Genome-wide analysis of the LAZ1 gene family in Gossypium hirsutum.

BACKGROUND: As the world's leading fiber crop and a major oil-producing crop, cotton fiber yield and fiber quality are affected by environmental stresses, especially heat, drought and salinity. The LAZ1 (Lazarus 1) family genes are responsive to abscisic acid, drought, and salt treatments. Currently, mining and functional analyses of LAZ1 family genes in cotton have not been reported. METHODS AND RESULTS: In this study, 20 GhLAZ1 genes, designated GhLAZ1-1 - GhLAZ1-20, were identified in the genome of Gossypium hirsutum through the construction of an HMM model, and their molecular properties, chromosomal localization, phylogeny, gene structure, evolutionary selection pressure, promoter cis elements and gene expression under salt stress were analyzed. With the exception of GhLAZ1-17 and GhLAZ1-20, the remaining 18 GhLAZ1 genes were unevenly localized on 13 chromosomes in G. hirsutum; evolutionary analysis showed that these genes could be divided into three subfamilies; and evolutionary selection pressure analysis demonstrated that the GhLAZ1 genes were all under purifying selection. Many elements related to light responses, hormone responses, and abiotic stresses were predicted on the GhLAZ1 family gene promoters, and real-time quantitative PCR results showed that GhLAZ1-2, GhLAZ1-8, and GhLAZ1-18 were upregulated significantly in salt-treated cotton leaves. CONCLUSIONS: Our results suggested that GhLAZ1 genes were involved in the salt tolerance mechanism in G. hirsutum and provided a reference for further exploring the function and molecular mechanism of LAZ1 genes.

Transcriptome, proteome and functional characterization reveals salt stress tolerance mechanisms in upland cotton (Gossypium hirsutum L.).

Uncovering the underlying mechanism of salt tolerance is important to breed cotton varieties with improved salt tolerance. In this study, transcriptome and proteome sequencing were performed on upland cotton (Gossypium hirsutum L.) variety under salt stress, and integrated analysis was carried out to exploit salt-tolerance genes in cotton. Enrichment analysis using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) was performed on differentially expressed genes (DEGs) obtained from transcriptome and proteome sequencing. GO enrichment was carried out mainly in the cell membrane, organelle, cellular process, metabolic process, and stress response. The expression of 23,981 genes was changed in physiological and biochemical processes such as cell metabolism. The metabolic pathways obtained by KEGG enrichment included glycerolipid metabolism, sesquiterpene and triterpenoid biosynthesis, flavonoid production, and plant hormone signal transduction. Combined transcriptome and proteome analysis to screen and annotate DEGs yielded 24 candidate genes with significant differential expression. The quantitative real-time polymerase chain reaction (qRT-PCR) validation of the candidate genes showed that two genes (Gh_D11G0978 and Gh_D10G0907) responded significantly to the induction of NaCl, and these two genes were further selected as target genes for gene cloning and functional validation through virus-induced gene silencing (VIGS). The silenced plants exhibited early wilting with a greater degree of salt damage under salt treatment. Moreover, they showed higher levels of reactive oxygen species (ROS) than the control. Therefore, we can infer that these two genes have a pivotal role in the response to salt stress in upland cotton. The findings in this research will facilitate the breeding of salt tolerance cotton varieties that can be grown on saline alkaline lands.

Genome-wide identification and analysis of the GUB_WAK_bind gene family in Gossypium hirsutum.

