title: C4 Photosynthesis in the Rice Paddy: Insights from the Noxious Weed Echinochloa glabrescens.
abstract: The C4 pathway is a highly complex trait that increases photosynthetic efficiency in more than 60 plant lineages. Although the majority of C4 plants occupy disturbed, arid, and nutrient-poor habitats, some grow in high-nutrient, waterlogged conditions. One such example is Echinochloa glabrescens, which is an aggressive weed of rice paddies. We generated comprehensive transcriptome datasets for C4 E. glabrescens and C3 rice to identify genes associated with adaption to waterlogged, nutrient-replete conditions, but also used the data to better understand how C4 photosynthesis operates in these conditions. Leaves of E. glabrescens exhibited classical Kranz anatomy with lightly lobed mesophyll cells having low chloroplast coverage. As with rice and other hygrophytic C3 species, leaves of E. glabrescens accumulated a chloroplastic phosphoenolpyruvate carboxylase protein, albeit at reduced amounts relative to rice. The arid-grown species Setaria italica (C4) and Brachypodium distachyon (C3) were also found to accumulate chloroplastic phosphoenolpyruvate carboxylase. We identified a molecular signature associated with C4 photosynthesis in nutrient-replete, waterlogged conditions that is highly similar to those previously reported from C4 plants that grow in more arid conditions. We also identified a cohort of genes that have been subjected to a selective sweep associated with growth in paddy conditions. Overall, this approach highlights the value of using wild species such as weeds to identify adaptions to specific conditions associated with high-yielding crops in agriculture.
authors.affiliation: Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (S.C., M.S., T.E.H., R.S.-U., J.A.P., J.M.H.);Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (S.K.);Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom (K.J.B., R.L.); andDepartment of Ecology and Evolutionary Biology, 25 Willcocks Street, University of Toronto, Toronto, Ontario, Canada M5S 3B2 (T.L.S.).
authors.forename: Sarah
authors.initials: S
authors.lastname: Covshoff
authors.affiliation: Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (S.C., M.S., T.E.H., R.S.-U., J.A.P., J.M.H.);Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (S.K.);Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom (K.J.B., R.L.); andDepartment of Ecology and Evolutionary Biology, 25 Willcocks Street, University of Toronto, Toronto, Ontario, Canada M5S 3B2 (T.L.S.).
authors.forename: Marek
authors.initials: M
authors.lastname: Szecowka
authors.affiliation: Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (S.C., M.S., T.E.H., R.S.-U., J.A.P., J.M.H.);Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (S.K.);Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom (K.J.B., R.L.); andDepartment of Ecology and Evolutionary Biology, 25 Willcocks Street, University of Toronto, Toronto, Ontario, Canada M5S 3B2 (T.L.S.).
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Hughes
authors.affiliation: Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (S.C., M.S., T.E.H., R.S.-U., J.A.P., J.M.H.);Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (S.K.);Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom (K.J.B., R.L.); andDepartment of Ecology and Evolutionary Biology, 25 Willcocks Street, University of Toronto, Toronto, Ontario, Canada M5S 3B2 (T.L.S.).
authors.forename: Richard
authors.identifier: http://orcid.org/0000-0001-8721-7197
authors.initials: R
authors.lastname: Smith-Unna
authors.affiliation: Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (S.C., M.S., T.E.H., R.S.-U., J.A.P., J.M.H.);Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (S.K.);Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom (K.J.B., R.L.); andDepartment of Ecology and Evolutionary Biology, 25 Willcocks Street, University of Toronto, Toronto, Ontario, Canada M5S 3B2 (T.L.S.).
authors.forename: Steven
authors.initials: S
authors.lastname: Kelly
authors.affiliation: Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (S.C., M.S., T.E.H., R.S.-U., J.A.P., J.M.H.);Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (S.K.);Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom (K.J.B., R.L.); andDepartment of Ecology and Evolutionary Biology, 25 Willcocks Street, University of Toronto, Toronto, Ontario, Canada M5S 3B2 (T.L.S.).
authors.forename: Karen J
authors.initials: KJ
authors.lastname: Bailey
authors.affiliation: Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (S.C., M.S., T.E.H., R.S.-U., J.A.P., J.M.H.);Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (S.K.);Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom (K.J.B., R.L.); andDepartment of Ecology and Evolutionary Biology, 25 Willcocks Street, University of Toronto, Toronto, Ontario, Canada M5S 3B2 (T.L.S.).
authors.forename: Tammy L
authors.initials: TL
authors.lastname: Sage
authors.affiliation: Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (S.C., M.S., T.E.H., R.S.-U., J.A.P., J.M.H.);Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (S.K.);Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom (K.J.B., R.L.); andDepartment of Ecology and Evolutionary Biology, 25 Willcocks Street, University of Toronto, Toronto, Ontario, Canada M5S 3B2 (T.L.S.).
authors.forename: Justin A
authors.initials: JA
authors.lastname: Pachebat
authors.affiliation: Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (S.C., M.S., T.E.H., R.S.-U., J.A.P., J.M.H.);Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (S.K.);Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom (K.J.B., R.L.); andDepartment of Ecology and Evolutionary Biology, 25 Willcocks Street, University of Toronto, Toronto, Ontario, Canada M5S 3B2 (T.L.S.).
authors.forename: Richard
authors.initials: R
authors.lastname: Leegood
authors.affiliation: Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom (S.C., M.S., T.E.H., R.S.-U., J.A.P., J.M.H.);Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom (S.K.);Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom (K.J.B., R.L.); andDepartment of Ecology and Evolutionary Biology, 25 Willcocks Street, University of Toronto, Toronto, Ontario, Canada M5S 3B2 (T.L.S.) jmh65@cam.ac.uk.
authors.forename: Julian M
authors.identifier: http://orcid.org/0000-0003-0662-7958
authors.initials: JM
authors.lastname: Hibberd
mesh_terms: D002736:Chloroplasts; D018556:Crops, Agricultural / Q000033:anatomy & histology / Q000235:genetics / Q000502:physiology; D031747:Echinochloa / Q000033:anatomy & histology / Q000235:genetics / Q000502:physiology*; D018506:Gene Expression Regulation, Plant; D012275:Oryza / Q000235:genetics* / Q000502:physiology; D010730:Phosphoenolpyruvate Carboxylase / Q000378:metabolism; D010788:Photosynthesis / Q000502:physiology*; D059828:Plant Cells / Q000648:ultrastructure; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D057685:Plant Weeds / Q000033:anatomy & histology / Q000235:genetics / Q000502:physiology*; D059467:Transcriptome
chemical_list: D010940:Plant Proteins; D010730:Phosphoenolpyruvate Carboxylase