Origin and Fates of TERT Gene Copies in Polyploid Plants

The gene coding for the telomerase reverse transcriptase (TERT) is essential for the maintenance of telomeres. Previously we described the presence of three TERT paralogs in the allotetraploid plant Nicotiana tabacum, while a single TERT copy was identified in the paleopolyploid model plant Arabidopsis thaliana. Here we examine the presence, origin and functional status of TERT variants in allotetraploid Nicotiana species of diverse evolutionary ages and their parental genome donors, as well as in other diploid and polyploid plant species. A combination of experimental and in silico bottom-up analyses of TERT gene copies in Nicotiana polyploids revealed various patterns of retention or loss of parental TERT variants and divergence in their functions. RT–qPCR results confirmed the expression of all the identified TERT variants. In representative plant and green algal genomes, our synteny analyses show that their TERT genes were located in a conserved locus that became advantageous after the divergence of eudicots, and the gene was later translocated in several plant groups. In various diploid and polyploid species, translocation of TERT became fixed in target loci that show ancient synapomorphy.

Privacy-Utility Equilibrium Protocol for Federated Aggregating Multiparty Genome Data

Cloud server aggregates a large amount of genome data from multi genome donors to facilitate scientific research. However, the untrusted cloud server is prone to violate privacy of aggregating genome data. Thus, each genome donor can randomly perturb her genome data using differential privacy mechanism before aggregating. But this is easy to lead to utility disaster of aggregating genome data due to the different privacy preferences of each genome donor, and privacy leakage of aggregating genome data because of the kinship between genome donors. The key challenge here is to achieve an equilibrium between privacy preserving and data utility of aggregating multiparty genome data. To this end, we proposed federated aggregation protocol of multiparty genome data (MGD-FAP) with privacy-utility equilibrium for guaranteeing desired privacy protection and desired data utility. First, we regarded the privacy budget and the accuracy as the desired privacy-utility metrics of genome data respectively. Second, we constructed the federated aggregation model of multiparty genome data by combining random perturbation method of genome data guaranteeing desired data utility with federated comparing update method of local privacy budget achieving desired privacy preserving. Third, we presented the MGD-FAP maintaining privacy-utility equilibrium under the federated aggregation model of multiparty genome data. Finally, our theoretical and experimental analysis showed that MGD-FAP can maintain privacy-utility equilibrium. The MGD-FAP is practical and feasible to ensure the privacy-utility equilibrium of cloud server aggregating multiparty genome data.

Identification of Bread and Durum Wheats from their Diploid Ancestral Species Based on Chloroplast DNA

Species that have been identified as the genome donors to cultivated polyploid durum and bread wheats (Triticum durum L. and T. aestivum L., respectively) are potential gene sources for the breeding of these two crops. Therefore, their accurate identification facilitates their use in the improvement of these crops. Based on chloroplast DNA analysis (rpL2 and rps16 introns, psbC-trnS, trnT-L, and trnL-F) using polymerase chain reaction (PCR) and PCR-restriction fragment length polymorphism (PCR-RFLP), an attempt was made in 2018 (Department of Molecular Biology and Biotechnology/AECS) to identify durum and bread wheats from each of their proposed diploid ancestral species (i.e., T. monococcum, T. urartu, Aegilops speltoides, and Ae. tauschii). The use of two PCR markers (psbC-trnS and trnL-F) and three PCR-RFLP locus-enzyme combinations (rps16 intron-Tru 1I, rpL2 intron-Taq I, and trnT-L-Taq I) allowed the identification of all species involved. Reliable and accurate identification of diploid ancestors of durum and bread wheats using these candidate species-specific cpDNA markers will be useful for wheat breeding programs, in situ and ex situ conservation efforts, verification of seed purity in commercial seed stocks, and ensuring identity and integrity of accessions held within a collection does not change through unwanted gene flow or by genetic drift after regeneration by seed.

Regeneration ofEscherichia colifrom Minicells through Lateral Gene Transfer

ABSTRACTRecently, artificial life has been created with artificial materials and methods. Life can be created when genomic DNA molecules are integrated in liposomes containing biochemical reactions for biogenic needs. However, it is not yet known whether the integration of these parts will be able to occur in nature and constitute a living system. I planned to regenerate bacteria from biologically active liposomes by inserting genomic DNA using only natural materials and methods. Minicells ofEscherichia coli, containing plasmids and activated SOS proteins, act as protocells. Four newE. colistrains were regenerated from minicells by inserting the genomes by using the system for conjugation between F−and Hfr strains. Cells of the four regenerated strains showed the same genetic markers as the two genome donors. Pulse-field gel electrophoresis of their genomes showed admixing of those of both donors. In addition, the genomes of the four regenerated strains had chimeric genome of the two donors. These results show that synthesis of life can occur in nature without artificial arrangement.IMPORTANCEWhat is the difference between inanimate objects and organisms? Organisms always have genomic DNA. When organisms lose their genomes, they can neither grow nor reproduce. As the result, organisms turn into inanimate objects without their genomes. In this study, I regenerated microbes from cells that had lost their genomes (cell corpses) by inserting another genome. All steps of regeneration used the natural behavior of microbes. The same regeneration of microbes could happen in nature. These primitive lives have plasticity, which accelerates evolution and provides various kinds of life in the world.

