Comparative Plastid Genomics of Neotropical Bulbophyllum (Orchidaceae; Epidendroideae)

Zavala-Páez, Michelle; Vieira, Leila do Nascimento; Baura, Valter A.; Balsanelli, Eduardo; Souza, Emanuel Maltempi de; Cevallos, Marco Cerna; Chase, Mark W.; Smidt, Eric de Camargo

doi:10.3389/fpls.2020.00799

Cited by 25 publications

(34 citation statements)

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“…Plastomes have several non-coding regions, but not all of them have been explored for phylogenetic studies [ 3 , 4 , 28 ]. Among the ten regions with the greatest SV% identified in our study, only five IGSs (e.g., accD-psaI , ndhF-rpl32 , trnS-trnG , psaC-ndhE , rps15 - ycf1 ) and one intron ( rpl16 ) were previously used and/or highlighted in angiosperm studies [ 3 , 38 , 51 ].…”

Section: Discussionmentioning

confidence: 99%

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The plastome sequence of Bactris gasipaes and evolutionary analysis in tribe Cocoseae (Arecaceae)

et al. 2021

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The family Arecaceae is distributed throughout tropical and subtropical regions of the world. Among the five subfamilies, Arecoideae is the most species-rich and still contains some ambiguous inter-generic relationships, such as those within subtribes Attaleinae and Bactridineae. The hypervariable regions of plastid genomes (plastomes) are interesting tools to clarify unresolved phylogenetic relationships. We sequenced and characterized the plastome of Bactris gasipaes (Bactridinae) and compared it with eight species from the three Cocoseae sub-tribes (Attaleinae, Bactridinae, and Elaeidinae) to perform comparative analysis and to identify hypervariable regions. The Bactris gasipaes plastome has 156,646 bp, with 113 unique genes. Among them, four genes have an alternative start codon (cemA, rps19, rpl2, and ndhD). Plastomes are highly conserved within tribe Cocoseae: 97.3% identity, length variation of ~2 kb, and a single ~4.5 kb inversion in Astrocaryum plastomes. The LSC/IR and IR/SSC junctions vary among the subtribes: in Bactridinae and Elaeidinae the rps19 gene is completely contained in the IR region; in the subtribe Attaleinae the rps19 gene is only partially contained in the IRs. The hypervariable regions selected according to sequence variation (SV%) and frequency of parsimony informative sites (PIS%) revealed plastome regions with great potential for molecular analysis. The ten regions with greatest SV% showed higher variation than the plastid molecular markers commonly used for phylogenetic analysis in palms. The phylogenetic trees based on the plastomes and the hypervariable regions (SV%) datasets had well-resolved relationships, with consistent topologies within tribe Cocoseae, and confirm the monophyly of the subtribes Bactridinae and Attaleinae.

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Section: Discussionmentioning

confidence: 99%

“…We estimated the variability of the sequences with the formula proposed by Shaw et al [ 27 ], adapted and used by Zavala-Páez et al [ 28 ]. First, we individually aligned each collinear coding sequence (CDS), intergenic spacers (IGS), and introns of the plastomes (list of species in S1 Table ) using MAFFT v.7 software [ 29 ].…”

Section: Methodsmentioning

confidence: 99%

The plastome sequence of Bactris gasipaes and evolutionary analysis in tribe Cocoseae (Arecaceae)

et al. 2021

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“…In addition, seven of the 11 ndh genes are located in SSC, so it is not surprising that ndh gene composition greatly influences the length of this region and, consequently, plastome size because it is the main distinctive feature among Pleurothallidinae genomes. This influence of ndh gene deletion/retention on the SSC size has been widely reported in the literature [53,54,63,64], but the importance of this region for orchid plastome size variation has only been observed for Pleurothallidinae and Bulbophyllum Thouars [29] thus far.…”

Section: Plos Onementioning

confidence: 79%

“…The advent of next-generation sequencing (NGS) has made plastome sequencing faster and more accessible [22], and they have become the main source of phylogenetic information for angiosperms [19,23]. In Orchidaceae, plastome sequences have been compared among genera and species to find the most-variable regions, termed mutational hotspots [24][25][26][27][28][29]. Hence, comparative analyses of complete plastome sequences of Pleurothallidinae can indicate better molecular markers, but thus far only three plastomes of the subtribe are publicly available.…”

