Chromosomal Distribution Research Articles

Varied chromosome distribution behaviours during meiosis in triploid Chinese chives contribute to the formation of viable pollen.

Triploids play an important role in the polyploidization process and are considered a bridge between diploids and polyploids. To inform plant polyploidization research and polyploid breeding, it is important to explore chromosome behaviour during triploid pollen development, pollen fertility problems in triploids and the potential value of utilizing triploids. In this study, acetocarmine, carbol fuchsin and fluorescence staining methods were used to observe microsporogenesis and microspore development in fertile triploid Chinese chives. The results revealed that some of the pollen mother cells were able to undergo equal chromosome distributions (approximately 36%), whereas other pollen mother cells formed lagging chromosomes, chromosome bridges, micronuclei and early cytoplasmic divisions during microsporogenesis, resulting in microspores of different sizes. Regardless of whether an equal tetrad or an abnormal polyad was formed, microspores were released from callose in a normal manner and contained nuclei. During the process of microspore development, most of the microspore nuclei disappeared gradually and ultimately formed empty pollen cells that lacked nuclei. During the meiosis of pollen mother cells in triploid Chinese chives, a variety of chromosome distribution behaviours contribute to the formation of some viable pollen.

Genome-wide characterization of the sunflower kinome: classification, evolutionary analysis and expression patterns under different stresses

Protein kinases play a significant role in plant responses to biotic and abiotic stresses, as well as in growth and development. While the kinome has been extensively investigated in crops such as Arabidopsis thaliana, soybean, common bean, and cotton, studies on protein kinases in sunflower remain limited. Our objective is to explore protein kinases in sunflower to bridge the research gap and enhance the understanding of their functions. We identified a total of 2,583 protein kinases from sunflower, which were classified into 22 families and 121 subfamilies. By comparing the subfamily members between sunflower and other species, we found that three subfamilies in sunflower—RLK-Pelle_CrRLK1L-1, RLK-Pelle_SD-2b, and RLK-Pelle_WAK—had undergone significant expansion. We then investigated the chromosomal distribution, molecular weight, isoelectric point, transmembrane domain, signal peptide, and structural and evolutionary diversity of the protein kinases. Through these studies, we have obtained a basic understanding of protein kinases in sunflower. To investigate the role of protein kinases in sunflower’s response to biotic and abiotic stresses, we obtained 534 transcriptome datasets from various research groups, covering eight types of abiotic stress and two types of biotic stress. For the first time, we overcame the batch effects in the data and utilized a gene scoring system developed by our lab to perform a comprehensive analysis of multiple transcriptome datasets from different research groups. Ultimately, 73 key protein kinases were identified from numerous candidates, and functional annotation revealed that they are key members of signaling pathways such as ABA, MAPK, and SOS, actively participating in sunflower’s response to biotic and abiotic stresses. In summary, through the exploration of protein kinases in sunflower, we have filled the gap in protein kinase research and provided a substantial amount of foundational data. By using the new scoring method to eliminate batch effects between transcriptome datasets, we achieved the first comprehensive analysis of large-scale transcriptome data. This method allows for a more thorough and detailed identification of key protein kinases that are widely regulated under various stress conditions, providing numerous candidate genes for sunflower stress resistance research.

Global identification of metal ion transporters in chickpea and delineating the role of CaYSL4 in orchestrating iron content

