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Background: PfAP2-EXP2 is located within chromosome 6 of Plasmodium falciparum recently identified to be undergoing an extensive selective sweep in West African isolates. The gene encoding this transcription factor, PfAP2-EXP2, is essential and thus likely subject to purifying selection that limits variants in the parasite population despite its genomic location. Methods: 72 Plasmodium falciparum field samples and 801 clinical sequences from the Pf6 MalariaGEN dataset of Ghanaian origin, were integrated and analysed. Results: A total of 14 single nucleotide variants of which 5 were missense variants, were identified after quality checks and filtering. Except for one, all identified variants were rare among the clinical samples obtained in this study (Minor allelic frequency < 0.01). Further results revealed a considerably low dN/dS value (0.208) suggesting the presence of purifying selection. Further, all the mutant amino acids were wildtype residues in AP2-EXP2 orthologous proteins—tentatively suggesting a genus-level conservation of amino acid residues. Computational analysis and predictions corroborated these findings. Conclusions: Despite the recent extensive selective sweep within chromosome 6 of West African isolates, PfAP2-EXP2 of Ghanaian origin exhibits low nucleotide diversity and very low dN/dS consistent with purifying selection acting to maintain the function of an essential gene. The conservation of AP2-EXP2 is an important factor that makes it a potential drug target. [ABSTRACT FROM AUTHOR]

Abstract Background PfAP2-EXP2 is located within chromosome 6 of Plasmodium falciparum recently identified to be undergoing an extensive selective sweep in West African isolates. The gene encoding this transcription factor, PfAP2-EXP2, is essential and thus likely subject to purifying selection that limits variants in the parasite population despite its genomic location. Methods 72 Plasmodium falciparum field samples and 801 clinical sequences from the Pf6 MalariaGEN dataset of Ghanaian origin, were integrated and analysed. Results A total of 14 single nucleotide variants of which 5 were missense variants, were identified after quality checks and filtering. Except for one, all identified variants were rare among the clinical samples obtained in this study (Minor allelic frequency

To investigate the nucleotide variation sites (SNPs) and expression differences of the fatty acid synthase gene (FASN) in Guizhou white goats, the relationship between the variation and body size traits was investigated. In this study, DNA was extracted from the blood of 100 samples of white goats from different regions in Guizhou province, China, and the variation sites were screened using pooled sequencing by mixing DNA samples, and 242 blood samples with body size traits were used for association analysis. The allele frequency, genotype frequency, homozygosity, heterozygosity and effective gene number were calculated by using PopGene 32.0 software, the population polymorphism information content was calculated by using PIC software (Version 0.6), and the state of genetic balance of the genes was analyzed by using the chi-square test. The mRNA of FASN gene expression levels in male and female goats were investigated by using real-time fluorescence quantitative PCR (RT-qPCR). The general linear mixed model of MINTAB software (Version 16.0) was used to analyze the association between FASN gene nucleotide mutation sites and body size traits. The results showed that there was one nucleotide mutation site g.141 C/T in the target fragment of FASN gene amplification, and revealed two alleles, C and T, and three genotypes CC, CT and TT. The genotype frequencies for CC, CT and TT were 0.4308, 0.4205 and 0.1487, respectively. The allele frequencies for C and T were 0.6410 and 0.3590, respectively. The genetic homozygosity (Ho) was higher than the heterozygosity (He). The χ2 test showed that the mutation site was in the Hardy–Weinberg equilibrium state (p > 0.05). The RT-qPCR results showed that the FASN gene had different expression levels in the longissimus dorsi muscle of male and female goats, and its expression was significantly higher in male goats than in female goats. The association analysis results showed that the mutation of the FASN gene had different effects on body size traits of male and female goats, and the presence of the populations of the T allele and the TT genotype recorded higher body size traits (body weight, heart girth and wither height) in female populations. Therefore, the site of the FASN gene can be used as a candidate marker for the early selection of growth traits in Guizhou white goats. [ABSTRACT FROM AUTHOR]

This study examined the genes related to immunity, metabolism, and antioxidants that may interact with the prevalence of postpartum endometritis in Ossimi sheep. We used fifty endometritis-positive Ossimi sheep and fifty that appeared to be normal. For the purpose of taking blood samples, each ewe had its jugular vein pierced. Nucleotide sequence differences for the immunological (alpha-2-macroglobulin, toll-like receptor 2, transforming growth factor beta, interleukin 1 receptor-associated kinase 3, high-mobility group box 1, Fc alpha and Mu receptor, and inducible nitric oxide synthase), metabolic (ADAM metallopeptidase with thrombospondin type 1 motif 20, potassium sodium-activated channel subfamily T member 2, Mitogen-activated protein kinase kinase kinase 4, FKBP prolyl isomerase 5, and relaxin family peptide receptor 1), and antioxidant (superoxide dismutase, catalase, NADH: ubiquinone oxidoreductase subunit s5, and Heme oxygenase-1) genes were found among sheep with endometritis and those in good condition utilizing PCR-DNA sequencing. Fisher's exact test revealed a significant difference in the probability of dispersal of all significant nucleotide changes between ewe groups with and without endometritis (p ˂ 0.01). In endometritis ewes, there was a considerable up-regulation of the expression levels of A2M, TLR2, IRAK3, HMGB1, FCAMR, iNOS, ADAMTS20, KCNT2, MAP3K4, FKBP5, RXFP1, and HMOX1. Conversely, there was a down-regulation of the genes that encode TGF-β, SOD, CAT, and NDUFS5. The kind of marker and its frequency in postparturient endometrtits significantly impacted the transcript levels of the indicators under analysis. The results validate that nucleotide changes and gene manifestation outlines in these candidates are significant predictors of the prevalence of endometritis in sheep. [ABSTRACT FROM AUTHOR]

Clonal evolution of chronic lymphocytic leukemia (CLL) often follows chemotherapy and is associated with adverse outcome, but also occurs in untreated patients, in which case its predictive role is debated. We investigated whether the selection and expansion of CLL clone(s) precede an aggressive disease shift. We found that clonal evolution occurs in all CLL patients, irrespective of the clinical outcome, but is faster during disease progression. In particular, changes in the frequency of nucleotide variants (NVs) in specific CLL-related genes may represent an indicator of poor clinical outcome.