BACKGROUND: Upland cotton is one of the main cultivated species of cotton, and salt stress is an important factor in its growth and development. Wall-associated receptor kinase galacturonan binding (GUB_WAK_bind) is an extracellular domain of wall-associated kinase (WAK), which can sense the environment and play a role in the response to plant stress. METHODS AND RESULTS: In this study, the GUB_WAK_bind gene in Gossypium hirsutum was identified and analyzed by bioinformatics at the whole genome level, including its physicochemical properties, evolutionary development, gene structure, chromosome positioning, cis-acting elements in the promoter, etc., and the expression of the GUB_WAK_bind genes under salt stress were analyzed by quantitative real-time polymerase chain reaction (qRT-PCR). A total of 22 GUB_WAK_bind gene members were identified in Gossypium hirsutum and divided into three subgroups by evolutionary development and motif analysis, most of which contained motif 5, which is similar to the motif pattern of subgroup members. The number of exons in this gene family is between 1 and 4, the number of introns is between 0 and 3, and 22 gene members are distributed on 14 chromosomes of Gossypium hirsutum. Almost all gene members have adverse stress response elements in their promoter region. The expression analysis in response to salt stress showed that the selected six genes were induced by NaCl stress with significant expression differences (P < 0.05). CONCLUSIONS: The results of this study have a certain reference value for understanding the evolution and function of GUB_WAK_bind genes and studying the salt tolerance genes of Gossypium hirsutum.

More efforts are needed for background surveys of zoonotic coronaviruses in animals.

Recently, a novel dog-origin coronavirus has been found in humans. The low similarity between the receptor-binding domain from this novel virus and other human-infecting coronaviruses in genus Alphacoronavirus suggests it might use a novel receptor or mechanism to enter human cells and also might trigger a novel immune response.

Mining of Potential Gene Resources for Breeding Nutritionally Improved Maize.

Maize is one of the leading food crops and its kernel is rich in starch, lipids, protein and other energy substances. In addition, maize kernels also contain many trace elements that are potentially beneficial to human health, such as vitamins, minerals and other secondary metabolites. However, gene resources that could be applied for nutrient improvement are limited in maize. In this review, we summarized 107 genes that are associated with nutrient content from different plant species and identified 246 orthologs from the maize genome. In addition, we constructed physical maps and performed a detailed expression pattern analysis for the 246 maize potential gene resources. Combining expression profiles and their potential roles in maize nutrient improvement, genetic engineering by editing or ectopic expression of these genes in maize are expected to improve resistant starch, oil, essential amino acids, vitamins, iron, zinc and anthocyanin levels of maize grains. Thus, this review provides valuable gene resources for maize nutrient improvement.

Genome-wide analysis reveals the spatiotemporal expression patterns of SOS3 genes in the maize B73 genome in response to salt stress.

BACKGROUND: Salt damage is an important abiotic stress that affects the growth and yield of maize worldwide. As an important member of the salt overly sensitive (SOS) signal transduction pathway, the SOS3 gene family participates in the transmission of stress signals and plays a vital role in improving the salt tolerance of plants. RESULTS: In this study, we identified 59 SOS3 genes in the maize B73 genome using bioinformatics methods and genome-wide analyses. SOS3 proteins were divided into 5 different subfamilies according to the phylogenetic relationships. A close relationship between the phylogenetic classification and intron mode was observed, with most SOS3 genes in the same group sharing common motifs and similar exon-intron structures in the corresponding genes. These genes were unequally distributed on five chromosomes of B73. A total of six SOS3 genes were identified as repeated genes, and 12 pairs of genes were proven to be segmentally duplicated genes, indicating that gene duplication may play an important role in the expansion of the SOS3 gene family. The expression analysis of 10 genes that were randomly selected from different subgroups suggested that all 10 genes were significantly differentially expressed within 48 h after salt treatment, of which eight SOS3 genes showed a significant decline while Zm00001d025938 and Zm00001d049665 did not. By observing the subcellular localization results, we found that most genes were expressed in chloroplasts while some genes were expressed in the cell membrane and nucleus. CONCLUSIONS: Our study provides valuable information for elucidating the evolutionary relationship and functional characteristics of the SOS3 gene family and lays the foundation for further study of the SOS3 gene family in the maize B73 genome.

Genome-wide identification and characterization of the CLASP_N gene family in upland cotton (Gossypium hirsutum L.).