Metal ion transporters (MITs) are vital to maintain proper metal homeostasis during growth and development of plants thereby necessitating their identification and characterization. Considering the economic importance of chickpea in human nutrition, the molecular behaviour and biological functions of the metal ion transporters (MIT) encoding gene families remains highly relevant in recent times. Global identification of MITs revealed a total of 12 CAXs, 6 CTRs, 11 MGTs, 15 MTPs, 9 NRAMPs, 16 OPTs, and 14 ZIPs responsible for metal ion transport. Assessment of phylogenetic relationships, chromosomal distribution, gene structure and motif analysis of MITs suggested their diverse functions. The yellow stripe-like (YSL) family of transporters is an important family whose members have been suggested to have a role in metal ion translocation and assimilation. Expression analysis of key YSLs including CaYSL1, CaYSL4, CaYSL6 and CaYSL16 indicated their significant involvement in conferring tolerance to Fe starvation. Notable was the expression of CaYSL4 that showed specific expression in flower, leaf, shoot, seed at 30 DAA and 40DAA after 7 and 10 day of Fe-deficiency treatment. It was found to be localized in the plasma membrane. RNAi-mediated silencing of CaYSL4 demonstrated its critical role in orchestrating Fe, Zn, Cu and Mn translocation in chickpea seeds. Collectively, the comprehensive analysis of MITs coupled with the functional role of CaYSL4 provides critical insight into the complex regulation of Fe ion transport and distribution that will enable breeding of nutritionally enhanced chickpea varieties.

Genome-Wide Identification of GATA Family Genes in Potato and Characterization of StGATA12 in Response to Salinity and Osmotic Stress.

GATA factors are evolutionarily conserved transcription regulators that are implicated in the regulation of physiological changes under abiotic stress. Unfortunately, there are few studies investigating the potential role of GATA genes in potato plants responding to salt and osmotic stresses. The physicochemical properties, chromosomal distribution, gene duplication, evolutionary relationships and classification, conserved motifs, gene structure, interspecific collinearity relationship, and cis-regulatory elements were analyzed. Potato plants were treated with NaCl and PEG to induce salinity and osmotic stress responses. qRT-PCR was carried out to characterize the expression pattern of StGATA family genes in potato plants subjected to salinity and osmotic stress. StGATA12 loss-of-function and gain-of-function plants were established. Morphological phenotypes and growth were indicated. Photosynthetic gas exchange was suggested by the net photosynthetic rate, transpiration rate, and stomatal conductance. Physiological indicators and the corresponding genes were indicated by enzyme activity and mRNA expression of genes encoding CAT, SOD, POD, and P5CS, and contents of H2O2, MDA, and proline. The expression patterns of StGATA family genes were altered in response to salinity and osmotic stress. StGATA12 protein is located in the nucleus. StGATA12 is involved in the regulation of potato plant growth in response to salinity and osmotic stress. Overexpression of StGATA12 promoted photosynthesis, transpiration, and stomatal conductance under salinity and osmotic stress. StGATA12 overexpression induced biochemical responses of potato plants to salinity and osmotic stress by regulating the levels of H2O2, MDA, and proline and the activity of CAT, SOD, and POD. StGATA12 overexpression induced the up-regulation of StCAT, StSOD, StPOD, and StP5CS against salinity and osmotic stress. StGATA12 could reinforce the ability of potato plants to resist salinity and osmosis-induced damages, which may provide an effective strategy to engineer potato plants for better adaptability to adverse salinity and osmotic conditions.

Clinal variation in autosomal satellite DNA clusters across a contact zone in Barker Frogs.

Contact zones between genetically divergent lineages offer a unique opportunity to explore gene flow and speciation dynamics. Because satellite DNAs (satDNAs) have high evolutionary rates, they may be useful for comparing related taxa and assessing contact zones. Here, we analyzed the distribution of chromosomal clusters of PcP190 satDNA across a contact zone between two distinct genetic lineages of a Neotropical species complex of frogs. The parental lineages, Physalaemus ephippifer and lineage 1B (L1B), exhibited pronounced divergence in the number of PcP190 clusters. We further expanded the geographic scope of this species complex by including two additional Brazilian localities in previously available cytogenetic and mitochondrial DNA datasets. The contact zone exhibited remarkable variation in the chromosomal distribution of PcP190 clusters among the autosomes; the only fixed autosomal site was found on chromosome 3. The highest numbers of PcP190 clusters were observed in specimens collected at sites near (approximately 320 km from) the distribution of L1B, whereas specimens from Dom Eliseu, which is near (approximately 330 km from) the distribution of P. ephippifer, had the lowest numbers of such clusters. Mitochondrial haplotypes also exhibited geographical variation across sites. Our findings expand the known contact zone of these Physalaemus lineages from 1,500 km2 to over 6,200 km2, demonstrating its extensive area, and emphasize the usefulness of satDNAs in studying contact zones.

