Search Results (472)

In this research, the mitochondrial genome of the Streptopelia decaocto was sequenced and examined for the first time to enhance the comprehension of the phylogenetic relationships within the Columbidae. The complete mitochondrial genome of Streptopelia decaocto (17,160 bp) was structurally similar to the recognized members of the Columbidae family, but with minor differences in gene size and arrangement. The structural AT content was 54.12%. Additionally, 150 mitochondrial datasets, representing valid species, were amassed in this investigation. Maximum likelihood (ML) and Bayesian inference (BI) phylogenetic trees and evolutionary time relationships of species were reconstructed based on cytb gene sequences. The findings from the phylogenetic evaluations suggest that the S. decaocto was classified under the Columbinae subfamily, diverging from the Miocene approximately 8.1 million years ago, indicating intricate evolutionary connections with its close relatives, implying a history of species divergence and geographic isolation. The diversification of the Columbidae commenced during the Late Oligocene and extended into the Miocene. This exploration offers crucial molecular data for the S. decaocto, facilitating the systematic taxonomic examination of the Columbidae and Columbiformes, and establishing a scientific foundation for species preservation and genetic resource management. Full article

The utility of the mitochondrial genomes (mitogenomes) in analyzing the evolutionary history of animals has been proven. Five deep-sea corals (Bathypathes sp.1, Bathypathes sp.2, Schizopathidae 1, Trissopathes sp., and Leiopathes sp.) were collected in the South China Sea (SCS). Initially, the structures and collinearity of the five deep-sea coral mitogenomes were analyzed. The gene arrangements in the five deep-sea coral mitogenomes were similar to those in the order Antipatharia, which evidenced their conservation throughout evolutionary history. Additionally, to elucidate the slow evolutionary rates in Hexacorallia mitogenomes, we conducted comprehensive analyses, including examining phylogenetic relationships, performing average nucleotide identity (ANI) analysis, and assessing GC-skew dissimilarity combining five deep-sea coral mitogenomes and 522 reference Hexacorallia mitogenomes. Phylogenetic analysis using 13 conserved proteins revealed that species clustered together at the order level, and they exhibited interspersed distributions at the family level. The ANI results revealed that species had significant similarities (identity > 85%) within the same order, while species from different orders showed notable differences (identity < 80%). The investigation of the Hexacorallia mitogenomes also highlighted that the GC-skew dissimilarity was highly significant at the order level, but not as pronounced at the family level. These results might be attributed to the slow evolution rate of Hexacorallia mitogenomes and provide evidence of mitogenomic diversity. Furthermore, divergence time analysis revealed older divergence times assessed via mitogenomes compared with nuclear data, shedding light on significant evolutionary events shaping distinct orders within Hexacorallia corals. Those findings provide new insights into understanding the slow evolutionary rates of deep-sea corals in all lineages of Hexacorallia using their mitogenomes. Full article

A 70-day feeding experiment was performed to investigate the effects of dietary vitamin E at different addition levels (0, 100, 200, and 400 mg/kg) on the growth, collagen content, antioxidant capacity, and expressions of genes related to the transforming growth factor beta (TGF-β)/Sma- and Mad-related protein (SMAD) signaling pathway in sea cucumbers (Apostichopus japonicus). The results showed that the A. japonicus in the group with 200 mg/kg vitamin E exhibited significantly higher growth rates, hydroxyproline (Hyp) and type III collagen contents, and superoxide dismutase (SOD) activity, as well as the upregulation of genes related to Tenascin, SMAD1, and TGF-β. Additionally, the A. japonicus in the group with 100 mg/kg vitamin E exhibited significantly higher body-wall indexes, denser collagen arrangements, improved texture quality, higher activities of glutathione peroxidase (GSH-Px) and peroxidase (POD), as well as the upregulation of genes related to collagen type I alpha 2 chain (COL1A2), collagen type III alpha 1 chain (COL3A1), and Sp-Smad2/3 (SMAD2/3). In contrast, the A. japonicus in the group with 400 mg/kg vitamin E showed a decrease in the growth rates, reduced Hyp contents, increased type I collagen contents, collagen fiber aggregation and a harder texture, along with the downregulation of genes related to the TGF-β/SMAD signaling pathway. Furthermore, the A. japonicus in the group with 400 mg/kg exhibited oxidative stress, reflected by the lower activities of SOD, GSH-Px, and POD. These results indicated that A. japonicus fed diets with the addition of 100–200 mg/kg vitamin E had improved collagen retention and texture quality by increasing the activities of antioxidant enzymes and the expressions of genes in the TGF-β/SMAD signaling pathway. However, the excessive addition of vitamin E (400 mg/kg) induced oxidative stress, which could increase the collagen degradation and fibrosis and pose a threat to the growth and texture quality of A. japonicus. Full article

