Recent Genome Duplications Facilitate Phenotypic Diversity of Hb Repertoire

Cyprinidae (Image by IHB)

The research team led by Pro. HE Shunping from Institute of Hydrobiology, Chinese Academy of Sciences (IHB) re-confirmed that recent genome duplications occurred in the polyploid fishes through a study on the genomic organization and evolution of the Cyprinidae hemoglobin repertoire.

Their results also indicated an evolutionary conservation of the genomic organization and expression patterns of hemoglobin genes in the diploid fishes. Moreover, genome duplications facilitated the phenotypic diversity reflected in both membership composition and intragenomic organization of Hb genes in the tetraploid species.

These features with species-specific changes in gene content is thought to have been derived by gene loss and fusion after genome duplication.

In this study, the genome and transcriptome data from eleven fish, including seven diploid and four tetraploid fish, were collected; Full complement Hb genes in the genomes were annotated, and the analyses of conserved synteny, molecular evolution, and sequence conservation were conducted.

To better understand the expression pattern of the Hb genes, researchers integrated the results with the expression profiles of the genes during ontogeny.

They detected the repeated evolutionary transitions of Hb gene expression during ontogeny in different species, involving the expression convergence of paralogous genes and expression divergence of orthologous genes. This may reflect changes in oxygenation properties among different species because different Hb isoforms have adapted to perform distinct oxygen loading/unloading tasks during ontogeny.

The study also revealed that the early and late expressed Hb genes were mostly located at the 3’ and 5’ end of the MN cluster, respectively, in most species studied.

Analyses of the physical organization revealed that the head-to-head and head-to-tail arrangement and alternating order of the hbα-hbβ pattern (including pseudogenes) was fairly conserved.

The Hb gene clusters in tetraploid species exhibited more variation in both composition and physical organization when compared with their diploid counterparts.

Repeated evolutionary transitions in the ontogenic regulation of Hb gene expression were identified.

It is expected that polyploidy fish generally possess more copies of Hb genes than diploid species due to the additional genome duplications.

However, gene loss and fusion after genome duplications helped to generate phenotypic changes in Cyprinidae Hb systems and may facilitate the evolutionary diversity on the gene function and expression pattern.

These changes might reflect the evolutionary advantage of expressing the multiple Hb isoforms to succeed in changing environmental oxygen conditions.

The survival, reproduction, and distribution of organisms are more or less affected by environmental O2 availability.

The physiologically optimal adaptation of organisms to environmental O2 availability is ultimately reflected in the balance of O2 demand (metabolism) and supply (storage and transport).

Hb plays an essential role in sustaining aerobic metabolism by transporting O2 from the respiratory exchange surfaces to the cells of respiring tissues.

The diversity of blood oxygen transport traits is the perfect reflection of physiological versatility for evolutionary success among vertebrates.

Whole-genome duplications (WGDs) are an important contributor to phenotypic innovations in evolutionary history. Evidence suggests that two successive rounds of whole-genome duplication that occurred early in vertebrate evolution may have played an important role in the evolution of vertebrate-specific innovations. However, little is known about the evolutionary consequences of recent genome duplications, especially the adaptive evolution from the molecular genetic level.

This study explored the contribution of recent genome duplication to the evolutionary adaptation to oxygen. Combining the relative studies in other teleost, the study revealed that the polyploidy fishes generally possess more copies of Hb gene than diploid.

The variation in Hb gene copy number has been regarded as a source of regulatory variation, which affects physiological difference in blood oxygen transport and aerobic energy metabolism and makes organisms to copy with the changing metabolic demands and environmental oxygen availability.

The results were published online in Science China Life Sciences. 

Conserved synteny of the Hb gene clusters from twelve representative
Cyprinidae fish (Figure by IHB)

Genomic organization of the Hb gene clusters of Cyprinidae fish (Figure by IHB)

Expression profiles of Hb genes in Wuchang bream