Abstract Detail


Huang, Weichen [1], Zhang, Lin [2], Columbus, J. Travis [3], Hu, Yi [1], Zhao, Yiyong [2], Tang, Lin [4], Guo, Zhenhua [5], Chen, Wenli [6], McKain, Michael [7], Bartlett, Madelaine [8], Huang, Chien-Hsun [2], Li, De-zhu [5], Ge, Song [6], Ma, Hong [1].

Nuclear gene-based phylogenomic study resolves Poaceae phylogeny and provides insight to the evolution of C4 photosynthesis.

The grass family Poaceae include rice, maize, wheat and other crops and are the most economically important angiosperm family that produces a large portion of food supply, both for human and livestock. Poaceae is also one of the largest plant families, consisting of over 11,000 species with a global distribution and contribute to diverse ecosystems. Poaceae species are classified into 12 subfamilies, with generally strong support for the monophyly of most subfamilies and two large multi-subfamily clades, BOP (three subfamilies with bamboo, rice, and wheat, respectively) and PACMAD (Panicoideae with maize and sorghum, and five other subfamilies). However, many relationships within subfamilies, among tribes and/or subtribes, remain uncertain, hindering evolutionary studies. There are two types (C3 and C4) of photosynthetic pathways in grasses; C3 photosynthesis is common in the BOP clade (including wheat, rice and bamboos) and three basal subfamilies, whereas C4 photosynthesis is only found in the PACMAD grasses. C4 grasses have specialized anatomy that improves the efficiency of photosynthesis under higher temperature. Partly due to this difference, C4 crops such as maize have higher yield compared with wheat and rice, both are C3. Efforts have been devoted to study of the transition from C3 to C4, and to engineering C4 pathway into C3 crops, in hope of improving the yield of C3 crops. However, unresolved grass phylogenetic relationship makes it hard to understand the evolutionary history of photosynthetic pathway type. To better resolve the Poaceae phylogeny and understand the evolution of photosynthesis, we used both transcriptomic and genomic datasets to cover 357 Poaceae species in 231 genera, representing 45 tribes and all 12 subfamilies. Over 1,200 low-copy nuclear genes were identified and retrieved, with several subsets obtained using additional criteria, and were used for single-gene trees and coalescent analyses to reconstruct a Poaceae phylogeny. We established a pipeline from de novo assembly of transcripts to selection of proper low-copy orthologous nuclear genes, thus reducing the impact from paralogs. Our results from multiple analyses strongly support the monophyly of 11 subfamilies and most tribes/subtribes; however, the subfamily Puelioideae was separated into two non-sister clades, one for each of the two previously defined tribes, supporting a hypothesis that places each tribe in a separate subfamily. In addition, in PACMAD, Aristidoideae is sister to a clade of other subfamilies and Panicoideae and Micrairoideae are sisters. Ancestral character reconstruction of photosynthesis supports the hypothesis of multiple independent origins of C4 photosynthesis in Poaceae. This is further supported by analysis of the ppc gene family that encodes the phosphoenolpyruvate carboxylase, which is a key enzyme in the C4 pathway. Results suggest that members of three different ppc subclades (ppc-aL1a, ppc-aL1b, and ppc-B2) were recruited as putative C4 ppc genes. This study provides valuable resources and a robust phylogenetic framework for studies of the grass family.

Related Links:
link to the paper

1 - The Pennsylvania State University, Department of Biology, 510 Mueller Laboratory, State College, PA, 16802, USA
2 - Fudan University, School of Life Sciences, 2005 Songhu Road, Shanghai, 200438, China
3 - Rancho Santa Ana Botanic Garden, 1500 North College Avenue, Claremont, CA, 91711.0, United States
4 - Zhejiang Univerisity, College of Life Sciences, Hangzhou, Zhejiang, 310058, China
5 - Kunming Institute of Botany, Kunming, Yunnan, 650201, China
6 - Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
7 - University Of Alabama, 411 Mary Harmon Bryant Hall, Tuscaloosa, AL, 35487, United States
8 - University Of Massachusetts Amherst, Biology Department, 611 North Pleasant St., 221 Morrill 3, Amherst, MA, 01003, United States

nuclear gene

Presentation Type: Oral Paper
Number: PHYLO II012
Abstract ID:284
Candidate for Awards:None

Copyright © 2000-2022, Botanical Society of America. All rights reserved