Complete Chloroplast Genomes ofSaccharum giganteum,Saccharum longisetosum,Cleistachne sorghoides, Sarga timorense, Narenga porphyrocomaandTripsacum dactyloides. Comparisons with ITS phylogeny and Placement withinSaccharum

Abstract

AcknowledgementsWe would like to thank Mr K-L Ma for collecting the S. timorense seeds and the N. porphyrocoma leaf material. We are grateful to Oxford Nanopore Technologies for support through their community access programme. We also thank the British Association of Sugar Technologists (BAST) for providing Saccharum hybrid cv SP80-3280 plant material. Abstract 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.

On the Validity of the Saccharum Complex and the Saccharinae Subtribe: A Re-assesment

“…The exception being the trans-Himalayan outgroup with a base chromosome count of 10 (Mehra & Sharna 1975). There is some evidence that many of the members of this clade are themselves hybrids (Lloyd Evans et al 2018;Lloyd Evans & Hughes 2020). Thus the different base chromosome number and separate hybrid origins of this grouping would seem to exclude them from Saccharum.…”

“…The revelaton that Sarga species are an hybrid and that their nuclear phylogenetic signals place them as a natural outgroup to the Saccharinae is a major finding (Estep et al 2014, Snyman et al 2018, Lloyd Evans and Hughes 2020. Thus, a genus that was not even considere as being closely related to Saccharum emerges as being more closely related than ¾ of the puroprted members of the Saccharum complex.…”

“…When the core Andropogoneae and Saccharinae diverged some 7.5 million years ago hybridization events ocurred between ancestral Sarga and Sorghum species. Sarga gained the Sorghum chloroplast type but retained its saccharinae-type genome (Estep et al 2014;Snyman et al 2017, Lloyd Evans et al 2019, Lloyd Evans and Hughes 2020.…”

Comparative Analysis of Chloroplast Genome in Saccharum spp. and Related Members of ‘Saccharum Complex’

“…In Saccharum , the complete cp genomes of Saccharum hybrid NCo310 [ 16 ], SP80-3280 [ 17 ], and RB867515 [ 18 ]; S. spontaneum SES205A, SES234B [ 19 ], and Yunnan 83-184 [ 20 ]; S. officinarum Badila and IJ76-514 were obtained in previous studies. More recently, the complete cp genomes of T. arundinaceum [ 21 , 22 ] and N. porphyrocoma [ 23 ] have been sequenced and assembled. The analysis of chloroplasts in Saccharum and related species focused on three aspects: (1) the structural features of the cp genome were compared with Saccharum species and other agronomically and industrially important monocots, such as Zea mays and Sorghum bicolor [ 16 ]; (2) the molecular classification of all Saccharum species and their nearest evolutionary neighbors was elucidated by plastid-based studies [ 23 ]; (3) the plastid view on sugarcane origins [ 20 ].…”

“…More recently, the complete cp genomes of T. arundinaceum [ 21 , 22 ] and N. porphyrocoma [ 23 ] have been sequenced and assembled. The analysis of chloroplasts in Saccharum and related species focused on three aspects: (1) the structural features of the cp genome were compared with Saccharum species and other agronomically and industrially important monocots, such as Zea mays and Sorghum bicolor [ 16 ]; (2) the molecular classification of all Saccharum species and their nearest evolutionary neighbors was elucidated by plastid-based studies [ 23 ]; (3) the plastid view on sugarcane origins [ 20 ]. These results have indicated the potential of this approach to elucidate the phylogenetic relationships within the ‘ Saccharum complex’.…”