1
|
Delfini C, Aliscioni SS, Acosta JM, Pensiero JF, Zuloaga FO. An Update of the Cenchrinae (Poaceae, Panicoideae, Paniceae) and a New Genus for the Subtribe to Clarify the Dubious Position of a Species of Panicum L. PLANTS (BASEL, SWITZERLAND) 2023; 12:749. [PMID: 36840098 PMCID: PMC9966601 DOI: 10.3390/plants12040749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/21/2023] [Accepted: 01/28/2023] [Indexed: 06/18/2023]
Abstract
Subtribe Cenchrinae, so-called as the "bristle clade", is a monophyletic group of panicoid grasses characterized by having sterile branches or bristles on the inflorescences in most of its species. Within this subtribe is also placed Panicum antidotale Retz., an "incertae sedis" species of Panicum L. which lacks bristles along the inflorescence. In this study, we present an update of the subtribe Cenchrinae based on molecular, morphological, and anatomical evidence to clarify the systematic position of P. antidotale in the Cenchrinae, excluding it from Panicum and establishing it in a new genus (i.e., Janochloa Zuloaga & Delfini); the morphological features distinguishing the new genus from other closely related taxa are properly discussed and an identification key to the 24 genera recognized within Cenchrinae is presented. We also add American Setaria species, not tested before, of subgenera Paurochaetium and Reverchoniae, discussing the position of these taxa in actual phylogeny of the genus as well as defining placements in the tree of Setaria species that were imprecisely located in previous analyses. A comparison with the results from other studies, comments on Stenotaphrum Trin. and a brief discussion on conflicting placements in Cenchrus and related taxa, and of Acritochaete Pilg. are also included.
Collapse
Affiliation(s)
- Carolina Delfini
- Instituto de Botánica Darwinion (ANCEFN–CONICET), Labardén 200, Casilla de Correo 22, San Isidro B1642HYD, Buenos Aires, Argentina
| | - Sandra S. Aliscioni
- Instituto de Botánica Darwinion (ANCEFN–CONICET), Labardén 200, Casilla de Correo 22, San Isidro B1642HYD, Buenos Aires, Argentina
- Cátedra de Botánica General, Facultad de Agronomía, Universidad de Buenos Aires, Av. San Martín 4453, Buenos Aires C1417DSE, Argentina
| | - Juan M. Acosta
- Instituto de Botánica Darwinion (ANCEFN–CONICET), Labardén 200, Casilla de Correo 22, San Isidro B1642HYD, Buenos Aires, Argentina
| | - José F. Pensiero
- Instituto de Ciencias Agropecuarias del Litoral, UNL–CONICET–FCA, Kreder 2805, Esperanza 3080HOF, Santa Fe, Argentina
| | - Fernando O. Zuloaga
- Instituto de Botánica Darwinion (ANCEFN–CONICET), Labardén 200, Casilla de Correo 22, San Isidro B1642HYD, Buenos Aires, Argentina
| |
Collapse
|
2
|
Delfini C, Salariato DL, Aliscioni SS, Zuloaga FO. Systematics and Phylogenetic Placement of Panicum L. Species within the Melinidinae Based on Morphological, Anatomical, and Molecular Data (Poaceae, Panicoideae, Paniceae). PLANTS (BASEL, SWITZERLAND) 2023; 12:399. [PMID: 36679111 PMCID: PMC10375907 DOI: 10.3390/plants12020399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 06/17/2023]
Abstract
Generic boundaries of the African species Panicum deustum Thunb., Panicum trichocladum Hack. ex K. Schum., and Panicum vollesenii Renvoize are analyzed and compared with related genera of the tribe Paniceae and the subtribe Melinidinae. Based on morphological (vegetative and reproductive characters including habit, ligules, inflorescence, spikelets, and ornamentation of the upper anthecium), anatomical (transverse section of leaves), and molecular data (three chloroplast markers), a new genus is proposed for P. deustum, while P. trichocladum and P. vollesenii are transferred to the genus Megathyrsus (Pilg.) B.K. Simon & S.W.L. Jacobs. The phylogenetic position of both taxa within the Melinidinae and their morphological affinities with other genera of the subtribe are also discussed. Additional studies on the Melinidinae will clarify the systematic position of the genera that are still in a doubtful position within the subtribe, such as Eriochloa and Urochloa.
