Sea urchin, commonly found on sashimi plates in fine restaurants, its unique taste makes foodies addicted, here is a quick test for you:
Which of the following statements about sea urchins is true?
A. Sea urchins are ancient creatures dating back 400 million years
B. Sea urchins are close relatives with starfish and sea cucumbers
C. Sea urchins have little guts and run away at the sight of the enemy
D. There are many types of sea urchins, and there are as many as 900 species
Answer: All of the above are correct
Not only that, sea urchins are also one of the earliest model organisms used in the history of biological sciences, and the research on sea urchin embryos plays a pivotal role in the development of early developmental biology.
Recently, a study on the genetic development of sea urchin embryos and larvae, jointly initiated by Duke University and Qingdao BGI Genomic Institute, showed the highly differentiated early life history of the two sea urchins through multi-omics joint analysis such as genomics and single-cell transcriptomics, revealed the impact of early events in sea urchin embryo formation patterns on evolution, and found that natural selection can rapidly reshape gene expression during development on a large scale. The findings were published in Nature Ecology & Evolution.
Screenshot of the official website of "Nature Ecology and Evolution"
According to existing studies, the interspecific divergence of the red sea urchin and the short-spined sea urchin occurred about 5 million years ago, and although it sounds a long time ago, they are already one of the closest relatives relative to the 500 million years of sea urchin history.
Theoretically, the characteristics of two sea urchins so closely related should be extremely similar. But in fact, there are huge differences in larval morphology, development process, predation habits and other aspects of red sea urchins and short-spined sea urchins, which have successfully aroused the interest of scientists.
The development pattern of the red sea urchin is more classic, and it is the development process from embryo to larvae that most sea urchin species will follow, and even the larval development of starfish has a similar morphology. The short-spined sea urchin, on the other hand, goes out of the niche route, and its embryonic development process is different from the beginning.
△ The first row of the picture: the classical development pattern represented by the red sea urchin
Fertilized egg-blastocyst-gastruloid-prismatic larvae-long-wristed larvae, mouthparts form, begin to feed on plankton microalgae to obtain nutrients for further growth and development, until the completion of metamorphosis development;
△ The second row of the picture: the derivative development pattern represented by the short spiny sea urchin
Starting with a larger egg cell with enough nutrients in the egg cell does not require feeding until metamorphosis is completed.
In order to explore the mystery that the two sea urchins are closely related but the embryonic development patterns are very different, the research team first used high-throughput sequencing technology to assemble the chromosome-level genomes of red sea urchins and short spiny sea urchins, respectively, the total genome sequences of the two sea urchins are 0.89 Gb and 1.06 Gb, each with 21 chromosomes, and there is a good collinear relationship between chromosomes. This also reconfirms the very close kinship between the two sea urchins at the molecular level.
Relying on the whole genome sequence obtained above, the research team found that there were no significant differences in the coding sequences of genes related to the early embryonic development gene regulatory network (dGRN) between red sea urchins and short spiny sea urchins, that is, extensive changes in the development and life history of embryonic and larval of short spiny sea urchins were not caused by major changes in the structure or function of the relevant genes themselves.
Since it is not a difference at the gene level, is the final expression different because the gene is regulated differently? The research team began targeting the chromatin open region (OCR).
Chromosomes are spiral-like structures formed by highly coiled chromatin curls, and when genes need to be expressed, the chromosomal region where the gene and the corresponding regulatory factor are located will open up to facilitate the binding of biological macromolecules such as enzymes.
Therefore, the open chromatin region can provide a large amount of gene expression regulation information, and its sequence changes also indicate that the expression and regulation of the corresponding gene may change.
The research team used ATAC sequencing technology to explore whether regulatory elements in the chromatin-open region had changed. The results showed that the short spiny sea urchin with changed embryonic morphology, the potential enhancer and promoter sequences in the chromatin open region were subject to obvious environmental selection, and there may be widespread positive selection for regulatory element functions within the genome. When the research team focused on the chromatin open regions near the dGRN-related gene, they found that these regions of the short-spined sea urchin changed more than other sea urchins, and the evolutionary speed of the relevant sequence and the frequency of chromatin state changes were 3 times that of other regions, which was not observed in other sea urchins.
In addition, to test whether the cell types during the development of two sea urchin embryos also changed, the researchers used single-cell sequencing technology to analyze the embryonic blastocysts of multiple sea urchins. The results suggest that in short-spined sea urchins, the early fate determination of cells in the embryo is delayed, and the role of key regulators of cell fate in osteoblast lines has also evolved.
Single cell sequencing of sea urchin embryos analyzes cell clustering results
Through further experiments, the research team verified the expression of key genes for cell differentiation during the development of short-spined sea urchin embryos. The experimental results show that during the embryonic development of short-spined sea urchins, the inhibitory effect and sequence similarity of the gene families of the two genes directly related to osteoblast differentiation have been significantly different, which also indicates that more profound evolutionary changes have occurred within the dGRN gene.
In this study, based on the differences in embryonic development patterns of two closely related sea urchins, this study conducted in-depth research on the gene regulatory network of early embryonic development based on the differences in embryonic development patterns of two closely related sea urchins, and found that natural selection can profoundly affect gene regulation on a genome-wide scale by changing the sequence of regulatory elements and chromatin accessibility in a short period of time, and show that in the face of natural selection, the conservation of developmental gene regulatory networks does not necessarily mean the limitation of development patterns, and related mechanisms may still evolve.
Dr. Guo Haobing of Qingdao BGI Institute of Genomics said, "This study provides new research ideas for the evolutionary development of marine organisms, discovers the profound impact of natural selection on species development and evolution in the developmental gene regulatory network, and lays a foundation for further revealing the deep mechanisms related to gene regulatory changes in the future." ”