Salinity tolerance was studied in chickpea accessions from a germplasm collection and in cultivars from Kazakhstan. After NaCl treatment, significant differences were found between genotypes, which could be arranged into three groups. Those that performed poorest were found in group 1, comprising five ICC accessions with the lowest chlorophyll content, the highest leaf necrosis (LN), Na⁺ accumulation, malondialdehyde (MDA) content, and a low glutathione ratio GSH/GSSG. Two cultivars, Privo-1 and Tassay, representing group 2, were moderate in these traits, while the best performance was for group 3, containing two other cultivars, Krasnokutsky-123 and Looch, which were found to have mostly green plants and an exact opposite pattern of traits. Marker–trait association (MTA) between 6K DArT markers and four traits (LN, Na⁺, MDA, and GSH/GSSG) revealed the presence of four possible candidate genes in the chickpea genome that may be associated with the three groups. One gene, ATP-binding cassette, CaABCC6, was selected, and three haplotypes, A, D1, and D2, were identified in plants from the three groups. Two of the most salt-tolerant cultivars from group 3 were found to have haplotype D2 with a novel identified SNP. RT-qPCR analysis confirmed that this gene was strongly expressed after NaCl treatment in the parental- and breeding-line plants of haplotype D2. Mass spectrometry of seed proteins showed a higher accumulation of glutathione reductase and S-transferase, but not peroxidase, in the D2 haplotype. In conclusion, the CaABCC6 gene was hypothesized to be associated with a better response to oxidative stress via glutathione metabolism, while other candidate genes are likely involved in the control of chlorophyll content and Na⁺ accumulation. Full article

Grafting alters the genetic and anatomical features of plants. Although grafting has been widely applied in plant propagation, the underlying processes that govern the effects of the procedure are not fully understood. Samples were collected to study the long-term influence of grafting on the leaf-shoot morphology, leaf-shoot anatomy, and genetic signature of the grafted plants. Citrulus lanatus (Thunb.) Matsum. & Nakai (cv. Lady) was used as the scion, and Lagenaria siceraria (Molina) Standl (cv. Argentario) as a rootstock. In grafted plants, leaf blades and petioles were 20.92% and 12.82% longer, respectively, while the midrib collenchyma was 35.68% thicker, and the diameter of the vessel member was 11.17% larger than in ungrafted plants. In the stem, grafting affected the arrangement and number of vascular bundles (from 1 to 2 rings). The thickness of the epidermis decreased by 69.79%, and the size of the external fascicular phloem decreased by 23.56%. The diameter of the vessel member of the grafted plants increased by 28.94%. Eight out of ten evaluated primers met the requirements (stability in both watermelons and bottle gourd, tissue-specific). In the genetic tests, we examined whether this change in the gene expression pattern is due to the grafting and, if so, to what extent. Seven out of eight tested Small Auxin Up-Regulated RNA (SAUR) genes were expressed in the ungrafted and grafted C. lanatus lines in four cases; the expression increased by more than 10% after grafting. The morpho-anatomical changes and genetic variation reported in this study for grafted lines of C. lanatus contribute to the understanding of the underlying mechanisms of plant growth observations resulting from grafting. Full article

