The ribosomal DNA (rDNA) constitutes a remarkably conserved DNA sequence within species, located in the area of the nucleolus, and responsible for coding three major types of rRNAs (18S, 5.8S and 28S). While historical investigations into rDNA focused on its structure and coding capabilities, recent research has turned to explore its functional roles in various biological processes. In this review, we summarize the main findings of rDNA methylation with embryonic development, aging and diseases in multiple species, including epigenetic alterations, related biological processes and potential applications of rDNA methylation. We present an overview of current related research and identify gaps in this field.

UNASSIGNED: Barbronia, a genus of freshwater macrophagous leeches, belongs to Erpobdelliformes (Salifidae: Clitellata: Annelida), and B. weberi, a well-known leech within this genus, has a worldwide distribution. However, the systematics of Barbronia have not yet been adequately investigated, primarily due to a few molecular markers, and only 20 Barbronia sequences available in the GenBank database. This gap significantly limits our understanding of the Barbronia species identification, as well as the phylogenetic placement of the genus Barbronia within Salifidae.
UNASSIGNED: Next-generation sequencing (NGS) was used to simultaneously capture the entire mitochondrial genome and the full-length 18S/28S rDNA sequences. The species boundary of Barbronia species was estimated using bGMYC and bPTP methods, based on all available Barbronia COI sequences. Uncorrected COI p-distance was calculated in MEGA. A molecular data matrix consisting of four loci (COI, 12S, 18S, and 28S rDNA) for outgroups (three Haemopis leeches) and 49 erpobdellid leeches, representing eight genera within the Suborder Erpobdelliformes was aligned using MAFFT and LocARNA. This matrix was used to reconstruct the phylogenetic relationship of Barbronia via Bayesian inference (BI) and the maximum likelihood (ML) method.
UNASSIGNED: The full lengths of the mitochondrial genome, 18S and 28S rDNAs of B. cf. gwalagwalensis, are 14847 bp, 1876 bp 1876 bp, and 2863 bp, respectively. Both bGMYC and bPTP results based on COI data are generally congruent, suggesting that the previously proposed taxa (B. arcana, B. weberi formosana, and B. wuttkei or Erpobdella wuttkei) are synonyms of B. weberi. The specimens listed in the B. gwalagwalensis group, however, are split into at least two Primary Species Hypotheses (PSHs). The p-distance of the first PSH is less than 1.3% but increased to 4.5% when including the secondary PSH (i.e., B. cf. gwalagwalensis). In comparison, the interspecific p-distance between the B. weberi group and the B. gwalagwalensis group ranged from 6.4% to 8.7%, and the intraspecific p-distance within the B. weberi group is less than 0.8%. Considering the species delimitation results and the sufficient large p-distance, the specimen sampled in China is treated as B. cf. gwalagwalensis. The monophyly of the four Erpobdelliformes families Salifidae, Orobdellidae, Gastrostomobdellidae sensu stricto and Erpobdellidae is well supported in ML and BI analysis based on a data of four markers. Within the Salifidae, a well-supported Barbronia is closely related to a clade containing Odontobdella and Mimobdella, and these three genera are sister to a clade consisted of Salifa and Linta. According to the results of this study, the strategy of simultaneous obtaining both whole mitochondria and nuclear markers from extensively sampled Salifids species using NGS is expected to fathom both the species diversity of B. gwalagwalensis and the evolutionary relationship of Salifidae.

DNA replication is a fundamental process ensuring the maintenance of the genome each time cells divide. This is particularly relevant early in development when cells divide profusely, later giving rise to entire organs. Here, we analyze and compare the genome replication progression in human embryonic stem cells, induced pluripotent stem cells, and differentiated cells. Using single-cell microscopic approaches, we map the spatio-temporal genome replication as a function of chromatin marks/compaction level. Furthermore, we mapped the replication timing of subchromosomal tandem repeat regions and interspersed repeat sequence elements. Albeit the majority of these genomic repeats did not change their replication timing from pluripotent to differentiated cells, we found developmental changes in the replication timing of rDNA repeats. Comparing single-cell super-resolution microscopic data with data from genome-wide sequencing approaches showed comparable numbers of replicons and large overlap in origins numbers and genomic location among developmental states with a generally higher origin variability in pluripotent cells. Using ratiometric analysis of incorporated nucleotides normalized per replisome in single cells, we uncovered differences in fork speed throughout the S phase in pluripotent cells but not in somatic cells. Altogether, our data define similarities and differences on the replication program and characteristics in human cells at different developmental states.