AbstractStephania cepharantha Hayata (S. cepharantha) is a common folk medicine herb in China with many therapeutic activities. This study used Illumina sequencing technology to construct a circular chloroplast genome map and compared it with that of other Stephania species. The genome of S. cepharantha is 158,052 bp in length, including a large single-copy region of 88,770 bp, a small single-copy region of 19,760 bp, and two reverse repeat regions of 49,522 bp. The genome encodes eight ribosomal ribonucleic acid (RNA) genes, 37 transfer RNA genes, and 85 protein-coding genes. Nucleotide variation analysis revealed that six highly variable regions of Stephania can be used as potential molecular markers for taxonomic research and evolutionary analysis. This study is the first chloroplast genome report on S. cepharantha, and it provides rich and valuable genetic information for understanding the evolutionary relationships and population inheritance of the species.

This study examined the genes related to immunity, metabolism, and antioxidants that may interact with the prevalence of postpartum endometritis in Ossimi sheep. We used fifty endometritis-positive Ossimi sheep and fifty that appeared to be normal. For the purpose of taking blood samples, each ewe had its jugular vein pierced. Nucleotide sequence differences for the immunological (alpha-2-macroglobulin, toll-like receptor 2, transforming growth factor beta, interleukin 1 receptor-associated kinase 3, high-mobility group box 1, Fc alpha and Mu receptor, and inducible nitric oxide synthase), metabolic (ADAM metallopeptidase with thrombospondin type 1 motif 20, potassium sodium-activated channel subfamily T member 2, Mitogen-activated protein kinase kinase kinase 4, FKBP prolyl isomerase 5, and relaxin family peptide receptor 1), and antioxidant (superoxide dismutase, catalase, NADH: ubiquinone oxidoreductase subunit s5, and Heme oxygenase-1) genes were found among sheep with endometritis and those in good condition utilizing PCR-DNA sequencing. Fisher’s exact test revealed a significant difference in the probability of dispersal of all significant nucleotide changes between ewe groups with and without endometritis (p ˂ 0.01). In endometritis ewes, there was a considerable up-regulation of the expression levels of A2M, TLR2, IRAK3, HMGB1, FCAMR, iNOS, ADAMTS20, KCNT2, MAP3K4, FKBP5, RXFP1, and HMOX1. Conversely, there was a down-regulation of the genes that encode TGF-β, SOD, CAT, and NDUFS5. The kind of marker and its frequency in postparturient endometrtits significantly impacted the transcript levels of the indicators under analysis. The results validate that nucleotide changes and gene manifestation outlines in these candidates are significant predictors of the prevalence of endometritis in sheep.

The McDonald and Kreitman test is one of the most powerful and widely used methods to detect and quantify recurrent natural selection in DNA sequence data. One of its main limitations is the underestimation of positive selection due to the presence of slightly deleterious variants segregating at low frequencies. Although several approaches have been developed to overcome this limitation, most of them work on gene pooled analyses. Here, we present the imputed McDonald and Kreitman test (impMKT), a new straightforward approach for the detection of positive selection and other selection components of the distribution of fitness effects at the gene level. We compare imputed McDonald and Kreitman test with other widely used McDonald and Kreitman test approaches considering both simulated and empirical data. By applying imputed McDonald and Kreitman test to humans and Drosophila data at the gene level, we substantially increase the statistical evidence of positive selection with respect to previous approaches (e.g. by 50% and 157% compared with the McDonald and Kreitman test in Drosophila and humans, respectively). Finally, we review the minimum number of genes required to obtain a reliable estimation of the proportion of adaptive substitution (a) in gene pooled analyses by using the imputed McDonald and Kreitman test compared with other McDonald and Kreitman test implementations. Because of its simplicity and increased power to detect recurrent positive selection on genes, we propose the imputed McDonald and Kreitman test as the first straightforward approach for testing specific evolutionary hypotheses at the gene level. The software implementation and population genomics data are available at the web-server imkt.uab.cat. [ABSTRACT FROM AUTHOR]

Phylogeographic research concerning Central China has been rarely conducted. Population genetic and phylogeography of Ziziphus jujuba var. spinosa (also called sour jujube) were investigated to improve our understanding of plant phylogeographic patterns in Central China. Single‐copy nuclear gene markers and complete chloroplast genome data were applied to 328 individuals collected from 21 natural populations of sour jujube in China. Nucleotide variation of sour jujube was relatively high (π = 0.00720, θw = 0.00925), which resulted from the mating system and complex population dynamics. Analysis of molecular variation analysis revealed that most of the total variation was attributed to variation within populations, and a high level of genetic differentiation among populations was detected (Fst = 0.197). Relatively low long‐distance dispersal capability and vitality of pollen contributed to high genetic differentiation among populations. Differences in the environmental conditions and long distance among populations further restricted gene flow. Structure clustering analysis uncovered intraspecific divergence between central and marginal populations. Migrate analysis found a high level of gene flow between these two intraspecific groups. Bayesian skyline plot detected population expansion of these two intraspecific groups. Network and phylogeny analysis of chloroplast haplotypes also found intraspecific divergence, and the divergence time was estimated to occur at about 55.86 Ma. Haplotype native to the Loess Plateau was more ancient, and multiple glacial refugia of sour jujube were found to locate at the Loess Plateau, areas adjacent to the Qinling Mountains and Tianmu Mountains. Species distribution model analysis found a typical contraction‐expansion model corresponding to the Quaternary climatic oscillations. In the future, the distribution of sour jujube may shift to high‐latitude areas. This study provides new insights for phylogeographic research of temperate plant species distributed in Central China and sets a solid foundation for the application of the scientific management strategy of Z. jujuba var. spinosa. [ABSTRACT FROM AUTHOR]

