Chromosomal Distribution Research Articles

Genome-Wide Identification and Characterization of YUCCA Gene Family in Mikania micrantha.

Auxin is a general coordinator for growth and development throughout plant lifespan, acting in a concentration-dependent manner. Tryptophan aminotransferases (YUCCA) family catalyze the oxidative decarboxylation of indole-3-pyruvic acid (IPA) to form indole-3-acetic acid (IAA) and plays a critical role in auxin homeostasis. Here, 18 YUCCA family genes divided into four categories were identified from Mikania micrantha (M. micrantha), one of the world's most invasive plants. Five highly conserved motifs were characterized in these YUCCA genes (MmYUCs). Transcriptome analysis revealed that MmYUCs exhibited distinct expression patterns in different organs and five MmYUCs showed high expression levels throughout all the five tissues, implying that they may play dominant roles in auxin biosynthesis and plant development. In addition, MmYUC6_1 was overexpressed in DR5::GUS Arabidopsis line to explore its function, which resulted in remarkably increased auxin level and typical elevated auxin-related phenotypes including shortened roots and elongated hypocotyls in the transgenic plants, suggesting that MmYUC6_1 promoted IAA biosynthesis in Arabidopsis. Collectively, these findings provided comprehensive insight into the phylogenetic relationships, chromosomal distributions, expression patterns and functions of the MmYUC genes in M. micrantha, which would facilitate the study of molecular mechanisms underlying the fast growth of M. micrantha and preventing its invasion.

The Cytogenetic Map of the Nile Crocodile (Crocodylus niloticus, Crocodylidae, Reptilia) with Fluorescence In Situ Localization of Major Repetitive DNAs.

Tandemly arranged and dispersed repetitive DNA sequences are important structural and functional elements that make up a significant portion of vertebrate genomes. Using high throughput, low coverage whole genome sequencing followed by bioinformatics analysis, we have identified seven major tandem repetitive DNAs and two fragments of LTR retrotransposons in the genome of the Nile crocodile (Crocodylus niloticus, 2n = 32). The repeats showed great variability in structure, genomic organization, and chromosomal distribution as revealed by fluorescence in situ hybridization (FISH). We found that centromeric and pericentromeric heterochromatin of C. niloticus is composed of previously described in Crocodylus siamensis CSI-HindIII and CSI-DraI repetitive sequence families, a satellite revealed in Crocodylus porosus, and additionally contains at least three previously unannotated tandem repeats. Both LTR sequences identified here belong to the ERV1 family of endogenous retroviruses. Each pericentromeric region was characterized by a diverse set of repeats, with the exception of chromosome pair 4, in which we found only one type of satellite. Only a few repeats showed non-centromeric signals in addition to their centromeric localization. Mapping of 18S-28S ribosomal RNA genes and telomeric sequences (TTAGGG)n did not demonstrate any co-localization of these sequences with revealed centromeric and pericentromeric heterochromatic blocks.

Transposable Elements as a Source of Novel Repetitive DNA in the Eukaryote Genome.

The impact of transposable elements (TEs) on the evolution of the eukaryote genome has been observed in a number of biological processes, such as the recruitment of the host's gene expression network or the rearrangement of genome structure. However, TEs may also provide a substrate for the emergence of novel repetitive elements, which contribute to the generation of new genomic components during the course of the evolutionary process. In this review, we examine published descriptions of TEs that give rise to tandem sequences in an attempt to comprehend the relationship between TEs and the emergence of de novo satellite DNA families in eukaryotic organisms. We evaluated the intragenomic behavior of the TEs, the role of their molecular structure, and the chromosomal distribution of the paralogous copies that generate arrays of repeats as a substrate for the emergence of new repetitive elements in the genome. We highlight the involvement and importance of TEs in the eukaryote genome and its remodeling processes.

MIKC-type MADS-box transcription factor gene family in peanut: Genome-wide characterization and expression analysis under abiotic stress.

