Environmental stress leads to genome streamlining in a widely distributed species of soil bacteria

Bacteria have highly flexible pangenomes, which are thought to facilitate evolutionary responses to environmental change, but the impacts of environmental stress on pangenome evolution remain unclear. Using a landscape pangenomics approach, I demonstrate that environmental stress leads to consistent, continuous reduction in genome content along four environmental stress gradients (acidity, aridity, heat, salinity) in naturally occurring populations of Bradyrhizobium diazoefficiens (widespread soil-dwelling plant mutualists). Using gene-level network and duplication functional traits to predict accessory gene distributions across environments, genes predicted to be superfluous are more likely lost in high stress, while genes with multi-functional roles are more likely retained. Genes with higher probabilities of being lost with stress contain significantly higher proportions of codons under strong purifying and positive selection. Gene loss is widespread across the entire genome, with high gene-retention hotspots in close spatial proximity to core genes, suggesting Bradyrhizobium has evolved to cluster essential-function genes (accessory genes with multifunctional roles and core genes) in discrete genomic regions, which may stabilise viability during genomic decay. In conclusion, pangenome evolution through genome streamlining are important evolutionary responses to environmental change. This raises questions about impacts of genome streamlining on the adaptive capacity of bacterial populations facing rapid environmental change.

Meta-Analysis of Qtl Associated With Starch Pasting Viscosity in Rice (Oryza Sativa L.)

Rapid Visco Analyzer (RVA) profiles are important traits for indicating rice quality, which are controlled by quantitative trait loci (QTL). In the past two decades, hundreds of QTL for rice RVA profiles have been detected, but without an integration study. Consistent QTL regions associated with rice RVA profiles by QTL meta-analysis with genetic information of 592 QTL for eight RVA profiles were studied. A total of 82 meta-QTL for RVA profiles were detected on 12 chromosomes. MQTL possessed narrower confidence intervals than the initial QTL and candidate genes were identified within each MQTL. These MQTL and candidate genes are beneficial for future marker-assisted selection gene cloning. Bangladesh J. Bot. 50(2): 269-276, 2021 (June)

Genome-Wide Investigation of N6-Methyladenosine Regulatory Genes and Their Roles in Tea (Camellia sinensis) Leaves During Withering Process

N6-methyladenosine (m6A), one of the internal modifications of RNA molecules, can directly influence RNA abundance and function without altering the nucleotide sequence, and plays a pivotal role in response to diverse environmental stresses. The precise m6A regulatory mechanism comprises three types of components, namely, m6A writers, erasers, and readers. To date, the research focusing on m6A regulatory genes in plant kingdom is still in its infancy. Here, a total of 34 m6A regulatory genes were identified from the chromosome-scale genome of tea plants. The expansion of m6A regulatory genes was driven mainly by whole-genome duplication (WGD) and segmental duplication, and the duplicated gene pairs evolved through purifying selection. Gene structure analysis revealed that the sequence variation contributed to the functional diversification of m6A regulatory genes. Expression pattern analysis showed that most m6A regulatory genes were differentially expressed under environmental stresses and tea-withering stage. These observations indicated that m6A regulatory genes play essential roles in response to environmental stresses and tea-withering stage. We also found that RNA methylation and DNA methylation formed a negative feedback by interacting with each other’s methylation regulatory genes. This study provided a foundation for understanding the m6A-mediated regulatory mechanism in tea plants under environmental stresses and tea-withering stage.

Genetic transformation of Paulownia elongata S. Y. Hu., mediated by Agrobacterium tumefaciens and biolistic system

Objective: The most appropriate conditions for genetic transformation through direct (bioballistic) and indirect (Agrobacterium tumefaciens) transformation systems in Paulownia elongata were established. Design/methodology/approach: Starting from in vitro propagation through both direct and indirect organogenesis, internodal stem segments with 0.5 to 1 cm length were determined as the best explant. The optimum dose for selection media was determined to be 15 mg L-1 of kanamycin. It was possible to obtain transgenic plants under both transformation systems. In the case of Agrobacterium tumefaciens, two hours of incubation, 48 h of co-cultivation, and optical density of 0.9 were used; while for bioballistics, the best conditions were 120 PSI of shot pressure, shot height at level 6 (16 cm), and vacuum pressure of 22 Hg mm, with particle inflow gun system (PIG). Results: Both systems produced complete transformants, chimeras, as well as those confirmed by histochemical X-GLUC and PCR analysis, producing a total of 14 positive plants by A. tumefaciens transformation from 26 trials and ten positive plants by the bioballistic system from 30 trials; a construction with chitinase and glucanase, NPT II selection gene and the GUS reporter gene were used. Findings/conclusions: So far, this has been the first report including integration of chitinase and glucanase genes.

