SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data

Ren

Molecular Ecology Resources

et al. 2020

Sponge gourd (Luffa cylindrica (L.) Roem.) or luffa is a diploid herbaceous plant with 26 chromosomes (2n = 26) and belongs to the family Cucurbitaceae. To address the limited knowledge of the genome of Luffa species, the chromosome‐level genome of L. cylindrica was assembled and analysed using PacBio long reads and Hi‐C data. We combined Hi‐C data with a draft genome assembly to generate chromosome‐length scaffolds. Thirteen scaffolds corresponding to the 13 chromosomes were assembled from 1,156 contigs to a final size of 669 Mb with a contig N50 size of 5 Mb and a scaffold N50 size of 53 Mb. After removing redundant sequences, 416.31 Mb (62.18% of the genome) of repeat sequences was detected. Subsequently, 31,661 protein‐coding genes with an average of 5.69 exons per gene were identified in the L. cylindrica genome using de novo methods, transcriptome data and homologue‐based approaches. In addition, 27,552 protein‐coding genes (87.02%) were annotated in five databases. According to the phylogenetic analysis, L. cylindrica is closely related to Cucurbita and Cucumis species and diverged from their common ancestor ~28.6–67.1 million years ago. Genome collinearity analysis was performed in Cucurbita moschata, Cucumis sativus and L. cylindrica, and it demonstrated a high degree of conserved gene order in these three species. The completeness of the genome will provide high‐quality genomic knowledge on breeding and reveal genetic variation in L. cylindrica.

Section: Resultsmentioning

confidence: 99%

Long‐read sequencing and de novo assembly of the Luffa cylindrica (L.) Roem. genome

Ren

Molecular Ecology Resources

et al. 2020

Insect Molecular Biology

“…Adapter sequences and low‐quality reads were trimmed from raw reads with SOAPnuke v. 1.5.2 (Chen et al, ) to generate clean reads. Trimmed clean reads were mapped to the T. urticae transcriptome assembly ASM23943v1 (RefSeq assembly accession: GCF_000239435.1; updated 25/5/2018; Grbić et al, ) using Salmon v. 0.9.1 (Patro et al, ) with default parameters.…”

Section: Methodsmentioning

confidence: 99%

Transcriptome of Tetranychus urticae embryos reveals insights into Wolbachia‐induced cytoplasmic incompatibility

et al. 2019

The endosymbiont Wolbachia is known for manipulating host reproduction in selfish ways. However, the molecular mechanisms have not yet been investigated in embryos. Here, we found that Wolbachia had no effect on the number of deposited eggs in Tetranychus urticae Koch (Acari: Tetranychidae) but caused two types of reproductive manipulation: killing uninfected female embryos via cytoplasmic incompatibility (CI) and increasing the hatching ratio of infected female embryos. RNA sequencing analyses showed that 145 genes were differentially expressed between Wolbachia‐infected (WI) and Wolbachia‐uninfected (WU) embryos. Wolbachia infection down‐regulated messenger RNA (mRNA) expression of glutathione S‐transferase that could buffer oxidative stress. In addition, 1613 and 294 genes were identified as CI‐specific up‐/down‐regulated genes. Compared to WU and WI embryos, embryos of CI cross strongly expressed genes involved in transcription, translation, tissue morphogenesis, DNA damage and mRNA surveillance. In contrast, most of the genes associated with energy production and metabolism were down‐regulated in the CI embryos compared to the WU and WI embryos, which provides some clues as to the cause of death of CI embryos. These results identify several genes that could be candidates for explaining Wolbachia‐induced CI. Our data form a basis to help elucidate the molecular consequences of CI in embryos.

“…S1). In order to reduce the effect of sequencing errors on the assembly, we used SOAPnuke v.1.5.6 (SOAPnuke, RRID:SCR_015025) [16] to filter out low-quality reads with adapters, high base error rate, and highly unknown base proportion, and obtained 177 Gb (272×) of clean data.…”

Section: Data Descriptionmentioning

confidence: 99%

Chromosome-level genome assembly of the spotted sea bass, Lateolabrax maculatus

Shao

Wang

et al. 2018

GigaScience

BackgroundThe spotted sea bass (Lateolabrax maculatus) is a valuable commercial fish that is widely cultured in China. While analyses using molecular markers and population genetics have been conducted, genomic resources are lacking.FindingsHere, we report a chromosome-scale assembly of the spotted sea bass genome by high-depth genome sequencing, assembly, and annotation. The genome scale was 0.67 Gb with contig and scaffold N50 length of 31 Kb and 1,040 Kb, respectively. Hi-C scaffolding of the genome resulted in 24 pseudochromosomes containing 77.68% of the total assembled sequences. A total of 132.38 Mb repeat sequences were detected, accounting for 20.73% of the assembled genome. A total of 22, 015 protein-coding genes were predicted, of which 96.52% were homologous to proteins in various databases. In addition, we constructed a phylogenetic tree using 1,586 single-copy gene families and identified 125 unique gene families in the spotted sea bass genome.ConclusionsWe assembled a spotted sea bass genome that will be a valuable genomic resource to understanding the biology of the spotted sea bass and will also lead to the development of molecular breeding techniques to generate spotted sea bass with better economic traits.