Collapse
Affiliation(s)
- Carolina Delfini
- Instituto de Botánica Darwinion (ANCEFN-CONICET), Labardén 200, Casilla de Correo 22, San Isidro B1642HYD, Argentina
| | - Diego L Salariato
- Instituto de Botánica Darwinion (ANCEFN-CONICET), Labardén 200, Casilla de Correo 22, San Isidro B1642HYD, Argentina
| | - Sandra S Aliscioni
- Instituto de Botánica Darwinion (ANCEFN-CONICET), Labardén 200, Casilla de Correo 22, San Isidro B1642HYD, Argentina
- Cátedra de Botánica General, Facultad de Agronomía, Universidad de Buenos Aires, Av. San Martín 4453, Buenos Aires C1417DSE, Argentina
| | - Fernando O Zuloaga
- Instituto de Botánica Darwinion (ANCEFN-CONICET), Labardén 200, Casilla de Correo 22, San Isidro B1642HYD, Argentina
| |
Collapse
|
3
|
Yang Q, Liu T, Wu T, Lei T, Li Y, Wang X. GGDB: A Grameneae genome alignment database of homologous genes hierarchically related to evolutionary events. PLANT PHYSIOLOGY 2022; 190:340-351. [PMID: 35789395 PMCID: PMC9434254 DOI: 10.1093/plphys/kiac297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
The genomes of Gramineae plants have been preferentially sequenced owing to their economic value. These genomes are often quite complex, for example harboring many duplicated genes, and are the main source of genetic innovation and often the result of recurrent polyploidization. Deciphering these complex genome structures and linking duplicated genes to specific polyploidization events are important for understanding the biology and evolution of plants. However, efforts have been hampered by the complexity of analyzing these genomes. Here, we analyzed 29 well-assembled and up-to-date Gramineae genome sequences by hierarchically relating duplicated genes in collinear regions to specific polyploidization or speciation events. We separated duplicated genes produced by each event, established lists of paralogous and orthologous genes, and ultimately constructed an online database, GGDB (http://www.grassgenome.com/). Homologous gene lists from each plant and between plants can be displayed, searched, and downloaded from the database. Interactive comparison tools are deployed to demonstrate homology among user-selected plants and to draw genome-scale or local alignment figures and gene-based phylogenetic trees corrected by exploiting gene collinearity. Using these tools and figures, users can easily detect structural changes in genomes and explore the effects of paleo-polyploidy on crop genome structure and function. The GGDB will provide a useful platform for improving our understanding of genome changes and functional innovation in Gramineae plants.
Collapse
Affiliation(s)
- Qihang Yang
- School of Life Science, North China University of Science and Technology, Tangshan, Hebei 063210, China
- Center for Genomics and Bio-computing, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Tao Liu
- School of Life Science, North China University of Science and Technology, Tangshan, Hebei 063210, China
- College of Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Tong Wu
- School of Life Science, North China University of Science and Technology, Tangshan, Hebei 063210, China
- Center for Genomics and Bio-computing, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Tianyu Lei
- School of Life Science, North China University of Science and Technology, Tangshan, Hebei 063210, China
- Center for Genomics and Bio-computing, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | - Yuxian Li
- School of Life Science, North China University of Science and Technology, Tangshan, Hebei 063210, China
- Center for Genomics and Bio-computing, North China University of Science and Technology, Tangshan, Hebei 063210, China
| | | |
Collapse
|
4
|
Tcherkez G, Farquhar GD. Rubisco catalytic adaptation is mostly driven by photosynthetic conditions - Not by phylogenetic constraints. JOURNAL OF PLANT PHYSIOLOGY 2021; 267:153554. [PMID: 34749030 DOI: 10.1016/j.jplph.2021.153554] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 10/19/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
The prevalence of phylogenetic constraints in Rubisco evolution has been emphasised recently by (Bouvier et al., 2021), who argued that phylogenetic inheritance limits Rubisco adaptation much more than the biochemical trade-off between specificity, CO2 affinity and turn-over. In this Opinion, we have critically examined how a phylogenetic signal can be computed with Rubisco kinetic properties and phylogenetic trees, and we arrive at a different conclusion. In particular, Rubisco's adaptation is partly driven by C4 vs. C3 photosynthetic conditions in Angiosperms, apparent phylogenetic signals being mostly due to either homoplasy, computation artefacts or the use of nearly identical sister species. While phylogenetic inheritance of an ancestral enzyme form probably has some role in Rubisco's adaptation landscape, it is a minor player, at least compared to microenvironmental conditions such as CO2 and O2 concentrations.