BACKGROUND: Cytoplasmic linker-associated proteins (CLASPs) are tubule proteins that can bind to microtubules and participate in regulating the structure and function of microtubules, which significantly affects the development and growth of plants. These proteins have been identified in Arabidopsis; however, little research has been performed in upland cotton. METHODS: In this study, the whole genome of the CLASP_N family was analyzed to provide theoretical support for the function of this gene family in the development of upland cotton fiber. Bioinformatics was used to analyze the family characteristics of CLASP_N in upland cotton, such as member identification, sequence characteristics, conserved domain structure and coevolutionary relationships. Real-time fluorescent quantitative PCR (qRT-PCR) was used to clarify the expression pattern of the upland cotton CLASP_N gene family in cotton fiber. RESULTS: At the genome-wide level, we identified 16 upland cotton CLASP_N genes. A chromosomal localization analysis revealed that these 16 genes were located on 13 chromosomes. The motif results showed that all CLASP_N proteins have the CLASP_N domain. Gene structure analysis showed that the structure and length of exons and introns were consistent in the subgroups. In the evolutionary analysis with other species, the gene family clearly diverged from the other species in the evolutionary process. A promoter sequence analysis showed that this gene family contains a large number of cis-acting elements related to a variety of plant hormones. qRT-PCR was used to clarify the expression pattern of the upland cotton CLASP_N gene family in cotton fiber and leaves, and Gh210800 was found to be highly expressed in the later stages of fiber development. The results of this study provide a foundation for further research on the molecular role of the CLASP_N genes in cotton fiber development.

Genome-Wide Analysis of the Cytochrome P450 Gene Family Involved in Salt Tolerance in Gossypium hirsutum.

Plant cytochrome P450 (P450) participates in a wide range of biosynthetic reactions and targets a variety of biological molecules. These reactions lead to various fatty acid conjugates, plant hormones, secondary metabolites, lignin, and various defensive compounds. In our previous research, transcriptome analysis was performed on the salt-tolerant upland cotton "Tongyan No. 1." Many differentially expressed genes (DEGs) belong to the P450 family, and their domains occur widely in plants. In this current research, P450 genes were identified in Gossypium hirsutum with the aid of bioinformatics methods for investigating phylogenetic relations, gene structure, cis-elements, chromosomal localization, and collinearity within a genome. qRT-PCR was conducted to analyze P450 gene expression patterns under salt stress. The molecular weights of the 156 P450 genes were in the range of 5,949.6-245,576.3 Da, and the length of the encoded amino acids for all the identified P450 genes ranged from 51 to 2,144. P450 proteins are divided into four different subfamilies based on phylogenetic relationship, gene structure, and chromosomal localization of gene replication. The length of P450 genes in upland cotton differs greatly, ranging from 1,500 to 13,000 bp. The number of exons in the P450 family genes ranged from 1 to 9, while the number of introns ranged from 0 to 8, and there were similar trends within clusters. A total of 31 cis-acting elements were identified by analyzing 1,500 bp promoter sequences. Differences were found in cis-acting elements among genes. The consistency between qRT-PCR and previous transcriptome analysis of salt tolerance DEGs indicated that they were likely to be involved in the salt tolerance of cotton seedlings. Our results provide valuable information on the evolutionary relationships of genes and functional characteristics of the gene family, which is beneficial for further study of the cotton P450 gene family.

The Causes of Chest Pain in Children and the Criteria for Targeted Myocardial Enzyme Testing in Identifying the Causes of Chest Pain in Children.