Genome-Wide Analysis of the Multidrug and Toxic Compound Extrusion Gene Family in the Tea Plant

The multidrug and toxic compound extrusion (MATE) family is the latest class of novel secondary transporters discovered in plants. However, there is currently no comprehensive analysis of the MATE gene family in the tea plant. In this study, 68 CsMATE genes were identified from the tea plant genome using bioinformatic methods. In general, we analyzed the evolutionary relationships, intron–exon structure, distribution in chromosomes, conserved domains, and gene expression patterns in different tissues and stresses of the CsMATE gene family. The 68 CsMATEs were phylogenetically divided into four major clusters (Class I to Class IV). The CsMATE genes within the same class exhibit similar structural features, while displaying certain distinctions across different classes. Evolutionary analysis indicated that the CsMATE gene family expanded mainly through gene duplication events, in addition to proximal duplication. Through the analysis of cis-acting elements, it was found that CsMATE genes may be involved in the growth, development, and stress response. Furthermore, we observed that certain CsMATE genes could be induced to exhibit expression under abiotic stress conditions such as low temperature, high salinity (NaCl), osmotic stress (PEG), and methyl jasmonate treatment (MeJA). The findings presented herein offer a crucial theoretical foundation for elucidating the biological functions of CsMATE genes, particularly in response to abiotic stress, and furnish valuable potential genetic resources for tea plant resistance breeding.

Repeatome Analysis and Satellite DNA Chromosome Patterns in Hedysarum Species.

The cosmopolitan genus Hedysarum L. (Fabaceae) is divided into sections Hedysarum, Stracheya, and Multicaulia. This genus includes many valuable medicinal, melliferous, and forage species. The species taxonomy and genome relationships within the sections are still unclear. We examined intra- and interspecific diversity in the section (sect.) Hedysarum based on repeatome analyses using NGS data, bioinformatic technologies, and chromosome FISH mapping of 35S rDNA, 5S rDNA, and the identified satellite DNA families (satDNAs). A comparison of repeatomes of H. alpinum, H. theinum, and H. flavescens revealed differences in their composition. However, similarity in sequences of most satDNAs indicated a close relationship between genomes within sect. Hedysarum. New effective satDNA chromosomal markers were detected, which is important for karyotype analyses within Hedysarum. Intra- and interspecific variability in the chromosomal distribution patterns of the studied markers were revealed, and species karyograms were constructed. These results provided new insight into the karyotype structures and genomic diversity within sect. Hedysarum, clarified the systematic position of H. sachalinense and H. arcticum, and confirmed the distant genomic relationships between species from sections Hedysarum and Multicaulia. Our findings are important for further comparative genome studies within the genus Hedysarum.

Comprehensive genome-wide characterization of the MIKC-type MADS-box family members and the dynamic expression profiling throughout the development of floral buds in Populus tomentosa

Poplar is a major silvicultural tree species for industrial production, with versatile applications in construction, furniture, pulp and biofuel. The phenotypic appearance of male or female floral buds in poplar trees, exhibits a strikingly similar morphology at corresponding developmental stages. However, there are significant differences in internal anatomical structures. The MIKC-type MADS-box transcription factor family plays an indispensable role in regulating the development of floral organs and increasing vegetative biomass, and it is also of great significance in elucidation of the aforementioned morphological differences. This study systematically analyzed the MIKC-type MADS-box transcription factor family in Populus tomentosa. A total of 100 MIKC-type MADS-box genes were identified, which were divided into 14 subfamilies. We examined the physicochemical properties, gene structure, conserved motifs, chromosome distribution, collinearity, promoter cis-acting elements, gene expression profiles, and protein-protein interaction network of these 100 MIKC-type MADS-box members. Excitingly, four clusters of PtMADS members exhibited a high level of abundant expression in the initial and mature floral buds of both male and female, suggesting critical significance in tuning the morphogenesis and development of floral organs, as well as in the modulation of reproductive fitness. The protein-protein interaction network diagram corroborated these findings, substantiating the speculated roles of these genes. Our findings lay a foundational framework for future functional explorations and potential applications of MIKC-type MADS-box genes in this industry tree species.

