Phylogenetic estimation and morphological evolution of Arundinarieae (Bambusoideae: Poaceae) based on plastome phylogenomic analysis

Attigala, Lakshmi; Wysocki, William P.; Duvall, Melvin R.; Clark, Lynn G.

doi:10.1016/j.ympev.2016.05.008

Cited by 59 publications

(103 citation statements)

References 40 publications

(85 reference statements)

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“…This result was consistent with previous findings (Attigala et al, 2016) in which a much higher of support to inter-generic relationships was observed in the cp genomic phylogeny within Arundinarieae tribe (Bambusoideae: Poaceae). The sister relationship between Paris s.s. and Daiswa + Trillium clade can be justified by the morphological synapomorphies of single whorl of net-veined leaves at stem apex and solitary flower ( Table 4 ).…”

Section: Discussionsupporting

confidence: 93%

Analysis of Complete Chloroplast Genome Sequences Improves Phylogenetic Resolution in Paris (Melanthiaceae)

Huang

Yang

et al. 2016

Front. Plant Sci.

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The genus Paris in the broad concept is an economically important group in the monocotyledonous family Melanthiaceae (tribe Parideae). The phylogeny of Paris was controversial in previous morphology-based classification and molecular phylogeny. Here, the complete cp genomes of eleven Paris taxa were sequenced, to better understand the evolutionary relationships among these plants and the mutation patterns in their chloroplast (cp) genomes. Comparative analyses indicated that the overall cp genome structure among the Paris taxa is quite similar. The triplication of trnI-CAU was found only in the cp genomes of P. quadrifolia and P. verticillata. Phylogenetic analyses based on the complete cp genomes did not resolve Paris as a monophyletic group, instead providing evidence supporting division of the twelve taxa into two segregate genera: Paris sensu strict and Daiswa. The sister relationship between Daiswa and Trillium was well supported. We recovered two fully supported lineages with divergent distribution in Daiswa; however, none of the previously recognized sections in Daiswa was resolved as monophyletic using plastome data, suggesting that the infrageneric relationships and biogeography of Daiswa species require further investigation. Ten highly divergent DNA regions, suitable for species identification, were detected among the 12 cp genomes. This study is the first successful attempt to provide well-supported evolutionary relationships in Paris based on phylogenomic analyses. The findings highlight the potential of the whole cp genomes for improving resolution in phylogeny as well as species identification in phylogenetically and taxonomically difficult plant genera.

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Section: Discussionsupporting

confidence: 93%

Analysis of Complete Chloroplast Genome Sequences Improves Phylogenetic Resolution in Paris (Melanthiaceae)

Huang

Yang

et al. 2016

Front. Plant Sci.

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“…Nonetheless, Ampelocalamuscalcareus was sister to all the other taxa of the tribe Arundinarieae in plastid and nuclear gene trees (Yang et al 2013, Ma et al 2014, Attigala et al 2016, Zhang et al 2016). The morphological similarity between the distantly related A.calcareus and those three genera ( Ampelocalamus , Drepanostachyum and Himalayacalamus ) demonstrated that morphological characters had undergone complex evolutionary trajectories in those taxa and also in the whole tribe and some important features in bamboo taxonomy were homoplastic or convergent that was illustrated in other studies of Arundinarieae and some tropical woody bamboos (Yang et al 2008, Tyrrell et al 2012, Attigala et al 2016). …”

Section: Discussionmentioning

confidence: 95%

“…Kuruna . However, relationships amongst them remain largely uncertain (Triplett and Clark 2010, Zeng et al 2010, Yang et al 2013, Attigala et al 2014, 2016, Ma et al 2014, Zhang et al 2016, Zhang et al 2017). Those lineages are strongly inconsistent with the morphological classification at the generic and subtribal levels (Keng and Wang 1996, Li 1997, 1999, Ohrnberger 1999).…”

