Lineage-specific Genome Duplication Research Articles

Draft Genome and Complete Hox-Cluster Characterization of the Sterlet (Acipenser ruthenus).

Background: Sturgeons (Chondrostei: Acipenseridae) are a group of “living fossil” fishes at a basal position among Actinopteri. They have raised great public interest due to their special evolutionary position, species conservation challenges, as well as their highly-prized eggs (caviar). The sterlet, Acipenser ruthenus, is a relatively small-sized member of sturgeons and has been widely distributing in both Europe and Asia. In this study, we performed whole genome sequencing, de novo assembly and gene annotation of the tarlet to construct its draft genome.Findings: We finally obtained a 1.83-Gb genome assembly (BUSCO completeness of 81.6%) from a total of 316.8-Gb raw reads generated by an Illumina Hiseq 2500 platform. The scaffold N50 and contig N50 values reached 191.06 and 18.88 kb, respectively. The sterlet genome was predicted to be comprised of 42.84% repeated sequences and to contain 22,184 protein-coding genes, of which 21,112 (95.17%) have been functionally annotated with at least one hit in public databases. A genetic phylogeny demonstrated that the sterlet is situated in the basal position among ray-finned fishes and 4dTv analysis estimated that a recent whole genome duplication occurred 21.3 million years ago. Moreover, seven Hox clusters carrying 68 Hox genes were characterized in the sterlet. Phylogeny of HoxA clusters in the sterlet and American paddlefish divided these sturgeons into two groups, confirming the independence of each lineage-specific genome duplication in Acipenseridae and Polyodontidae.Conclusions: This draft genome makes up for the lack of genomic and molecular data of the sterlet and its Hox clusters. It also provides a genetic basis for further investigation of lineage-specific genome duplication and the early evolution of ray-finned fishes.

Pck-ing up steam: Widening the salmonid gluconeogenic gene duplication trail

Rainbow trout have, as salmonid fish species, undergone sequential genome duplication events in their evolutionary history. In addition to a teleost-specific whole genome duplication approximately 320–350 million years ago, rainbow trout and salmonids in general underwent an additional salmonid lineage-specific genome duplication event approximately 80 million years ago. Through the recent sequencing of salmonid genome sequences, including the rainbow trout, the identification and study of duplicated genes has become available. A particular focus of interest has been the evolution and regulation of rainbow trout gluconeogenic genes, as recent molecular and gene expression evidence points to a possible contribution of previously uncharacterized gluconeogenic gene paralogues to the rainbow trout long-studied glucose intolerant phenotype. Since the publication of the initial rainbow trout genome draft, resequencing and annotation have further improved genome coverage. Taking advantage of these recent improvements, we here identify a salmonid-specific genome duplication of ancestral mitochondrial phosphoenolpyruvate carboxykinase 2 isoenzyme, we termed pck2a and pck2b. Cytosolic phosphoenolpyruvate carboxykinase (Pck1) and, more recently mitochondrial Pck2, are considered to be the rate-limiting enzymes in de novo gluconeogenesis. Following in silico confirmation of salmonid pck2a and pck2b evolutionary history, we simultaneously profiled cytosolic pck1 and mitochondrial pck2a and pck2b expression in rainbow trout liver under several experimental conditions known to regulate hepatic gluconeogenesis. Cytosolic pck1 abundance was increased by nutritional (diets with a high protein to carbohydrate ratio compared to diets with a low carbohydrate to protein ratio) and glucoregulatory endocrine factors (glucagon and cortisol), revealing that the well-described transcriptional regulation of pck1 in mammals is present in rainbow trout. Conversely, and in contrast to mammals, we here describe endocrine regulation of pck2a (decrease in abundance in response to glucagon infusion), and nutritional, social-status-dependent and hypoxia-dependent regulation of pck2b. Specifically, pck2b transcript abundance increased in trout fed a diet with a low protein to carbohydrate ratio compared to a diet with a high protein to carbohydrate ratio, in dominant fish compared to subordinate fish as well as hypoxia. This specific and differential expression of rainbow trout pck2 ohnologues is indicative of functional diversification, and possible functional consequences are discussed in light of the recently highlighted gluconeogenic roles of mitochondrial pck2 in mammalian models.