Abstract Phylogeographic research concerning Central China has been rarely conducted. Population genetic and phylogeography of Ziziphus jujuba var. spinosa (also called sour jujube) were investigated to improve our understanding of plant phylogeographic patterns in Central China. Single‐copy nuclear gene markers and complete chloroplast genome data were applied to 328 individuals collected from 21 natural populations of sour jujube in China. Nucleotide variation of sour jujube was relatively high (π = 0.00720, θw = 0.00925), which resulted from the mating system and complex population dynamics. Analysis of molecular variation analysis revealed that most of the total variation was attributed to variation within populations, and a high level of genetic differentiation among populations was detected (Fst = 0.197). Relatively low long‐distance dispersal capability and vitality of pollen contributed to high genetic differentiation among populations. Differences in the environmental conditions and long distance among populations further restricted gene flow. Structure clustering analysis uncovered intraspecific divergence between central and marginal populations. Migrate analysis found a high level of gene flow between these two intraspecific groups. Bayesian skyline plot detected population expansion of these two intraspecific groups. Network and phylogeny analysis of chloroplast haplotypes also found intraspecific divergence, and the divergence time was estimated to occur at about 55.86 Ma. Haplotype native to the Loess Plateau was more ancient, and multiple glacial refugia of sour jujube were found to locate at the Loess Plateau, areas adjacent to the Qinling Mountains and Tianmu Mountains. Species distribution model analysis found a typical contraction‐expansion model corresponding to the Quaternary climatic oscillations. In the future, the distribution of sour jujube may shift to high‐latitude areas. This study provides new insights for phylogeographic research of temperate plant species distributed in Central China and sets a solid foundation for the application of the scientific management strategy of Z. jujuba var. spinosa.

The tree Cryptomeria japonica var. sinensis is native to China and is an important forest species widely used for wood production. Here, we sequenced the complete chloroplast (cp) genomes of six wild and six cultivated accessions of this tree. The 12 cp genomes ranged from 131,379 to 131,528 bp. The GC content was 35.4%, similar to other gymnosperm species. The cp genomes lacked typical inverted repeat (IR) regions and encoded 118 genes. Most genes appeared in one copy and 17 genes contained introns. Two multi-copy genes (trnM-CAU × 3, trnQ-UUG × 2) were identified. And 59–61 simple sequence repeats (SSRs) were identified in the whole cp genomes, and most SSR loci consisted of A or T bases. Phylogenetic analysis indicated that wild and cultivated accessions were not clearly differentiated. Our results will provide useful information for the conservation and utilization of this variety. Supplemental data for this article is available online at https://doi.org/10.1080/13102818.2021.1932592 .

Stephania cepharantha Hayata (S. cepharantha) is a common folk medicine herb in China with many therapeutic activities. This study used Illumina sequencing technology to construct a circular chloroplast genome map and compared it with that of other Stephania species. The genome of S. cepharantha is 158,052 bp in length, including a large single-copy region of 88,770 bp, a small single-copy region of 19,760 bp, and two reverse repeat regions of 49,522 bp. The genome encodes eight ribosomal ribonucleic acid (RNA) genes, 37 transfer RNA genes, and 85 protein-coding genes. Nucleotide variation analysis revealed that six highly variable regions of Stephania can be used as potential molecular markers for taxonomic research and evolutionary analysis. This study is the first chloroplast genome report on S. cepharantha, and it provides rich and valuable genetic information for understanding the evolutionary relationships and population inheritance of the species. [ABSTRACT FROM AUTHOR]

Rubus hirsutus is a type of tonifying kidney-essence herb that belongs to the Rosaceae family, and has been commonly used to treat multiple diseases, such as polyuria, impotence, and infertility. In this study, we determined the complete chloroplast sequence of R. hirsutus and conduced a comparative analysis within the genus Rubus. The assembled chloroplast (cp.) genome is 156,380 bp in length with a GC content of 37.0% and shares a conserved quadripartite structure within the other cp. genomes in this genus. A total of 132 unique genes were annotated in the cp. genome of R. hirsutus, which contained 87 protein-coding genes, 37 tRNAs, and eight rRNAs. Seventeen duplicated genes were identified in the inverted repeats region. Furthermore, 70 simple sequence repeats and 35 long repeats were detected in total in the R. hirsutus chloroplast genome. Eight mutational hotspots were identified in the cp. genome of this species with higher nucleotide variations in non-coding regions than those of coding regions. Furthermore, the gene order, codon usage, and repeat sequence distribution were highly consistent in Rubus according to the results of a comparative analysis. A phylogenetic analysis indicated that there was a sister relationship between R. hirsutus and R. chingii. Overall, the complete chloroplast genome of R. hirsutus and the comparative analysis will help to further the evolutionary study, conservation, phylogenetic reconstruction, and development of molecular barcodes for the genus Rubus. [ABSTRACT FROM AUTHOR]

SNPs are the most common nucleotide variations in the genome. Functional SNPs in the coding region, known as nonsynonymous SNPs (nsSNPs), change amino acid residues and affect protein function. Identifying functional SNPs is an uphill task as it is difficult to correlate between variation and phenotypes in association studies. Computational in silico analysis provides an opportunity to understand the SNPs functional impact to proteins and facilitate experimental approaches in understanding the relationship between the phenotype and genotype. Advancement in sequencing technologies contributed to sequencing thousands of genomes. As a result, many public databases have been designed incorporating this sequenced data to explore nucleotide variations. In this study, we explored functional SNPs in the rice GPAT family (as a model plant gene family), using 3000 Rice Genome Sequencing Project data. We identified 1056 SNPs, among hundred rice varieties in 26 GPAT genes, and filtered 98 nsSNPs. We further investigated the structural and functional impact of these nsSNPs using various computational tools and shortlisted 13 SNPs having high damaging effects on protein structure. We found that rice GPAT genes can be influenced by nsSNPs and they might have a major effect on regulation and function of GPAT genes. This information will be useful to understand the possible relationships between genetic mutation and phenotypic variation, and their functional implication on rice GPAT proteins. The study will also provide a computational pathway to identify SNPs in other rice gene families.

