New high‐quality peach ( Prunus persica L. Batsch) genome assembly to analyze the molecular evolutionary mechanism of volatile compounds in peach fruits

2021 ◽  
Author(s):  
Ke Cao ◽  
Xuanwen Yang ◽  
Yong Li ◽  
Gengrui Zhu ◽  
Weichao Fang ◽  
...  
2021 ◽  
Vol 11 (10) ◽  
pp. 4658
Author(s):  
Magdalena Januszek ◽  
Paweł Satora

Quality of plum jerkum is significantly associated to the profile of volatile compounds. Therefore, we decided to assess the impact of various fermentation types on selected properties of plum jerkums, especially compounds which contribute to the aroma of the finished product. We used the following yeast strains: S. cerevisiae S1, H. uvarum H2, and Ethanol RED (S. cerevisiae). Moreover, we considered spontaneous fermentation. S. cerevisiae and H. uvarum strains were isolated during the fermentation of Čačanska Lepotica or Węgierka Dąbrowicka (plum cultivars), respectively. As for fermentation type, spontaneous fermentation of H. uvarum H2 provided the best results. It could be associated to the fact that plum juices fermented with H. uvarum H2 presented the highest concentration of terpenoids, esters, or some higher alcohols. In the current paper, application of indigenous strains of yeasts resulted in the required oenological characteristics, e.g., highest fermentation efficiency and concentration of ethanol was determined in juices fermented with Ethanol RED (S. cerevisiae) and also with S. cerevisiae S1. Our results suggested that indigenous strains of yeasts present in plums demonstrate great potential for the production of plum jerkums of high quality.


Author(s):  
Yi‐Ming Weng ◽  
Charlotte B. Francoeur ◽  
Cameron R. Currie ◽  
David H. Kavanaugh ◽  
Sean D. Schoville

Author(s):  
Hui Zhang ◽  
Yuexing Wang ◽  
Ce Deng ◽  
Sheng Zhao ◽  
Peng Zhang ◽  
...  

Author(s):  
Tomas N Generalovic ◽  
Shane A McCarthy ◽  
Ian A Warren ◽  
Jonathan M D Wood ◽  
James Torrance ◽  
...  

Abstract Hermetia illucens L. (Diptera: Stratiomyidae), the Black Soldier Fly (BSF) is an increasingly important species for bioconversion of organic material into animal feed. We generated a high-quality chromosome-scale genome assembly of the BSF using Pacific Bioscience, 10X Genomics linked read and high-throughput chromosome conformation capture sequencing technology. Scaffolding the final assembly with Hi-C data produced a highly contiguous 1.01 Gb genome with 99.75% of scaffolds assembled into pseudochromosomes representing seven chromosomes with 16.01 Mb contig and 180.46 Mb scaffold N50 values. The highly complete genome obtained a BUSCO completeness of 98.6%. We masked 67.32% of the genome as repetitive sequences and annotated a total of 16,478 protein-coding genes using the BRAKER2 pipeline. We analysed an established lab population to investigate the genomic variation and architecture of the BSF revealing six autosomes and an X chromosome. Additionally, we estimated the inbreeding coefficient (1.9%) of a lab population by assessing runs of homozygosity. This provided evidence for inbreeding events including long runs of homozygosity on chromosome five. Release of this novel chromosome-scale BSF genome assembly will provide an improved resource for further genomic studies, functional characterisation of genes of interest and genetic modification of this economically important species.


2019 ◽  
Vol 19 (2) ◽  
pp. 485-496 ◽  
Author(s):  
Wenbo Chen ◽  
Xiaowei Yang ◽  
Guillaume Tetreau ◽  
Xiaozhao Song ◽  
Cathy Coutu ◽  
...  

Toxins ◽  
2018 ◽  
Vol 10 (12) ◽  
pp. 488 ◽  
Author(s):  
Shiyong Zhang ◽  
Jia Li ◽  
Qin Qin ◽  
Wei Liu ◽  
Chao Bian ◽  
...  

Naturally derived toxins from animals are good raw materials for drug development. As a representative venomous teleost, Chinese yellow catfish (Pelteobagrus fulvidraco) can provide valuable resources for studies on toxin genes. Its venom glands are located in the pectoral and dorsal fins. Although with such interesting biologic traits and great value in economy, Chinese yellow catfish is still lacking a sequenced genome. Here, we report a high-quality genome assembly of Chinese yellow catfish using a combination of next-generation Illumina and third-generation PacBio sequencing platforms. The final assembly reached 714 Mb, with a contig N50 of 970 kb and a scaffold N50 of 3.65 Mb, respectively. We also annotated 21,562 protein-coding genes, in which 97.59% were assigned at least one functional annotation. Based on the genome sequence, we analyzed toxin genes in Chinese yellow catfish. Finally, we identified 207 toxin genes and classified them into three major groups. Interestingly, we also expanded a previously reported sex-related region (to ≈6 Mb) in the achieved genome assembly, and localized two important toxin genes within this region. In summary, we assembled a high-quality genome of Chinese yellow catfish and performed high-throughput identification of toxin genes from a genomic view. Therefore, the limited number of toxin sequences in public databases will be remarkably improved once we integrate multi-omics data from more and more sequenced species.