Gene duplication and genetic innovation in cereal genomes.

Organisms continuously require genetic variation to adapt to fluctuating environments, yet major evolutionary events are episodic, making the relationship between genome evolution and organismal adaptation of considerable interest. Here, by genome-wide comparison of sorghum, maize, and rice SNPs, we investigated reservoirs of genetic variations with high precision. For sorghum and rice, which have not experienced whole-genome duplication in 96 million years or more, tandem duplicates accumulate relatively more SNPs than paralogous genes retained from genome duplication. However, maize, which experienced lineage-specific genome duplication and has a relatively larger supply of paralogous duplicates, shows SNP enrichment in paralogous genes. The proportion of genes showing signatures of recent positive selection is higher in small-scale (tandem and transposed) than genome-scale duplicates in sorghum, but the opposite is true in maize. A large proportion of recent duplications in rice are species-specific; however, most recent duplications in sorghum are derived from ancestral gene families. A new retrotransposon family was also a source of many recent sorghum duplications, illustrating a role in providing variation for genetic innovations. This study shows that diverse evolutionary mechanisms provide the raw genetic material for adaptation in taxa with divergent histories of genome evolution.

Kiss and Tell: Deletion of Kisspeptins and Receptors Reveal Surprising Results

The well-known expression “Kiss and Tell” usually refers to revealing one’s sexual exploits or private matters. In the case of the transcription activator-like effector nucleases gene knockout studies by Tang et al (1), sequential removal of the 2 known kisspeptins and their receptors surprisingly reveals that this system is not required for reproduction. The authors rightly note that this challenges the idea that kisspeptin neurons are central regulators of vertebrate reproduction (eg, Refs. 2, 3 among many). To date, most observations leading to this conclusion are based on studies in mammals, including humans, rats, and mice, and thus may not reflect the diversity of neuroendocrine control mechanisms across the vertebrate groups. On the surface, this lack-of-effect study in zebrafish could be quite discouraging, except in the light of the evolution of neuropeptidergic systems controlling reproductive function. Zebrafish are members of a group of fish called teleosts. Teleosts are wonderfully diverse in their reproductive strategies, often beautiful, economically important, and there are nearly 30 000 species currently known (4). The evolutionof these ray-finned fishgoesbackapproximately 200 million years before present, after undergoing the third lineage-specific genome duplication (5). Complete or partial gene duplications in many teleosts have presented real challenges when trying to sort out the evolution and specific functions of reproductive neuropeptides. Many neuropeptides, neurotransmitter synthesis enzymes, and neurohormone receptors duplicated and/or mutated over time, resulting in an array of novel molecular substrates for the evolution of hormone systems. This may be one reason that teleosts are successful, being both widespread in distribution and fecund. These evolutionary duplication events in teleosts have generated multiple numbers of genes and peptides in comparison with their mammalian counterparts. For example, it has been observed that most fish species harbor 2 or 3 distinct GnRH genes and peptides (6, 7). Their location and functions are different, and early GnRH knockdown studies in trout revealed that reproduction may continue even with reduced GnRH levels (8). Subsequent studies revealed a more important role for the hypophysiotropic forms of GnRH in tilapia (9) and common carp (10). In both cases, reproduction was not inhibited in all animals expressing the GnRH antisense transgene. For the common carp, a close relative of zebrafish (family Cyprinidae, eg, carps, minnows, and goldfish), abnormal sexual development and infertility were observed in about 40% of the animals expressing the antisense transgene targeting the hypophysiotropic form of GnRH (10). On the other hand, the remaining 60% had normal gonads with sperm or eggs (10), indicating that reproduction was still possible in these carp. What about the kisspeptin knockout fish? Through rigorous analysis, the authors demonstrated that spermatogenesis, folliculogenesis, and reproductive capacity were not impaired in 6 mutant lines missing kisspeptins or kisspeptin receptors (1). It should be noted that thekisspeptin systemhasbeendescribed indetail in several fish, and there are significant differences between species, and in comparison with mammals. If one considers only zebrafish, Kah’s group (11), using specific antibodies, has clearly demonstrated that there are 2 independent kisspeptin systems (kiss1 and kiss2). The first is the habenular kiss1 system that is likely involved in nonreproductive activities, perhaps metabolic control. On the other hand, distribution of kiss2 neurons in hypophysiotropic areas