β-amylase is a thermostable enzyme that hydrolyses starch during cooking of sweetpotato (Ipomoea batatas) storage roots, thereby influencing eating quality. Its activity is known to vary amongst genotypes but the genetic diversity of the beta-amylase gene (Amyβ) is not well studied. Amyβ has a highly conserved region between exon V and VI, forming part of the enzyme's active site. To determine the gene diversity, a 2.3 kb fragment, including the conserved region of the Amyβ gene was sequenced from 25 sweetpotato genotypes. The effect of sequence variation on gene expression, enzyme activity, and firmness in cooked roots was determined. Six genotypes carrying several SNPs within exon V, linked with an AT or ATGATA insertion in intron V were unique and clustered together. The genotypes also shared an A336E substitution in the amino acid sequence, eight residues upstream of a substrate-binding Thr344. The genotypes carrying this allele exhibited low gene expression and low enzyme activity. Enzyme activity was negatively correlated with firmness (R = −0.42) in cooked roots. This is the first report of such an allele, associated with low enzyme activity. These results suggest that genetic variation within the AmyB locus can be utilized to develop markers for firmness in sweetpotato breeding.

SNPs are the most common nucleotide variations in the genome. Functional SNPs in the coding region, known as nonsynonymous SNPs (nsSNPs), change amino acid residues and affect protein function. Identifying functional SNPs is an uphill task as it is difficult to correlate between variation and phenotypes in association studies. Computational in silico analysis provides an opportunity to understand the SNPs functional impact to proteins and facilitate experimental approaches in understanding the relationship between the phenotype and genotype. Advancement in sequencing technologies contributed to sequencing thousands of genomes. As a result, many public databases have been designed incorporating this sequenced data to explore nucleotide variations. In this study, we explored functional SNPs in the rice GPAT family (as a model plant gene family), using 3000 Rice Genome Sequencing Project data. We identified 1056 SNPs, among hundred rice varieties in 26 GPAT genes, and filtered 98 nsSNPs. We further investigated the structural and functional impact of these nsSNPs using various computational tools and shortlisted 13 SNPs having high damaging effects on protein structure. We found that rice GPAT genes can be influenced by nsSNPs and they might have a major effect on regulation and function of GPAT genes. This information will be useful to understand the possible relationships between genetic mutation and phenotypic variation, and their functional implication on rice GPAT proteins. The study will also provide a computational pathway to identify SNPs in other rice gene families. [ABSTRACT FROM AUTHOR]

Abstract Clonal evolution of chronic lymphocytic leukemia (CLL) often follows chemotherapy and is associated with adverse outcome, but also occurs in untreated patients, in which case its predictive role is debated. We investigated whether the selection and expansion of CLL clone(s) precede an aggressive disease shift. We found that clonal evolution occurs in all CLL patients, irrespective of the clinical outcome, but is faster during disease progression. In particular, changes in the frequency of nucleotide variants (NVs) in specific CLL-related genes may represent an indicator of poor clinical outcome.

Abstract Background Myogenic Differentiation 1 (MyoD) is a crucial master switch in regulating muscle-specific gene transcription. Forced expression of myoD is equipped to induce several cell lineages into myoblast, which then differentiate and fuse into myotube. Pig is one of the most significant livestock supplying meat, and has been classified into lean, fat and miniature pig breeds. However, the mechanisms underlying muscle mass variation among different pig breeds have remained unclear. Considering the important effect of MyoD on muscle development, it remains to be investigated whether the difference in muscle mass is caused by its single nucleotide polymorphisms (SNPs) which are the major differences among pig breeds at DNA level. Results In this study, we identified the locations of porcine myoD regulatory regions including proximal regulatory region (PRR), distal regulatory region (DRR), and core enhancer (CE) region. There are 8 SNPs in the regulatory regions and 6 SNPs in gene body region, which were identified from lean, fat and miniature pig populations. However, these SNPs have no effects on its temporal expression and transcriptional activity which might lead to the distinction in postnatal muscle mass. In addition, overexpression of myoD clones across from amphibious to mammals including xenopus tropicalis, chicken, mouse and pig whose gene identities vary from 68 to 84%, could promote myogenesis in NIH3T3 fibroblasts cells. Conclusions These results proved that myoD nucleotide variations from different pig populations have no effect on muscle mass, suggesting that the function of myoD is highly conserved not only among different pig breeds, but also across different species. Thus, it would be futile to discover SNPs affecting muscle mass in pig populations with normal muscle development.

The natural resistance-associated macrophage protein 1 (NRAMP1) gene in chickens, which exists on chromosome 7, is thought to play a significant role in disease resistance. Variations in this gene have been documented and have played crucial roles in the variations in the resistance and/or susceptibility that is expressed by individuals and different groups of animal species. In this study, the NRAMP1 gene was studied for single nucleotide polymorphism (SNP) variability between indigenous and exotic chicken breeds. The gene was amplified using the polymerase chain reaction (PCR) method and sequenced and analyzed. Six SNPs, both synonymous and non-synonymous (C3700T, G3702C, A3712C, C3714G, C3693G, and G3705T), were detected in the gene in both indigenous and exotic chicken types. One allele form was detected among all the sample animals that were studied. A phylogenetic tree revealed that the indigenous chicken type and the exotic broiler chicken type are genetically similar with respect to this gene. However, the exotic layer chicken type is genetically suggested to be distantly related to both the indigenous and broiler chicken types, indicating that the gene has probably been evolving both within and among different poultry species.