Aims: Chest pain is a common complaint at pediatric cardiology clinics and often leads to an extensive cardiac evaluation. In this study, we analyzed the causes of chest pain in Chinese children and developed diagnostic procedures and criteria for targeted myocardial enzyme testing. Methods and Results: We retrospectively analyzed the clinical data of patients aged below 18 years visiting our hospital for chest pain between 2005 and 2019. Based on auxiliary exams and clinical diagnosis, we developed diagnostic procedures and criteria for targeted myocardial enzyme testing in children with chest pain. A total of 7,251 children were included in this study. The chest pain was of cardiac origin in 581 patients (8.0%). The incidence of non-cardiac chest pain was significantly higher in the preschool group and the school-age group than in the adolescent group (93.5 vs. 93.8 vs. 90.3%, P < 0.05). Among children with cardiac chest pain, the most common concomitant symptom was chest tightness (67.0%). Myocardial enzyme testing was performed in 5,408 patients and was abnormal in 453 patients. We developed a diagnostic procedure and criteria for targeted myocardial enzyme testing using pertinent history, physical examination, and ECG findings or UCG finding. Applying the diagnostic procedure and criteria could lead to the reduction in myocardial enzyme testing while still capturing all cardiac diagnoses. Conclusion: In children, chest pain is mostly benign and rarely cardiac. During diagnosis, targeted myocardial enzyme testing based on medical history and physical examination can effectively reduce resource use.

RNA Binding Proteins RZ-1B and RZ-1C Play Critical Roles in Regulating Pre-mRNA Splicing and Gene Expression during Development in Arabidopsis.

Nuclear-localized RNA binding proteins are involved in various aspects of RNA metabolism, which in turn modulates gene expression. However, the functions of nuclear-localized RNA binding proteins in plants are poorly understood. Here, we report the functions of two proteins containing RNA recognition motifs, RZ-1B and RZ-1C, in Arabidopsis thaliana. RZ-1B and RZ-1C were localized to nuclear speckles and interacted with a spectrum of serine/arginine-rich (SR) proteins through their C termini. RZ-1C preferentially bound to purine-rich RNA sequences in vitro through its N-terminal RNA recognition motif. Disrupting the RNA binding activity of RZ-1C with SR proteins through overexpression of the C terminus of RZ-1C conferred defective phenotypes similar to those observed in rz-1b rz-1c double mutants, including delayed seed germination, reduced stature, and serrated leaves. Loss of function of RZ-1B and RZ-1C was accompanied by defective splicing of many genes and global perturbation of gene expression. In addition, we found that RZ-1C directly targeted FLOWERING LOCUS C (FLC), promoting efficient splicing of FLC introns and likely also repressing FLC transcription. Our findings highlight the critical role of RZ-1B/1C in regulating RNA splicing, gene expression, and many key aspects of plant development via interaction with proteins including SR proteins.

Targeted degradation of the cyclin-dependent kinase inhibitor ICK4/KRP6 by RING-type E3 ligases is essential for mitotic cell cycle progression during Arabidopsis gametogenesis.

Following meiosis, plant gametophytes develop through two or three rounds of mitosis. Although the ontogeny of gametophyte development has been defined in Arabidopsis thaliana, the molecular mechanisms regulating mitotic cell cycle progression are not well understood. Here, we report that RING-H2 group F 1a (RHF1a) and RHF2a, two RING-finger E3 ligases, play an important role in Arabidopsis gametogenesis. The rhf1a rhf2a double mutants are defective in the formation of male and female gametophytes due to interphase arrest of the mitotic cell cycle at the microspore stage of pollen development and at female gametophyte stage 1 of embryo sac development. We demonstrate that RHF1a directly interacts with and targets a cyclin-dependent kinase inhibitor ICK4/KRP6 (for Interactors of Cdc2 Kinase 4/Kip-related protein 6) for proteasome-mediated degradation. Inactivation of the two redundant RHF genes leads to the accumulation of ICK4/KRP6, and reduction of ICK4/KRP6 expression largely rescues the gametophytic defects in rhf1a rhf2a double mutants, indicating that ICK4/KRP6 is a substrate of the RHF E3 ligases. Interestingly, in situ hybridization showed that ICK4/KRP6 was predominantly expressed in sporophytes during meiosis. Our findings indicate that RHF1a/2a-mediated degradation of the meiosis-accumulated ICK4/KRP6 is essential to ensure the progression of subsequent mitoses to form gametophytes in Arabidopsis.