Transcriptional divergence of the duplicated hypoxia-inducible factor alpha genes in zebrafish

Oxygen availability has been a major force in shaping the physiological evolution of animals. Under reduced oxygen availability (hypoxia) major changes in gene expression are mediated by hypoxia-inducible factors (HIF alphas). Tetrapods have three hif alpha genes, whereas zebrafish (Danio rerio) and other cyprinids have six due to a teleost lineage-specific genome duplication. We studied the transcriptional divergence of the six teleost-specific hif alphas by inspecting the tissue-specific transcription patterns in adult zebrafish and by monitoring the early developmental transcription of normoxia- and hypoxia-grown zebrafish embryos. Overall we observed the highest hif alpha mRNA levels in tissues that are important for hypoxic survival, including the brain, gill and heart. Of the paralogs that have not previously received attention (hif alpha-1A, hif alpha-2B and hif alpha-3B) especially the hif alpha-2B transcription levels suggest functional relevance. The hif alpha-1A/B paralogs that have considerable coding sequence divergence displayed more overall transcriptional divergence than the hif alpha-2A/B paralog pair. The hif alpha-2A/B paralogs that are similarly conserved in coding sequence had a divergent transcription pattern during early development. When zebrafish grown in modest hypoxia were compared to normoxia grown fish, only hif alpha-3A transcription was significantly altered. These results suggest that, in zebrafish, the evolutionary retention of each hif alpha paralog pair has involved unique patterns of coding sequence divergence, adult tissue-specific transcriptional divergence or developmental transcriptional divergence.

Fish Suppressors of Cytokine Signaling (SOCS): Gene Discovery, Modulation of Expression and Function

The intracellular suppressors of cytokine signaling (SOCS) family members, including CISH and SOCS1 to 7 in mammals, are important regulators of cytokine signaling pathways. So far, the orthologues of all the eight mammalian SOCS members have been identified in fish, with several of them having multiple copies. Whilst fish CISH, SOCS3, and SOCS5 paralogues are possibly the result of the fish-specific whole genome duplication event, gene duplication or lineage-specific genome duplication may also contribute to some paralogues, as with the three trout SOCS2s and three zebrafish SOCS5s. Fish SOCS genes are broadly expressed and also show species-specific expression patterns. They can be upregulated by cytokines, such as IFN-γ, TNF-α, IL-1β, IL-6, and IL-21, by immune stimulants such as LPS, poly I:C, and PMA, as well as by viral, bacterial, and parasitic infections in member- and species-dependent manners. Initial functional studies demonstrate conserved mechanisms of fish SOCS action via JAK/STAT pathways.

