Evolutionary history and pan-genome dynamics of strawberry (Fragaria spp.)

Strawberry (Fragaria spp.) has emerged as a model system for various fundamental and applied research in recent years. In total, the genomes of five different species have been sequenced over the past 10 y. Here, we report chromosome-scale reference genomes for five strawberry species, including three newly sequenced species’ genomes, and genome resequencing data for 128 additional accessions to estimate the genetic diversity, structure, and demographic history of key Fragaria species. Our analyses obtained fully resolved and strongly supported phylogenies and divergence times for most diploid strawberry species. These analyses also uncovered a new diploid species (Fragaria emeiensis Jia J. Lei). Finally, we constructed a pan-genome for Fragaria and examined the evolutionary dynamics of gene families. Notably, we identified multiple independent single base mutations of the MYB10 gene associated with white pigmented fruit shared by different strawberry species. These reference genomes and datasets, combined with our phylogenetic estimates, should serve as a powerful comparative genomic platform and resource for future studies in strawberry.

Chromosome-Scale Genome and Comparative Transcriptomic Analysis Reveal Transcriptional Regulators of β-Carotene Biosynthesis in Mango

Mango (2n = 2x = 40) is an important tropical/subtropical evergreen fruit tree grown worldwide and yields nutritionally rich and high-value fruits. Here, a high-quality mango genome (396 Mb, contig N50 = 1.03 Mb) was assembled using the cultivar “Irwin” from Florida, USA. A total of 97.19% of the sequences were anchored to 20 chromosomes, including 36,756 protein-coding genes. We compared the β-carotene content, in two different cultivars (“Irwin” and “Baixiangya”) and growth periods. The variation in β-carotene content mainly affected fruit flesh color. Additionally, transcriptome analysis identified genes related to β-carotene biosynthesis. MiPSY1 was proved to be a key gene regulating β-carotene biosynthesis. Weighted gene co-expression network analysis, dual luciferase, and yeast one-hybrid assays confirmed that transcription factors (TFs) MibZIP66 and MibHLH45 activate MiPSY1 transcription by directly binding to the CACGTG motif of the MiPSY1 promoter. However, the two TFs showed no significant synergistic effect on promoter activity. The results of the current study provide a genomic platform for studying the molecular basis of the flesh color of mango fruit.

PROMISE: a real-world clinical-genomic database to address knowledge gaps in prostate cancer

Purpose Prostate cancer is a heterogeneous disease with variable clinical outcomes. Despite numerous recent approvals of novel therapies, castration-resistant prostate cancer remains lethal. A “real-world” clinical-genomic database is urgently needed to enhance our characterization of advanced prostate cancer and further enable precision oncology. Methods The Prostate Cancer Precision Medicine Multi-Institutional Collaborative Effort (PROMISE) is a consortium whose aims are to establish a repository of de-identified clinical and genomic patient data that are linked to patient outcomes. The consortium structure includes a (1) bio-informatics committee to standardize genomic data and provide quality control, (2) biostatistics committee to independently perform statistical analyses, (3) executive committee to review and select proposals of relevant questions for the consortium to address, (4) diversity/inclusion committee to address important clinical questions pertaining to racial disparities, and (5) patient advocacy committee to understand patient perspectives to improve patients’ quality of care. Results The PROMISE consortium was formed by 16 academic institutions in early 2020 and a secure RedCap database was created. The first patient record was entered into the database in April 2020 and over 1000 records have been entered as of early 2021. Data entry is proceeding as planned with the goal to have over 2500 patient records by the end of 2021. Conclusions The PROMISE consortium provides a powerful clinical-genomic platform to interrogate and address data gaps that have arisen with increased genomic testing in the clinical management of prostate cancer. The dataset incorporates data from patient populations that are often underrepresented in clinical trials, generates new hypotheses to direct further research, and addresses important clinical questions that are otherwise difficult to investigate in prospective studies.

De Novo Transcriptomic Analyses Revealed Some Detoxification Genes and Related Pathways Responsive to Noposion Yihaogong® 5% EC (Lambda-Cyhalothrin 5%) Exposure in Spodoptera frugiperda Third-Instar Larvae

The fall armyworm, Spodoptera frugiperda (J.E. Smith) (Lepidoptera: Noctuidae), is a polyphagous, invasive insect pest which causes significant losses in important crops wherever it has spread. The use of pesticides in agriculture is a key tool in the management of many important crop pests, including S. frugiperda, but continued use of insecticides has selected for various types of resistance, including enzyme systems that provide enhanced mechanisms of detoxification. In the present study, we analyzed the de novo transcriptome of S. frugiperda larvae exposed to Noposion Yihaogong® 5% emulsifiable concentrate (EC) insecticide focusing on detoxification genes and related pathways. Results showed that a total of 1819 differentially expressed genes (DEGs) were identified in larvae after being treated with Noposion Yihaogong® 5% EC insecticide, of which 863 were up- and 956 down-regulated. Majority of these differentially expressed genes were identified in numerous Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, including metabolism of xenobiotics and drug metabolism. Furthermore, many of S. frugiperda genes involved in detoxification pathways influenced by lambda-cyhalothrin stress support their predicted role by further co-expression network analysis. Our RT-qPCR results were consistent with the DEG’s data of transcriptome analysis. The comprehensive transcriptome sequence resource attained through this study enriches the genomic platform of S. frugiperda, and the identified DEGs may enable greater molecular underpinnings behind the insecticide-resistance mechanism caused by lambda-cyhalothrin.