Whole genome duplication in coast redwood (Sequoia sempervirens) and its implications for explaining the rarity of polyploidy in conifers

Whereas polyploidy is common and an important evolutionary factor in most land plant lineages it is a real rarity in gymnosperms. Coast redwood (Sequoia sempervirens) is the only hexaploid conifer and one of just two naturally polyploid conifer species. Numerous hypotheses about the mechanism of polyploidy in Sequoia and parental genome donors have been proffered over the years, primarily based on morphological and cytological data, but it remains unclear how Sequoia became polyploid and why this lineage overcame an apparent gymnosperm barrier to whole-genome duplication (WGD). We sequenced transcriptomes and used phylogenetic inference, Bayesian concordance analysis, and paralog age distributions to resolve relationships among gene copies in hexaploid coast redwood and its close relatives. Our data show that hexaploidy in the coast redwood lineage is best explained by autopolyploidy or, if there was allopolyploidy, this was restricted to within the Californian redwood clade. We found that duplicate genes have more similar sequences than would be expected given evidence from fossil guard cell size which suggest that polyploidy dates to the Eocene. Conflict between molecular and fossil estimates of WGD can be explained if diploidization occurred very slowly following whole genome duplication. We extrapolate from this to suggest that the rarity of polyploidy in conifers may be due to slow rates of diploidization in this clade.

Nuclear and chloroplast DNA phylogeny reveals complex evolutionary history of Elymus pendulinus

Evidence accumulated over the last decade has shown that allopolyploid genomes may undergo complex reticulate evolution. In this study, 13 accessions of tetraploid Elymus pendulinus were analyzed using two low-copy nuclear genes (RPB2 and PepC) and two regions of chloroplast genome (Rps16 and trnD-trnT). Previous studies suggested that Pseudoroegneria (St) and an unknown diploid (Y) were genome donors to E. pendulinus, and that Pseudoroegneria was the maternal donor. Our results revealed an extreme reticulate pattern, with at least four distinct gene lineages coexisting within this species that might be acquired through a possible combination of allotetraploidization and introgression from both within and outside the tribe Hordeeae. Chloroplast DNA data identified two potential maternal genome donors (Pseudoroegneria and an unknown species outside Hordeeae) to E. pendulinus. Nuclear gene data indicated that both Pseudoroegneria and an unknown Y diploid have contributed to the nuclear genome of E. pendulinus, in agreement with cytogenetic data. However, unexpected contributions from Hordeum and unknown aliens from within or outside Hordeeae to E. pendulinus without genome duplication were observed. Elymus pendulinus provides a remarkable instance of the previously unsuspected chimerical nature of some plant genomes and the resulting phylogenetic complexity produced by multiple historical reticulation events.

Molecular phylogeny and reticulate origins of several American polyploid Hordeum species

The phylogeny of diploid species in the genus Hordeum has been studied intensively. Although the origin of American polyploid species has been analyzed using multiple-copy internal transcribed spacer sequences, the origins of these species in Hordeum remain unclear. The objectives of our study were to elucidate the origins of American polyploid species and to explore phylogenetic relationships of these polyploids to diploid Hordeum and other diploid species in Triticeae using a single copy of a nuclear gene, disrupted meiotic cDNA1 (DMC1). DMC1 sequences from nine Hordeum polyploid species were analyzed. Sequence comparisons revealed that one copy of sequences from polyploid species Hordeum fuegianum , Hordeum jubatum , and Hordeum tetraploidum showed a 82 bp miniature inverted-repeat terminal element (MITE) (Stowaway) insertion, which was also detected in the Triticeae diploid species Australopyrum species (W genome) and Taeniatherum caput-medusae (Ta genome). Maximum parsimony and Bayesian analysis suggested that diploid Hordeum brachyantherum subsp. californicum is one ancestor of polyploids Hordeum arizonicum , H. brachyantherum subsp. brachyantherum , Hordeum depressum , and Hordeum procerum . The other ancestor of tetraploid H. depressum is probably Hordeum euclaston . Hordeum cordobense was suggested to be one of the genome donors to hexaploid H. procerum. The diploid Hordeum flexuosum and tetraploid H. tetraploidum were suggested as the parents to hexaploid species Hordeum parodii . The result is that one sequence from each of three Hordeum tetrapolyploids, including H. fuegianum, H. jubatum, and H. tetraploidum, and one from Hordeum hexaploid H. arizonicum fall outside the Hordeum clade of the DMC1 phylogenetic tree, therefore representing another example of complex evolutionary history. Our data may shed light on future phylogenetic studies in Triticeae, especially for the polyploids, by broadening the scope of investigations through sampling more genome types in Poaceae, not only from the tribe Triticeae.