Passion fruit (Passiflora edulis), a medicinal plant, was introduced into China in the early 19th century, is mainly cultivated in southern provinces (Liang et al. 2019). During March 2023, a survey was carried out and 167 samples were taken from passion fruit cultivated area in Yulin (22.6570263°E; 110.1765019°N) apart from the planting base appeared yellow leaves, stunted growth, and distinctive galls on the roots. Within the galls, Meloidogyne sp. females and egg masses were observed. From the rhizosphere soil, second-stage juveniles (J2) were extracted, and population density was 105/500 g soil. The species was determined to be Meloidogyne enterolobii based on morphological characteristics, including female perineal pattern, and genetic analyses. Female (n = 10) perineal patterns showed oval shape, with coarse and smooth striae, dorsal arch rounded to square, and lateral lines not distinct. The male head cap was high and rounded, with the head region only slightly set off from the body, knobs large, ovoid to rounded. The measurements of males (n = 10) included body length, 1,230.7 ± 244.94 (997 to 1,569) µm; a, 38.58 ± 7.8 (33.45 to 47.05) µm; c, 113.03 ± 26.22 (80.82 to 144.23) µm; stylet, 15.68 ± 1.1 (14.5 to 17.4) µm; spicules, 31.83 ± 2.84 (28.69 to 36.1) µm; tail, 11.09 ± 1.72 (8.02 to 13.38) µm; and gubernaculum length, 8.34 ± 0.28 (8.11 to 8.98) µm. Measurements of J2 (n = 20) included body length, 455.75 ± 44.94 (381 to 512) µm; a, 26.32 ± 3.89 (18.18 to 32.70) µm; c, 8.56 ± 1.2 (6.36 to 10.80) µm; stylet, 12.44 ± 0.76 (11.2 to 13.8) µm; DGO, 3.65 ± 0.54 (2.84 to 4.68) µm; tail, 53.89 ± 6.36 (39.8 to 62.2) µm; and hyaline tail terminus, 11.77 ± 2.83 (7.14 to 16.2) µm. These morphological characteristics are similar to those reported in the original description of M. enterolobii (Yang and Eisenback 1983). The sequences of the partial ITS region was amplified with V5367 (5\'-TTGATTACGTCCCTGCCCTTT-3\') and 26S (5\'-TTTCACTCGCCGTTACTAAGG-3\') primers (Vrain et al. 1992). The region between cytochrome oxidase subunit II (COII) and the 16S rRNA mitochondrial DNA (mtDNA COII) was also amplified with the primers C2F3 (5\'-GGTCAATGTTCAGAAATTTGTGG-3\') (Powers and Harris 1993) and MRH106 (5\'-AATTTCTAAAGACTTTTCTTAGT-3\') (Stanton et al. 1997). The ITS region yielded a fragment of 757 bp (OR072957) and mtDNA COII of 706 bp (OR078415). A BLAST search indicated the sequences were 100% identical to several sequences of M. enterolobii (MT406250, MH756127 and AY831967, MN269940, respectively). To confirm pathogenicity, 20 passion fruit (P. edulis Sim. f. flavicarpa) 30-day-old seedlings were transplanted into pots with an autoclaved mixture of sand and field soil (3:1) and maintained in the glasshouse at 25 ± 2°C with 65 ± 5% relative humidity. After eight weeks, fifteen plants were inoculated with 500 J2/pot (nematode culture collected from the original field), and another five uninoculated plants served as a control. Two months later, aboveground symptoms were similar to those observed in the field. Nematode reproduction occurred and root galls were observed. The reproduction factor (nematode final population density/initial population density) was 4.8. The disease caused by M. enterolobii was severe in Yulin city of Guangxi. Guangxi is an important area for passion fruit culture, with about 2000 ha, which is responsible for two-thirds of China production (Xing et al. 2020). This is the first record of P. edulis natural infection with M. enterolobii in the Yulin City of Guangxi, China.