Poplar coma, the fluff-like appendages of seeds originating from the differentiated surface cells of the placenta and funicle, aids in the long-distance dispersal of seeds in the spring. However, it also poses hazards to human safety and causes pollution in the surrounding environment. Unraveling the regulatory mechanisms governing the initiation and development of coma is essential for addressing this issue comprehensively. In this study, strand-specific RNA-seq was conducted at three distinct stages of coma development, revealing 1888 lncRNAs and 52,810 mRNAs. The expression profiles of lncRNAs and mRNAs during coma development were analyzed. Subsequently, potential target genes of lncRNAs were predicted through co-localization and co-expression analyses. Integrating various types of sequencing data, lncRNA-miRNA-TF regulatory networks related to the initiation of coma were constructed. Utilizing identified differentially expressed genes encoding kinesin and actin, lncRNA-miRNA-mRNA regulatory networks associated with the construction and arrangement of the coma cytoskeleton were established. Additionally, relying on differentially expressed genes encoding cellulose synthase, sucrose synthase, and expansin, lncRNA-miRNA-mRNA regulatory networks related to coma cell wall synthesis and remodeling were developed. This study not only enhances the comprehension of lncRNA but also provides novel insights into the molecular mechanisms governing the initiation and development of poplar coma. Full article

A potential biocontrol agent for American foulbrood (AFB), the Paenibacillus bacteriophage phJNUCC32, was isolated from Baengnokdam in Halla Mountain. This study aimed to investigate its genomic characteristics through whole-genome sequencing. The genome of phJNUCC32 was found to be 62,871 base pairs in length, with a G + C content of 51.98%. Phylogenetic analysis classified phJNUCC32 within the unclassified Caudoviricetes bacteriophage category. The genome prediction confirmed the absence of virulence factors and antibiotic-resistance genes, ensuring its genetic safety. A total of 63 coding DNA sequences were identified, revealing a modular arrangement. Notably, the annotation of gene function indicates that phJNUCC32 harbors the holin/lysin system, suggesting significant potential for controlling bacterial infections in AFB and agriculture. Full article

Rubus includes a group of important plants with medicinal and culinary significance, as well as ornamental value. However, due to its status as one of the largest genera in the Rosaceae family and frequent occurrences of apomixis, hybridization, and polyploidy among its species, the morphological identification of this genus is highly challenging. The plastid genome serves as a valuable tool for studying the evolutionary relationships among plants. Therefore, based on the raw data of the whole genomes from six popular Rubus taxa, the complete Cp genomes were assembled, annotated, and subjected to comparative and phylogenetic analyses. In this research, six newly complete Cp genomes were reported, which all had a representative quadripartite formation, with a similar GC content (37.06%–37.26%), and their size ranged from 155,493 bp to 156,882 bp. They all encode 111 unique genes, containing 79 PCGs, 28 tRNA, and 4 rRNA. The analysis of gene structure of different groups showed that the sequence and content of genes were relatively conservative, and there was no gene rearrangement. Most of their PCGs had a high frequency codon usage bias and all genes were in purifying selection states. A nucleotide variable analysis revealed that the IR areas had less variation than the SC areas, and there was the greatest diversity in the SSC area. Eleven hypervariable areas were identified, containing rpl32-trnL, rpl32, rps16-trnQ, trnT-trnL, trnQ-psbK, trnK-rps16, and rps15-ycf1, which could be used as labels for genetic diversity and taxa identification. The phylogenetic trees of 72 Rosaceae plants were constructed based on ML and BI methods. The results strongly support the theory that the Rubus genus was a monophyletic group and sampled species could be arranged into seven subgenera. Overall, this study sheds its new light into the phylogeny of the Rubus genus, providing valuable insights for future studies of the Cp genomes from the expanded taxa of the Rosaceae family. Full article

The spleen is the largest peripheral immune organ of the organism, accounting for 25% of the total lymphoid tissue of the body. During HS, the spleen is damaged due to the elevated environment, which seriously affects life performance and broilers’ health. This study aimed to investigate the mechanism of chronic HS damage to broiler spleen tissues. The broilers were typically raised until they reached 21 days of age, after which they were arbitrarily allocated into two groups: an HS group and a cntrol group. The HS group was subjected to a temperature of 35 °C for 10 h each day, starting at 21 days of age. At 35 and 42 days of age, spleen and serum samples were obtained from the broilers. The results showed that after HS, a significant decrease in productive performance was observed at 42 days of age (p < 0.01), and the spleen index, and bursa index were significantly decreased (p < 0.01). T-AOC of the organism was significantly decreased (p < 0.05), GSH-PX, SOD, and CAT antioxidant factors were significantly decreased (p < 0.01), and MDA was significantly elevated (p < 0.01). HS also led to a significant increase in cytokines IL-6, TNF-α, and INF-γ and a significant decrease in IL-4 in the spleen. The histopathologic results showed that the spleen’s red-white medulla was poorly demarcated. The cells were sparsely arranged after HS. After HS, the expression of TLRs, MYD88, and NF-κB genes increased significantly. The expression of HSP70 increased significantly, suggesting that HS may induces an inflammatory response in broiler spleens through this signaling pathway, which may cause pathological damage to broiler spleens, leading to a decrease in immune function and progressively aggravating HS-induced damage with the prolongation of HS. Full article