Author(s):  
Yuanchao Liu ◽  
Longhua Huang ◽  
Huiping Hu ◽  
Manjun Cai ◽  
Xiaowei Liang ◽  
...  

Abstract Ganoderma leucocontextum, a newly discovered species of Ganodermataceae in China, has diverse pharmacological activities. G. leucocontextum was widely cultivated in southwest China, but the systematic genetic study has been impeded by the lack of a reference genome. Herein, we present the first whole-genome assembly of G. leucocontextum based on the Illumina and Nanopore platform from high-quality DNA extracted from a monokaryon strain (DH-8). The generated genome was 50.05 Mb in size with a N50 scaffold size of 3.06 Mb, 78,206 coding sequences and 13,390 putative genes. Genome completeness was assessed using the Benchmarking Universal Single-Copy Orthologs (BUSCO) tool, which identified 96.55% of the 280 Fungi BUSCO genes. Furthermore, differences in functional genes of secondary metabolites (terpenoids) were analyzed between G. leucocontextum and G. lucidum. G. leucocontextum has more genes related to terpenoids synthesis compared to G. lucidum, which may be one of the reasons why they exhibit different biological activities. This is the first genome assembly and annotation for G. leucocontextum, which would enrich the toolbox for biological and genetic studies in G. leucocontextum.


Author(s):  
Valentina Peona ◽  
Mozes P.K. Blom ◽  
Luohao Xu ◽  
Reto Burri ◽  
Shawn Sullivan ◽  
...  

AbstractGenome assemblies are currently being produced at an impressive rate by consortia and individual laboratories. The low costs and increasing efficiency of sequencing technologies have opened up a whole new world of genomic biodiversity. Although these technologies generate high-quality genome assemblies, there are still genomic regions difficult to assemble, like repetitive elements and GC-rich regions (genomic “dark matter”). In this study, we compare the efficiency of currently used sequencing technologies (short/linked/long reads and proximity ligation maps) and combinations thereof in assembling genomic dark matter starting from the same sample. By adopting different de-novo assembly strategies, we were able to compare each individual draft assembly to a curated multiplatform one and identify the nature of the previously missing dark matter with a particular focus on transposable elements, multi-copy MHC genes, and GC-rich regions. Thanks to this multiplatform approach, we demonstrate the feasibility of producing a high-quality chromosome-level assembly for a non-model organism (paradise crow) for which only suboptimal samples are available. Our approach was able to reconstruct complex chromosomes like the repeat-rich W sex chromosome and several GC-rich microchromosomes. Telomere-to-telomere assemblies are not a reality yet for most organisms, but by leveraging technology choice it is possible to minimize genome assembly gaps for downstream analysis. We provide a roadmap to tailor sequencing projects around the completeness of both the coding and non-coding parts of the genomes.


2021 ◽  
Author(s):  
Yinqing Yang ◽  
Kang Zhang ◽  
Ya Xiao ◽  
Lingkui Zhang ◽  
Yile Huang ◽  
...  

Rubus corchorifolius (Shanmei or mountain berry, 2n =14) is widely distributed in China, and its fruit has high nutritional and medicinal values. Here, we report a high-quality chromosome-scale genome assembly of Shanmei, with a size of 215.69 Mb and encompassing 26696 genes. Genome comparisons among Rosaceae species show that Shanmei and Fupenzi(Rubus chingii Hu) are most closely related, and then is blackberry (Rubus occidentalis). Further resequencing of 101 samples of Shanmei collected from four regions in provinces of Yunnan, Hunan, Jiangxi and Sichuan in South China reveals that the Hunan population of Shanmei possesses the highest diversity and may represent the relatively more ancestral population. Moreover, the Yunnan population undergoes strong selection based on nucleotide diversity, linkage disequilibrium and the historical effective population size analyses. Furthermore, genes from candidate genomic regions that show strong divergence are significantly enriched in flavonoid biosynthesis and plant hormone signal transduction, indicating the genetic basis of adaptation of Shanmei to the local environments. The high-quality genome sequences and the variome dataset of Shanmei provide valuable resources for breeding applications and for elucidating the genome evolution and ecological adaptation of Rubus species.


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