A survey on de novo assembly methods for single-molecular sequencing

Background:The single-molecular sequencing(SMS)is under rapid development and generating increasingly long and accurate sequences.De novo assembly of genomes from SMS sequences is a critical step for many genomic studies.To scale well with the developing trends of SMS,many de novo assemblers for SMS have been released.These assembly workflows can be categorized into two different kinds:the correction-and-assembly strategy and the assembly-and-correction strategy,both of which are gaining more and more attentions.Results:In this article we make a discussion on the characteristics of errors in SMS sequences・We then review the currently widely applied de novo assemblers for SMS sequences.We also describe computational methods relevant to de novo assembly,including the alignment methods and the error correction methods.Benchmarks are provided to analyze their performance on different datasets and to provide use guides on applying the computation methods.Conclusion:We make a detailed review on the latest development of de novo assembly and some relevant algorithms for SMS,including their rationales,solutions and results.Besides,we provide use guides on the algorithms based on their benchmark results.Finally we conclude the review by giving some developing trends of third generation sequencing(TGS).

Gm Ms1 encodes a kinesin-like protein essential for male fertility in soybean(Glycine max L.)

The application of heterosis is a promising approach for greatly increasing yield in soybean(Glycine max L.). Nuclear male sterility is essential for hybrid seed production and the utilization of heterosis. Here we report the cloning of the gene underlying the soybean male-sterile mutant ms-1,which has been widely used for recurrent selection in soybean breeding programs. We initially delimited the ms1 locus to a 16.15 kb region on chromosome13, based on SLAF_BSA sequencing followed by genotyping of an F_(2) population segregating for the locus. Compared with the same region in fertile plants, the mutant region lacks a sequence of approximately 38.7 kb containing five protein-coding genes, including an ortholog of the kinesin-like protein gene NACK2, named Gm Ms1. The Gm Ms1 knockout plants generated via CRISPR/Casmediated gene editing displayed a complete malesterile phenotype. Metabolic profiling showed that fertile anthers accumulated starch and sucrose normally, whereas sterile anthers had higher anthocyanin levels and lower flavonoid levels and lower antioxidant enzyme activities. These results provide insights into the molecular mechanisms governing male sterility and demonstrate that Gm Ms1 could be used to create male-sterile lines through targeted mutagenesis. These findings pave the way for designing seed production technology and an intelligent male-sterile line system to utilize heterosis in soybean.