Identification and Expression Analysis of TCP Transcription Factors Under Abiotic Stress in Phoebe bournei.

The TCP gene family encodes plant transcription factors crucial for regulating growth and development. While TCP genes have been identified in various species, they have not been studied in Phoebe bournei (Hemsl.). This study identified 29 TCP genes in the P. bournei genome, categorizing them into Class I (PCF) and Class II (CYC/TB1 and CIN). We conducted analyses on the PbTCP gene at both the protein level (physicochemical properties) and the gene sequence level (subcellular localization, chromosomal distribution, phylogenetic relationships, conserved motifs, and gene structure). Most P. bournei TCP genes are localized in the nucleus, except PbTCP9 in the mitochondria and PbTCP8 in both the chloroplast and nucleus. Chromosomal mapping showed 29 TCP genes unevenly distributed across 10 chromosomes, except chromosome 8 and 9. We also analyzed the promoter cis-regulatory elements, which are mainly involved in plant growth and development and hormone responses. Notably, most PbTCP transcription factors respond highly to light. Further analysis revealed three subfamily genes expressed in five P. bournei tissues: leaves, root bark, root xylem, stem xylem, and stem bark, with predominant PCF genes. Using qRT-PCR, we examined six representative genes-PbTCP16, PbTCP23, PbTCP7, PbTCP29, PbTCP14, and PbTCP15-under stress conditions such as high temperature, drought, light exposure, and dark. PbTCP14 and PbTCP15 showed significantly higher expression under heat, drought, light and dark stress. We hypothesize that TCP transcription factors play a key role in growth under varying light conditions, possibly mediated by auxin hormones. This work provides insights into the TCP gene family's functional characteristics and stress resistance regulation in P. bournei.

Identifying Calmodulin and Calmodulin-like Protein Members in Canavalia rosea and Exploring Their Potential Roles in Abiotic Stress Tolerance.

Calmodulins (CaMs) and calmodulin-like proteins (CMLs) belong to families of calcium-sensors that act as calcium ion (Ca2+) signal-decoding proteins and regulate downstream target proteins. As a tropical halophyte, Canavalia rosea shows great resistance to multiple abiotic stresses, including high salinity/alkalinity, extreme drought, heat, and intense sunlight. However, investigations of calcium ion signal transduction involved in the stress responses of C. rosea are limited. The CaM and CML gene families have been identified and characterized in many other plant species. Nevertheless, there is limited available information about these genes in C. rosea. In this study, a bioinformatic analysis, including the gene structures, conserved protein domains, phylogenetic relationships, chromosome distribution, and gene synteny, was comprehensively performed to identify and characterize CrCaMs and CrCMLs. A spatio-temporal expression assay in different organs and environmental conditions was then conducted using the RNA sequencing technique. Additionally, several CrCaM and CrCML members were then cloned and functionally characterized using the yeast heterogeneous expression system, and some of them were found to change the tolerance of yeast to heat, salt, alkalinity, and high osmotic stresses. The results of this study provide a foundation for understanding the possible roles of the CrCaM and CrCML genes, especially for halophyte C. rosea's natural ecological adaptability for its native habitats. This study also provides a theoretical basis for further study of the physiological and biochemical functions of plant CaMs and CMLs that are involved in tolerance to multiple abiotic stresses.

Comparative satellite DNA mapping in species of the genus Prochilodus (Teleostei, Characiformes) and its evolutionary implications.