Fine Mapping of Hybrid Necrosis Gene Ne1 in Common Wheat (Triticum Aestivum L.)

Hybrid necrosis is characterized as progressive chlorosis and necrosis of plant leaves, tillers or whole plants premature death in certain wheat hybrids, which is caused by the combination of two complementary loci Ne1 and Ne2 located on chromosome arms 5BL and 2BS, respectively. Hybrid necrosis s is a serious barrier for combining desirable traits from various genotypes of wheat and the full utilization of heterosis in wheat. In this study, we fine mapped Ne1 on chromosome 5BL, and finally delimited Ne1 to a 4.06-Mb region with large heterogeneous inbred families (HIFs) from the RILs of ‘Zhengnong 17’ × ‘Yangbaimai’. Further characterization of the near isogenic lines derived from HIFs confirmed that Ne1 was tightly linked with a 2.89-Mb fragment that is deleted in Zhengnong 17. Additionally, a diagnostic InDel marker 5B-InDel385 for Ne1 was developed and was used to assess the existence of Ne1 in a diverse panel of 501 wheat accessions. Among them, 122 (61%) out of 200 landraces showed the presence of Ne1 gene, whereas only 79 (26%) out of 301 modern cultivars carried the Ne1 gene. The drastic decrease of Ne1 frequency in modern cultivars indicates that the Ne1 has been subjected to heavily selection pressure. This study provides a good foundation for the marker-assisted selection, gene cloning and functional studies of Ne1 in wheat.

Urbanization and Evolution in Aquatic Environments

Human impacts on freshwater and marine ecosystems have long been of special concern due to water’s essential role in ecosystem functioning and human civilization. Urban development causes a large number of changes in all types of aquatic environments, from small ephemeral pools to rivers to great lakes to expansive coastal habitats. These changes can strongly influence evolution of life in the water by altering selection, gene flow, and genetic drift. Yet our understanding of the evolutionary consequences of urbanization on aquatic organisms is still in early stages. This chapter reviews the impacts of urbanization on aquatic taxa, examining the evolutionary consequences (known or likely) of four major types of urban-induced changes to ecosystems: biotic interactions, physical environment, temperature, and pollution. By drawing connections between literature on ecological and evolutionary impacts in aquatic urban environments, the chapter concludes that (1) several anthropogenic factors seem to commonly drive evolutionary and phenotypic change (organic-compound pollution, altered temperature, and hydrologic shifts), (2) predictability of evolutionary changes are often taxa specific, and may commonly depend on the focal ‘scale’ (e.g., whole-organism performance, morphology, or gene), and (3) there are a few key ‘frontier topics’ (altered biotic interactions, artificial light, sound pollution, and fragmentation) where additional research on phenotypic evolution would be particularly informative.

Functional analysis of cancer gene subtype from co-clustering and classification

<span lang="EN-MY">Cancer is a heterogeneity genetic disease with huge phenotypic alterations among dissimilar cancers types or even between same cancer types. Recent expansions of genome-wide profiling technologies offer a chance to explore molecular changes variations throughout advancement of cancer. Therefore, various statistical and machine learning algorithms have been designed and developed for the handling and interpretation of high-throughput microarray molecular data. Discovery of molecular subtypes studies have permitted the cancer to be allocated into similar groups that are deliberated to port similar molecular and clinical characteristics. Thus, the main objective of this research is to discover cancer gene subtypes and classify genes to obtain higher accuracy. In particular improved co-clustering algorithm used to discover cancer subtypes. And then supervised infinite feature selection gene selection method was combined with multi class SVM for classification of selected genes and further biological analysis. The analysis on breast cancer and glioblastoma multiforme evidences that top genes involved in cancer and the pathways present in both cancer top genes. The functional analysis is useful in medical and pharmaceutical field for cancer diagnosis and prognosis.</span>

