The aquatic beetle Cybister rugosus has experienced ongoing habitat loss, a decline in population numbers and confirmed extinctions among insular populations in Japan. It has recently been classified on the Red List as endangered by the Japanese Ministry of Environment and has been designated a specified class II nationally rare species of wild fauna and flora. To design effective conservation strategies for this species, it is essential to compile data on its genetic variation to ascertain its genetic diversity and population structure. Previous studies found low levels of genetic variation in the COI gene among Japanese insular populations and failed to detect a fine population structure. Thus, we developed ten novel microsatellite markers for C. rugosus, using whole-genome shotgun sequencing. The degree of polymorphism for these markers was characterized using summary statistics describing the genetic variation in 49 individuals from populations in Cambodia and on the islands of the Ryukyu Archipelago. Microsatellite data indicated differentiation among the insular populations in Japan, which could not be clearly shown in the COI data, and some insular populations showed low levels of genetic diversity. The newly developed microsatellite markers will contribute to future ecological and evolutionary studies on this species and to conservation research.

DNA methylation is essential for transcriptional regulation and the maintenance of chromosome stability, and its precise inheritance upon DNA replication is indispensable for cellular homeostasis. The DNMT1/UHRF1 complex is critical in copying DNA methylation with accessory proteins, including CDCA7 and HELLS. The DNMT1/UHRF1 complex is also crucial for maintaining DNA methylation at imprinting control regions during preimplantation development against genome-wide DNA demethylation, an essential process for early embryos to acquire totipotency. Pathogenic variants in the genes involved in the mechanism of DNA methylation maintenance result in immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome, multilocus imprinting disturbance (MLID), autosomal dominant cerebellar ataxia, deafness, and narcolepsy (ADCADN), neuropathy, hereditary sensory, type 1E (HSN1E), Kleefstra syndrome 1 (KLEFS1) and immunodeficiency 96 (IMD96). This review discusses recent progress in understanding the molecular pathogenesis of these diseases, with a particular focus on ICF syndrome and MLID.

Intraspecific variations in specialized metabolites play a crucial role in the adaptive response to diverse environments. Two major subspecies, japonica and indica, are observed in Asian cultivated rice (Oryza sativa L.). Previously, we identified (3R)-β-tyrosine, a novel nonproteinogenic β-amino acid in plants, along with the enzyme tyrosine aminomutase (TAM1), required for β-tyrosine biosynthesis, in the japonica cultivar Nipponbare. Notably, TAM1 and β-tyrosine preferentially distributed in japonica cultivars compared with indica cultivars. Considering its phytotoxicity and antimicrobial activity, intraspecific variations in β-tyrosine may contribute to defensive potentials of japonica rice. Investigation of the evolutionary trajectory of TAM1 and β-tyrosine should enhance our understanding of evolution of rice defense. However, their distribution patterns in Oryza rufipogon, the direct ancestor of O. sativa, remain unclear. Therefore, in this study, we extensively examined TAM1 presence/absence and β-tyrosine contents involving 110 genetically and geographically diverse O. rufipogon and revealed that they are characteristically observed in the ancestral subpopulation of japonica rice, while being absent or slightly accumulated in other subpopulations. Thus, we conclude that TAM1 and β-tyrosine in japonica rice are likely derived from its ancestral subpopulation. Furthermore, the high and low TAM1 possession rates and β-tyrosine contents in japonica and indica rice, respectively, could be attributed to distribution patterns of TAM1 and β-tyrosine in their ancestral subpopulations. This study provides fundamental insights into evolution of rice defense.