Satellite DNA (satDNA) sequences are dynamic components of the eukaryotic genome, that can play significant roles in species diversification. The Prochilodontidae family, which includes 21 Neotropical fish species, is characterized by a conserved karyotype of 2n = 54 biarmed chromosomes, with variation in some species and populations regarding the presence or absence of B chromosomes. This study aimed to investigate whether the chromosomal distribution of specific satDNA sequences is conserved among three Prochilodus species (P. lineatus, P. costatus, and P. argenteus) regarding organization and number of loci, and to compare their genomes using comparative genomic hybridization (CGH). Our results demonstrated that most satDNA sequences share a similar distribution pattern across the three species, and CGH analysis corroborated that their karyotypes are very similar in terms of repetitive DNA distribution. We also identified a potential CENP-B box sequence within PliSat01, a satDNA located in the pericentromeric region of all analyzed species. In contrast, PliSat04 and PliSat14 displayed differential locations and variations in the number of loci per genome, underscoring the dynamic nature of repetitive sequences even in species with otherwise highly conserved genomes. These findings represent the first evidence of karyotype diversification in Prochilodus, highlighting the evolutionary dynamism of satDNA sequences.

Identification of AP2/ERF Transcription Factors and Characterization of AP2/ERF Genes Related to Low-Temperature Stress Response and Fruit Development in Luffa

Plant-specific APETALA2/Ethylene-Responsive Factor (AP2/ERF) transcription factors are involved in the regulation of genes associated with the growth and developmental processes of numerous plants. Although AP2/ERF proteins from other species have been intensively studied, no studies have been reported on the AP2/ERF family of Luffa cylindrica, an important vegetable of the cucurbit family, and one of the most popular vegetables in the world. In this study, 133 genes (315–6696 bp) encoding LcAP2/ERF proteins with complete AP2/ERF domains were identified according to the luffa P93075 genome. These LcAP2/ERF genes were subsequently classified and analyzed for their gene structures, chromosomal distribution locations, promoter cis-acting elements, conserved structural domains of encoded proteins, and responses to abiotic stresses. The LcAP2/ERF genes were identified and divided into five phylogenetic groups (AP2, DREBs, ERFs, RAV, and soloists). These genes were unevenly distributed across 13 chromosomes. An analysis of gene structures indicated the LcAP2/ERF genes contained 0–11 introns (average of 4.4). Additionally, 16 motifs were identified in the LcAP2/ERF proteins that were conserved across different phylogenetic groups. Moreover, 11 cis-acting elements associated with response to the environment were analyzed in a 2000 bp region upstream of the LcAP2/ERF gene promoters. A transcriptome analysis involving RNA-seq data revealed tissue-specific LcAP2/ERF expression profiles and the diversity in LcAP2/ERF expression. The effects of low-temperature stress on LcAP2/ERF expression were determined. Furthermore, fruit-development-related and low-temperature-induced expressional changes were verified by RT-qPCR analyses of 14 differentially expressed LcAP2/ERF genes in luffa. Our findings will help clarify the evolution of the luffa AP2/ERF family, while also providing valuable insights for future studies on AP2/ERF functions.

Frequencies of house fly proto-Y chromosomes across populations are predicted by temperature heterogeneity within populations.

Sex chromosomes often differ between closely related species and can even be polymorphic within populations. Species with multifactorial sex determination segregate for multiple different sex determining loci within populations, making them uniquely informative of the selection pressures that drive the evolution of sex chromosomes. The house fly (Musca domestica) is a model species for studying multifactorial sex determination because male determining genes have been identified on all six of the chromosomes, which means that any chromosome can be a "proto-Y". Natural populations of house fly also segregate for a recently derived female-determining locus, meaning house flies also have a proto-W chromosome. The different proto-Y chromosomes are distributed along latitudinal clines on multiple continents, their distributions can be explained by seasonality in temperature, and they have temperature-dependent effects on physiological and behavioral traits. It is not clear, however, how the clinal distributions interact with the effect of seasonality on the frequencies of house fly proto-Y and proto-W chromosomes across populations. To address this question, we measured the frequencies of house fly proto-Y and proto-W chromosomes across nine populations in the United States of America. We confirmed the clinal distribution along the eastern coast of North America, but it is limited to the eastern coast. In contrast, annual mean daily temperature range predicts proto-Y chromosome frequencies across the entire continent. Our results therefore suggest that temperature heterogeneity can explain the distributions of house fly proto-Y chromosomes in a way that does not depend on the cline.