Comparative Genome-wide Analysis and Expression Profiling of Histone Acetyltransferase (HAT) Gene Family in Response to Hormonal Applications, Metal and Abiotic Stresses in Cotton

Post-translational modifications are involved in regulating diverse developmental processes. Histone acetyltransferases (HATs) play vital roles in the regulation of chromation structure and activate the gene transcription implicated in various cellular processes. However, HATs in cotton, as well as their regulation in response to developmental and environmental cues, remain unidentified. In this study, 9 HATs were identified from Gossypium raimondi and Gossypium arboretum, while 18 HATs were identified from Gossypium hirsutum. Based on their amino acid sequences, Gossypium HATs were divided into three groups: CPB, GNAT, and TAFII250. Almost all the HATs within each subgroup share similar gene structure and conserved motifs. Gossypium HATs are unevenly distributed on the chromosomes, and duplication analysis suggests that Gossypium HATs are under strong purifying selection. Gene expression analysis showed that Gossypium HATs were differentially expressed in various vegetative tissues and at different stages of fiber development. Furthermore, all the HATs were differentially regulated in response to various stresses (salt, drought, cold, heavy metal and DNA damage) and hormones (abscisic acid (ABA) and auxin (NAA)). Finally, co-localization of HAT genes with reported quantitative trait loci (QTL) of fiber development were reported. Altogether, these results highlight the functional diversification of HATs in cotton growth and fiber development, as well as in response to different environmental cues. This study enhances our understanding of function of histone acetylation in cotton growth, fiber development, and stress adaptation, which will eventually lead to the long-term improvement of stress tolerance and fiber quality in cotton.

Gene Subset Selection for Leukemia Classification Using Microarray Data

Background: Cancer subtype identification is an active research field which helps in the diagnosis of various cancers with proper treatments. Leukemia is one such cancer with various subtypes. High throughput technologies such as Deoxyribo Nucleic Acid (DNA) microarray are highly active in the field of cancer detection and classification alternatively. Objective: Yet, a precise analysis is important in microarray data applications as microarray experiments provide huge amount of data. Gene selection techniques promote microarray usage in the field of medicine. The objective of gene selection is to select a small subset of genes, which are the most informative in classification. associations while known disease-lncRNA associations are required only. Method: In this study, multi-objective evolutionary algorithm is used for gene subset selection in Leukemia classification. An initial redundant and irrelevant gene removal is followed by multiobjective evolutionary based gene subset selection. Gene subset selection highly influences the perfect classification. Thus, selecting the appropriate algorithm for subset selection is important. Results: The performance of the proposed method is compared against the standard genetic algorithm and evolutionary algorithm. Three Leukemia microarray datasets were used to evaluate the performance of the proposed method. Perfect classification was achieved for all the datasets only with few significant genes using the proposed approach. Conclusion: Thus, it is obvious that the proposed study perfectly classifies Leukemia with only few significant genes.</P>

The Genetic Structure of Turnip mosaic Virus Population Reveals the Rapid Expansion of a New Emergent Lineage in China

Turnip mosaic virus (TuMV) is one of the most widespread and economically important virus infecting both crop and ornamental species of the family Brassicaceae. TuMV isolates can be classified to five phylogenetic lineages, basal-B, basal-BR, Asian-BR, world-B and Orchis. To understand the genetic structure of TuMV from radish in China, the 3&prime;-terminal genome of 90 TuMV isolates were determined and analyzed with other Chinese isolates available. The results showed that the Chinese TuMV isolates from radish formed three groups: Asian-BR, basal-BR and world-B. More than half of these isolates (52.54%) were clustered to basal-BR group, and could be further divided into three sub-groups. The TuMV basal-BR isolates in the sub-groups I and II were genetically homologous with Japanese ones, while those in sub-group III formed a distinct lineage. Sub-populations of TuMV basal-BR II and III were new emergent and in a state of expansion. The Chinese TuMV radish populations were under negative selection. Gene flow between TuMV populations from Tai&rsquo;an, Weifang and Changchun was frequent.