Hoxclusters of the bichir (Actinopterygii,Polypterus senegalus) highlight unique patterns of sequence evolution in gnathostome phylogeny

Teleost fishes have extra Hox gene clusters owing to shared or lineage-specific genome duplication events in rayfinned fish (actinopterygian) phylogeny. Hence, extrapolating between genome function of teleosts and human or even between different fish species is difficult. We have sequenced and analyzed Hox gene clusters of the Senegal bichir (Polypterus senegalus), an extant representative of the most basal actinopterygian lineage. Bichir possesses four Hox gene clusters (A, B, C, D); phylogenetic analysis supports their orthology to the four Hox gene clusters of the gnathostome ancestor. We have generated a comprehensive database of conserved Hox noncoding sequences that include cartilaginous, lobe-finned, and ray-finned fishes (bichir and teleosts). Our analysis identified putative and known Hox cis-regulatory sequences with differing depths of conservation in Gnathostoma. We found that although bichir possesses four Hox gene clusters, its pattern of conservation of noncoding sequences is mosaic between outgroups, such as human, coelacanth, and shark, with four Hox gene clusters and teleosts, such as zebrafish and pufferfish, with seven or eight Hox gene clusters. Notably, bichir Hox gene clusters have been invaded by DNA transposons and this trend is further exemplified in teleosts, suggesting an as yet unrecognized mechanism of genome evolution that may explain Hox cluster plasticity in actinopterygians. Taken together, our results suggest that actinopterygian Hox gene clusters experienced a reduction in selective constraints that surprisingly predates the teleost-specific genome duplication.

Independent and dynamic reallocation of pitx gene expression during vertebrate evolution, with emphasis on fish pituitary development

Several transcription regulators play key roles during pituitary morphogenesis. Well known intrinsic signals of the adenohypophysis such as the K 50 paired-like homeodomain proteins regulate commitment, proliferation, differential specification and maintenance of adenohypophyseal cells. We have cloned and successively characterized the mRNA localization of three pitx gene-pairs and three of their splice variants in salmon, pitx1α, pitx1β; pitx2α, pitx2β; pitx3α, pitx3β; pitx1αsh, pitx1βsh and pitx2αA. The high level of conservation between the pitx paralog-pairs indicates that they likely arose from lineage-specific genome duplication. We also report the isolation of a pitx1 gene in zebrafish. Comparative ISH studies of zebrafish, salmon and mouse pitx genes indicate both conservation and divergence of spatial expression domains in vertebrates. Significant differences were observed between the expressions of pitx orthologs during pituitary development. We suggest that the ancestral pituitary expression at early and late events of morphogenesis is preserved in different species through complementary shuffling of expression between the distinct pitx members of the family. Moreover, ISH analysis of the pitx salmon repertoire shows rapid evolution in this lineage, differences in spatio-temporal expression are observed between gene duplicates.

Retention of the duplicated cellular retinoic acid‐binding protein 1 genes (crabp1a and crabp1b) in the zebrafish genome by subfunctionalization of tissue‐specific expression

The cellular retinoic acid-binding protein type I (CRABPI) is encoded by a single gene in mammals. We have characterized two crabp1 genes in zebrafish, designated crabp1a and crabp1b. These two crabp1 genes share the same gene structure as the mammalian CRABP1 genes and encode proteins that show the highest amino acid sequence identity to mammalian CRABPIs. The zebrafish crabp1a and crabp1b were assigned to linkage groups 25 and 7, respectively. Both linkage groups show conserved syntenies to a segment of the human chromosome 15 harboring the CRABP1 locus. Phylogenetic analysis suggests that the zebrafish crabp1a and crabp1b are orthologs of the mammalian CRABP1 genes that likely arose from a teleost fish lineage-specific genome duplication. Embryonic whole mount in situ hybridization detected zebrafish crabp1b transcripts in the posterior hindbrain and spinal cord from early stages of embryogenesis. crabp1a mRNA was detected in the forebrain and midbrain at later developmental stages. In adult zebrafish, crabp1a mRNA was localized to the optic tectum, whereas crabp1b mRNA was detected in several tissues by RT-PCR but not by tissue section in situ hybridization. The differential and complementary expression patterns of the zebrafish crabp1a and crabp1b genes imply that subfunctionalization may be the mechanism for the retention of both crabp1 duplicated genes in the zebrafish genome.