Genome-Wide Identification and Expression Analysis of SNAP Gene Family in Wheat

Background/Objectives: The SNAP gene family is a class of proteins containing a SNAP domain, which plays a crucial role in the growth and development of plants. Methods: Bioinformatics methods were used to systematically analyze the gene structure, phylogenetic evolution, chromosomal distribution, physicochemical properties, conserved motifs, and cis-acting elements of the TaSNAP family members. Results: The TaSNAP family comprises members that encode proteins ranging between 120 and 276 amino acids, with isoelectric points spanning from 4.87 to 7.92. Phylogenetic analysis elucidated the categorization of the eight TaSNAP into three distinct subfamilies, wherein members of the same subfamily display marked similarities in their gene structures. Chromosomal mapping revealed the distribution of TaSNAP family members across chromosomes 2A, 2B, 2D, 7A, 7B, and 7D. Utilizing the Plant CARE tool, we identified ten elements linked to plant hormones and four associated with stress responses. Expression analysis via qRT-PCR was performed to assess the levels of the eight TaSNAP genes in various tissues and under diverse abiotic stress conditions. The results indicated heightened expression of most genes in roots compared to spikes. Notably, under ABA stress, the majority of genes exhibited upregulation, whereas certain genes were downregulated under PEG stress, implying a substantial role for SNAP protein in wheat growth and development. Conclusions: This study conducted a comprehensive bioinformatics analysis of each member of the wheat SNAP family, laying a crucial foundation for future functional investigations.

Genome-wide identification and expression analysis of SlKFB gene family (Solanum lycopersicum) and the molecular mechanism of SlKFB16 and SlKFB34 under drought

Environmental stress significantly affects plant growth and productivity. The effects of drought stress on plants are reflected primarily in enzyme activity, membrane systems, and cell-water loss. Here, the Kelch repeat F-box (KFB) protein family in tomato was systematically identified and analysed. Using bioinformatics, we identified 37 SlKFB family members in the tomato genome and analysed their protein structure, phylogenetic relationships, chromosome distribution, and expression under drought or biotic-stress conditions. Transcriptome data revealed that SlKFB members exhibit differential responses to drought stress, with significant differences in SlKFB16 and SlKFB34 expression. Functional analysis revealed that SlKFB16 functions in the cytoplasm and SlKFB34 in the nucleus and cytoplasm. Under drought stress, SlKFB16 and SlKFB34-silencing significantly reduced reactive oxygen species scavenging and resistance to drought stress. These findings provide a reference for further studies of the mechanisms of SlKFB16 and SlKFB34 in drought stress in tomato as well as a foundation for enhancing their resistance to drought stress.

Identification of WRKY transcription factors in Rosa chinensis and analysis of their expression response to alkali stress response

Breeding abiotic stress-tolerant varieties of Rosa chinensis is a paramount goal in horticulture. WRKY transcription factors, pivotal in plant responses to diverse stressors, offer potential targets for enhancing stress resilience in R. chinensis. Using bioinformatics and genomic data, we identified RcWRKY transcription factor genes, characterised their chromosomal distribution, phylogenetic relationships, structural attributes, collinearity, and expression patterns in response to saline stress. Leveraging bidirectional database searches, we pinpointed 66 RcWRKY genes, categorised into three groups. All except RcWRKY60 encoded DNA Binding Domain and Zinc Finger Motif regions of the WRKY domain. Expansion of the RcWRKY gene family was propelled by 19 segmental, and 2 tandem, duplications. We unveiled 41 and 15 RcWRKY genes corresponding to 50 AtWRKY and 17 OsWRKY orthologs respectively, indicating postdivergence expansion. Expression analyses under alkaline stress pinpointed significant alterations in 54 RcWRKY genes. Integration of functional roles from their Arabidopsis orthologs and cis-acting elements within their promoters, along with quantitative reverse transcription PCR validation, underscored the importance of RcWRKY27 and 29 in R. chinensis’ alkaline stress response. These findings offer insights into the biological roles of RcWRKY transcription factors, as well as the regulatory dynamics governing R. chinensis’ growth, development, and stress resilience.

