Scientists have successfully produced genome assemblies for two previously undocumented hidden-neck turtles. This research reveals a novel three-dimensional structure of genomes among reptiles, birds, and mammals, which could aid in creating better conservation methods for turtles and enhance our understanding of vertebrate genome evolution and chromosomal arrangement.
Researchers from UAB and Iowa State University have accomplished the genome assemblies of two hidden-neck turtle species, which have not been published before. The findings introduced a new three-dimensional genome structure within the phylogenetic group that includes reptiles, birds, and mammals, potentially leading to improved conservation strategies for turtles and further studies on vertebrate genome and chromosomal evolution.
The investigation was spearheaded by Aurora Ruiz-Herrera from UAB and Nicole Valenzuela from Iowa State University, alongside collaborators from the Institute of Evolutionary Biology (CSIC-UPF) and Earlham College. Published in Genome Research, the study emphasizes the significant role of chromatin, the three-dimensional configuration that organizes genetic material within the cell nucleus, in regulating gene activity and its evolutionary implications.
The scientists achieved de novo genome assemblies (without a pre-existing reference model) for two cryptodiran turtle species known as short-necked turtles, utilizing a blend of gene sequencing and expression techniques. These two species belong to different lineages, each exhibiting distinct sex-chromosome evolution: one with XX/XY chromosomes like humans and other mammals, and another with ZZ/ZW chromosomes similar to those found in birds and butterflies. Furthermore, the team uncovered a new three-dimensional chromatin configuration in both lineages: they observed a chromosomal folding pattern that facilitates interactions between centromeres and telomeres, in addition to the typical fusion/fission events in linear genomes. These insights present fresh information about 3D chromatin architecture in amniotes, a group that includes reptiles, birds, and mammals.
“We propose that the unique chromosomal patterns observed in these turtles stem from an ancestral amniote state characterized by significant chromosome associations that were retained during genomic restructuring in turtles and other vertebrates,” explains Nicole Valenzuela, a researcher in the Department of Ecology, Evolution and Organismal Biology at Iowa State University.
“These discoveries expand our comprehension of sex chromosome evolution and establish a strong basis for forthcoming inquiries into genome evolution and chromosomal organization in vertebrates,” adds Aurora Ruiz-Herrera, who works in the Department of Cell Biology, Physiology and Immunology, and the Institute of Biotechnology and Biomedicine (IBB) at UAB.
A critical model for scientific exploration
The authors of the article emphasize that examining turtle genomes offers vital insights that could change our understanding of biology and evolution. Due to their impressive lifespan and disease resilience, turtles serve as a remarkable model for various scientific fields, including biomedicine and conservation efforts. Analyzing their genome is essential for pinpointing the specific genes linked to these advantageous traits, which might contribute to advancements in human medicine, particularly in relation to aging and disease resistance.
Moreover, the turtle genome presents a distinctive perspective on evolution: these reptiles have thrived for over 250 million years, enduring mass extinction periods and adjusting to different habitats. Investigating their genetic material is crucial for grasping the adaptation and survival mechanisms that are vital for preserving not only turtles but also other species.
The initial turtle genome assemblies were released more than ten years ago. Since then, twelve genome assemblies of Chelonians have been documented, with nine having their gene sequences identified. “These newly generated assemblies increase this compilation and underscore the significance of high-quality genomic resources for the progress of evolutionary and developmental biology,” concludes Aurora Ruiz-Herrera.