Peanut (Arachis hypogaea) is one of the most important economic crops around the world, especially since it provides vegetable oil and high-quality protein for humans. Proteins encoded by MADS-box transcription factors are widely involved in regulating plant growth and development as well as responses to abiotic stresses. However, the MIKC-type MADS-box TFs in peanut remains currently unclear. Hence, in this study, 166 MIKC-type MADS-box genes were identified in both cultivated and wild-type peanut genomes, which were divided into 12 subfamilies. We found a variety of development-, hormone-, and stress-related cis-acting elements in the promoter region of peanut MIKC-type MADS-box genes. The chromosomal distribution of peanut MADS-box genes was not random, and gene duplication contributed to the expansion of the MADS-box gene family. The interaction network of the peanut AhMADS proteins was established. Expression pattern analysis showed that AhMADS genes were specifically expressed in tissues and under abiotic stresses. It was further confirmed via the qRT-PCR technique that five selected AhMADS genes could be induced by abiotic and hormone treatments and presented different expressive profiles under various stresses. Taken together, these findings provide valuable information for the exploration of candidate genes in molecular breeding and further study of AhMADS gene functions.

WRKY transcription factor family in lettuce plant (Lactuca sativa): Genome-wide characterization, chromosome location, phylogeny structures, and expression patterns.

WRKY transcription factors (TF) have been identified in many plant species and play critical roles in multiple stages of growth and development and under various stress conditions. As one of the most popular vegetable crops, asparagus lettuce has important medicinal and nutritional value. However, study of WRKY TFs family in asparagus lettuce is limited. With the lettuce (Lactuca sativa L.) genome publication, we identified 76 WRKY TFs and analyzed structural characteristics, phylogenetic relationships, chromosomal distribution, interaction network, and expression profiles. The 76 LsWRKY TFs were phylogenetically classified as Groups I, II (IIa-IIe), and III. Cis element analysis revealed complex regulatory relationships of LsWRKY genes in response to different biological progresses. Interaction network analysis indicated that LsWRKY TFs could interact with other proteins, such as SIB (sigma factor binding protein), WRKY TFs, and MPK. The WRKYIII subfamily genes showed different expression patterns during the progress of asparagus lettuce stem enlargement. According to qRT-PCR analysis, abiotic stresses (drought, salt, low temperature, and high temperature) and phytohormone treatment could induce specific LsWRKYIII gene expression. These results will provide systematic and comprehensive information on LsWRKY TFs and lay the foundation for further clarification of the regulatory mechanism of LsWRKY, especially LsWRKYIII TFs, involved in stress response and the progress of plant growth and development.

Discovery of DNA polymorphisms via genome-resequencing and development of molecular markers between two barley cultivars.

Genome resequencing uncovers genome-wide DNA polymorphisms that are useful for the development of high-density InDel markers between two barley cultivars. Discovering genomic variations and developing genetic markers are crucial for genetics studies and molecular breeding in cereal crops. Although InDels (insertions and deletions) have become popular because of their abundance and ease of detection, discovery of genome-wide DNA polymorphisms and development of InDel markers in barley have lagged behind other cereal crops such as rice, maize and wheat. In this study, we re-sequenced two barley cultivars, Golden Promise (GP, a classic British spring barley variety) and Hua30 (a Chinese spring barley variety), and mapped clean reads to the reference Morex genome, and identified in total 13,933,145 single nucleotide polymorphisms (SNPs) and 1,240,456 InDels for GP with Morex, 11,297,100 SNPs and 781,687 InDels for Hua30 with Morex, and 13,742,399 SNPs and 1,191,597 InDels for GP with Hua30. We further characterized distinct types, chromosomal distribution patterns, genome location, functional effect, and other features of these DNA polymorphisms. Additionally, we revealed the functional relevance of these identified SNPs/InDels regarding different flowering times between Hua30 and GP within 17 flowering time genes. Furthermore, we developed a series of InDel markers and validated them experimentally in 43 barley core accessions, respectively. Finally, we rebuilt population structure and phylogenetic tree of these 43 barley core accessions. Collectively, all of these genetic resources will facilitate not only the basic research but also applied research in barley.

Genome-wide characterization of soybean RALF genes and their expression responses to Fusarium oxysporum.