Extrachromosomal circular DNAs in prostate adenocarcinoma: global characterizations and a novel prediction model.

The role of focal amplifications and extrachromosomal circular DNA (eccDNA) is still uncertain in prostate adenocarcinoma (PRAD). Here, we first mapped the global characterizations of eccDNA and then investigate the characterization of eccDNA-amplified key differentially expressed encoded genes (eKDEGs) in the progression, immune response and immunotherapy of PRAD. Circular_seq was used in conjunction with the TCGA-PRAD transcriptome dataset to sequence, annotate, and filter for eccDNA-amplified differentially expressed coding genes (eDEGs) in PRAD and para-cancerous normal prostate tissues. Afterwards, risk models were created and eKDEGs linked to the PRAD prognosis were identified using Cox and Lasso regression analysis. The immune microenvironment of the risk model was quantified using a variety of immunological algorithms, which also identified its characteristics with regard to immunotherapy, immune response, and immune infiltration. In this research, there was no significant difference in the size, type, and chromosomal distribution of eccDNA in PRAD and para-cancerous normal prostate tissues. However, 4,290 differentially expressed eccDNAs were identified and 1,981 coding genes were amplified. Following that, 499 eDEGs were tested in conjunction with the transcriptome dataset from TCGA-PRAD. By using Cox and Lasso regression techniques, ZNF330 and PITPNM3 were identified as eKDEGs of PRAD, and a new PRAD risk model was conducted based on this. Survival analysis showed that the high-risk group of this model was associated with poor prognosis and validated in external data. Immune infiltration analysis showed that the model risks affected immune cell infiltration in PRAD, not only mediating changes in immune cell function, but also correlating with immunophenotyping. Furthermore, the high-risk group was negatively associated with anti-CTLA-4/anti-PD-1 response and mutational burden. In addition, Tumor Immune Dysfunction and Exclusion analyses showed that high-risk group was more prone to immune escape. Drug sensitivity analyses identified 10 drugs, which were instructive for PRAD treatment. ZNF330 and PITPNM are the eKDEGs for PRAD, which can be used as potential new prognostic markers. The two-factor combined risk model can effectively assess the survival and prognosis of PRAD patients, but also can predict the different responses of immunotherapy to PRAD patients, which may provide new ideas for PRAD immunotherapy.

Distinct patterns of satDNA distribution in holocentric chromosomes of spike-sedges (Eleocharis, Cyperaceae).

Eleocharis R. Br. (Cyperaceae) species are known for having holocentric chromosomes, which enable rapid karyotype differentiation. High intra- and interspecific variations in chromosome numbers and genome sizes are documented for different Eleocharis species, frequently accompanied by fluctuations in the repetitive DNA fraction. However, a lack of detailed analysis has hampered a better understanding of the interplay between holocentricity and repetitive DNA evolution in this genus. In our study, we confirmed the holocentricity of Eleocharis chromosomes by immunostaining against the kinetochore protein KNL1 and the cell-cycle dependent posttranslational modifications histone H2AThr121ph and H3S10ph. We further studied the composition and chromosomal distribution of the main satellite DNA repeats found in the newly sequenced species Eleocharis maculosa, Eleocharis geniculata, Eleocharis parodii, Eleocharis elegans, and Eleocharis montana. Five of the six satellites discovered were arranged in clusters, while EmaSAT14 was distributed irregularly along the chromatid length in a line-like manner. EmaSAT14 monomers were present in a few copies in few species across the Eleocharis phylogenetic tree. Nonetheless, they were accumulated within a restricted group of Maculosae series, subgenus Eleocharis. The data indicates that the amplification and line-like distribution of EmaSAT14 along chromatids may have occurred recently within a section of the genus.

