A multilocus phylogenetic analysis reveals the monophyly of a recircumscribed papilionoid legume tribe Diocleae with well-supported generic relationships

Queiroz, Luciano Paganucci de; Pastore, José Floriano Barêa; Cardoso, Domingos; Snak, Cristiane; Lima, Ana Luísa de Carvalho; Gagnon, Edeline; Vatanparast, Mohammad; Holland, Ailsa E.; Egan, Ashley N.

doi:10.1016/j.ympev.2015.04.016

Cited by 64 publications

(57 citation statements)

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“…Mucuna is variously allied with monotypic Haymondia wallichii (DC.) A.N.Egan & B.Pan bis [4, 61] or with tribe Desmodieae [4, 62–64]. The addition of our transcriptomic data representing the Mucuna lineage thus fills a void within the developing resource base of transcriptomic data available for comparative evolutionary studies across legumes.…”

Section: Discussionmentioning

confidence: 99%

Transcriptomic resources for the medicinal legume Mucuna pruriens: de novo transcriptome assembly, annotation, identification and validation of EST-SSR markers

et al. 2017

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BackgroundThe medicinal legume Mucuna pruriens (L.) DC. has attracted attention worldwide as a source of the anti-Parkinson’s drug L-Dopa. It is also a popular green manure cover crop that offers many agronomic benefits including high protein content, nitrogen fixation and soil nutrients. The plant currently lacks genomic resources and there is limited knowledge on gene expression, metabolic pathways, and genetics of secondary metabolite production. Here, we present transcriptomic resources for M. pruriens, including a de novo transcriptome assembly and annotation, as well as differential transcript expression analyses between root, leaf, and pod tissues. We also develop microsatellite markers and analyze genetic diversity and population structure within a set of Indian germplasm accessions.ResultsOne-hundred ninety-one million two hundred thirty-three thousand two hundred forty-two bp cleaned reads were assembled into 67,561 transcripts with mean length of 626 bp and N50 of 987 bp. Assembled sequences were annotated using BLASTX against public databases with over 80% of transcripts annotated. We identified 7,493 simple sequence repeat (SSR) motifs, including 787 polymorphic repeats between the parents of a mapping population. 134 SSRs from expressed sequenced tags (ESTs) were screened against 23 M. pruriens accessions from India, with 52 EST-SSRs retained after quality control. Population structure analysis using a Bayesian framework implemented in fastSTRUCTURE showed nearly similar groupings as with distance-based (neighbor-joining) and principal component analyses, with most of the accessions clustering per geographical origins. Pair-wise comparison of transcript expression in leaves, roots and pods identified 4,387 differentially expressed transcripts with the highest number occurring between roots and leaves. Differentially expressed transcripts were enriched with transcription factors and transcripts annotated as belonging to secondary metabolite pathways.ConclusionsThe M. pruriens transcriptomic resources generated in this study provide foundational resources for gene discovery and development of molecular markers. Polymorphic SSRs identified can be used for genetic diversity, marker-trait analyses, and development of functional markers for crop improvement. The results of differential expression studies can be used to investigate genes involved in L-Dopa synthesis and other key metabolic pathways in M. pruriens.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3780-9) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Transcriptomic resources for the medicinal legume Mucuna pruriens: de novo transcriptome assembly, annotation, identification and validation of EST-SSR markers

et al. 2017

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“…To accomplish this aim, all major lineages of the papilionoids (Cardoso et al, 2012a(Cardoso et al, , 2013a were included, mostly from previously published matK sequences (e.g., Hu et al, 2000;Lavin et al, 2001Lavin et al, , 2003McMahon and Hufford, 2004;Wojciechowski et al, 2004;Queiroz et al, 2010Queiroz et al, , 2015Queiroz and Lavin, 2011;Delgado-Salinas et al, 2011;Cardoso et al 2012aCardoso et al , 2013aCardoso et al , 2015Snak et al, 2016).…”

Section: Taxon Sampling and Molecular Datamentioning

confidence: 99%

“…For example, dramatic shuffling in the placement of genera has also been necessary within the species-rich canavanine-accumulating clade (Wojciechowski et al, 2004;Silva et al, 2012;Sirichamorn et al, 2012Sirichamorn et al, , 2014Queiroz et al, 2015). There are, however, few cases of generic interchange between lineages below (less inclusive) or above the (more inclusive) the node defining the canavanineaccumulating clade.…”

Section: Introductionmentioning

confidence: 99%

A molecular phylogeny reveals the Cuban enigmatic genus Behaimia as a new piece in the Brongniartieae puzzle of papilionoid legumes