Genomic Competition for Noise Reduction Shaped Evolutionary Landscape of Mir-4673

The genomic platform that informs evolution of microRNA cascades remains unknown. Here we capitalized on the recent evolutionary trajectory of hominin-specific miRNA-4673 (Dokumcu et al., 2018) encoded in intron 4 of notch-1 to uncover the identity of one such precursor genomic element and the selective forces acting upon it. The miRNA targets genes that regulate Wnt/β-catenin signalling cascade. Primary sequence of the microRNA and its target region in Wnt modulating genes evolved from homologous signatures mapped to homotypic cis-clusters recognised by TCF3/4 and TFAP2A/B/C families. Integration of homologous TFAP2A/B/C cis-clusters (short range inhibitor of β-catenin (Li and Dashwood, 2004)) into the transcriptional landscape of Wnt cascade genes can reduce noise in gene expression (Blake et al., 2003). Probabilistic adoption of miRNA secondary structure by one such cis-signature in notch-1 reflected selection for superhelical curvature symmetry of precursor DNA to localize a nucleosome that overlapped the latter cis-cluster. By replicating the cis-cluster signature, non-random interactions of the miRNA with key Wnt modulator genes expanded the transcriptional noise buffering capacity via a coherent feed-forward loop mechanism (Hornstein and Shomron, 2006). In consequence, an autonomous transcriptional noise dampener (the cis-cluster/nucleosome) evolved into a post-transcriptional one (the miRNA). The findings suggest a latent potential for remodelling of transcriptional landscape by miRNAs that capitalize on non-random distribution of genomic cis-signatures.

Tissue sampling for genomic testing in a community-based center.

e18000 Background: Genomic testing requires greater quality than routine clinical diagnostic tests. As genomic testing proliferates and becomes more widespread, adjustments in processes may be needed by community-based pathology, radiology, and surgery groups. Both tissue quality and quantity parameters are essential for successful completion of next-generation sequencing (NGS) panels. Methods: A NGS genomic platform ( > 600 genes) was implemented in a hybrid academic community-based cancer institute, with success/failure rates recorded.. Data were collected from the electronic medical records and biorepository data system. Descriptive statistics assessed success or failure rates by tissue quality or quantity with subgroup analyses by disease sites (primary/metastases), collection procedure, and specimen age. Results: From 6/2015-2/2017, 809 NGS tests yielded 143 (17%) failures [specimen quality (34%) and specimen quantity (66%)]. Of the failed tests, specimens were collected from 26 primary disease sites [lung (21%)] and 18 metastatic sites [liver (29%), lymph node (19%), and lung, omentum, brain, and peritoneal specimens (all < 10%)]. Of the failed tests, all bronchoscopy, EBUS, and peritoneal fluid specimens and the majority of FNAs (78%) were due to insufficient tissue quantity, whereas surgical resection or excision had more issues with quality of the specimen (60%). Of note, surgical specimens ranged from 2005-2016; NGS quality initiatives were implemented system-wide in 2015, leading to substantially fewer failed tests. Cores biopsies had fewer quantity (24%) or quality (18%) issues. The number of tests failing due to insufficient quantity also declined due to education and communication processes implemented. Conclusions: The majority of NGS tests provided valuable information. Implementation of systematic tissue collection (core biopsies) and processing, for primary lung and lung and liver metastases using core biopsies consistently provided the fewest failures and implementing NGS-specific processes improved NGS success rates.

Determination of brown planthopper resistant genes in some rice varieties by molecular markers

Brown plant hopper (Nilaparvata lugens Stal.) is the one of dangerous pests for rice that were reported in most of rice growing countries. Twenty seven BPH resistance genes have been detected in cultivated and wild rice. However, each resistance gene is able to resist with only strain or certain biotype. Besides, many studies indicated that the toxicity of BPH strains tend to change and loss the resistance of rice lines. The breeding of rice varieties that resist to many BPH biotypes is being the breeders towards. With helping of the development of molecular markers and genetic engineering, the breeders are hopping to identify the molecular markers that linked tightly with BPH resistance genes and develop the rice varieties can gather many resistance genes in a well genomic platform. In this study, we assessed the resistance of rice lines of Vietnam and imported rice lines. The resistance was ditermined by using assessement method in the galvanized box and molecular markers linkage with resistance genes (Bph1, bph2, Bph3, Bph9 and Bph17). The results showed that there was a high affinity between the two methods with 70.59% and 86.27% of lines that have the resistance (respectively). Among of 51 surveyed rice lines, 44 lines (86.27%) were determined to have at least one marker linkage with resistance genes. 19 lines (37.25%) harbored two or three markers linkage with resistance genes. These lines will be a good genetic resource for screening and breeding the resistant rice varieties.