RALFs (RAPID ALKALINIZATION FACTORs) are small peptides required for plant growth, development and immunity. RALF has recently been discovered to regulate plant resistance to fungal infection. However, little is known in crops, particularly in soybean. Here, 27 RALFs were identified in the genome of Glycine max. All Glycine max RALFs (GmRALFs) and 34 Arabidopsis RALFs were classified into 12 clades via the phylogenetic analyses. Gene structures, conserved motifs, chromosome distribution and cis-elements were analyzed in this study. Furthermore, 18 GmRALFs were found in response to Fusarium oxysporum (F. oxysporum) infection in soybean and to have distinct expression patterns. Among them, secretory function of two GmRALFs were identified, and three GmRALFs were detected to interact with FERONIA in Glycine max (GmFERONIA, GmFER). Our current study systematically identified and characterized GmRALFs in the soybean genome, laying a groundwork for further functional analyses and soybean breeding.

Agro-Morphological and Cytogenetic Characterization of Colchicine-Induced Tetraploid Plants of Polemonium caeruleum L. (Polemoniaceae).

Polemonium caeruleum L. (Polemoniaceae) is a valuable medicinal herb with a wide spectrum of biological activities. Under natural conditions, the productivity of this species is rather low. In this study, colchicine-induced tetraploid plants (2n = 4x = 36) of P. caeruleum were obtained, and for the first time, their morphological and cytogenetic characterization was performed. In the tetraploid plants, raw material productivity and also the content of triterpene saponins were significantly higher than in the control diploids. The analysis of chromosome behavior at meiosis and FISH chromosome mapping of 45S and 5S rDNA generally demonstrated stability of both genomes in the tetraploid plants. Based on chromosome morphology and distribution patterns of the studied molecular cytogenetic markers, all chromosome pairs in karyotypes were identified, and chromosome karyograms and idiograms of P. caeruleum were constructed. The revealed specific microdiagnostic characteristics of P. caeruleum (strongly sinuous cells and anomocytic stomata of the leaf epidermis, and also glandular hairs along the veins) could be useful for raw material identification. In the obtained tetraploids, the predominance of large stomata on the lower leaf epidermis was determined. The studied tetraploids can be used in various breeding programs to obtain high-quality pharmaceutical raw materials of P. caeruleum.

Genome-wide identification of foxtail millet's TRX family and a functional analysis of SiNRX1 in response to drought and salt stresses in transgenic Arabidopsis.

Thioredoxins (TRXs) are small-molecule proteins with redox activity that play very important roles in the growth, development, and stress resistance of plants. Foxtail millet (Setaria italica) gradually became a model crop for stress resistance research because of its advantages such as its resistance to sterility and its small genome. To date, the thioredoxin (TRX) family has been identified in Arabidopsis thaliana, rice and wheat. However, studies of the TRX family in foxtail millet have not been reported, and the biological function of this family remains unclear. In this study, 35 SiTRX genes were identified in the whole genome of foxtail millet through bioinformatic analysis. According to phylogenetic analysis, 35 SiTRXs can be divided into 13 types. The chromosome distribution, gene structure, cis-elements and conserved protein motifs of 35 SiTRXs were characterized. Three nucleoredoxin (NRX) members were further identified by a structural analysis of TRX family members. The expression patterns of foxtail millet’s SiNRX members under abiotic stresses showed that they have different stress-response patterns. In addition, subcellular localization revealed that SiNRXs were localized to the nucleus, cytoplasm and membrane. Further studies demonstrated that the overexpression of SiNRX1 enhanced Arabidopsis’ tolerance to drought and salt stresses, resulting in a higher survival rate and better growth performance. Moreover, the expression levels of several known stress-related genes were generally higher in overexpressed lines than in the wild-type. Thus, this study provides a general picture of the TRX family in foxtail millet and lay a foundation for further research on the mechanism of the action of TRX proteins on abiotic stresses.