Abstract Background Liriodendron is a genus of Magnoliaceae, which consists of two relict species, Liriodendron chinense and L. tulipifera. Although the morphologies are highly similar, the two species exhibit different adaptive capacity. Dehydrins (DHNs) are abiotic stresses resistant proteins in planta, which are associated with adaptive evolution. To better understand the evolution divergence between L. chinense and L. tulipifera and how DHN genes are associated with adaptation evolution, we firstly investigated the DNA polymorphisms of the LcDHN-like gene in 21 L. chinense and 6 L. tulipifera populations. Results A 707 bp LcDHN-like gene was cloned, which included a 477 bp open reading frame (ORF) and coding 158 amino acids. 311 LcDHN-like gDNA sequences were obtained from 70 L. chinense and 35 L. tulipifera individuals. The AMOVA and phylogenetic relationship analysis showed significant differences between the two species. A higher genetic diversity was observed in L. tulipifera compared to L. chinense, in consistent with the higher adaptive capacity of L. tulipifera. Our data also suggested that the LcDHN-like genes’ polymorphisms were under neutral mutation and purifying selection model in the L. chinense and L. tulipifera populations, respectively. The distinct expanding range and rate between the two species, haplotypes shared only in L.chinense’s nearby populations, and wide dispersals in L. tulipifera could contribute to the obscure east-west separation in L. chinense and entirely unordered phylogeny in L. tulipifera. The completely separated nonsynonymous substitution at position 875 and the higher range scope of aliphatic index in L. tulipifera populations may be related with its higher adaptive capacity. Taken together, our study suggests LcDHN-like gene is a potential mark gene responsible for adaptive evolution divergence in Liriodendron. Conclusions Significant differences and completely distinct haplogroups between L. chinense and L. tulipifera showed that the two species have evolved into different directions. The more widely distribution, earlier haplogroups divergence events, and richer SNPs variations in L. tulipifera could imply its stronger adaptation in this species. And potential effect of the allelic variations in LcDHN-like gene may reflect the difference of water stress and chill tolerance between L. chinense and L. tulipifera, which could provide some information for further adaption evolution studies of Liriodendron.

The tree Cryptomeria japonica var. sinensis is native to China and is an important forest species widely used for wood production. Here, we sequenced the complete chloroplast (cp) genomes of six wild and six cultivated accessions of this tree. The 12 cp genomes ranged from 131,379 to 131,528 bp. The GC content was 35.4%, similar to other gymnosperm species. The cp genomes lacked typical inverted repeat (IR) regions and encoded 118 genes. Most genes appeared in one copy and 17 genes contained introns. Two multi-copy genes (trnM-CAU × 3, trnQ-UUG × 2) were identified. And 59–61 simple sequence repeats (SSRs) were identified in the whole cp genomes, and most SSR loci consisted of A or T bases. Phylogenetic analysis indicated that wild and cultivated accessions were not clearly differentiated. Our results will provide useful information for the conservation and utilization of this variety. Supplemental data for this article is available online at https://doi.org/10.1080/13102818.2021.1932592. [ABSTRACT FROM AUTHOR]

Tandemly arranged paralogous genes lbe and lbl are members of the Drosophila NK homeobox family. We analyzed population samples of Drosophila melanogaster from Africa, Europe, North and South America, and single strains of D. sechellia, D. simulans, and D. yakuba within two linked regions encompassing partial sequences of lbe and lbl. The evolution of lbe and lbl is highly constrained due to their important regulatory functions. Despite this, a variety of forces have shaped the patterns of variation in lb genes: recombination, intragenic gene conversion and natural selection strongly influence background variation created by linkage disequilibrium and dimorphic haplotype structure. The two genes exhibited similar levels of nucleotide diversity and positive selection was detected in the noncoding regions of both genes. However, synonymous variability was significantly higher for lbe: no nonsynonymous changes were observed in this gene. We argue that balancing selection impacts some synonymous sites of the lbe gene. Stability of mRNA secondary structure was significantly different between the lbe (but not lbl) haplotype groups and may represent a driving force of balancing selection in epistatically interacting synonymous sites. Balancing selection on synonymous sites may be the first, or one of a few such observations, in Drosophila. In contrast, recurrent positive selection on lbl at the protein level influenced evolution at three codon sites. Transcription factor binding-site profiles were different for lbe and lbl, suggesting that their developmental functions are not redundant. Combined with our previous results on nucleotide variation in esterase and other homeobox genes, these results suggest that interplay of balancing and directional selection may be a general feature of molecular evolution in Drosophila and other eukaryote genomes.

