Evolutionary histories of legume genomes and mechanisms of genome remodeling

Evolutionary genomics analysis of plants aims to reveal and help us to understand the history of genome evolution that plants have undergone. So far, many specific topics and questions of genome evolution have been studied and answered. However, there are still a large number of questions to which the answers are unknown or not clear. In this dissertation, I focus on two specific topics of evolutionary genomics: (1) genome size evolution following genomic rearrangements in plants; (2) ancestral genome reconstruction in legumes. Using a model of two wild peanut relatives in which one genome experienced large rearrangements, we find that the main determinant in genome size reduction is a set of inversions which experienced subsequent net sequence removal in the inverted regions. We observe a general pattern in which sequence is lost more rapidly at newly distal (telomeric) regions than it is gained at newly proximal (pericentromeric) regions – resulting in net sequence loss in the inverted regions. The major driver of this process is recombination, determined by the chromosomal location. Any type of genomic rearrangement that exposes proximal regions to higher recombination rates can cause genome size reduction by this mechanism. Sequence loss in those regions was primarily due to removal of transposable elements. Illegitimate recombination is likely the major mechanism responsible for the sequence removal, rather than unequal intrastrand recombination. We also measure the relative rate of genome size reduction in these two Arachis diploids. We also test our model in other plant species and find that it applies in all cases examined, suggesting our model is widely applicable. Inversions occurring in tetraploid cultivated peanut after the polyploidization event provide us an excellent opportunity to examine the model of genome size reduction following genomic rearrangements in polyploidy. It is also a good opportunity to understand the genome size reduction process at its early stage, since the inversions are quite recent (likely younger than 10,000 years). We observe that the model of genome size reduction still holds in the recently-derived tetraploid peanut as it does in the much earlier-diverging diploid progenitors. We find that the genome size reduction process starts with differences in very long sequence deletions and then spreads to mid-length sequence deletions later. We measure the relative rate of size reduction of the inverted region in tetraploid peanut, finding that it is higher than the rates calculated in our previous study between Arachis diploids. We argue this is because the rate of size reduction is more rapid in the early generations after the inversion. We describe the reconstruction of a hypothetical ancestral genome for the papilionoid legumes, in order to help us better understand the evolutionary histories of these legumes. We use a novel method for identifying informative markers, to reconstruct the ancestral genomes for selected legume species, including Glycine max, which has a recent exclusive WGD event. We infer that the reconstructed most recent common ancestor of all selected legume species (all within the Papilionoideae) has 9 chromosomes. The model then predicts that chromosome numbers reduced to 8 in Medicago truncatula and Cicer arietinum separately, through two separate single fusion events. In Lotus japonicus, a series of rearrangement events is the major cause of the chromosome number reduction to 6. We infer that the chromosome number increased mostly independently in Cajanus cajan, Glycine max, Phaseolus vulgaris and Vigna radiata. In Arachis (A. duranensis and A. ipaensis), there was an increase in chromosome number prior to their divergence. The chromosome structural evolution described here is consistent with the phylogenetic distribution of a large collection of chromosome counts in the legumes

A Mechanism for Genome Size Reduction Following Genomic Rearrangements

The factors behind genome size evolution have been of great interest, considering that eukaryotic genomes vary in size by more than three orders of magnitude. Using a model of two wild peanut relatives, Arachis duranensis and Arachis ipaensis, in which one genome experienced large rearrangements, we find that the main determinant in genome size reduction is a set of inversions that occurred in A. duranensis, and subsequent net sequence removal in the inverted regions. We observe a general pattern in which sequence is lost more rapidly at newly distal (telomeric) regions than it is gained at newly proximal (pericentromeric) regions – resulting in net sequence loss in the inverted regions. The major driver of this process is recombination, determined by the chromosomal location. Any type of genomic rearrangement that exposes proximal regions to higher recombination rates can cause genome size reduction by this mechanism. In comparisons between A. duranensis and A. ipaensis, we find that the inversions all occurred in A. duranensis. Sequence loss in those regions was primarily due to removal of transposable elements. Illegitimate recombination is likely the major mechanism responsible for the sequence removal, rather than unequal intrastrand recombination. We also measure the relative rate of genome size reduction in these two Arachis diploids. We also test our model in other plant species and find that it applies in all cases examined, suggesting our model is widely applicable