Metal chelating and anti-radical activity of Salvia officinalis in the ameliorative effects against uranium toxicity

Uranium is a highly radioactive heavy metal that is toxic to living things. In this study, physiological, cytogenetic, biochemical and anatomical toxicity caused by uranium and the protective role of sage (Salvia officinalis L.) leaf extract against this toxicity were investigated with the help of Allium test. Germination percentage, root length, weight gain, mitotic index (MI), micronucleus (MN) formation, chromosomal aberrations (CAs), superoxide dismutase (SOD) and catalase (CAT) enzyme activities, malondialdehyde (MDA) levels and changes in root meristem cells were used as indicators of toxicity. In the experimental stage, a total of six groups, one of which was the control, were formed. Group I was treated with tap water, while group II and III were treated only with sage (190 mg/L and 380 mg/L). Groups IV, V and VI were germinated with uranyl acetate dihydrate (0.1 mg/mL), uranyl acetate dihydrate + 190 mg/L sage and uranyl acetate dihydrate + 380 mg/L sage, respectively. Allium cepa L. bulbs of each group were germinated for 72 h, and at the end of the period, routine preparation techniques were applied and physiological, cytogenetic, biochemical and anatomical analyzes were performed. As a result, uranium application caused a significant decrease (p < 0.05) in all physiological parameters and MI values. MN, CAs numbers, SOD and CAT enzyme activities and MDA levels increased significantly (p < 0.05) with uranium application. Uranium promoted CAs in the root tip cells in the form of fragment, vagrant chromosome, sticky chromosome, bridge and unequal distribution of chromatin. In addition, it caused anatomical damages such as epidermis cell damage, cortex cell damage and flattened cell nucleus in root tip meristem cells. Sage application together with uranium caused significant (p < 0.05) increases in physiological parameters and MI values and significant decreases in MN, CAs, SOD and CAT activities and MDA levels. In addition, the application of sage resulted in improvement in the severity of anatomical damages induced by uranium. It was determined that the protective role of sage observed for all parameters investigated was even more pronounced at dose of 380 mg/L. The protective role of sage against uranium toxicity is related to its antioxidant activity, and sage has 82.8% metal chelating and 72.9% DPPH removal activity. As a result, uranyl acetate exhibited versatile toxicity in A. cepa, caused cytotoxicity by decreasing the MI rate, and genotoxicity by increasing the frequencies of MN and CAs. And also, Sage acted as a toxicity-reducing agent by displaying a dose-dependent protective role against the toxic effects induced by uranyl acetate.

Evolutionary characterization of miR396s in Poaceae exemplified by their genetic effects in wheat and maize

MiR396s play important roles in regulating plant growth and stress response, and great potential for crop yield promotion was anticipated. For more comprehensive and precise understanding of miR396s in Poaceae, we analyzed the phylogenetic linkage, gene expression, and chromosomal distribution of miR396s in this study. Although the mature miR396s’ sequences were mostly conserved, differential expression patterns and chromosomal distribution were found among Poaceae species including the major cereal crops rice, wheat, and maize. Consistently, in comparison with rice, wheat and maize plants transformed with the target mimicry construct of miR396 (MIM396) exhibited differential effects on grain size and disease resistance. While the TaMIM396 plants showed increased grain size, panicle length and sensitivity to B. graminis, the ZmMIM396 plants didn’t show obvious changes in grain size and disease resistance. In Addition, several GROWTH-REGULATING FACTOR (GRF) genes in wheat and maize were repressed by miR396s, which could be reversed by MIM396, confirming the conserved regulatory roles of miR396 on GRFs. While providing new solution to enhance grain yield in wheat and revealing potential regulatory variations of miR396s in controlling grain size and disease resistance in different crops, this study gives clues to further explore miR396s’ functions in other Poaceae species.