Background: Breast units (BUs) provide breast cancer (BC) care, including prevention, treatment, and genetic assessment. Genetic research has highlighted BRCA1/2 mutations as key hereditary BC risk factors. BRCA testing is crucial for personalized treatment and prevention strategies. However, the integration of BRCA testing in Italian BUs faces multiple challenges. This study, by Senonetwork Italia, aimed to evaluate genetic testing practices and identify obstacles within Italian BUs. Methods: Senonetwork Italia conducted a 16-question web-based survey involving 153 BUs. The survey assessed aspects of BRCA testing, including timing, urgency, counseling, patient selection, and multi-gene panels. Results: Of the 153 BUs, 109 (71.2%) responded. Testing before surgery was performed by 70.6% of centers, with urgent cases acknowledged by 87.2%. Most centers (56.0%) arranged urgent pre-test counseling within a week. BRCA mutation status influenced treatment decisions in 99.1% of cases. Multi-gene panels were used by 33.0% of centers for all genetic counseling cases, while 56.0% followed standard referral criteria. The main challenges included cost, reimbursement, and reporting timelines. Conclusions: This survey highlights significant variations in BRCA testing practices across Italian BUs and identifies key logistical and financial challenges. There is a need for standardized practices of genetic testing to ensure personalized and effective BC management in Italy. Full article

RNC1, a plant-specific gene, is known for its involvement in splicing group II introns within maize chloroplast. However, its role in chloroplast development and global gene expression remains poorly understood. This study aimed to investigate the role of RNC1 in chloroplast development and identify the genes that mediate its function in the development of entire tomato plants. Consistent with findings in maize, RNC1 silencing induced dwarfism and leaf whitening in tomato plants. Subcellular localization analysis revealed that the RNC1 protein is localized to both the nucleus and cytoplasm, including the stress granule and chloroplasts. Electron microscopic examination of tomato leaf transverse sections exposed significant disruptions in the spatial arrangement of the thylakoid network upon RNC1 silencing, crucial for efficient light energy capture and conversion into chemical energy. Transcriptome analysis suggested that RNC1 silencing potentially impacts tomato plant development through genes associated with all three categories (biological processes, cellular components, and molecular functions). Overall, our findings contribute to a better understanding of the critical role of RNC1 in chloroplast development and its significance in plant physiology. Full article

Zygotic genome activation (ZGA) is a pivotal event in mammalian embryogenesis, marking the transition from maternal to zygotic control of development. During the ZGA process that is characterized by the intricate cascade of gene expression, who tipped the first domino in a meticulously arranged sequence is a subject of paramount interest. Recently, Dux, Obox and Nr5a2 were identified as pioneer transcription factors that reside at the top of transcriptional hierarchy. Through co-option of retrotransposon elements as hubs for transcriptional activation, these pioneer transcription factors rewire the gene regulatory network, thus initiating ZGA. In this review, we provide a snapshot of the mechanisms underlying the functions of these pioneer transcription factors. We propose that ZGA is the starting point where the embryo’s own genome begins to influence development trajectory, therefore in-depth dissecting the functions of pioneer transcription factors during ZGA will form a cornerstone of our understanding for early embryonic development, which will pave the way for advancing our grasp of mammalian developmental biology and optimizing in vitro production (IVP) techniques. Full article