BACKGROUND: Satellite repeats are one of the most rapidly evolving components in eukaryotic genomes and play vital roles in genome regulation, genome evolution, and speciation. As a consequence, the composition, abundance and chromosome distribution of satellite repeats often exhibit variability across various species, genome, and even individual chromosomes. However, we know little about the satellite repeat evolution in allopolyploid genomes.
RESULTS: In this study, we investigated the satellite repeat signature in five okra (Abelmoschus esculentus) accessions using genomic and cytogenetic methods. In each of the five accessions, we identified eight satellite repeats, which exhibited a significant level of intraspecific conservation. Through fluorescence in situ hybridization (FISH) experiments, we observed that the satellite repeats generated multiple signals and exhibited variations in copy number across chromosomes. Intriguingly, we found that five satellite repeats were interspersed with centromeric retrotransposons, signifying their involvement in centromeric satellite repeat identity. We confirmed subgenome-biased amplification patterns of these satellite repeats through existing genome assemblies or dual-color FISH, indicating their distinct dynamic evolution in the allotetraploid okra subgenome. Moreover, we observed the presence of multiple chromosomes harboring the 35 S rDNA loci, alongside another chromosomal pair carrying the 5 S rDNA loci in okra using FISH assay. Remarkably, the intensity of 35 S rDNA hybridization signals varied among chromosomes, with the signals predominantly localized within regions of relatively weak DAPI staining, associated with GC-rich heterochromatin regions. Finally, we observed a similar localization pattern between 35 S rDNA and three satellite repeats with high GC content and confirmed their origin in the intergenic spacer region of the 35 S rDNA.
CONCLUSIONS: Our findings uncover a unique satellite repeat signature in the allotetraploid okra, contributing to our understanding of the composition, abundance, and chromosomal distribution of satellite repeats in allopolyploid genomes, further enriching our understanding of their evolutionary dynamics in complex allopolyploid genomes.

Red Noctiluca scintillans is a common heterotrophic dinoflagellate that forms blooms in temperate, subtropical, and tropical coastal ecosystems. The diet of this species plays an important role in its cell growth, development, and reproduction. Because limited gene diversity data are available regarding prey of this species, its diet in Daya Bay during a boreal winter bloom is reported using an integrated approach involving light microscopy, single cell isolation and plastid 16S rDNA cloning, and 18S rDNA V4 and V9 region amplification using isolated cells and environmental DNA as templates with high-throughput sequencing. While conventional light microscopy reveals the diet of this species to comprise Coscinodiscus sp. and Stephanopyxis turris (diatoms), copepod eggs, and detritus, plastid gene diversity identifies a diet comprising diatoms, cyanobacteria, and bacteria, and 18S rDNA high-throughput sequencing reveals a diet comprising 36 eukaryote families (primarily copepods, as well as diatoms, dinoflagellates, Ochrophyta, Haptophytes, Chordata, Cercozoans, Chlorophyta, Polychaeta, and ciliates). Dietary staples include copepods, diatoms, dinoflagellates, Ochrophyta, and Synechococcus. High copepod abundance in prey may reflect their relatively high abundance in environmental seawater. Thus, N. scintillans is generally omnivorous but prefers dominant phytoplankton taxa, including Rhizosoleniaceae, Leptocylindraceae, and Cymatosiraceae (diatoms), as well as Gonyaulacaceae (dinoflagellates). An integrated multi-disciplinary approach provides a more comprehensive picture of N. scintillans diet in Daya Bay, and an improved understanding of this species\' ecological niche and trophic role in marine ecosystems.

BACKGROUND: The Pacific abalone, Haliotis discus hannai, is one of the most commercially important marine shellfish in China. Cell engineering breeding is an important tool in abalone genetic breeding, and the triploids obtained through this method have high commercial value. However, current research mainly focuses on establishing induction methods and evaluating the growth traits of triploids, while there is a lack of basic research on triploid cytogenetics.
METHODS: In this study, Cytogenetic analysis of triploid Haliotis discus hannai larvae (produced by chemical treatment) and diploid larvae was performed.
RESULTS: The results showed that triploid H. discus hannai had a chromosome number of 3n = 54, consisting of 30 metacentric (m) and 24 submetacentric (sm) chromosomes, while the diploids had a chromosome number of 2n = 36, consisting of 20 metacentric (m) and 16 submetacentric (sm) chromosomes. Notably, both triploids and diploids displayed variation in the number of NORs and/or their diameter. The average number of NORs in triploid was significantly higher than that in diploids (p < 0.05), but the average diameter of NORs of triploid was no significant different from that of diploid (p > 0.05). Additionally, 5S rDNA localization to 3 submetacentric chromosomes was observed in triploids, compared to 2 submetacentric chromosomes in diploids. The number of 18S rDNA sites displayed positional conservancy and quantitative variability in both diploids and triploids. Specifically, 18S rDNA was found at the end of the chromosome in both groups, with triploids exhibiting a significantly higher number of loci than diploids (p < 0.01).
CONCLUSIONS: This study provides valuable insights into the cytogenetic characteristics of triploid H. discus hannai, which could facilitate further research on the stability of the chromosome set in this species.

