Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce.

ABSTRACT: Lettuce (Lactuca sativa) is a major crop and a member of the large, highly successful Compositae family of flowering plants. Here we present a reference assembly for the species and family. This was generated using whole-genome shotgun Illumina reads plus in vitro proximity ligation data to create large superscaffolds; it was validated genetically and superscaffolds were oriented in genetic bins ordered along nine chromosomal pseudomolecules. We identify several genomic features that may have contributed to the success of the family, including genes encoding Cycloidea-like transcription factors, kinases, enzymes involved in rubber biosynthesis and disease resistance proteins that are expanded in the genome. We characterize 21 novel microRNAs, one of which may trigger phasiRNAs from numerou

SUBMITTER: Reyes-Chin-Wo S 

PROVIDER: S-EPMC5394340 | biostudies-literature | 2017 Apr

REPOSITORIES: biostudies-literature