Nucleosomes are complexes of DNA and histone proteins that form the basis of eukaryotic chromatin. Eukaryotic histones are descended from archaeal homologs; however, how this occurred remains unclear. Our previous genetic analysis of the budding yeast nucleosome identified 26 histone residues conserved between Saccharomyces cerevisiae and Trypanosoma brucei: 15 that are lethal when mutated and 11 that are synthetically lethal with deletion of the FEN1 nuclease. These residues are partially conserved in nucleosomes of a variety of giant viruses, allowing us to follow the route by which they were established in the LECA (last eukaryotic common ancestor). We analyzed yeast nucleosome genetic data to generate a model for the emergence of the eukaryotic nucleosome. In our model, histone H2B-H2A and H4-H3 doublets found in giant virus nucleosomes facilitated the formation of the acidic patch surface and nucleosome entry sites of the eukaryotic nucleosome, respectively. Splitting of the H2B-H2A doublet resulted in the H2A variant H2A.Z, and subsequent splitting of the H4-H3 doublet led to a eukaryote-specific domain required for chromatin binding of H2A.Z. We propose that the LECA emerged when the newly split H3 N-terminus horizontally acquired a common N-tail found in extinct pre-LECA lineages and some extant giant viruses. This hypothesis predicts that the emergence of the H3 variant CENP-A and the establishment of CENP-A-dependent chromosome segregation occurred after the emergence of the LECA, implying that the root of all eukaryotes is assigned within Euglenida.

The ClinVar accession number on p. 176 (SCV002817173) should be replaced with the correct number, SCV002817373.The PDF file for DOI: https://doi.org/10.1266/ggs.22-00138 has been replaced with the corrected version as of November 6, 2024.

Primula secundiflora is an insect-pollinated, perennial herb belonging to the section Proliferae (Primulaceae) that exhibits considerable variation in its mating system, with predominantly outcrossing populations comprising long-styled and short-styled floral morphs and selfing populations comprising only homostyles. To facilitate future investigations of the population genetics and mating patterns of this species, we developed 25 microsatellite markers from P. secundiflora using next-generation sequencing and measured polymorphism and genetic diversity in a sample of 30 individuals from three natural populations. The markers displayed high polymorphism, with the number of observed alleles per locus ranging from three to 16 (mean = 8.36). The observed and expected heterozygosities ranged from 0.100 to 1.000 and 0.145 to 0.843, respectively. Twenty-one of the loci were also successfully amplified in P. denticulata. These microsatellite markers should provide powerful tools for investigating patterns of population genetic diversity and the evolutionary relationships between distyly and homostyly in P. secundiflora.

In Saccharomyces cerevisiae, boundaries formed by DNA sequence-dependent or -independent histone modifications stop the spread of the heterochromatin region formed via the Sir complex. However, it is unclear whether the histone modifiers that control DNA sequence-independent boundaries function in a chromosome-specific or -nonspecific manner. In this study, we evaluated the effects of the SAGA complex, a histone acetyltransferase (HAT) complex, and its relationship with other histone-modifying enzymes to clarify the mechanism underlying boundary regulation of the IMD2 gene on the right subtelomere of chromosome VIII. We found that Spt8, a component of the SAGA complex, is important for boundary formation in this region and that the inclusion of Spt8 in the SAGA complex is more important than its interaction with TATA-binding protein and TFIIS. In addition to SAGA, various HAT-related factors, such as NuA4 and Rtt109, also functioned in this region. In particular, the SAGA complex induced weak IMD2 expression throughout the cell, whereas NuA4 induced strong expression. These results indicate that multiple HATs contribute to the regulation of boundary formation and IMD2 expression on the right subtelomere of chromosome VIII and that IMD2 expression is determined by the balance between these factors.

Next-generation RNA sequencing analysis was performed to develop 13 novel expressed sequence tag-simple sequence repeat markers to evaluate the genetic variation in the near-threatened halophyte Limonium tetragonum (Thunb.) A. A. Bullock. In the four populations examined, the total number of alleles at each locus ranged from two to seven, with an average of 3.1. The average observed and expected heterozygosity ranged from 0.00 to 0.13 and 0.28 to 0.78, respectively. Three of the 13 loci had the same homozygous alleles within populations, but different alleles among populations. Compared to other halophytes, relatively low genetic diversity was observed in this species. Further studies are necessary to determine the population demography of L. tetragonum and to clarify the cause of its low genetic diversity.