Genome-wide identification and expression analysis of the SPL gene family and its response to abiotic stress in barley (Hordeum vulgare L.)

BackgroundSquamosa promoter-binding protein-like (SPL) is a plant-specific transcription factor that is widely involved in the regulation of plant growth and development, including flower and grain development, stress responses, and secondary metabolite synthesis. However, this gene family has not been comprehensively evaluated in barley, the most adaptable cereal crop with a high nutritional value.ResultsIn this study, a total of 15 HvSPL genes were identified based on the Hordeum vulgare genome. These genes were named HvSPL1 to HvSPL15 based on the chromosomal distribution of the HvSPL genes and were divided into seven groups (I, II, III, V, VI, VII, and VIII) based on the phylogenetic tree analysis. Chromosomal localization revealed one pair of tandem duplicated genes and one pair of segmental duplicated genes. The HvSPL genes exhibited the highest collinearity with the monocotyledonous plant, Zea mays (27 pairs), followed by Oryza sativa (18 pairs), Sorghum bicolor (16 pairs), and Arabidopsis thaliana (3 pairs), and the fewest homologous genes with Solanum lycopersicum (1 pair). The distribution of the HvSPL genes in the evolutionary tree was relatively scattered, and HvSPL proteins tended to cluster with SPL proteins from Z. mays and O. sativa, indicating a close relationship between HvSPL and SPL proteins from monocotyledonous plants. Finally, the spatial and temporal expression patterns of the 14 HvSPL genes from different subfamilies were determined using quantitative real-time polymerase chain reaction (qRT-PCR). Based on the results, the HvSPL gene family exhibited tissue-specific expression and played a regulatory role in grain development and abiotic stress. HvSPL genes are highly expressed in various tissues during seed development. The expression levels of HvSPL genes under the six abiotic stress conditions indicated that many genes responded to stress, especially HvSPL8, which exhibited high expression under multiple stress conditions, thereby warranting further attention.ConclusionIn this study, 15 SPL gene family members were identified in the genome of Hordeum vulgare, and the phylogenetic relationships, gene structure, replication events, gene expression, and potential roles of these genes in millet development were studied. Our findings lay the foundation for exploring the HvSPL genes and performing molecular breeding of barley.

Identification of autophagy gene family in potato and the role of StATG8a in salt and drought stress.

Autophagy is a highly conserved method of recycling cytoplasm components in eukaryotes. It plays an important role in plant growth and development, as well as in response to biotic and abiotic stresses. Although autophagy-related genes (ATGs) have been identified in several crop species, their particular role in potato (Solanum tuberosum L.) remains unclear. Several transcription factors and signaling genes in the transgenic lines of the model plant Arabidopsis thaliana, such as AtTSPO, AtBES1, AtPIP2;7, AtCOST1 as well as AtATI1/2, ATG8f, GFP-ATG8F-HA, AtDSK2, AtNBR1, AtHKT1 play crucial functions under drought and salt stresses, respectively. In this study, a total of 29 putative StATGs from 15 different ATG subfamilies in the potato genome were identified. Their physicochemical properties, evolutionary connections, chromosomal distribution, gene duplication, protein-protein interaction network, conserved motifs, gene structure, interspecific collinearity relationship, and cis-regulatory elements were analyzed. The results of qRT-PCR detection of StATG expression showed that 29 StATGs were differentially expressed in potato's leaves, flowers, petiole, stem, stolon, tuber, and root. StATGs were dynamically modulated by salt and drought stresses and up-regulated under salt and drought conditions. Our results showed that the StATG8a localized in the cytoplasm and the nucleus. Potato cultivar "Atlantic" overexpressing or downregulating StATG8a were constructed. Based on physiological, biochemical, and photosynthesis parameters, potato lines overexpressing StATG8a exhibited 9 times higher drought and salt tolerance compared to non-transgenic plants. In contrast, the potato plants with knockdown expression showed a downtrend in drought and salt tolerance compared to non-transgenic potato lines. These results could provide new insights into the function of StATG8a in salt and drought response and its possible mechanisms.