PT  - JOURNAL ARTICLE
AU  - Evans, Dyfed Lloyd
AU  - Hughes, Ben
TI  - Complete Chloroplast Genomes of <em>Saccharum giganteum</em>, <em>Saccharum longisetosum</em>, <em>Cleistachne sorghoides, Sarga timorense, Narenga porphyrocoma</em> and <em>Tripsacum dactyloides</em>. Comparisons with ITS phylogeny and Placement within <em>Saccharum</em>
AID  - 10.1101/2020.06.12.149476
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.06.12.149476
4099  - http://biorxiv.org/content/early/2020/06/14/2020.06.12.149476.short
4100  - http://biorxiv.org/content/early/2020/06/14/2020.06.12.149476.full
AB  - The first complete chloroplast and Internal Transcribed Sequence (ITS) cassette sequences for the species: Saccharum giganteum, Saccharum longisetosum, Cleistachne sorghoides, Saccharum narenga and Tripsacum dactyloides are presented. Corresponding sequences for a new isolate of Sarga timorense were assembled. Phylogenetic analyses place S. giganteum, S. longisetosum and S. narenga within the Saccharinae but distinct from Saccharum, whilst C. sorghoides emerges as a member of genus Sarga and Tripsacum datyloides as a member of the Tripsacinae. Comparison of chloroplast and ITS phylogenies reveal complex reticulate evolution within the Saccharinae, with S. giganteum, S. longisetosum and S. narenga, despite having the same base chromosome count (15) having different evolutionary origins; making them members of different genera and not members of genus Saccharum. The importance of reticulate evolution in the origins of Andropogoneae, particularly the Saccharinae and the unique positions of Saccharum and Miscanthus is discussed.Competing Interest StatementThe authors declare that there is no conflict of interest. However, to aid transparency, DLlE is a non-remunerated Senior Scientist and Lead Informatician for CSS, whilst BH is an informatician and biochemist at CSS. CSS (Cambridge Sequencing Services) is a non-profit organization dedicated to the advancement of sequencing technologies.