Collapse
Affiliation(s)
- Guillaume Tcherkez
- Institut de Recherche and Horticulture et Semences, INRAe Angers, Université D'Angers, 42 Rue Georges Morel, 49070, Beaucouzé, France; Research School of Biology, ANU College of Science, Australian National University, 2601, Canberra ACT, Australia.
| | - Graham D Farquhar
- Research School of Biology, ANU College of Science, Australian National University, 2601, Canberra ACT, Australia
| |
Collapse
|
5
|
Chen Y, Zhu X, Loukopoulos P, Weston LA, Albrecht DE, Quinn JC. Genotypic identification of Panicum spp. in New South Wales, Australia using DNA barcoding. Sci Rep 2021; 11:16055. [PMID: 34362980 PMCID: PMC8346583 DOI: 10.1038/s41598-021-95610-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 07/16/2021] [Indexed: 02/07/2023] Open
Abstract
Australia has over 30 Panicum spp. (panic grass) including several non-native species that cause crop and pasture loss and hepatogenous photosensitisation in livestock. It is critical to correctly identify them at the species level to facilitate the development of appropriate management strategies for efficacious control of Panicum grasses in crops, fallows and pastures. Currently, identification of Panicum spp. relies on morphological examination of the reproductive structures, but this approach is only useful for flowering specimens and requires significant taxonomic expertise. To overcome this limitation, we used multi-locus DNA barcoding for the identification of ten selected Panicum spp. found in Australia. With the exception of P. buncei, other native Australian Panicum were genetically separated at the species level and distinguished from non-native species. One nuclear (ITS) and two chloroplast regions (matK and trnL intron-trnF) were identified with varying facility for DNA barcode separation of the Panicum species. Concatenation of sequences from ITS, matK and trnL intron-trnF regions provided clear separation of eight regionally collected species, with a maximum intraspecific distance of 0.22% and minimum interspecific distance of 0.33%. Two of three non-native Panicum species exhibited a smaller genome size compared to native species evaluated, and we speculate that this may be associated with biological advantages impacting invasion of non-native Panicum species in novel locations. We conclude that multi-locus DNA barcoding, in combination with traditional taxonomic identification, provides an accurate and cost-effective adjunctive tool for further distinguishing Panicum spp. at the species level.