The natural resistance-associated macrophage protein 1 (NRAMP1) gene in chickens, which exists on chromosome 7, is thought to play a significant role in disease resistance. Variations in this gene have been documented and have played crucial roles in the variations in the resistance and/or susceptibility that is expressed by individuals and different groups of animal species. In this study, the NRAMP1 gene was studied for single nucleotide polymorphism (SNP) variability between indigenous and exotic chicken breeds. The gene was amplified using the polymerase chain reaction (PCR) method and sequenced and analyzed. Six SNPs, both synonymous and non-synonymous (C3700T, G3702C, A3712C, C3714G, C3693G, and G3705T), were detected in the gene in both indigenous and exotic chicken types. One allele form was detected among all the sample animals that were studied. A phylogenetic tree revealed that the indigenous chicken type and the exotic broiler chicken type are genetically similar with respect to this gene. However, the exotic layer chicken type is genetically suggested to be distantly related to both the indigenous and broiler chicken types, indicating that the gene has probably been evolving both within and among different poultry species. [ABSTRACT FROM AUTHOR]

This study has mainly focused on ecological issues of Section Heterobalanus, which contains about nine sclerophyllous alpine species and occurs mainly in the China Mountains. To investigate the population history and demography of an endemic oak species (Quercus aquigolioides, Fagaceae) from the Himalaya- Hengduan Mountains region, and elucidate how the unique climatic conditions and heterogeneous topography resulted the uplift of the QTP shaped the genetic diversity and evolutionary history of the species. We sequenced and analyzed a total 1406 base pairs from chloroplast DNA (cpDNA) trnT-L sequences for 296 individuals from 19 populations across the species' geographic range. Based on these data, we constructed the genealogical relationships and coalescent analysis was used to test demographic hypotheses. 38 haplotypes were identified based on cpDNA variation, and of overall 38 haplotypes, 33 hyplotypes are restricted to single population. High levels of haplotype diversity (Hd=0.948) and low levels of nucleotide diversity (p=0.1976) were detected within the whole species, and a great amount of variation occurred among populations within groups (57.3%). The phylogenetic result demonstrated that Q. aquifolioides cpDNA hyplotypes have three main genetic lineages with distinct distribution. And these genetic lineages resulted by two main bottlenecks in the species took place at 9.37Ma and 8.41Ma, and they have undergone several genetic bottlenecks for a time span of ca. 9 million years. Significant interpopulation differentiation and phylogeopgraphic structure were also detected (GST=0.629, NST= 0.946, NST>GST, P<0.01), and the mismatch distribution analyses indicated a demographic equilibrium for Q. aquifolioides. But as a result of its complex topography, the overall network gave no clear indication regarding demographic process. Together with fossil evidence, the results strongly suggested that multiple microrefugia of Q. aquifolioides existing and the microrefugia were scattered throughout the present geographical range before the Last Glacial Maximum (LGM). Although this species seems to have post-glacial expansion, Q. aquifolioides did not undergo marked changes in population sizes from the late Miocene. And the uplift of the QTP contributed to the phylogeny of cpDNA hyplotypes and differentiation among the population by heterogeneous topographies and climatic change formed the uplift. The two main genetic bottlenecks at ca. 9Ma could contribute to the uplift of eastern and southern QTP at 13-8Ma and strengthen of Asian Summer monsoon at same time causing by the uplift. And several genetic differentiations at ca. 3Ma could confirm with the uplift of the QTP since 3.6Ma. It was reasonable to conclude that the Mio-Pliocene growth of the QTP and the accompanied climatic changes could account for the modern pattern of Q. aquifolioides phylogenetic structure in the HHMs region: first, the center and northern QTP drought and the different evaluation in south and east margin at 13-8Ma made the three main different lineages (NW group and other all). Then the asynchronous and heterogeneous uplifting of QTP in different regions during 9-0.7 Ma resulted to the difference time of the bottleneck in the different lineages. These findings have wide implications for understanding plant species' responses to the uplift of QTP and climatic change with it. [ABSTRACT FROM AUTHOR]

Background: Liriodendron is a genus of Magnoliaceae, which consists of two relict species, Liriodendron chinense and L. tulipifera. Although the morphologies are highly similar, the two species exhibit different adaptive capacity. Dehydrins (DHNs) are abiotic stresses resistant proteins in planta, which are associated with adaptive evolution. To better understand the evolution divergence between L. chinense and L. tulipifera and how DHN genes are associated with adaptation evolution, we firstly investigated the DNA polymorphisms of the LcDHN-like gene in 21 L. chinense and 6 L. tulipifera populations. Results: A 707 bp LcDHN-like gene was cloned, which included a 477 bp open reading frame (ORF) and coding 158 amino acids. 311 LcDHN-like gDNA sequences were obtained from 70 L. chinense and 35 L. tulipifera individuals. The AMOVA and phylogenetic relationship analysis showed significant differences between the two species. A higher genetic diversity was observed in L. tulipifera compared to L. chinense, in consistent with the higher adaptive capacity of L. tulipifera. Our data also suggested that the LcDHN-like genes' polymorphisms were under neutral mutation and purifying selection model in the L. chinense and L. tulipifera populations, respectively. The distinct expanding range and rate between the two species, haplotypes shared only in L.chinense's nearby populations, and wide dispersals in L. tulipifera could contribute to the obscure east-west separation in L. chinense and entirely unordered phylogeny in L. tulipifera. The completely separated nonsynonymous substitution at position 875 and the higher range scope of aliphatic index in L. tulipifera populations may be related with its higher adaptive capacity. Taken together, our study suggests LcDHN-like gene is a potential mark gene responsible for adaptive evolution divergence in Liriodendron. Conclusions: Significant differences and completely distinct haplogroups between L. chinense and L. tulipifera showed that the two species have evolved into different directions. The more widely distribution, earlier haplogroups divergence events, and richer SNPs variations in L. tulipifera could imply its stronger adaptation in this species. And potential effect of the allelic variations in LcDHN-like gene may reflect the difference of water stress and chill tolerance between L. chinense and L. tulipifera, which could provide some information for further adaption evolution studies of Liriodendron. [ABSTRACT FROM AUTHOR]

Lipin 1 plays an important role in lipid metabolism. In this study; we searched for variation in the ovine lipin 1 gene (LPIN1) in three gene regions (a 5′ non-coding region; a region containing an alternatively spliced exon in intron 4; and a region containing coding exon 6) using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis. The greatest amount of alleles was found in coding exon 6; with five sequences being detected. The effect of variation in this exon was investigated in 242 New Zealand Romney lambs derived from 12 sire-lines. The presence of variant E3 was associated with a decrease in birth weight (p = 0.005) and the proportion of leg yield (p = 0.045), but with an increase in hot carcass weight (p = 0.032) and the proportion of loin yield (p = 0.014). The presence of variant B3 was associated with an increased pre-weaning growth rate (p = 0.041), whereas the presence of variant C3 was associated with an increase in shoulder yield (p < 0.001). These results suggest that ovine LPIN1 variation may have value as a genetic marker for improving meat production and carcass traits.

