Understanding the Vitis species at the genomic level is important for cultivar improvement of grapevine. Here we report whole-genome genetic variation at single-base resolution of 472 Vitis accessions, which cover 48 out of 60 extant Vitis species from a wide geographic distribution. The variation helps to identify a recent dramatic expansion and contraction of effective population size in the domesticated grapevines and that cultivars from the pan-Black Sea region have a unique demographic history in comparison to the other domesticated cultivars. We also find selective sweeps for berry edibility and stress resistance improvement. Furthermore, we find associations between candidate genes and important agronomic traits, such as berry shape and aromatic compounds. These results demonstrate resource value of the resequencing data for illuminating the evolutionary biology of Vitis species and providing targets for grapevine genetic improvement.

We elucidate grapevine evolution and domestication histories with 3525 cultivated and wild accessions worldwide. In the Pleistocene, harsh climate drove the separation of wild grape ecotypes caused by continuous habitat fragmentation. Then, domestication occurred concurrently about 11,000 years ago in Western Asia and the Caucasus to yield table and wine grapevines. The Western Asia domesticates dispersed into Europe with early farmers, introgressed with ancient wild western ecotypes, and subsequently diversified along human migration trails into muscat and unique western wine grape ancestries by the late Neolithic. Analyses of domestication traits also reveal new insights into selection for berry palatability, hermaphroditism, muscat flavor, and berry skin color. These data demonstrate the role of the grapevines in the early inception of agriculture across Eurasia.

Background. Idiopathic membranous nephropathy (IMN) is a major cause of adult nephrotic syndromes, and reliable noninvasive biomarkers for diagnosis and monitoring are urgently needed. In this study, we performed small RNA (sRNA) sequencing to explore sRNA profiles of urinary exosomes derived from IMN patients and healthy controls (CON) to provide clues for identifying novel noninvasive sRNA biomarkers for IMN. Methods. Urine samples were collected from five healthy controls and six patients with IMN. High-throughput sequencing was used to screen sRNA expression profiles of urinary exosomes from patients with IMN in two independent cohorts. Results. Urinary exosomes were successfully isolated and used to obtain exosomal sRNAs. We screened 131 differentially expressed miRNAs, including 28 specifically expressed miRNAs, then explored the top 10 specifically expressed miRNAs in all IMN individuals. The specifically expressed miRNAs and differentially expressed miRNAs provide potential biomarkers for IMN. Additionally, we discovered numerous sRNAs derived from genomic repetitive sequences, which could represent an exciting new area of research. Conclusion. Herein, we revealed significant differences in expression profiles of urinary exosomal miRNAs and repetitive region-derived sRNAs between patients with IMN and healthy controls. The findings could facilitate the development of potential molecular targets for membranous nephropathy.

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Shangri-La is a wine region that has the highest altitude vineyards in China. This is the first study investigated the biodiversity of non-Saccharomyces yeasts associated with spontaneous fermentation of Cabernet Sauvignon wines produced from two sub-regions (Lancang River and Jinsha River) of Shangri-La. The culturable yeasts were preliminarily classified based on their colonial morphology on the Wallerstein Laboratory nutrient agar plates. Yeast species were identified by the sequencing of the 26S rRNA D1/D2 region and the 5.8S rRNA ITS region. Twenty-five non-Saccharomyces yeast species belonging to sixteen genera were isolated and identified in Shangri-La wine region. Candida, Hanseniaspora, Pichia, and Starmerella were found in both sub-regions, but the Lancang River showed more diverse yeast species than the Jinsha River. Shangri-La not only exhibited high diversity of non-Saccharomyces yeasts, and furthermore, seven species of non-Saccharomyces yeasts were exclusively found in this region, including B. bruxellensis, D. hansenii, M. guilliermondii, S. vini, S. diversa, T. delbrueckii and W. anomalus, which might play an important role in distinctive regional wine characteristics. This study provide a relatively comprehensive analysis of indigenous non-Saccharomyces yeasts associated with Cabernet Sauvignon from Shangri-La, and has significance for exploring ‘microbial terroir’ of wine regions in China.

Red bayberry is a sweet, tart fruit native to China and grown widely in the south. The key organic compounds forming the distinctive aroma in red bayberry, are terpenoids, mainly β-caryophyllene and α-pinene. However, the key genes responsible for different terpenoids are still unknown. Here, transcriptome analysis on samples from four cultivars, during fruit development, with different terpenoid production, provided candidate genes for volatile organic compound (VOC) production. Terpene synthases (TPS) are key enzymes regulating terpenoid biosynthesis, and 34 TPS family members were identified in the red bayberry genome. MrTPS3 in chromosome 2 and MrTPS20 in chromosome 7 were identified as key genes regulating β-caryophyllene and α-pinene synthesis, respectively, by qRT-PCR. Subcellular localization and enzyme activity assay showed that MrTPS3 was responsible for β-caryophyllene (sesquiterpenes) production and MrTPS20 for α-pinene (monoterpenes). Notably, one amino acid substitution between dark color cultivars and light color cultivars resulted in the loss of function of MrTPS3, causing the different β-caryophyllene production. Our results lay the foundation to study volatile organic compounds (VOCs) in red bayberry and provide potential genes for molecular breeding.

In the original version of this Article, in the last paragraph of the first section of the Results, the ratios of SNPs located in the intergenic regions, SNPs located in the coding sequences, and indels located in the coding regions are incorrectly written as '71.2%', '4.6%', and '1.4%', respectively. These ratios should read as '73.7%', '4.0%', and '1.3%', respectively. In addition, the estimated ratio of indels in the coding regions that could cause frameshift mutations is incorrectly written as '66.7%'. It should read as '66.9%'. Furthermore, authors' given names and surnames of Reference 47 are switched. The authors' names should read 'Grassi F., De Mattia F., Zecca G., Sala F., & Labra M.'. These have been corrected in both the PDF and HTML versions of the Article.

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