Section: Introductionmentioning

confidence: 99%

A new genus of temperate woody bamboos (Poaceae, Bambusoideae, Arundinarieae) from a limestone montane area of China

Zhang¹,

Ma²,

D³

2018

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Ampelocalamuscalcareus is a climbing and slender bamboo, known from south Guizhou, China. This species grows in broadleaved forests of limestone montane areas. Recent molecular phylogenetic analyses demonstrated that A.calcareus was sister to all other lineages of the tribe Arundinarieae rather than a member of Ampelocalamus. The morphological features and habitats of A.calcareus and related genera including Ampelocalamus, Drepanostachyum and Himalayacalamus were compared and discussed. The characteristics of the branch complements, nodes and foliage leaves distinguish A.calcareus from morphologically similar taxa. On the basis of molecular and morphological evidence, we propose to establish a new genus, Hsuehochloa, to accommodate A.calcareus and to honour the late Chinese bamboo taxonomist Chi-Ju Hsueh (Ji-Ru Xue). In addition, we describe the inflorescence of Hsuehochloa for the first time.

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“…Chloroplast (cp) genome sequencing, by providing more genetic information, has proven itself as a method offering great potential for the resolution of historically difficult problems in phylogenetics (Jansen et al, 2007; Moore et al, 2007, 2010; Barrett et al, 2013, 2014; Ma et al, 2014; Stull et al, 2015; Attigala et al, 2016; Huang et al, 2016). Here, we present the complete cp genomes of Davidia involucrata , Nyssa sinensis , and Camptotheca acuminata through Illumina sequencing and a reference-guided assembly of the de novo contigs.…”

Section: Introductionmentioning

confidence: 99%

Comparative and Phylogenetic Analyses of the Complete Chloroplast Genomes of Three Arcto-Tertiary Relicts: Camptotheca acuminata, Davidia involucrata, and Nyssa sinensis

Yang

2017

Front. Plant Sci.

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The Arcto-Tertiary relict genera, Camptotheca, Davidia, and Nyssa represent deep lineages in the asterid order Cornales. Recent phylogenetic studies suggested that these genera should be placed in a newly circumscribed family, Nyssaceae. However, because these analyses were based upon a few genes, it is prudent and necessary to examine further evidence before adopting this taxonomic treatment. In this study, we determined the complete chloroplast (cp) genomes of Camptotheca acuminata, Davidia involucrata, and Nyssa sinensis. Their cp genomes ranged from 156,672 to 158,409 bp, which included 115 genes, and their genome features were highly similar to those of other species within the order Cornales. The phylogenetic relationships among the genera Camptotheca, Davidia, Nyssa, and 23 related taxa in the asterids were analyzed based on 73 protein-coding genes from the cp genomes. All of the previously recognized major clades (namely Cornales, Ericales, Campanulids, and Lamiids) in the asterids, as well as their relationships, were recovered with robust support. A clade including the genera Davidia, Nyssa, Camptotheca, and Diplopanax, was resolved as a well-supported monophyletic group, which was fully separated from the family Cornaceae by the family Hydrangeaceae. Our results provide novel evidence to support the acceptance of the family Nyssaceae outlined by the updated Angiosperm Phylogeny Group.

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Phylogenetic estimation and morphological evolution of Arundinarieae (Bambusoideae: Poaceae) based on plastome phylogenomic analysis

Cited by 59 publications

References 40 publications

Analysis of Complete Chloroplast Genome Sequences Improves Phylogenetic Resolution in Paris (Melanthiaceae)

Analysis of Complete Chloroplast Genome Sequences Improves Phylogenetic Resolution in Paris (Melanthiaceae)

A new genus of temperate woody bamboos (Poaceae, Bambusoideae, Arundinarieae) from a limestone montane area of China

Comparative and Phylogenetic Analyses of the Complete Chloroplast Genomes of Three Arcto-Tertiary Relicts: Camptotheca acuminata, Davidia involucrata, and Nyssa sinensis

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