title: Phylogenetic inference and SSR characterization of tropical woody bamboos tribe Bambuseae (Poaceae: Bambusoideae) based on complete plastid genome sequences.
abstract: The complete plastome sequencing is an efficient option for increasing phylogenetic resolution and evolutionary studies, as well as may greatly facilitate the use of plastid DNA markers in plant population genetic studies. Merostachys and Guadua stand out as the most common and the highest potential utilization bamboos indigenous of Brazil. Here, we sequenced the complete plastome sequences of the Brazilian Guadua chacoensis and Merostachys sp. to perform full plastome phylogeny and characterize the occurrence, type, and distribution of SRRs using 20 Bambuseae species. The determined plastome sequence of Merostachys sp. and G. chacoensis is 136,334 and 135,403 bp in size, respectively, with an identical gene content and typical quadripartite structure consisting of a pair of IRs separated by the LSC and SSC regions. The Maximum Likelihood and Bayesian Inference analyses produced phylogenomic trees identical in topology. These trees supported monophyly of Paleotropical and Neotropical Bamboos clades. The Neotropical bamboos segregated into three well-supported lineages, Chusqueinae, Guaduinae, and Arthrostylidiinae, with the last two forming a well-supported sister relationship. Paleotropical bamboos segregated into two well-supported lineages, Hickeliinae and Bambusinae + Melocanninae. We identified 141.8 cpSSR in Bambuseae plastomes and an inferior value (38.15) for plastome coding sequences. Among them, we identified 16 polymorphic SSR loci, with number of alleles varying from 3 to 10. These 16 polymorphic cpSSR loci in Bambuseae plastome can be assessed for the intraspecific level of polymorphism, leading to innovative highly sensitive phylogeographic and population genetics studies for this tribe.
authors.affiliation: Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Rodovia Admar Gonzaga, 1346, Florianópolis, Santa Catarina, 88040-900, Brazil.
authors.forename: Leila do Nascimento
authors.initials: Ldo N
authors.lastname: Vieira
authors.affiliation: Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Rodovia Admar Gonzaga, 1346, Florianópolis, Santa Catarina, 88040-900, Brazil.
authors.forename: Karina Goulart
authors.initials: KG
authors.lastname: Dos Anjos
authors.affiliation: Instituto Carlos Chagas, Fundação Oswaldo Cruz, Rua Professor Algacyr Munhoz Mader, 3775, bloco C, Cidade Industrial, Curitiba, Brazil.|Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Rua Coronel Francisco H. dos Santos s/n, Curitiba, Paraná, 81531-980, Brazil.
authors.forename: Helisson
authors.initials: H
authors.lastname: Faoro
authors.affiliation: Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Rodovia Admar Gonzaga, 1346, Florianópolis, Santa Catarina, 88040-900, Brazil.
authors.forename: Hugo Pacheco de Freitas
authors.initials: HP
authors.lastname: Fraga
authors.affiliation: Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Rodovia Admar Gonzaga, 1346, Florianópolis, Santa Catarina, 88040-900, Brazil.
authors.forename: Thiago Machado
authors.initials: TM
authors.lastname: Greco
authors.affiliation: Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Rua Coronel Francisco H. dos Santos s/n, Curitiba, Paraná, 81531-980, Brazil.
authors.forename: Fábio de Oliveira
authors.initials: Fde O
authors.lastname: Pedrosa
authors.affiliation: Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Rua Coronel Francisco H. dos Santos s/n, Curitiba, Paraná, 81531-980, Brazil.
authors.forename: Emanuel Maltempi
authors.initials: EM
authors.lastname: de Souza
authors.affiliation: Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Avenida Peter Henry Rolfs s/n, Viçosa, Minas Gerais, 36570-000, Brazil.
authors.forename: Marcelo
authors.initials: M
authors.lastname: Rogalski
authors.affiliation: Departamento de Microbiologia, Universidade de São Paulo, Avenida Professor Lineu Prestes, 1374 - Ed. Biomédicas II - Sala 250 - 2o. Andar, São Paulo, São Paulo, 05508-900, Brazil.
authors.forename: Robson Francisco
authors.initials: RF
authors.lastname: de Souza
authors.affiliation: Laboratório de Fisiologia do Desenvolvimento e Genética Vegetal, Programa de Pós-graduação em Recursos Genéticos Vegetais, Universidade Federal de Santa Catarina, Rodovia Admar Gonzaga, 1346, Florianópolis, Santa Catarina, 88040-900, Brazil. miguel.guerra@ufsc.br.
authors.forename: Miguel Pedro
authors.initials: MP
authors.lastname: Guerra
mesh_terms: D056426:Genetic Loci; D054627:Genome, Plastid; D010802:Phylogeny; D018087:Plastids / Q000235:genetics*; D006109:Poaceae / Q000235:genetics*; D017422:Sequence Analysis, DNA
keywords: Molecular phylogeny; Next-generation; Plastome; Poaceae; Woody bamboos