Genetica最新文献

Due to the increase in demand for food production worldwide, the cultivation of improved varieties is used as a strategy in order to maximize production. The improved Maradol papaya variety was introduced to the Yucatan Peninsula (YP), Mexico, the Mesoamerican diversity area of papaya, in the 1990s. The domesticated and wild papaya belong to the same species (Carica papaya L.), which promotes gene flow from crops to their wild relatives, threatening the genetic diversity of wild papaya populations in the region. In this study, we used a population genomic approach to evaluate the impact of domesticated-to-wild gene flow on the genetic structure and diversity of wild papaya in the YP. We used 2054 SNP markers for 227 wild individuals from 15 collection sites and 127 domesticated individuals from 13 Maradol papaya plantations. We found, (a) the presence of individuals that may be the result of a hybridization process between wild and domesticated papaya; (b) a higher genetic diversity in the wild group (H_E = 0.18) in comparison to the domesticated group (H_E = 0.09); and (c) low migration rates from domesticated to wild plants (m = 0.005). The domesticated-to-wild gene flow in C. papaya can have a negative effect on the genetic diversity and adaptive potential of wild populations from this region. The conservation of crop wild relatives should be a priority since they are part of various ecological processes and are considered natural reservoirs of genetic diversity for crops.

The taxonomic concepts and phylogenetic relations among genera of the family Mniaceae have given rise to much controversy in recent years, including Mnium, Plagiomnium, and Pohlia. Chloroplast genome study of these genera will be helpful to reflect the fact of this relationship. In this study, we sequenced three species in the Plagiomnium genus using an Illumina HiSeq 4000 platform. The complete chloroplast genomes of P. rostratum, P. succulentum and P. vesicatum were 125,196 bp, 124,689 bp, and 124,663 bp in length, which all contained a quadripartite structure including two copies of the invert repeats (IR, 10,120 bp, 9,818 bp, and 9,665 bp), one large single copy region (LSC, 86,395 bp, 86,299 bp, and 86,532 bp), and one single copy region (SSC, 18,561 bp, 18,754 bp, and 18,801 bp). The overall GC contents were 29.8%, 30.5%, and 30.5% respectively. The simple sequence repeats (SSRs) were detected in conjunction with Plagiomnium acutum, with variable sites genes observed: rpoC2, ycf1, and ycf2. Combined with the other three sequences published in Mniaceae, analyses of codon usage, repeats sequences, GC contents, and gene features revealed similarities among the seven species in Mniaceae. The trend of nucleotide diversity (Pi) in the seven complete chloroplast genomes showed Pi > 0.056: trnI-rpl23, petG-petL-psbE, trnK-chlB, trnG-trnR-atpA, rpoB-trnC-ycf66, ndhB, trnN-ndhF, and rps15-ycf1. We confirmed the phylogenetic relationships that Plagiomnium genus is a sister group with Mnium, while the Pohlia genus is not a monophyletic group. Phylogenetic analyses corroborated the monophyly of Mniaceae and supported the transfer of the Pohlia genus into Mniaceae.

The basic helix-loop-helix (bHLH) family is one of the three major transcription factor families that play important transcriptional regulatory roles in plant growth and development. One of the most crucial elements in defining Lagerstroemia indica's decorative qualities is flower color. However, the function of the bHLH transcription factor family in L. indica anthocyanin glycoside synthesis has not been clarified. Using the transcriptome data of flower color, 79 LibHLH genes were found in this study. Phylogenetic analysis showed that the LibHLH genes can be divided into 16 subfamilies, and most of the genes in the same subfamily have similar conserved motifs. The total anthocyanin glycoside content of L. indica 'Zihua Guifei' petals was determined during three developmental stages of the petals' growth. The results showed that the total anthocyanin glycoside content grew gradually with growth and development, and that it accumulated most during the full bloom stage. By using gene expression analysis, protein interaction network analysis, and bioinformatics, it was possible to determine which member of the III f family, LibHLH29, is important for the synthesis of anthocyanin glycosides in L. indica. Its expression was confirmed by qRT-PCR, and the results were essentially compatible with the transcriptome data. It was more prominent in the light-colored bloom stage the color-transition stage of L. indica 'Zihua Guifei'. It can be further investigated as a major candidate gene for regulating anthocyanin glycoside synthesis in L. indica, thus laying the foundation for an in-depth study of the interactions among transcription factors.