Evolutionary histories of legume genomes and mechanisms of genome remodeling

Evolutionary genomics analysis of plants aims to reveal and help us to understand the history of genome evolution that plants have undergone. So far, many specific topics and questions of genome evolution have been studied and answered. However, there are still a large number of questions to which the answers are unknown or not clear. In this dissertation, I focus on two specific topics of evolutionary genomics: (1) genome size evolution following genomic rearrangements in plants; (2) ancestral genome reconstruction in legumes. Using a model of two wild peanut relatives in which one genome experienced large rearrangements, we find that the main determinant in genome size reduction is a set of inversions which experienced subsequent net sequence removal in the inverted regions. We observe a general pattern in which sequence is lost more rapidly at newly distal (telomeric) regions than it is gained at newly proximal (pericentromeric) regions – resulting in net sequence loss in the inverted regions. The major driver of this process is recombination, determined by the chromosomal location. Any type of genomic rearrangement that exposes proximal regions to higher recombination rates can cause genome size reduction by this mechanism. Sequence loss in those regions was primarily due to removal of transposable elements. Illegitimate recombination is likely the major mechanism responsible for the sequence removal, rather than unequal intrastrand recombination. We also measure the relative rate of genome size reduction in these two Arachis diploids. We also test our model in other plant species and find that it applies in all cases examined, suggesting our model is widely applicable. Inversions occurring in tetraploid cultivated peanut after the polyploidization event provide us an excellent opportunity to examine the model of genome size reduction following genomic rearrangements in polyploidy. It is also a good opportunity to understand the genome size reduction process at its early stage, since the inversions are quite recent (likely younger than 10,000 years). We observe that the model of genome size reduction still holds in the recently-derived tetraploid peanut as it does in the much earlier-diverging diploid progenitors. We find that the genome size reduction process starts with differences in very long sequence deletions and then spreads to mid-length sequence deletions later. We measure the relative rate of size reduction of the inverted region in tetraploid peanut, finding that it is higher than the rates calculated in our previous study between Arachis diploids. We argue this is because the rate of size reduction is more rapid in the early generations after the inversion. We describe the reconstruction of a hypothetical ancestral genome for the papilionoid legumes, in order to help us better understand the evolutionary histories of these legumes. We use a novel method for identifying informative markers, to reconstruct the ancestral genomes for selected legume species, including Glycine max, which has a recent exclusive WGD event. We infer that the reconstructed most recent common ancestor of all selected legume species (all within the Papilionoideae) has 9 chromosomes. The model then predicts that chromosome numbers reduced to 8 in Medicago truncatula and Cicer arietinum separately, through two separate single fusion events. In Lotus japonicus, a series of rearrangement events is the major cause of the chromosome number reduction to 6. We infer that the chromosome number increased mostly independently in Cajanus cajan, Glycine max, Phaseolus vulgaris and Vigna radiata. In Arachis (A. duranensis and A. ipaensis), there was an increase in chromosome number prior to their divergence. The chromosome structural evolution described here is consistent with the phylogenetic distribution of a large collection of chromosome counts in the legumes.</p

Integrated Impacts of Non-Ideal Factors on the Vibration Characteristics of Permanent Magnet Synchronous Motors for Electric Vehicles

