-
Qvist Estes posted an update 10 days ago
In addition to Wurfbainia longiligularis, the ψycf1 was discovered among the 25 Zingiberaceae species. The shared protein coding genes from 52 Zingiberales plants and four other family species as out groups were used to construct phylogenetic trees distinguished by maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) and showed that Musaceae was the basal group in Zingiberales, and Curcuma had a close relationship with Stahlianthu. Besides this, Curcuma flaviflora was clustered together with Zingiber. Its distribution area (Southeast Asia) overlaps with the latter. Maybe hybridization occur in related groups within the same region. This may explain why Zingiberaceae species have a complex phylogeny, and more samples and genetic data were necessary to confirm their relationship. This study provide the reliable information and high-quality chloroplast genomes and genome resources for future Zingiberaceae research.Phytophthora root rot (PRR) caused by Phytophthora sojae is a serious disease of soybean. The most effective disease-control strategy is to deploy resistant cultivars carrying Rps genes. Soybean cultivar Yudou25 can effectively resist pathotypes of P. sojae in China. Previous studies have mapped the Rps gene in Yudou25, RpsYD25, on chromosome 3. In this study, at first RpsYD25 was located between SSR markers Satt1k3 (2.2 cM) and BARCSOYSSR_03_0253 (4.5 cM) by using an F23 population containing 165 families derived from Zaoshu18 and Yudou25. Then the recombination sites were identified in 1127 F34 families derived from Zaoshu18 and Yudou25 using the developed PCR-based SNP, InDel and SSR markers, and RpsYD25 was finely mapped in the a 101.3 kb genomic region. In this region, a zinc ion binding and nucleic acid binding gene Glyma.03g034700 and two NBS-LRR genes Glyma.03g034800 and Glyma.03g034900 were predicted as candidate genes of RpsYD25, and five co-segregated SSR markers with RpsYD25 were identified and validated to be diagnostic markers. Combined with the resistance reaction to multiple P. sojae isolates, seven of 178 soybean genotypes were detected to contain RpsYD25 using the five co-segregated SSR markers. The soybean genotypes carrying RpsYD25 and the developed co-segregated markers can be effectively applied in the breeding for P. sojae resistance in China.Functional assays that assess mRNA splicing can be used in interpretation of the clinical significance of sequence variants, including the Lynch syndrome-associated mismatch repair (MMR) genes. The purpose of this study was to investigate the contribution of splicing assay data to the classification of MMR gene sequence variants. We assayed mRNA splicing for 24 sequence variants in MLH1, MSH2, and MSH6, including 12 missense variants that were also assessed using a cell-free in vitro MMR activity (CIMRA) assay. Selleckchem Eprosartan Multifactorial likelihood analysis was conducted for each variant, combining CIMRA outputs and clinical data where available. We collated these results with existing public data to provide a dataset of splicing assay results for a total of 671 MMR gene sequence variants (328 missense/in-frame indel), and published and unpublished repair activity measurements for 154 of these variants. There were 241 variants for which a splicing aberration was detected 92 complete impact, 33 incomplete impact, and 116 where it was not possible to determine complete versus incomplete splicing impact. Splicing results mostly aided in the interpretation of intronic (72%) and silent (92%) variants and were the least useful for missense substitutions/in-frame indels (10%). MMR protein functional activity assays were more useful in the analysis of these exonic variants but by design they were not able to detect clinically important splicing aberrations identified by parallel mRNA assays. The development of high throughput assays that can quantitatively assess impact on mRNA transcript expression and protein function in parallel will streamline classification of MMR gene sequence variants.The domestic Bactrian camel is indispensable to agricultural production in the desertification area of China owning to its endurance to hunger and thirst, cold resistance, drought resistance, and good long-distance transportation. Therefore, it is necessary to investigate the genetic diversity, genetic structure, and genes with important roles in the evolution of this species. In this study, 1,568,087 SNPs were identified in 47 domestic Bactrian camels inhabiting four regions of China, namely Inner Mongolia, Gansu, Qinghai, and Xinjiang, by restriction site associated DNA sequencing (RAD-seq). The SNP data were used for nucleotide diversity analysis (π) and linkage disequilibrium (LD) attenuation analysis to elucidate the genetic diversity of the domestic Bactrian camel in the four regions studied. Results showed that Xinjiang camels had the highest nucleotide diversity and the fastest decay rate of the LD coefficient; therefore, Xinjiang camels had the highest genetic diversity. Structure analysis, principalllular component. Binding represented the main molecular function. In addition, the shared selected genes of the domestic Bactrian camel in the four regions of China were significantly enriched in the long-term depression pathway. The research should enable further study of the genetic resources of the domestic Bactrian camel, as well as the conservation of these resources.Apomixis, an asexual mode of reproduction through seeds, has immense scope for crop improvement due to its ability to fix hybrid vigor. In C. ciliaris, a predominantly apomictically reproducing range grass, apomixis is genetically controlled by an apospory-specific-genomic-region (ASGR) which is enriched with retrotransposons. Earlier studies showed insertional polymorphisms of a few ASGR-specific retrotransposons between apomictic and sexual plants of C. ciliaris. REs are mainly regulated at the transcriptional level through cytosine methylation. To understand the possible association of ASGR-specific retrotransposon to apomixis, the extent and pattern of differential methylation of Gy163 RE and its impact on transcription were investigated in two genotypes each of apomictic and sexual plants of C. ciliaris. We observed that Gy163 encodes for an integrase domain of RE Ty3-Gypsy, is differentially methylated between reproductive tissues of apomictic and sexual plants. However, leaf tissues did not exhibit differential methylation between apomictic and sexual plants.