Genome-wide identification of the CDPK gene family reveals the CDPK-RBOH pathway potential involved in improving chilling tolerance in peach fruit

Calcium-dependent protein kinase (CDPK), as an essential calcium receptor, plays a major role in the perception and decoding of intracellular calcium signaling in plant development and stress responses. Here, the CDPK gene family was analyzed at the genome-wide level in peach. This study identified 17 PpCDPK gene members from the peach genome, and systematically investigated phylogenetic relationships, conserved motifs, exon-intron structures, chromosome distribution, and cis-acting elements of each PpCDPK gene using bioinformatics. Furthermore, the expression levels of most PpCDPK genes were significantly changed under the CaCl2, EBR, GB, cold shock, hot water treatments, and various temperatures in the cold storage of peach fruits. RNA-seq data showed that PpCDPK2, PpCDPK7, PpCDPK10, and PpCDPK13 were related to postharvest chilling stress in peach. The interaction network of PpCDPK7 protein showed that the interaction between PpCDPK7 and PpRBOH may be the intersectional point of Ca2+ and ROS signal transmission during cold storage of peach fruits. These systematic analyses are helpful to further characterize the regulation of PpCDPKs and CDPK-RBOH mediated signal cascades in postharvest chilling injury in peach fruit.

PSXII-1 CNV and Cnvr Detection from High-Density SNP Genotyping in Holstein Cattle

Abstract Copy number variation (CNV) represents an important source of genetic variation complementary to single nucleotide polymorphism (SNP) and provides valuable insights into the genetic architecture of complex traits in humans and livestock animals. However, many factors affect CNV detection, including sample size. Previous studies in Holstein cattle have only used hundreds of individuals. Therefore, in the present study, CNVs were identified from high-density genotype array data in 3,529 Holstein cows from 16 herds located in 7 U.S. states. CNVs were derived from 546,802 autosomal SNP markers with MAF &amp;gt; 0.05 and call rate &amp;gt; 0.90 using the intensity signals at each SNP position in a hidden Markov model implemented in PennCNV software. The log R ratio (LRR) values were corrected based on the guanine-cytosine content in the genomic regions located 500 kb upstream and downstream of each marker. After detection, CNVs presenting LRR ≤ 0.30, B allele frequency drift &amp;lt; 0.01, waviness factor ≤ 0.05, number of SNPs &amp;gt; 10 and length &amp;gt; 1 kb were merged into CNV regions (CNVR) using CNVRanger. A total of 1,881 non-redundant CNV events spanning the entire genome were identified in 1,771 cows, with a mean of 10 CNVs per individual and ranging from 1 to 27. The highest percentage of CNV calls was located on BTA7 (16%), while only 9 CNVs were identified on BTA9. The CNV calls were grouped into 685 CNVRs covering 3.07% of the bovine autosomal genome. The number of CNVRs with copy loss and gain were 356 and 310, and both types were observed in 19 regions. The chromosomal distribution of CNVR revealed that BTA7 harbors 38 CNVRs, while only 2 were detected on BTA28. These results will support further research on the contribution of CNVs and CNVRs to the genetic architecture of complex traits in Holstein cattle.

The Chromosome Number and rDNA Loci Evolution in Onobrychis (Fabaceae).

The evolution of chromosome number and ribosomal DNA (rDNA) loci number and localisation were studied in Onobrychis Mill. Diploid and tetraploid species, as well as two basic chromosome numbers, x = 7 and x = 8, were observed among analysed taxa. The chromosomal distribution of rDNA loci was presented here for the first time using fluorescence in situ hybridisation (FISH) with 5S and 35S rDNA probes. Onobrychis species showed a high polymorphism in the number and localisation of rDNA loci among diploids, whereas the rDNA loci pattern was very similar in polyploids. Phylogenetic relationships among the species, inferred from nrITS sequences, were used as a framework to reconstruct the patterns of basic chromosome number and rDNA loci evolution. Analysis of the evolution of the basic chromosome numbers allowed the inference of x = 8 as the ancestral number and the descending dysploidy and polyploidisation as the major mechanisms of the chromosome number evolution. Analyses of chromosomal patterns of rRNA gene loci in a phylogenetic context resulted in the reconstruction of one locus of 5S rDNA and one locus of 35S rDNA in the interstitial chromosomal position as the ancestral state in this genus.

Computational benchmarking of putative KIFC1 inhibitors.

