Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies

Abstract

Brassica rapa comprises several important cultivated vegetables and oil crops. Current reference genome assemblies of Brassica rapa are quite fragmented and not highly contiguous, thereby limiting extensive genetic and genomic analyses. Here, we report an improved assembly of the B. rapa genome (v3.0) using single-molecule sequencing, optical mapping, and chromosome conformation capture technologies (Hi-C). Relative to the previous reference genomes, our assembly features a contig N50 size of 1.45 Mb, representing a ~30-fold improvement. We also identified a new event that occurred in the B. rapa genome ~1.2 million years ago, when a long terminal repeat retrotransposon (LTR-RT) expanded. Further analysis refined the relationship of genome blocks and accurately located the centromeres in the B. rapa genome. The B. rapa genome v3.0 will serve as an important community resource for future genetic and genomic studies in B. rapa. This resource will facilitate breeding efforts in B. rapa, as well as comparative genomic analysis with other Brassica species.

A chromosome-scale assembly of allotetraploid Brassica juncea (AABB) elucidates comparative architecture of the A and B genomes

“…We have reported a highly contiguous genome assembly of B. juncea variety Varuna, an oleiferous type belonging to the Indian gene pool of mustard, using long-read SMRT sequencing and optical mapping. The B. juncea assembly reported here has given contig N50 value of >5Mb, comparable to the other recent SMRT based genome assemblies [9][10][11][12][13][14] . We found recursive optical mapping with three different labeling reactions to be highly useful for correcting mis-assemblies.…”

“…Recent genome sequencing efforts have relied exclusively on high coverage SMRT sequencing, both for the de-novo genome assemblies and for improving earlier assembled draft genomes that used the second-generation technologies [8][9][10][11][12][13] . Amongst the Brassica species -assembly of B. rapa Chiifu has been improved by additional data from ~57x SMRT sequencing, BioNano optical mapping, and Hi-C reads 14 . Highly contiguous de-novo assemblies have been generated for two new lines of B. rapa and B. oleracea by Nanopore long-read sequencing and optical mapping 15 .…”

A chromosome-scale genome assembly of Isatis indigotica, an important medicinal plant used in traditional Chinese medicine

“…Continuity and completeness are important indicators of genome assembly. PacBio-based genome assembly plus error corrections based on Illumina data could greatly improve continuity and completeness [56][57][58][59] . Our genome assembly of I. indigotica by this strategy showed a highly resolved result with an N50 = 1.22 Mb and longest contig length = 8.99 Mb.…”

Reconstructing the evolutionary history of a functionally diverse gene family reveals complexity at the genetic origins of novelty

“…Another weakness of commonly used homology-based annota on pipelines is that they a empt to align an en re protein or mRNA sequence with a genomic sequence, a prac ce that is very likely to miss alterna ve splicing variants or pseudogenes, informa on concerning which is crucial in evolu onary studies (Danchin et al 2018;Zhang et al 2018) . In addi on, these pipelines have trouble annota ng tandem-array duplica ons, especially when there's high similarity between the copies (Zallot et al 2016;Nobre et al 2016) .…”