5S ribosomal DNAs (rDNAs) are arranged in tandem and are often under-represented in genome assemblies. In the present study, we performed a global and in-depth analysis of the 5S rDNAs in the model insect Tribolium castaneum and its closely related species Tribolium freemani. To accomplish this goal, we used our recently published genome assemblies based on Nanopore and PacBio long-read sequencing. Although these closely related species share the 5S rRNA gene sequence with high homology, they show a different organization of the 5S rDNA locus. Analysis of 5S rDNA arrays in T. castaneum revealed a typical tandemly repeated organization characterized by repeat units consisting of the 121 bp long 5S rRNA gene and the 71 bp long nontranscribed spacer (NTS). In contrast, T. freemani showed a much more complex organization of 5S rDNA arrays characterized by two patterns. The first is based on the association of 5S rRNA gene with arrays of a satellite DNA, representing the NTS sequence of the 5S rDNA genes in T. freemani. The second, more complex type is characterized by a somewhat less frequent occurrence of the 5S rRNA gene and its association with longer satellite DNA arrays that are regularly interrupted by Jockey-like retrotransposons. This organization, in which the ribosomal gene is associated with two completely different repetitive elements such as satellite DNAs and retrotransposons, suggests that the 5S rRNA gene, regardless of its crucial function in the genome, could be a subject of extremely dynamic genomic rearrangements. Full article

Mealy peaches are dry and flavorless, which reduces their consumer acceptance. A deeper understanding of the mechanism underlying mealiness is crucial to enhancing peach fruit quality. In this study, comparative profiling was conducted on CP13, CP14, CM, and RM peaches. Sensory evaluation indicated that CP13 and CM are non-mealy clingstone and freestone peaches, respectively, and CP14 and RM are mealy freestone peaches. Both CP13 and CP14, identified as stony hard (SH) peaches, exhibited minimal ethylene release, whereas CM and RM, identified as melting flesh (MF) peaches, released high amounts of ethylene during the ripening process. Scanning electron microscopy (SEM) microstructure observation indicated that cells in the flesh tissue of mealy peaches, CP14 (SH) and RM (MF), were intact and separated, with large intercellular spaces and irregular arrangements. The main factor that promotes mealiness is differences in pectin metabolism, which impact cell wall composition. The fluctuations in polygalacturonase (PG) and pectin methylesterase (PME) activity between mealy and non-mealy peaches were the main factor contributing to mealiness. However, the changes in cell wall metabolism that caused these fluctuations did not have a clear direction. Using transcriptome analysis and weighted gene co-expression network analysis (WGCNA), we were able to identify forty differentially expressed genes (DEGs) that are associated with mealy patterns. Among these DEGs, genes encoding PG were significantly upregulated in mealy peaches (CP14 and RM) compared to non-mealy peaches (CP13 and CM). PpPG1 was the main effector gene for mealiness, while PpPG2, PpEGase2, PpEXP1, PpEXP3, PpAGP2, PpIAA4, and PpABA2 were identified as candidate genes regulating peach mealiness. These findings provide a solid experimental basis for understanding the textual distinctions between mealy and non-mealy peaches. Full article

In this in vivo study on hairless mice, we examined the effects of light-emitting diode (LED) treatment applied prior to ultraviolet B (UVB) irradiation. We found that pre-treating with LED improved skin morphological and histopathological conditions compared to those only exposed to UVB irradiation. In our study, histological evaluation of collagen and elastic fibers after LED treatment prior to UVB irradiation showed that this pretreatment significantly enhanced the quality of fibers, which were otherwise poor in density and irregularly arranged due to UV exposure alone. This suggests that LED treatment promotes collagen and elastin production, leading to improved skin properties. Additionally, we observed an increase in Claudin-1 expression and a reduction in nuclear factor-erythroid 2-related factor 2 (Nrf-2) and heme-oxygenase 1 (HO-1) expression within the LED-treated skin tissues, suggesting that LED therapy may modulate key skin barrier proteins and oxidative stress markers. These results demonstrate that pretreatment with LED light can enhance the skin’s resistance to UVB-induced damage by modulating gene regulation associated with skin protection. Further investigations are needed to explore the broader biological effects of LED therapy on other tissues such as blood vessels. This study underscores the potential of LED therapy as a non-invasive approach to enhance skin repair and counteract the effects of photoaging caused by UV exposure. Full article