The centrosome in animal cells is instrumental in spindle pole formation, nucleation, proper alignment of microtubules during cell division, and distribution of chromosomes in each daughter cell. Centrosome amplification involving structural and numerical abnormalities in the centrosome can cause chromosomal instability and dysregulation of the cell cycle, leading to cancer development and metastasis. However, disturbances caused by centrosome amplification can also limit cancer cell survival by activating mitotic checkpoints and promoting mitotic catastrophe. As a smart escape, cancer cells cluster their surplus of centrosomes into pseudo-bipolar spindles and progress through the cell cycle. This phenomenon, known as centrosome clustering (CC), involves many proteins and has garnered considerable attention as a specific cancer cell-targeting weapon. The kinesin-14 motor protein KIFC1 is a minus end-directed motor protein that is involved in CC. Because KIFC1 is upregulated in various cancers and modulates oncogenic signaling cascades, it has emerged as a potential chemotherapeutic target. Many molecules have been identified as KIFC1 inhibitors because of their centrosome declustering activity in cancer cells. Despite the ever-increasing literature in this field, there have been few efforts to review the progress. The current review aims to collate and present an in-depth analysis of known KIFC1 inhibitors and their biological activities. Additionally, we present computational docking data of putative KIFC1 inhibitors with their binding sites and binding affinities. This first-of-kind comparative analysis involving experimental biology, chemistry, and computational docking of different KIFC1 inhibitors may help guide decision-making in the selection and design of potent inhibitors.

Comprehensive analysis of the LHT gene family in tobacco and functional characterization of NtLHT22 involvement in amino acids homeostasis.

Amino acids are vital nitrogen (N) sources for plant growth, development, and yield. The uptake and translocation of amino acids are mediated by amino acid transporters (AATs). The AATs family including lysine-histidine transporters (LHTs), amino acid permeases (AAPs), and proline transporters (ProTs) subfamilies have been identified in various plants. However, little is known about these genes in tobacco. In this study, we identified 23 LHT genes, the important members of AATs, in the tobacco genome. The gene structure, phylogenetic tree, transmembrane helices, chromosomal distribution, cis-regulatory elements, and expression profiles of NtLHT genes were systematically analyzed. Phylogenetic analysis divided the 23 NtLHT genes into two conserved subgroups. Expression profiles confirmed that the NtLHT genes were differentially expressed in various tissues, indicating their potential roles in tobacco growth and development. Cis-elements analysis of promoters and expression patterns after stress treatments suggested that NtLHT genes probable participate in abiotic stress responses of tobacco. In addition, Knock out and overexpression of NtLHT22 changed the amino acids homeostasis in the transgenic plants, the contents of amino acids were significantly decreased in NtLHT22 overexpression plants than wild-type. The results from this study provide important information for further studies on the molecular functions of the NtLHT genes.

Genome-wide identification and transcriptome analysis of the heavy metal-associated (HMA) gene family in Tartary buckwheat and their regulatory roles under cadmium stress

Heavy metal-associated (HMA) genes are those related to heavy metal transport and detoxification in plants. HMA genes have not been reported in Tartary buckwheat so far. In this study, we accessed the HMA genes of Tartary buckwheat by genome-wide identification for the first time. A total of 56 HMA genes were identified, including 36 ATX1 (antioxidant protein1) genes, 13 HIPP (heavy metal-associated isoprenylated plant protein) genes, and 7 P1B-ATPase (P1B-type adenosine triphosphatase) genes. These gene structures, motif compositions, chromosomal distribution, phylogenetic relationship, duplication events, interaction networks, cis-acting elements, and transcriptional expression under cadmium (Cd) stress were investigated. Among them, genes in HIPP and ATX1 subfamilies were more closely related. The 56 HMA genes were involved in the regulation of metal ion transport and homeostasis by binding metal ions, likely triggered by signals transducted by plant hormones. Fifteen of these HMA genes played regulatory roles under Cd stress. FtP1bA1 was identified to be a core gene involved in the defense regulation of Cd stress. Our results provide not only the first overview and characteristics of HMA genes in the whole genome of Tartary buckwheat but also a valuable reference for the functional analysis of HMA genes under Cd stress. Understanding changes in gene regulation induced by Cd stress lays the foundation for breeding resistant varieties.