The auxin response factor (ARF) is a plant-specific transcription factor that regulates the expression of auxin response genes by binding directly to their promoters. They play an important role in the regulation of plant growth and development, as well as in the response to biotic and abiotic stresses. However, the identification and functional analysis of ARFs in Fagopyrum dibotrys are still unclear. In this study, a total of 26 FdARF genes were identified using bioinformatic methods. Their chromosomal location, gene structure, physical and chemical properties of their encoded protein, subcellular location, phylogenetic tree, conserved motifs and cis-acting elements in FdARF promoters were analyzed. The results showed that 26 FdARF genes were unevenly distributed on 8 chromosomes, with the largest distribution on chromosome 4 and the least distribution on chromosome 3. Most FdARF proteins are located in the nucleus, except for the proteins FdARF7 and FdARF21 located to the cytoplasm and nucleus, while FdARF14, FdARF16, and FdARF25 proteins are located outside the chloroplast and nucleus. According to phylogenetic analysis, 26 FdARF genes were divided into 6 subgroups. Duplication analysis indicates that the expansion of the FdARF gene family was derived from segmental duplication rather than tandem duplication. The prediction based on cis-elements of the promoter showed that 26 FdARF genes were rich in multiple stress response elements, suggesting that FdARFs may be involved in the response to abiotic stress. Expression profiling analysis showed that most of the FdARF genes were expressed in the roots, stems, leaves, and tubers of F. dibotrys, but their expression exhibits a certain degree of tissue specificity. qRT-PCR analysis revealed that most members of the FdARF gene were up- or down-regulated in response to abiotic stress. The results of this study expand our understanding of the functional role of FdARFs in response to abiotic stress and lay a theoretical foundation for further exploration of other functions of FdARF genes.

Here we intend to shift the "DNA- and information-centric" conception of biological inheritance, with the accompanying exclusion of any non-DNA matter, to a "poly-matter network" framework which, in addition to DNA, considers the action of other cellular membranous constituents. These cellular structures, in particular organelles and plasma membranes, express "landscapes" of specific topologies at their surfaces, which may become altered in response to certain environmental factors. These so-called "membranous environmental landscapes" (MELs), which replicate by self-organization / autopoiesis rather than self-assembly, are transferred from donor to acceptor cells by various - vesicular and non-vesicular - mechanisms and exert novel features in the acceptor cells. The "DNA-centric" conception may be certainly explanatorily sufficient for the transfer of heritable phenotype variation to acceptor cells following the copying of DNA in donor cells and thereby for the phenomenon of biological inheritance of traits. However, it is not causally sufficient. With the observation of phenotype variation, as initially manifested during bacterial transformation, the impact of environmental factors, such as nutrition and stress, in the differential regulation of gene expression has been widely accepted and resulted in intense efforts to resolve the underlying epigenetic mechanisms. However, these are explained under a conceptual frame where the DNA (and associated proteins) are the only matter of inheritance. In contrast, it is our argumentation that inheritance can only be adequately understood as the transfer of DNA in concert with non-DNA matter in a "poly-matter network" conception. The adequate inclusion of the transfer of non-DNA matter is still a desideratum of future genetic research, which may pave the way for the experimental elucidation not only of how DNA and membrane matter act in concert to enable the inheritance of innate traits, but also whether they interact for that of acquired biological traits. Moreover, the "poly-matter network" conception may open new perspectives for an understanding of the pathogenesis of "common complex" diseases.

Biologists currently have an assortment of high-throughput sequencing techniques allowing the study of population dynamics in increasing detail. The utility of genetic estimates depends on their ability to recover meaningful approximations while filtering out noise produced by artifacts. In this study, we empirically compared the congruence of two reduced representation approaches (genotyping-by-sequencing, GBS, and whole-exome sequencing, WES) in estimating genetic diversity and population structure using SNP markers typed in a small number of wild jaguar (Panthera onca) samples from South America. Due to its targeted nature, WES allowed for a more straightforward reconstruction of loci compared to GBS, facilitating the identification of true polymorphisms across individuals. We therefore used WES-derived metrics as a benchmark against which GBS-derived indicators were compared, adjusting parameters for locus assembly and SNP filtering in the latter. We observed significant variation in SNP call rates across samples in GBS datasets, leading to a recurrent miscalling of heterozygous sites. This issue was further amplified by small sample sizes, ultimately impacting the consistency of summary statistics between genotyping methods. Recognizing that the genetic markers obtained from GBS and WES are intrinsically different due to varying evolutionary pressures, particularly selection, we consider that our empirical comparison offers valuable insights and highlights critical considerations for estimating population genetic attributes using reduced representation datasets. Our results emphasize the critical need for careful evaluation of missing data and stringent filtering to achieve reliable estimates of genetic diversity and differentiation in elusive wildlife species.

