The first genome for the Cape Primrose Streptocarpus rexii (Gesneriaceae), a model plant for studying meristem-driven shoot diversity

Kanae Nishii, Michelle Hart, Nathan Kelso, Sadie Barber, Yun-Yu Chen, Marian Thomson, Urmi Trivedi, Alexander D Twyford, Michael Möller

Research output: Contribution to journalArticlepeer-review

Abstract

Cape Primroses (Streptocarpus, Gesneriaceae) are an ideal study system for investigating the genetics underlying species diversity in the angiosperms. Streptocarpus rexii has served as a model species for plant developmental research for over five decades due to its unusual extended meristem activity present in the leaves. In this study, we sequenced and assembled the complete nuclear, chloroplast and mitochondrial genomes of S. rexii using Oxford Nanopore Technologies long read sequencing. Two flow cells of PromethION sequencing resulted in 32 billion reads and were sufficient to generate a draft nuclear genome assembly spanning 776 Mbp of the 929 Mbp haploid genome size. The final assembly contained 5,855 nuclear contigs (766 Mbp) with an N50 of 3.7 Mbp and an L50 of 57. Over 70% of the draft genome was identified as repeats. A genome repeat library of Gesneriaceae was generated and used for genome annotation, with a total of 45,045 genes annotated in the S. rexii genome. Ks plots of the paranomes suggested a recent whole genome duplication event, shared between S. rexii and P. huaijiensis. A new chloroplast and mitochondrial genome assembly method, based on contig coverage and identification, was developed, and successfully used to assemble both organellar genomes of S. rexii. This method was developed into a pipeline and proved widely applicable. The nuclear genome of S. rexii and other datasets generated and reported here will be invaluable resources for further research to aid in the identification of genes involved in morphological variation underpinning plant diversification.
Original languageEnglish
Article numbere388
Number of pages17
JournalPlant Direct
Volume6
Issue number4
Early online date3 Apr 2022
DOIs
Publication statusE-pub ahead of print - 3 Apr 2022

Keywords

  • genome assembly
  • gesneriaceae
  • high molecular weight DNA
  • oxford nanopore technologies
  • PLCL pipeline
  • streptocarpus rexii

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