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Yeast has been extensively studied and engineered due to its genetic amenability. Projects like Sc2.0 and Sc3.0 have demonstrated the feasibility of constructing synthetic yeast genomes, yielding promising results in both research and industrial applications. In contrast, plant synthetic genomics has faced challenges due to the complexity of plant genomes. However, recent advancements of the project SynMoss, utilizing the model moss plant Physcomitrium patens, offer opportunities for plant synthetic genomics. The shared characteristics between P. patens and yeast, such as high homologous recombination rates and dominant haploid life cycle, enable researchers to manipulate P. patens genomes similarly, opening promising avenues for research and application in plant synthetic biology. In conclusion, harnessing insights from yeast synthetic genomics and applying them to plants, with P. patens as a breakthrough, shows great potential for revolutionizing plant synthetic genomics., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Since the first synthetic gene was synthesized in 1970s, the efficiency and the capacity of made-to-order DNA sequence synthesis has increased by several orders of magnitude. Advances in DNA synthesis and assembly over the past years has resulted in a steep drop in price for custom made DNA. Similar effects were observed in DNA sequencing technologies which underpin DNA-reading projects. Today, synthetic DNA sequences with more than 10000bps and turn-around times of a few weeks are commercially available. This enables researchers to perform large-scale projects to write synthetic chromosomes and characterize their functionalities in vivo. Synthetic genomics opens up new paradigms to study the genome fundamentals and engineer novel biological functions., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Loss-of-function study is an effective approach to research gene functions. However, currently most of such studies have ignored an important problem (in this paper, we call it "off-target" problem), that is, if the target gene is an overlapping gene (A gene whose expressible nucleotides overlaps with that of another one), loss-of-function mutation by deleting the complete open reading frame (ORF) may also cause the gene it overlaps lose function, resulting a phenotype which may be rather different from that of single gene deletion. Therefore, when doing such studies, the loss-of-function mutations should be carefully designed to guarantee only the function of the target gene will be abolished. In this paper, we present PyMut, an easy-to-use web tool for biologists to design such mutations. To the best of our knowledge, PyMut is the first tool that aims to solve the "off-target" problem regarding the overlapping genes. Our web server is freely available at http://www.bioinfo.tsinghua.edu.cn/∼liuke/PyMut/index.html.

Benefited from the rapid development of high-throughput sequencing, genome editing, DNA synthesis and functional genomics, synthetic genomics gains the momentum in this century. The entire genomes of several viruses and one prokaryote have been chemically synthesized and applied to drive normal cellular processes. The first eukaryotic genome synthesis project (Sc2.0) is on-going and about half of the genome has been synthesized and functionally tested. The Human Genome Project-Write (HGP-Write) was proposed in 2016, which pushes the tide of synthetic genomics to a position we have never seen before. Technologies on genome-scale design and DNA synthesis have been rapidly developed, aiming to construct a more predictable and controllable genome at reasonable cost. The generation of synthetic organisms not only has promising applications for industry, environment, healthy and basic researches, but also raises ethic and policy concerns. This review presents the development of synthetic genomics, with emphasis on technologies for whole genome design, synthesis and assembly. We also discussed ethics, prospective and challenge in synthetic genomics. As one of the major branches in synthetic biology, synthetic genomics is still at its infant stage. A lot of excitement will come in the next few years.

The forfeiting of photosynthetic capabilities has occurred independently many times throughout eukaryotic evolution. But almost all non-photosynthetic plants and algae still retain a colorless plastid and an associated genome, which performs fundamental processes apart from photosynthesis. Unfortunately, little is known about the forces leading to photosynthetic loss; this is largely because there is a lack of data from transitional species. Here, we compare the plastid genomes of two "transitional" green algae: the photosynthetic, mixotrophic Auxenochlorella protothecoides and the non-photosynthetic, obligate heterotroph Prototheca wickerhamii. Remarkably, the plastid genome of A. protothecoides is only slightly larger than that of P. wickerhamii, making it among the smallest plastid genomes yet observed from photosynthetic green algae. Even more surprising, both algae have almost identical plastid genomic architectures and gene compositions (with the exception of genes involved in photosynthesis), implying that they are closely related. This close relationship was further supported by phylogenetic and substitution rate analyses, which suggest that the lineages giving rise to A. protothecoides and P. wickerhamii diverged from one another around six million years ago.

Summary: Synthetic genomics involves the design, assembly, and transfer of artificially synthesized DNA fragments into target hosts to replace the native genome and construct viable forms of life. With advances in DNA synthesis and assembly techniques, the application of synthetic genomics in viruses, bacteria, and yeast has improved our knowledge of genome organization and function. Multicellular eukaryotic organisms are characterized by larger genomes, more complex epigenetic regulation, and widespread transposable elements, making genome synthesis challenging. Recently, the first synthetic multicellular eukaryotic organism was generated in the model plant Physcomitrium patens with a partially synthetic chromosome arm. Here, we introduce the design and assembly principles of moss genome synthesis. We also discuss the remaining technical barriers in the application of synthetic genomics in seed plants. [ABSTRACT FROM AUTHOR]

We report the establishment of an efficient and heritable gene mutagenesis method in the silkworm Bombyx mori using modified type II clustered regularly interspaced short palindromic repeats (CRISPR) with an associated protein (Cas9) system. Using four loci Bm-ok, BmKMO, BmTH, and Bmtan as candidates, we proved that genome alterations at specific sites could be induced by direct microinjection of specific guide RNA and Cas9-mRNA into silkworm embryos. Mutation frequencies of 16.7–35.0% were observed in the injected generation, and DNA fragments deletions were also noted. Bm-ok mosaic mutants were used to test for mutant heritability due to the easily determined translucent epidermal phenotype of Bm-ok-disrupted cells. Two crossing strategies were used. In the first, injected Bm-ok moths were crossed with wild-type moths, and a 28.6% frequency of germline mutation transmission was observed. In the second strategy, two Bm-ok mosaic mutant moths were crossed with each other, and 93.6% of the offsprings appeared mutations in both alleles of Bm-ok gene (compound heterozygous). In summary, the CRISPR/Cas9 system can act as a highly specific and heritable gene-editing tool in Bombyx mori. [ABSTRACT FROM AUTHOR]

We report the establishment of an efficient and heritable gene mutagenesis method in the silkworm Bombyx mori using modified type II clustered regularly interspaced short palindromic repeats (CRISPR) with an associated protein (Cas9) system. Using four loci Bm-ok, BmKMO, BmTH, and Bmtan as candidates, we proved that genome alterations at specific sites could be induced by direct microinjection of specific guide RNA and Cas9-mRNA into silkworm embryos. Mutation frequencies of 16.7–35.0% were observed in the injected generation, and DNA fragments deletions were also noted. Bm-ok mosaic mutants were used to test for mutant heritability due to the easily determined translucent epidermal phenotype of Bm-ok-disrupted cells. Two crossing strategies were used. In the first, injected Bm-ok moths were crossed with wild-type moths, and a 28.6% frequency of germline mutation transmission was observed. In the second strategy, two Bm-ok mosaic mutant moths were crossed with each other, and 93.6% of the offsprings appeared mutations in both alleles of Bm-ok gene (compound heterozygous). In summary, the CRISPR/Cas9 system can act as a highly specific and heritable gene-editing tool in Bombyx mori. [ABSTRACT FROM AUTHOR]