Collapse
Affiliation(s)
- Yuchi Chen
- grid.1037.50000 0004 0368 0777School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW Australia ,grid.1680.f0000 0004 0559 5189Graham Centre for Agricultural Innovation, Charles Sturt University and NSW Department of Primary Industries, Wagga Wagga, NSW Australia ,grid.1008.90000 0001 2179 088XMelbourne Veterinary School, The University of Melbourne, Werribee, VIC Australia
| | - Xiaocheng Zhu
- grid.1680.f0000 0004 0559 5189Graham Centre for Agricultural Innovation, Charles Sturt University and NSW Department of Primary Industries, Wagga Wagga, NSW Australia ,grid.1680.f0000 0004 0559 5189Wagga Wagga Agricultural Institute, NSW Department of Primary Industries, Wagga Wagga, NSW Australia
| | - Panayiotis Loukopoulos
- grid.1037.50000 0004 0368 0777School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW Australia ,grid.1008.90000 0001 2179 088XMelbourne Veterinary School, The University of Melbourne, Werribee, VIC Australia
| | - Leslie A. Weston
- grid.1037.50000 0004 0368 0777School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW Australia ,grid.1680.f0000 0004 0559 5189Graham Centre for Agricultural Innovation, Charles Sturt University and NSW Department of Primary Industries, Wagga Wagga, NSW Australia
| | - David E. Albrecht
- grid.467784.e0000 0001 2231 5722Australian National Herbarium, Centre for Australian National Biodiversity Research (a Joint Venture Between Parks Australia and CSIRO), Canberra, Australian Capital Territory, Australia
| | - Jane C. Quinn
- grid.1037.50000 0004 0368 0777School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW Australia ,grid.1680.f0000 0004 0559 5189Graham Centre for Agricultural Innovation, Charles Sturt University and NSW Department of Primary Industries, Wagga Wagga, NSW Australia
| |
Collapse
|
6
|
Sonawane BV, Koteyeva NK, Johnson DM, Cousins AB. Differences in leaf anatomy determines temperature response of leaf hydraulic and mesophyll CO 2 conductance in phylogenetically related C 4 and C 3 grass species. THE NEW PHYTOLOGIST 2021; 230:1802-1814. [PMID: 33605441 DOI: 10.1111/nph.17287] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 02/02/2021] [Indexed: 06/12/2023]
Abstract
Leaf hydraulic and mesophyll CO2 conductance are both influenced by leaf anatomical traits, however it is poorly understood how the temperature response of these conductances differs between C4 and C3 species with distinct leaf anatomy. This study investigated the temperature response of leaf hydraulic conductance (Kleaf ), stomatal (gs ) and mesophyll (gm ) conductance to CO2 , and leaf anatomical traits in phylogenetically related Panicum antidotale (C4 ) and P. bisulcatum (C3 ) grasses. The C4 species had lower hydraulic conductance outside xylem (Kox ) and Kleaf compared with the C3 species. However, the C4 species had higher gm compared with the C3 species. Traits associated with leaf water movement, Kleaf and Kox , increased with temperature more in the C3 than in the C4 species, whereas traits related to carbon uptake, Anet and gm , increased more with temperature in the C4 than the C3 species. Our findings demonstrate that, in addition to a CO2 concentrating mechanism, outside-xylem leaf anatomy in the C4 species P. antidotale favours lower water movement through the leaf and stomata that provides an additional advantage for greater leaf carbon uptake relative to water loss with increasing leaf temperature than in the C3 species P. bisulcatum.
Collapse
Affiliation(s)
- Balasaheb V Sonawane
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Nuria K Koteyeva
- Laboratory of Anatomy and Morphology, V. L. Komarov Botanical Institute of Russian Academy of Sciences, Prof. Popov Street 2, St Petersburg, 197376, Russia
| | - Daniel M Johnson
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, 30602, USA
| | - Asaph B Cousins
- School of Biological Sciences, Washington State University, Pullman, WA, 99164, USA
| |
Collapse
|
7
|
Tashima M, Yabiku T, Ueno O. Coleataenia prionitis, a C 4-like species in the Poaceae. PHOTOSYNTHESIS RESEARCH 2021; 147:211-227. [PMID: 33393063 DOI: 10.1007/s11120-020-00808-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 12/01/2020] [Indexed: 06/12/2023]
Abstract
C4-like plants represent the penultimate stage of evolution from C3 to C4 plants. Although Coleataenia prionitis (formerly Panicum prionitis) has been described as a C4 plant, its leaf anatomy and gas exchange traits suggest that it may be a C4-like plant. Here, we reexamined the leaf structure and biochemical and physiological traits of photosynthesis in this grass. The large vascular bundles were surrounded by two layers of bundle sheath (BS): a colorless outer BS and a chloroplast-rich inner BS. Small vascular bundles, which generally had a single BS layer with various vascular structures, also occurred throughout the mesophyll together with BS cells not associated with vascular tissue. The mesophyll cells did not show a radial arrangement typical of Kranz anatomy. These features suggest that the leaf anatomy of C. prionitis is on the evolutionary pathway to a complete C4 Kranz type. Phosphoenolpyruvate carboxylase (PEPC) and pyruvate, Pi dikinase occurred in the mesophyll and outer BS. Glycine decarboxylase was confined to the inner BS. Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) accumulated in the mesophyll and both BSs. C. prionitis had biochemical traits of NADP-malic enzyme type, whereas its gas exchange traits were close to those of C4-like intermediate plants rather than C4 plants. A gas exchange study with a PEPC inhibitor suggested that Rubisco in the mesophyll could fix atmospheric CO2. These data demonstrate that C. prionitis is not a true C4 plant but should be considered as a C4-like plant.