The Acinetobacter baumannii virulence protein Bap is encoded by a large gene and contains both variable sequence and repetitive modules. To date, four primer sets targeting different regions of bap have been designed, but no study has evaluated all these primers simultaneously for detection of bap. Here, we assessed the effect of primer sets Bap I-IV, on detection of bap both in silico and in vitro. Using the primer set Bap II, all 143 tested strains yielded an amplicon corresponding to the bap gene. This primer set showed the highest sensitivity (100, 95% CI: 97·9-100%) compared to the other primer sets. This study demonstrates that primer set Bap II performs with optimal efficiency for detection of the bap gene among different strains. Significance and Impact of the Study This study investigated the effect of nucleotide variation on PCR detection of the bap gene in various Acinetobacter baumannii strains. Since bap is the target gene for many detection assays, this variation can affect the detection efficiency. Here we present a primer set Bap II with optimal detection efficiency amongst 143 different strains, as shown by in silico and in vitro evidence. [ABSTRACT FROM AUTHOR]

Background: Analysis of phylogenetic relationship of 91 isolates of Phellinus noxius obtained from 46 plant species in Taiwan did not show distinct grouping based on ITS sequences. Results: However, the ITS nucleotides showed 20 different kinds of variations including single nucleotide polymorphisms, deletion and insertion in ITS1 and ITS2, but none in 5.8 S. The Taiwanese isolates of P. noxius were dividable into long (type L), median (type M) and short (type S) groups based on ITS sequence length. Two isolates with identical ITS sequence belonged to types L. Type M with 72 isolates was further divided into 33 subtypes, while types S with 17 isolates was further divided into two subtypes. Conclusion: Phylogenetic analysis of ITS sequences among Phellinus species showed that isolates of P. noxius were in the same clade distinctly separated from other Phellinus species. [ABSTRACT FROM AUTHOR]

In summer 2015, cucumber and tomato plants with collaps and decline symptoms were collected from fields in Bajgah and Kaftarak regions in Fars province and transported to the laboratory. After isolation of the causal agent, single spore colonies were derived prior to morphological identification. Colonies on PDA plates were buff or salmon pink; the mycelium was slimy with sparse or absent aerial hyphae. Conidiophores were solitary, unbranched or rarely irregularly branched and the conidiogenous cells could be described as phialidic, hyaline and smooth. Occasionally the conidiogenous cells showed one septa near the base. Conidia were aggregated in slimy heads, hyaline, ellipsoidal, tapering gradually to rounded apex and base, septate or aseptate. These characteristics are typical of Plectosphaerella cucumerina (Lindf.) W. Gams. (anamorph: Plectsporium tabacinum). The internal transcribed spacer (ITS) region of the isolates was amplified using primers ITS1 and ITS4 and sequenced. Blast analysis of the sequences showed identity of the isolates to P. cucumerina. Based on sequence analysis of ITS region, the fungal isolates showed nucleotide variation. Bajgah and Kaftarak isolates were identified as two molecular subgroups. Pathogenicity tests were also conducted on tomato, cucumber, pepper, watermelon and melon plants. 3-4 weeks after inoculation, 70% inoculated plants showed symptoms including wilting, root and collar rot, dwarfing of stem and root and death of seedling. This is the first report of P. cucumerina causing tomato and cucumber collapse in Iran with characterization of the fungus based on morphological, pathogenicity and molecular data. [ABSTRACT FROM AUTHOR]

Small double-stranded RNAs (dsRNAs) of approximately 21-nucleotides in size, referred to as small interfering RNA (siRNA) duplexes, can induce sequence-specific posttranscriptional gene silencing, or RNA interference (RNAi). Since chemically synthesized siRNA duplexes were found to induce RNAi in mammalian cells, RNAi has become a powerful reverse genetic tool for suppressing the expression of a gene of interest in mammals, including human, and its application has been expanding to various fields. Recent studies further suggest that synthetic siRNA duplexes have the potential for specifically inhibiting the expression of an allele of interest without suppressing the expression of other alleles, i.e., siRNA duplexes likely confer allele-specific silencing. Such gene silencing by RNAi is an advanced technique with very promising applications. In this review, I would like to discuss the potential utility of allele-specific silencing by RNAi as a therapeutic method for dominantly inherited diseases, and describe possible improvements in siRNA duplexes for enhancing their efficacy.