Genome-wide identification, characterization and expression analysis of the ABA receptor PYL gene family in response to ABA, photoperiod, and chilling in vegetative buds of Liriodendron chinense

Abscisic acid (ABA) is a signaling phytohormone in plants to improve stress adaption under harsh environments. ABA is sensed by the pyrabactin resistance1/PYR1-like/regulatory components of the ABA receptor (PYR1/PYL/RCAR) (named PYLs) and is the core regulator of ABA stress signaling. ABA receptor PYL gene family have been well studied in rubber tree, apple, Theobroma cacao, Ricinus communis, and Vitis vinifera. We first revealed the genome-wide comprehensive analysis to classify the PYL genes in the L. chinense. This study highlighted the seven LchiPYL genes in the L. chinense genome. The detailed investigations about gene structure variations, chromosomal distributions, phylogenetic tree, 3D structure, motif analysis, cis-regulatory elements, subcellular location, and expression profiles in buds and stress responses were carried out in this article. Phylogenetic tree analysis exploited that the seven LchiPYL genes were divided into four groups (Group I–IV) from L. chinense, and three were highly linked with other species. By analyzing the cis-elements in the promoters, we identified five hormones-, six stress-, three growth and biological process, and two metabolic-related responsive elements. The expression analysis showed that all seven genes were up-and down-regulated against response to ABA, photoperiod, chilling, and chilling + photoperiod treatments. Our findings opened up new future research directions and provided insight into the PYL family genes in Liriodendron chinense.

Differentially reset transcriptomes and genome bias response orchestrate wheat response to phosphate deficiency.

Phosphorus (P) is an essential macronutrient for all organisms. Phosphate (Pi) deficiency reduces grain yield and quality in wheat. Understanding how wheat responds to Pi deficiency at the global transcriptional level remains limited. We revisited the available RNA-seq transcriptome from Pi-starved wheat roots and shoots subjected to Pi starvation. Genome-wide transcriptome resetting was observed under Pi starvation, with a total of 917 and 2338 genes being differentially expressed in roots and shoots, respectively. Chromosomal distribution analysis of the gene triplets and differentially expressed genes (DEGs) revealed that the D genome displayed genome induction bias and, specifically, the chromosome 2D might be a key contributor to Pi-limiting triggered gene expression response. Alterations in multiple metabolic pathways pertaining to secondary metabolites, transcription factors and Pi uptake-related genes were evidenced. This study provides genomic insight and the dynamic landscape of the transcriptional changes contributing to the hexaploid wheat during Pi starvation. The outcomes of this study and the follow-up experiments have the potential to assist the development of Pi-efficient wheat cultivars.

Genome-Wide Identification and Expression Analysis of eIF Family Genes from Brassica rapa in Response to TuMV Resistance.

Brassica rapa is one of the most important leafy vegetables worldwide, and has a long history of cultivation. However, it has not been possible to completely control the damage of turnip mosaic virus (TuMV), a serious virus in B. rapa, to production. In this study, the genome-wide identification and expression detection of eIF family genes from B. rapa in response to TuMV resistance were analyzed, including the identification of eIF family genes, chromosomal distribution, three-dimensional (3D) structure and sequence logo analyses, and the expression characterization as well as differential metabolite analysis of eIF family genes in resistant/susceptible lines, which may further prove the whole-genome tripling (WGT) event in B. rapa evolution and provide evidence for the functional redundancy and functional loss of multicopy eIF genes in evolution. A qRT-PCR analysis revealed that the relative expressions of eIF genes in a susceptible line (80461) were higher than those in a resistant line (80124), which may prove that, when TuMV infects host plants, the eIF genes can combine with the virus mRNA 5′ end cap structure and promote the initiation of virus mRNA translation in the susceptible B. rapa line. In addition, the metabolite substances were detected, the differences in metabolites between disease-resistant and disease-susceptible plants were mainly manifested by altered compounds such as flavonoids, jasmonic acid, salicylic acid, ketones, esters, etc., which inferred that the different metabolite regulations of eIF family genes and reveal the resistance mechanisms of eIF genes against TuMV in brassica crops. This study may lay a new theoretical foundation for revealing eIF family gene resistance to TuMV in B. rapa, as well as advancing our understanding of virus–host interactions.