Collapse
Affiliation(s)
- Maho Tashima
- Graduate School of Bioresources and Environmental Sciences, Kyushu University, Motooka, Fukuoka, 819-0395, Japan
| | - Takayuki Yabiku
- Graduate School of Bioresources and Environmental Sciences, Kyushu University, Motooka, Fukuoka, 819-0395, Japan
| | - Osamu Ueno
- Faculty of Agriculture, Kyushu University, Motooka, Fukuoka, 819-0395, Japan.
| |
Collapse
|
8
|
Hyun J, Do HDK, Jung J, Kim JH. Development of molecular markers for invasive alien plants in Korea: a case study of a toxic weed, Cenchrus longispinus L., based on next generation sequencing data. PeerJ 2019; 7:e7965. [PMID: 31737445 PMCID: PMC6855208 DOI: 10.7717/peerj.7965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/30/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Genomic data play an important role in plant research because of its implications in studying genomic evolution, phylogeny, and developing molecular markers. Although the information of invasive alien plants was collected, the genomic data of those species have not been intensively studied. METHODS We employ the next generation sequencing and PCR methods to explore the genomic data as well as to develop and test the molecular markers. RESULTS In this study, we characterize the chloroplast genomes (cpDNA) of Cenchrus longispinus and C. echinatus, of which the lengths are 137,144 and 137,131 bp, respectively. These two newly sequenced genomes include 78 protein-coding genes, 30 tRNA, and four rRNA. There are 56 simple single repeats and 17 forward repeats in the chloroplast genome of C. longispinus. Most of the repeats locate in non-coding regions. However, repeats can be found in infA, ndhD, ndhH, ndhK, psbC, rpl22, rpoC2, rps14, trnA-UGC, trnC-GCA, trnF-GAA, trnQ-UUG, trnS-UGA, trnS-GCU, and ycf15. The phylogenomic analysis revealed the monophyly of Cenchrus but not Panicum species in tribe Paniceae. The single nucleotide polymorphism sites in atpB, matK, and ndhD were successfully used for developing molecular markers to distinguish C. longispinus and related taxa. The simple PCR protocol for using the newly developed molecular markers was also provided.
Collapse
Affiliation(s)
- JongYoung Hyun
- Department of Life Science, Gachon University, Seongnam, Gyeonggi, Korea
| | - Hoang Dang Khoa Do
- Department of Life Science, Gachon University, Seongnam, Gyeonggi, Korea
| | - Joonhyung Jung
- Department of Life Science, Gachon University, Seongnam, Gyeonggi, Korea
| | - Joo-Hwan Kim
- Department of Life Science, Gachon University, Seongnam, Gyeonggi, Korea
| |
Collapse
|
9
|
Acosta JM, Zuloaga FO, Reinheimer R. Nuclear phylogeny and hypothesized allopolyploidization events in the Subtribe Otachyriinae (Paspaleae, Poaceae). SYST BIODIVERS 2019. [DOI: 10.1080/14772000.2019.1572035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Juan M. Acosta
- Instituto de Botánica Darwinion (CONICET-ANCEFN), Labardén 200, Casilla de Correo 22, B1642HYD, San Isidro, Buenos Aires, Argentina
| | - Fernando O. Zuloaga
- Instituto de Botánica Darwinion (CONICET-ANCEFN), Labardén 200, Casilla de Correo 22, B1642HYD, San Isidro, Buenos Aires, Argentina
| | - Renata Reinheimer
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, FBCB, Santa Fe, Argentina
| |
Collapse
|