Grass plastomes reveal unexpected paraphyly with endemic species of Micrairoideae from India and new haplotype markers in Arundinoideae.
OBJECTIVE
We investigated the little-studied Arundinoideae/Micrairoideae clade of grasses with an innovative plastome phylogenomic approach. This method gives robust results for taxa of uncertain phylogenetic placement. Arundinoideae comprise ∼45 species, although historically was much larger. Arundinoideae is notable for the widely invasivePhragmites australis. Micrairoideae comprise nine genera and ∼200 species. Some are threatened with extinction, includingHubbardia, someIsachnespp., andLimnopoa. Two micrairoid genera,EriachneandPheidochloa, exhibit C4photosynthesis in this otherwise C3subfamily and represent an independent origin of the C4pathway among grasses.


METHODS
Five new plastomes were sequenced with next-generation sequencing-by-synthesis methods. Plastomes were assembled by de novo methods and phylogenetically analyzed with eight other recently published arundinoid or micrairoid plastomes and 11 outgroup species. Stable carbon isotope ratios were determined for micrairoid and arundinoid species to investigate ambiguities in the proxy evidence for C4photosynthesis.


RESULTS
Phylogenomic analyses showed strong support for ingroup nodes in the Arundinoideae/Micrairoideae subtree, including a paraphyletic clade of Hubbardieae with Isachneae. Anatomical, biochemical, and positively selected sites data are ambiguous with regard to the photosynthetic pathways in Micrairoideae. Species ofHubbardia,Isachne, andLimnopoawere definitively shown by δ13C measurements to be C3andEriachneto be C4.


CONCLUSIONS
Our plastome phylogenomic analyses for Micrairoideae are the first phylogenetic results to indicate paraphyly between Isachneae and Hubbardieae. The definitive δ13C data for four genera of Micrairoideae indicates the breadth of variation possible in the proxy evidence for photosynthetic pathways of both C3and C4taxa.
Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, Illinois 60115 USA mel-duvall@niu.edu.
Melvin R
MR
Duvall
Department of Botany, Shivaji University, Kolhapur 416 004, India.
Shrirang R
SR
Yadav
Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, Illinois 60115 USA.
Sean V
SV
Burke
Biological Sciences, Northern Illinois University, 1425 W. Lincoln Hwy, DeKalb, Illinois 60115 USA.
William P
WP
Wysocki
D002244:Carbon / Q000378:metabolism; D057486:Carbon Cycle; D002247:Carbon Isotopes; D019143:Evolution, Molecular; D054627:Genome, Plastid / Q000235:genetics*; D006239:Haplotypes; D059014:High-Throughput Nucleotide Sequencing; D007194:India; D010788:Photosynthesis / Q000235:genetics; D010802:Phylogeny; D006109:Poaceae / Q000145:classification / Q000235:genetics*; D013045:Species Specificity
D002247:Carbon Isotopes; D002244:Carbon
Arundinoideae; C3/C4 photosynthesis; Hubbardia; Micrairoideae; Phragmites australis; Poaceae; plastome phylogenomics; rbcL evolution