The genus Jatropha (Euphorbiaceae) contains species that are of significant economic and ornamental value. However, Jatropha breeding material is rather limited due to incomplete information regarding phylogenetic relationships among germplasm resources. Phylogenetic analyses were performed based on the internal transcribed spacer of nuclear ribosomal DNA (nrDNA ITS), two chloroplast regions ( trnL-F and rbcL), and the combined (ITS+ trnL-F+ rbcL) dataset among twenty-five specimens representing six key Jatropha species. Phylogenetic relationships of Jatropha were well resolved between subgenus Curcas and subgenus Jatropha, and demonstrated the intermediate position of section Polymorphae among sections of both subgenera. Jatropha curcas and J. integerrima demonstrated a close phylogenetic relationship. The molecular data agreed with the morphological classification that recognized J. multifida and J. podagrica in sec. Peltatae. The distinct intraspecific divergence that occurred in J. curcas could be attributed to restricted gene flow caused by geographical isolation and different ecological conditions. Phylograms produced with trnL-F and rbcL sequence data suggested slow rates of sequence divergence among Jatropha spp., while the ITS gene tree had good resolution suggesting high genetic variation of ITS among Jatropha species. [ABSTRACT FROM AUTHOR]

Background: Mungbean (Vigna radiata [L.] R. Wilczek) is an important legume crop with high nutritional value in South and Southeast Asia. The crop plant is susceptible to a storage pest caused by bruchids (Callosobruchus spp.). Some wild and cultivated mungbean accessions show resistance to bruchids. Genomic and transcriptomic comparison of bruchid-resistant and -susceptible mungbean could reveal bruchid-resistant genes (Br) for this pest and give insights into the bruchid resistance of mungbean. Results: Flow cytometry showed that the genome size varied by 61 Mb (mega base pairs) among the tested mungbean accessions. Next generation sequencing followed by de novo assembly of the genome of the bruchid-resistant recombinant inbred line 59 (RIL59) revealed more than 42,000 genes. Transcriptomic comparison of bruchid-resistant and -susceptible parental lines and their offspring identified 91 differentially expressed genes (DEGs) classified into 17 major and 74 minor bruchid-resistance-associated genes. We found 408 nucleotide variations (NVs) between bruchid-resistant and -susceptible lines in regions spanning 2 kb (kilo base pairs) of the promoters of 68 DEGs. Furthermore, 282 NVs were identified on exons of 148 sequence-changed-protein genes (SCPs). DEGs and SCPs comprised genes involved in resistant-related, transposable elements (TEs) and conserved metabolic pathways. A large number of these genes were mapped to a region on chromosome 5. Molecular markers designed for variants of putative bruchid-resistance-associated genes were highly diagnostic for the bruchid-resistant genotype. Conclusions: In addition to identifying bruchid-resistance-associated genes, we found that conserved metabolism and TEs may be modifier factors for bruchid resistance of mungbean. The genome sequence of a bruchid-resistant inbred line, candidate genes and sequence variations in promoter regions and exons putatively conditioning resistance as well as markers detecting these variants could be used for development of bruchid-resistant mungbean varieties. [ABSTRACT FROM AUTHOR]

Historical tectonism and climate oscillations can isolate and contract the geographical distributions of many plant species, and they are even known to trigger species divergence and ultimately speciation. Here, we estimated the nucleotide variation and speciation in three closely related Populus species, Populus tremuloides, P. tremula and P. davidiana, distributed in North America and Eurasia. We analysed the sequence variation in six single-copy nuclear loci and three chloroplast (cp DNA) fragments in 497 individuals sampled from 33 populations of these three species across their geographic distributions. These three Populus species harboured relatively high levels of nucleotide diversity and showed high levels of nucleotide differentiation. Phylogenetic analysis revealed that P. tremuloides diverged earlier than the other two species. The cp DNA haplotype network result clearly illustrated the dispersal route from North America to eastern Asia and then into Europe. Molecular dating results confirmed that the divergence of these three species coincided with the sundering of the Bering land bridge in the late Miocene and a rapid uplift of the Qinghai-Tibetan Plateau around the Miocene/Pliocene boundary. Vicariance-driven successful allopatric speciation resulting from historical tectonism and climate oscillations most likely played roles in the formation of the disjunct distributions and divergence of these three Populus species. [ABSTRACT FROM AUTHOR]

Micro-RNA (miRNA) genes encode abundant small regulatory RNAs that play key roles during development and in homeostasis by fine tuning and buffering gene expression. This layer of regulatory control over transcriptional networks is preserved by selection across deep evolutionary time, yet selection pressures on individual miRNA genes in contemporary populations remain poorly characterized in any organism. Here, we quantify nucleotide variability for 129 miRNAs in the genome of the nematode Caenorhabditis remanei tounderstandthemicroevolutionof this important classof regulatorygenes. Our analysis of threepopulation samples and C. remanei's sister species revealed ongoing natural selection that constrains evolution of all sequence domains within miRNA hairpins. We also show that new miRNAs evolve faster than older miRNAs but that selection nevertheless favors their persistence. Despite the ongoing importance of purging of new mutations, we discover a trove of >400 natural miRNA sequence variants that include single nucleotide polymorphisms in seed motifs, indels that ablatemiRNAfunctional domains, and origination of new miRNAs by duplication. Moreover, we demonstrate substantial nucleotide divergence of pre-miRNA hairpin alleles between populations andsister species. These findings from the first global survey ofmiRNAmicroevolution in Caenorhabditis support the idea that changes in gene expression, mediated through divergence in miRNA regulation, can contribute to phenotypic novelty and adaptation to specific environments in the present day as well as the distant past. [ABSTRACT FROM AUTHOR]

Helianthus is an economically important and genetically diverse genus, containing both evolutionary model species and cultivated species. Genetic variation within this genus has been examined at many different scales, from genome size changes to chromosomal structure to nucleotide variation. The growing amount of genomic resources within the genus has yielded insights into the importance of paleopolyploid events, and how transposable elements can cause rapid genome size increases. The rapidly evolving chromosomes in Helianthus have provided a system whereby it has been possible to study how chromosomal rearrangements impact speciation, adaptation and introgression. Population and quantitative genetic studies have used the abundant nucleotide variation to identify a number of candidate genes which may be involved in both local adaptation and domestication. The results from these investigations have provided basic knowledge about evolution and how to utilize genetic resources for both agriculture and conservation. Targeting Helianthus for further study as new technologies emerge will allow for a better understanding of how different types of genomic variation interact and contribute to phenotypic variation in a complex system that is ecologically and economically significant. [ABSTRACT FROM AUTHOR]