A large-scale sampling was undertaken during a research cruise across the South China Sea in August 2016, covering an area of about 100,000 km2 to investigate the molecular diversity and distributions of micro-eukaryotic protists, with a focus on the potentially harmful microalgal (HAB) species along the east coast of Peninsular Malaysia. Environmental DNAs from 30 stations were extracted and DNA metabarcoding targeting the V4 and V9 markers in the 18S rDNA was performed. Many protistan molecular units, including previously unreported HAB taxa, were discovered for the first time in the water. Our findings also revealed interesting spatial distribution patterns, with a marked signal of compositional turnover between latitudinal regimes of water masses, where dinophytes and diatom compositions were among the most strongly enhanced at the fronts, leading to distinct niches. Our results further confirmed the widespread distribution of HAB species, such as the toxigenic Alexandrium tamiyavaichii and Pseudo-nitzschia species, and the fish-killing Margalefidinium polykrikoides and Karlodinium veneficum. The molecular information obtained from this study provides an updated HAB species inventory and a toolset that could facilitate existing HAB monitoring schemes in the region to better inform management decisions.

Discrimination of chromosome is essential for chromosome manipulation or visual chromosome characterization. Oligonucleotide probes can be employed to simplify the procedures of chromosome identification in molecular cytogenetics due to its simplicity, fastness, cost-effectiveness, and high efficiency. So far, however, visual identification of cotton chromosomes remains unsolved. Here, we developed 16 oligonucleotide probes for rapid and accurate identification of chromosomes in Gossypium hirsutum: 9 probes, of which each is able to distinguish individually one pair of chromosomes, and seven probes, of which each distinguishes multiple pairs of chromosomes. Besides the identification of Chrs. A09 and D09, we first find Chr. D08, which carries both 45S and 5S rDNA sequences. Interestingly, we also find Chr. A07 has a small 45S rDNA size, suggesting that the size of this site on Chr. A07 may have reduced during evolution. By the combination of 45S and 5S rDNA sequences and oligonucleotide probes developed, 10 chromosomes (Chrs. 3-7, and 9-13) in A subgenome and 7 (Chrs. 1-2, 4-5, and 7-9) in D subgenome of cotton are able to be recognized. This study establishes cotton oligonucleotide fluorescence in situ hybridization technology for discrimination of chromosomes, which supports and guides for sequence assembling, particularly, for tandem repeat sequences in cotton.

During fertilization, DAXX (death domain-associated protein) mediates histone variant H3.3 incorporation into heterochromatin, which plays an important role in the maintenance of genomic integrity. rDNA, the ribosomal gene, is included in the first wave of gene activation after fertilization. Our and other studies indicated that loss of Daxx disturbs rDNA heterochromatinization and promotes rDNA transcription without change in protein expression of H3.3. However, maternal and zygotic deletion of Daxx impairs blastocyst development. Whether Daxx knockdown affects H3.3 expression and improves the rDNA transcription in preimplantation development has not been reported. In the present study, we injected HA-labelled H3.3 (H3.3-HA) into oocytes during ICSI procedure, and detected H3.3 and DAXX by immunofluorescent staining. Then, we knockdowned Daxx and detected the gene expression levels of Daxx, H3.3, 18s and 47s rRNA. We also performed immunofluorescent staining of B23, γH2A and EdU incorporation to demonstrate nuclear structure, DNA damage and replication. We found injection of H3.3-HA did not impair preimplantation development. Daxx siRNA did not change expression of H3.3 mRNA, and the development of two-cell embryos and blastocysts, but the overall replication and expression levels of rRNA were increased compared with that in the control group. Finally, knockdown of DAXX did not aggravate the DNA damage but loosened the nucleolus. We concluded that Daxx knockdown promoted DNA replication and rDNA transcription, but did not affect H3.3 expression and subsequent preimplantation development.