Despite being identified in previous articles, the pathogenesis-related 10 (PR-10) protein remains relatively overlooked and has yet to be fully characterized in numerous plant species. This research employs a comprehensive data mining approach to in silico characterize PR-10 proteins in cassava, a vital crop plant globally. In this study, the focus was on in silico identified 53 cassava PR-10 proteins, which can be categorized into two main subgroups: 34 major latex proteins (MLPs) and 13 major allergen proteins, Pru ar 1, based on their phylogenetic relationship. The genome collinearity analysis with the rubber tree showed a possible evolutionary relationship of the PR-10 gene between these two Euphorbiaceae species, specifically on their chromosome 15. Notably, MLP423 and other MLP proteins were identified in various previously published cassava transcriptome datasets in response to biotic treatments from diverse phytopathogens, including anthracnose fungus, viruses, and bacterial blight. Ligand prediction and molecular docking of three MLP423 proteins have revealed potential interaction with cytokinin and abscisic acid hormones. Their expressions and predicted binding affinities are discussed here, highlighting their role as contributors to cassava's defense network against key diseases.

Hydrocotyle himalaica from Bhutan, a perennial herb that thrives from 1500 to 2600 m, possesses both ecological importance and medicinal properties. The plastome analysis revealed a length of 153,383 bp, showing variation from conspecific taxa in China. Its standard structure comprises two IR regions (18,336 bp IRa and 18,336 bp IRb), an LSC region of 97,944 bp, and an SSC region of 18,767 bp, with a GC content of 37.63%. Non-coding regions showed higher mutation susceptibility, with Pi values from 0.006 to 0.107. An AT-rich codon bias was consistent across all 18 Hydrocotyle species. Nucleotide composition and GC% in coding sequences differed among the species. The codon preference in Hydrocotyle is shaped by multiple factors, with natural selection being the primary influence, as indicated by the ENC-plot, PR2-plot, and Neutrality-plot. Codon usage patterns varied, with RSCU values from 0 to 2.23. Codons ending in A or U had RSCU > 1, while those ending in C or G had RSCU < 1. GC2 content surpassed GC3 and GC1 in most genes. The phylogenetic analysis placed H. himalaica, sourced from Kanglung, Bhutan, within the monophyly of the Hydrocotyloideae subfamily. However, the species showed weaker bootstrap support (BS < 50) with H. javanica and H. hookeri subsp., a deviation from a prior report on the same species from Jiangkou, Guizhou, China. This analysis highlighted the genomic characteristics and evolutionary relationships of H. himalaica from Bhutan, underscoring the need for a comprehensive phylogenetic, ecological, and botanical characterization to confirm intra-specific variation within Hydrocotyle species.

As one of the most important parts of plants, the genetic mechanisms of photosynthesis or the response of leaf to a single abiotic and biotic stress have been well studied. However, few researches have involved in the integration of data analysis from system level in leaf tissue under multiple abiotic stresses by utilizing biological networks. In this study, the weighted gene co-expression network analysis (WGCNA) strategy was used to integrate multiple data in leaf tissue of Populus species under different sample treatments. The gene co-expression networks were constructed and functional modules were identified by selecting the suitable soft threshold power β in the procedure of WGCNA. The identified hub genes and gene modules were annotated by agriGO, NetAffx Analysis Center, The Plant Genome Integrative Explorer (PlantGenIE) and other annotation tools. The annotation results have displayed that the highly correlated modules and hub genes are involved in the important biological processes or pathways related to module traits. The efficiency of the WGCNA strategy can generate comprehensive understanding of gene module-traits associations in leaf tissue, which will provide novel insight into the genetic mechanism of Populus species.

DNA barcoding based on COI sequences has been highly informative for the taxonomic assessment of many fish species due to its high rate of species identification. Accordingly, numerous studies have employed this method to encompass species checklists of different areas, assessment of cryptic diversity, biodiversity monitoring, and other applications. Furthermore, most of the success of COI DNA barcoding relies on a comprehensive database (BOLD Systems) that holds sequences and detailed records of millions of species and applies a system (BIN) that clusters short DNA barcodes to generate OTUs. Besides COI, the 16S rDNA has proven to be suitable for the molecular identification of several taxa, and the combination of both markers could be advantageous in investigating species composition in the Neotropics. The family Paralichthyidae comprises over 60 flatfish species. Most of them inhabit tropical areas and remain understudied. Here, we evaluated the diversity of Paralichthyidae species along the Brazilian coast through COI and 16S DNA barcodes. Combining our dataset with BOLD (COI) and GenBank (16S) public records, we conducted tree-based and genetic distance analyses along with BIN-based and species delimitation methods. Our results were consistent for both markers, and we identified eight species of paralichthyids among our samples with high confidence. Interestingly, our analyses indicate several cases where public records assigned to the same species might be sequences from multiple species. Therefore, we provide new records and occurrences and explore important issues regarding misidentification and putative cryptic diversity for several species.