynchus mykiss
2023, Heliyon
Neuropeptides are a group of peptides derived from precursor proteins synthesized in neuronal and nonneuronal cells. The classical functions of neuropeptides have been extensively studied in mammals, including neuromodulation in the central nervous system, molecular signaling in the peripheral nervous system, and immunomodulation associated mainly with anti-inflammatory activity. In contrast, in teleosts, studies of the immunomodulatory function of these neuropeptides are limited. In Oncorhynchus mykiss, vasoactive intestinal peptide (VIP) mRNA sequences have not been cloned, and the role of VIP in modulating the immune system has not been studied. Furthermore, in relation to other neuropeptides with possible immunomodulatory function, such as ghrelin, there are also few studies. Therefore, in this work, we performed molecular cloning, identification, and phylogenetic analysis of three VIP precursor sequences (prepro-VIP1, VIP2 and VIP3) in rainbow trout. In addition, the immunomodulatory function of both neuropeptides was evaluated in an in vitro model using the VIP1 sequence identified in this work and a ghrelin sequence already studied in O. mykiss. The results suggest that the prepro-VIP2 sequence has the lowest percentage of identity with respect to the other homologous sequences and is more closely related to mammalian orthologous sequences. VIP1 induces significant expression of both pro-inflammatory (IFN-γ, IL-1β) and anti-inflammatory (IL-10 and TGF-β) cytokines, whereas ghrelin only induces significant expression of proinflammatory cytokines such as IL-6 and TNF-α.
Transcriptome analysis revealed the existence of family-specific regulation of growth traits in grass carp
2023, Genomics
The grass carp (Ctenopharyngodon idella) is the world's most prolific freshwater fish. Little is known, however, about the functional genes and genetic regulatory networks that govern its growth traits. We created three grass carp families in this study by using two grass carp parents with fast-growing offspring and two grass carp parents with slow-growing offspring, namely the fast-growing × fast-growing family (FF), the slow-growing × slow-growing family (SS), and the fast-growing × slow-growing family (FS). Under the satiation and starvation feeding modes, the average body weight of these families' offspring exhibited a consistent ordering (FF > FS > SS). The transcriptomes of grass carp whole brain and hepatopancreas were then acquired for each family, and it was discovered that the number of differentially expressed genes (DEGs) in the different organs demonstrated family specificity. DEGs were mostly identified in the hepatopancreas of FF and the whole brain of SS, but they were more evenly distributed in FS. There were 14 DEGs that were found in all three families, including three that were negatively correlated in hepatopancreas (ahsg2, lect2) or in brain (drd5), and 11 that were positively connected in hepatopancreas (sycn, pabpc4, zgc:112294, cel, endou, ela2, prss3, zbtb41, ela3) or in brain (fabp7, endod1). The deletion of ahsg2 boosted the growth rate only in certain zebrafish, suggesting that the growth-promoting effects of ahsg2 varies among individuals. Furthermore, we examined the SNP in each family and conducted preliminary research on the probable genetic pathways of family-specific control of growth traits. The family specificity of the growth regulation mechanism of grass carp at the transcriptional level was revealed for the first time in this study, and it was discovered that growth differences among individuals in the FF family were primarily due to differences in nutrient metabolism, whereas growth differences among individuals in the SS family may be primarily due to differences in foraging ability caused by differences in brain development. This research adds to our understanding of the genetic regulatory mechanism of grass carp growth.
The importance of thyroid hormone signaling during early development: Lessons from the zebrafish model
2023, General and Comparative Endocrinology
The zebrafish is an optimal experimental model to study thyroid hormone (TH) involvement in vertebrate development. The use of state-of-the-art zebrafish genetic tools available for the study of the effect of gene silencing, cell fate decisions and cell lineage differentiation have contributed to a more insightful comprehension of molecular, cellular, and tissue-specific TH actions. In contrast to intrauterine development, extrauterine embryogenesis observed in zebrafish has facilitated a more detailed study of the development of the hypothalamic-pituitary-thyroid axis. This model has also enabled a more insightful analysis of TH molecular actions upon the organization and function of the brain, the retina, the heart, and the immune system. Consequently, zebrafish has become a trendy model to address paradigms of TH-related functional and biomedical importance. We here compilate the available knowledge regarding zebrafish developmental events for which specific components of TH signaling are essential.
Association study between relative expression levels of eight genes and growth rate in Hungarian common carp (Cyprinus carpio): Association study between relative expression levels of eight genes
2022, Saudi Journal of Biological Sciences
Citation Excerpt :
TLRs, the first line of defense that recognizes microbial pathogenic molecules in the body, are one of the best-studied immune receptors for detecting infection in mammals (Palti, 2018). The major feature of TLRs in the fish genome is the high degree of similarity to the mammalian TLR system (Palti, 2018), but the number of duplicated TLR genes is high due to several fish-specific duplication events (Ohno, 1999). Causey et al. (2019) studied immunostimulated silver salmon (Oncorhynchus kisutch) from three experimental groups that had the same genetic background but showed strongly divergent growth rates.
One of the most important issues in improving the competitiveness of the fish production sector is to improve the growth rate of fish. The genetic background to this trait is at present poorly understood. In this study, we compared the relative gene expression levels of the Akt1s1, FGF, GH, IGF1, MSTN, TLR2, TLR4 and TLR5 genes in blood in groups of common carps (Cyprinus carpio), which belonged to different growth types and phenotypes. Fish were divided into groups based on growth rate (normal group: n = 6; slow group: n = 6) and phenotype (scaled group: n = 6; mirror group: n = 6). In the first 18 weeks, we measured significant differences (p < 0.05) between groups in terms of body weight and body length. Over the next 18 weeks, the fish in the slow group showed more intense development. In the same period, the slow group was characterized by lower expression levels for most genes, whereas GH and IGF1 mRNA levels were higher compared to the normal group. We found that phenotype was not a determining factor in differences of relative expression levels of the genes studied.
Astrocytic contribution to glutamate-related central respiratory chemoreception in vertebrates
2021, Respiratory Physiology and Neurobiology
Central respiratory chemoreceptors play a key role in the respiratory homeostasis by sensing CO₂ and H⁺ in brain and activating the respiratory neural network. This ability of specific brain regions to respond to acidosis and hypercapnia is based on neuronal and glial mechanisms. Several decades ago, glutamatergic transmission was proposed to be involved as a main mechanism in central chemoreception. However, a complete identification of mechanism has been elusive. At the rostral medulla, chemosensitive neurons of the retrotrapezoid nucleus (RTN) are glutamatergic and they are stimulated by ATP released by RTN astrocytes in response to hypercapnia. In addition, recent findings show that caudal medullary astrocytes in brainstem can also contribute as CO₂ and H⁺ sensors that release D-serine and glutamate, both gliotransmitters able to activate the respiratory neural network. In this review, we describe the mammalian astrocytic glutamatergic contribution to the central respiratory chemoreception trying to trace in vertebrates the emergence of several components involved in this process.

View all citing articles on Scopus

^☆: Unspecified

View full text

Regular ArticleGene duplication and the uniqueness of vertebrate genomes circa 1970–1999☆

Abstract

Genomics

FEBS Lett

Sex Chromosomes and Sex-linked Genes.

Evolution by Gene Duplication.

So much junk DNA in our genome,

La quantita di ADN per nucles negli eriticiti di latimeria

R C Inst Lumb Cl Sc Mat Nat

Evolution of cellular DNA contents in teleost fishes

Am Nat

Regular Article
Gene duplication and the uniqueness of vertebrate genomes circa 1970–1999☆