Queiroz

São-Mateus

Delgado‐Salinas

et al. 2017

Molecular Phylogenetics and Evolution

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This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. E-mail address: luciano.paganucci@gmail.com (L.P. de Queiroz). ABSTRACTThe papilionoid legume tribe Brongniartieae comprises a collection of 13 genera with disparate morphologies that were previously positioned in at least three remotely related tribes. The Brongniartieae displays a wide geographical disjunction between Australia and the New World and previous phylogenetic studies had provided conflicting results about the relationships between the American and Australian genera. We carry out phylogenetic analyses of (1) a plastid matK dataset extensively sampled across legumes to solve the enigmatic relationship of the Cuban-endemic monospecific genus Behaimia; and (2) multilocus datasets with focus on all genera ever referred toBrongniartieae. These analyses resulted in a well-resolved and strongly-supported phylogenetic tree of the Brongniartieae. Increased molecular sampling in papilionoid legume phylogeny has dramatically changed our understanding of the evolution and taxonomic classification in this species rich lineage of economically and ecologically important legumes (family Leguminosae).The prevailing traditional hypotheses of generic relationships assumed that the papilionate flower would be a signature of the most "derived" groups, whereas the more caesalpinioid and mimosoid-like floral organizations, involving undifferentiated petals and free stamens, marked mostly the "primitive" tribes within the subfamily Papilionoideae (Polhill, 1981a). Hence, such an evolutionary perspective has largely influenced the way in which the modern subfamily, tribe, and even genus-level classification of legumes was built (LPWG, 2013(LPWG, , 2017. In the past 15 years, molecular phylogenetic studies have underpinned dramatic taxonomic changes after revealing unexpected relationships, suggesting that floral architecture is relatively labile in the early-branching papilionoid lineages (e.g. Pennington et al., 2001;Wojciechowski et al., 2004; Cardoso et al., 2012aCardoso et al., , 2013aCardoso et al., , 2015Ramos et al., 2016).The recent examples of broad phylogenetic re-alignments that were unexpectedly revealed in the early-branching genera of Papilionoideae (Cardoso et al., 2012a(Cardoso et al., , 2012b(Cardoso et al., , 2012c(Cardoso et al., , 2013a(Cardoso et al., , 2017Ramos et al., 2016; Castellanos et al., in press) are not an exception across legumes. For example, dramatic shuffling in the placement of genera has also been necessary within the species-rich canavanine-accumulating clade (Wojciechowski et al., 2004;Silva et al., 2012;Sirichamorn et al., ...

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“…Stirt. [Egan and Crandall 2008; Dludlu et al 2013], Dioclea Kunth, and Galactia P. Browne [De Queiroz et al 2015]). In many other legume groups extensive non-monophyly of genera has been reported, but phylogenies with increased molecular and taxonomic sampling are necessary to provide the robust evidence needed to establish new generic systems (e.g.…”

Section: Introductionmentioning

confidence: 99%

A new generic system for the pantropical Caesalpinia group (Leguminosae)

Gagnon

Bruneau

Hughes

et al. 2016

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The Caesalpinia group is a large pantropical clade of ca. 205 species in subfamily Caesalpinioideae (Leguminosae) in which generic delimitation has been in a state of considerable flux. Here we present new phylogenetic analyses based on five plastid and one nuclear ribosomal marker, with dense taxon sampling including 172 (84%) of the species and representatives of all previously described genera in the Caesalpinia group. These analyses show that the current classification of the Caesalpinia group into 21 genera needs to be revised. Several genera (Poincianella, Erythrostemon, Cenostigma and Caesalpinia sensu Lewis, 2005) are non-monophyletic and several previously unclassified Asian species segregate into clades that merit recognition at generic rank. In addition, the near-completeness of our taxon sampling identifies three species that do not belong in any of the main clades and these are recognised as new monospecific genera. A new generic classification of the Caesalpinia group is presented including a key for the identification of genera, full generic descriptions, illustrations (drawings and photo plates of all genera), and (for most genera) the nomenclatural transfer of species to their correct genus. We recognise 26 genera, with reinstatement of two previously described genera (Biancaea Tod., Denisophytum R. Vig.), re-delimitation and expansion of several others (Moullava, Cenostigma, Libidibia and Erythrostemon), contraction of Caesalpinia s.s. and description of four new ones (Gelrebia, Paubrasilia, Hererolandia and Hultholia), and make 75 new nomenclatural combinations in this new generic system.

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A multilocus phylogenetic analysis reveals the monophyly of a recircumscribed papilionoid legume tribe Diocleae with well-supported generic relationships

Cited by 64 publications

References 62 publications

Transcriptomic resources for the medicinal legume Mucuna pruriens: de novo transcriptome assembly, annotation, identification and validation of EST-SSR markers

Transcriptomic resources for the medicinal legume Mucuna pruriens: de novo transcriptome assembly, annotation, identification and validation of EST-SSR markers

A molecular phylogeny reveals the Cuban enigmatic genus Behaimia as a new piece in the Brongniartieae puzzle of papilionoid legumes

A new generic system for the pantropical Caesalpinia group (Leguminosae)

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