The nonlinear electromagnetic vibration of the motor is a major factor that deteriorates the noise, vibration, and hardness (NVH) performance of a vehicle’s electric drive system. Considering the nonlinear characteristics of the inverter, the nonsinusoidal distribution of the air-gap magnetic field, the cogging torque, and the current measurement error, a mathematical model of a permanent magnet synchronous motor of an electric vehicle was established, and its dynamic and electromagnetic vibration characteristics under different speed–load conditions were simulated and analyzed. The results show that the nonlinear characteristics of the inverter and nonsinusoidal distribution of the air-gap magnetic field cause the odd current harmonics, such as the 5th, 7th, 11th, and 13th, which lead to the 6th and its integer multiple order fluctuations of the electromagnetic torque. Moreover, the vibration amplitude is intensified under the coupling action of the nonlinear characteristics of the inverter and the nonsinusoidal distribution of the air-gap magnetic field. The current measurement error produces the 1st and 2nd harmonics of the d- and q-axes currents, which result in the 1st and 2nd order fluctuations of the electromagnetic torque. The cogging torque mainly leads to a 12th order torque ripple of the electromagnetic torque. In addition, the non-ideal factors cause a sharp deterioration in the system vibration state under high-speed and heavy-load conditions. This study provides a theoretical reference for the mathematical modeling and electromagnetic vibration research of permanent magnet synchronous motors, considering non-ideal factors comprehensively

Analysis of Microbial Diversity and Community Structure in the Rhizosphere of Cigar Tobacco in Different Agroecological Zones

To reveal the influence of ecological zones on the structure of microbial communities in cigar rhizosphere soils, Yunnan's cigar tobacco production region was first divided into three ecological zones. Soil samples were collected at maturity and the community structure of fungi and bacteria in the rhizosphere soil was analyzed using 18S rRNA and 16S rRNA high-throughput sequencing techniques. The results showed that the dominant fungi were Ascomycota, Mortrellomycota, and Basidiomycota, and the dominant bacteria were Ascomycota and Proteobacteria. The dominant genera and relative abundances of fungi and bacteria differ at the genus level. Ecoregions may affect the community structure and distribution of fungal and bacterial diversity in the rhizospheric soil of cigars at maturity, which may provide a theoretical basis for the selection of high-quality cigar-producing regions in the future

Table3_A novel risk score model based on fourteen chromatin regulators-based genes for predicting overall survival of patients with lower-grade gliomas.XLSX

Background: Low grade gliomas(LGGs) present vexatious management issues for neurosurgeons. Chromatin regulators (CRs) are emerging as a focus of tumor research due to their pivotal role in tumorigenesis and progression. Hence, the goal of the current work was to unveil the function and value of CRs in patients with LGGs.Methods: RNA-Sequencing and corresponding clinical data were extracted from The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA) database. A single-cell RNA-seq dataset was sourced from the Gene Expression Omnibus (GEO) database. Altogether 870 CRs were retrieved from the published articles in top academic journals. The least absolute shrinkage and selection operator (LASSO) algorithm and Cox regression analysis were applied to construct the prognostic risk model. Patients were then assigned into high- and low-risk groups based on the median risk score. The Kaplan–Meier (K-M) survival curve and receiver operating characteristic curve (ROC) were performed to assess the prognostic value. Sequentially, functional enrichment, tumor immune microenvironment, tumor mutation burden, drug prediction, single cell analysis and so on were analyzed to further explore the value of CR-based signature. Finally, the expression of signature genes were validated by immunohistochemistry (IHC) and quantitative real-time PCR (qRT-PCR).Results: We successfully constructed and validated a 14 CRs-based model for predicting the prognosis of patients with LGGs. Moreover, we also found 14 CRs-based model was an independent prognostic factor. Functional analysis revealed that the differentially expressed genes were mainly enriched in tumor and immune related pathways. Subsequently, our research uncovered that LGGs patients with higher risk scores exhibited a higher TMB and were less likely to be responsive to immunotherapy. Meanwhile, the results of drug analysis offered several potential drug candidates. Furthermore, tSNE plots highlighting the magnitude of expression of the genes of interest in the cells from the scRNA-seq assay. Ultimately, transcription expression of six representative signature genes at the mRNA level was consistent with their protein expression changes.Conclusion: Our findings provided a reliable biomarker for predicting the prognosis, which is expected to offer new insight into LGGs management and would hopefully become a promising target for future research.</p