Section: Introductionmentioning

confidence: 99%

Plastid phylogenomics of Pleurothallidinae (Orchidaceae): Conservative plastomes, new variable markers, and comparative analyses of plastid, nuclear, and mitochondrial data

et al. 2021

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We present the first comparative plastome study of Pleurothallidinae with analyses of structural and molecular characteristics and identification of the ten most-variable regions to be incorporated in future phylogenetic studies. We sequenced complete plastomes of eight species in the subtribe and compared phylogenetic results of these to parallel analyses of their nuclear ribosomal DNA operon (26S, 18S, and 5.8S plus associated spacers) and partial mitochondrial genome sequences (29–38 genes and partial introns). These plastomes have the typical quadripartite structure for which gene content is similar to those of other orchids, with variation only in the composition of the ndh genes. The independent loss of ndh genes had an impact on which genes border the inverted repeats and thus the size of the small single-copy region, leading to variation in overall plastome length. Analyses of 68 coding sequences indicated the same pattern of codon usage as in other orchids, and 13 protein-coding genes under positive selection were detected. Also, we identified 62 polymorphic microsatellite loci and ten highly variable regions, for which we designed primers. Phylogenomic analyses showed that the top ten mutational hotspots represent well the phylogenetic relationships found with whole plastome sequences. However, strongly supported incongruence was observed among plastid, nuclear ribosomal DNA operon, and mitochondrial DNA trees, indicating possible occurrence of incomplete lineage sorting and/or introgressive hybridization. Despite the incongruence, the mtDNA tree retrieved some clades found in other analyses. These results, together with performance in recent studies, support a future role for mitochondrial markers in Pleurothallidinae phylogenetics.

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“…Most notably, this includes the plastid genome, which has been used extensively for phylogenetics. The ease of this method has meant that it has surged in popularity over recent years, in many organisms, but also in angiosperms and orchids specifically (Parks et al, 2009; Edger et al, 2018; Li, Yi, et al, 2019; Kim et al, 2020; Zavala-Páez et al, 2020). This has perpetuated the plastid-marker bias in phylogenetic studies of orchids but also greatly improved the results from these analyses.…”

Section: Discussionmentioning

confidence: 99%

Hundreds of nuclear and plastid loci yield insights into orchid relationships

Pérez‐Escobar

Dodsworth

Bogarín³

et al. 2020

Preprint

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Premise of the studyEvolutionary relationships in the species-rich Orchidaceae have historically relied on organellar DNA sequences and limited taxon sampling. Previous studies provided a robust plastid-maternal phylogenetic framework, from which multiple hypotheses on the drivers of orchid diversification have been derived. However, the extent to which the maternal evolutionary history of orchids is congruent with that of the nuclear genome has remained uninvestigated.MethodsWe inferred phylogenetic relationships from 294 low-copy nuclear genes sequenced/obtained using the Angiosperms353 universal probe set from 75 species representing 69 genera, 16 tribes and 24 subtribes. To test for topological incongruence between nuclear and plastid genomes, we constructed a tree from 78 plastid genes, representing 117 genera, 18 tribes and 28 subtribes and compared them using a co-phylogenetic approach. The phylogenetic informativeness and support of the Angiosperms353 loci were compared with those of the 78 plastid genes.Key ResultsPhylogenetic inferences of nuclear datasets produced highly congruent and robustly supported orchid relationships. Comparisons of nuclear gene trees and plastid gene trees using the latest co-phylogenetic tools revealed strongly supported phylogenetic incongruence in both shallow and deep time. Phylogenetic informativeness analyses showed that the Angiosperms353 genes were in general more informative than most plastid genes.ConclusionsOur study provides the first robust nuclear phylogenomic framework for Orchidaceae plus an assessment of intragenomic nuclear discordance, plastid-nuclear tree incongruence, and phylogenetic informativeness across the family. Our results also demonstrate what has long been known but rarely documented: nuclear and plastid phylogenetic trees are not fully congruent and therefore should not be considered interchangeable.

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Comparative Plastid Genomics of Neotropical Bulbophyllum (Orchidaceae; Epidendroideae)

Cited by 25 publications

References 98 publications

The plastome sequence of Bactris gasipaes and evolutionary analysis in tribe Cocoseae (Arecaceae)

The plastome sequence of Bactris gasipaes and evolutionary analysis in tribe Cocoseae (Arecaceae)

Plastid phylogenomics of Pleurothallidinae (Orchidaceae): Conservative plastomes, new variable markers, and comparative analyses of plastid, nuclear, and mitochondrial data

Hundreds of nuclear and plastid loci yield insights into orchid relationships

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