RNA-assisted assembly of Physaria fendleri genome

Advances in assembly algorithms have allowed diverse strategies of genome construction to become available. The use of a hybrid assembler (run with paired-end short read data and short read-derived super-reads) can provide a starting set of contigs from which a high quality assembly can be made, however short read genomic DNA reads do not often give the coverage to assemble contigs large enough for accurate scaffolding and eventual super-scaffolding. This becomes an even bigger challenge when working with highly heterozygous species, as haplotigs contaminate the already-limited template pool that can be used for scaffolding and gap-filling. This project's goal is to use an original strand-specific RNA seq data set to improve a meta-assembly of alternative oilseed crop Physaria fendleri, addressing issues with heterozygosity and taking advantage of reference-based methods. This processed assembly will then be used for analysis of a transcriptomics experiment looking at the effect of inhibiting fatty acid elongation on central carbon metabolism.

汇编算法的进步使得多样化的基因组构建策略得以实现。采用混合组装器（使用配对末端短读数据及其衍生出的超长读数据）能够提供一组起始的连续片段，从而制作出高质量的组装。然而，由于短读基因组DNA读数通常无法提供足够的覆盖范围来组装足够大的连续片段以进行准确的框架构建和最终的超级框架构建，这成为了一个更大的挑战。在处理高度杂合物种时，这一问题尤为突出，因为单倍型片段会污染本就有限的模板库，从而影响框架构建和间隙填充。本项目旨在利用一个独特的链特异性RNA测序数据集，以提高替代油料作物Physaria fendleri的元组装质量，解决杂合性问题，并充分利用基于参考的方法。随后，处理后的组装将被用于分析转录组实验，以研究抑制脂肪酸延长对中心碳代谢的影响。