Using phylogenomics to reconstruct phylogenetic relationships within tribe Polygonateae (Asparagaceae), with a special focus on Polygonatum

Floden, Aaron; Schilling, Edward E.

doi:10.1016/j.ympev.2018.08.017

Cited by 35 publications

(49 citation statements)

References 75 publications

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“…We reconstructed a phylogeny employing the GTR þ G model and 1000 bootstrap replicates under the maximum-likelihood (ML) inference in RAxML-HPC v.8.2.10 on the CIPRES cluster (Miller et al 2010). The ML tree (Figure 1) was consistent with the most recent phylogenetic study on Polygonateae (Asparagaceae) (Floden and Schilling 2018). Reineckia carnea exhibited the closest relationship with Rohdea chinensis.…”

supporting

confidence: 64%

Complete chloroplast genome of Reineckia carnea and its implications for the phylogenetic position within Nolinoideae (Asparagaceae)

Sun

Cao²,

et al. 2019

Mitochondrial DNA Part B

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Reineckia carnea is an important horticultural and medicinal plant in East Asia. Here, we determined the first complete chloroplast genome of R. carnea using genome skimming approach. The cp genome was 157,059 bp long, with a large single-copy region (LSC) of 85,474 bp and a small single-copy region (SSC) of 18,535 bp separated by a pair of inverted repeats (IRs) of 26,525 bp. It encodes 132 genes, including 86 protein-coding genes, 38 tRNA genes, and eight ribosomal RNA genes. The phylogenetic analysis indicated that R. carnea is close related to Rohdea chinensis.

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supporting

confidence: 64%

Complete chloroplast genome of Reineckia carnea and its implications for the phylogenetic position within Nolinoideae (Asparagaceae)

Sun

Cao²,

et al. 2019

Mitochondrial DNA Part B

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“…The phylogenetic relationship of the Nolinoideae taxa has not been resolved in earlier studies. The reason for this is that the Nolinoideae subfamily consists of three major tribe clades, namely, Polygonateae, Aspidistreae and Ophiopogoneae, and is weakly supported in the phylogenetic tree [47]. Moreover, in the Polygonateae clade, several Polygonatum species were characterized and their phylogenetic relationships have been resolved recently [9,11,14,15].…”

Section: Discussionmentioning

confidence: 99%

“…However, the genus Liriope made the sister group to the Aspidistreae tribe clade with very weak bootstrap value (26%). Floden and Schilling [47] revealed that the Maianthemum is not sister to Disporopsis, Heteropolygonatum and Polygonatum and suggested that Maianthemum does not belong to the Polygonateae tribe based on petA-psbJ + ITS analyses. In contrast, our results showed that Maianthemum is a sister to Disporopsis, Heteropolygonatum and Polygonatum and it belongs to the Polygonateae tribe based on 75 plastid protein-coding genes.…”

Section: Discussionmentioning

confidence: 99%

The Complete Chloroplast Genome Sequence of the Speirantha gardenii: Comparative and Adaptive Evolutionary Analysis

Raman¹,

Park²

2020

Agronomy

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The plant “False Lily of the Valley”, Speirantha gardenii is restricted to south-east China and considered as an endemic plant. Due to its limited availability, this plant was less studied. Hence, this study is focused on its molecular studies, where we have sequenced the complete chloroplast genome of S. gardenii and this is the first report on the chloroplast genome sequence of Speirantha. The complete S. gardenii chloroplast genome is of 156,869 bp in length with 37.6% GC, which included a pair of inverted repeats (IRs) each of 26,437 bp that separated a large single-copy (LSC) region of 85,368 bp and a small single-copy (SSC) region of 18,627 bp. The chloroplast genome comprises 81 protein-coding genes, 30 tRNA and four rRNA unique genes. Furthermore, a total of 699 repeats and 805 simple-sequence repeats (SSRs) markers are identified in the genome. Additionally, KA/KS nucleotide substitution analysis showed that seven protein-coding genes have highly diverged and identified nine amino acid sites under potentially positive selection in these genes. Phylogenetic analyses suggest that S. gardenii species has a closer genetic relationship to the Reineckea, Rohdea and Convallaria genera. The present study will provide insights into developing a lineage-specific marker for genetic diversity and gene evolution studies in the Nolinoideae taxa.

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“…Polygonatum (Asparagaceae) is a widespread temperate genus with approximate 75 species distributed throughout the temperate Northern Hemisphere, centered in the Eastern Himalaya and Indo-Burma biodiversity hotspots [1]. Plants growth and development are interconnected processes, producing under the effects of heredity (genotype) and environmental factors.…”

Section: Introductionmentioning

confidence: 99%

The Impact of Ecologic Factors on Growth and Development of Two Polygonatum Species

Omarov¹

2019

AJPS

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Using phylogenomics to reconstruct phylogenetic relationships within tribe Polygonateae (Asparagaceae), with a special focus on Polygonatum

Cited by 35 publications

References 75 publications

Complete chloroplast genome of Reineckia carnea and its implications for the phylogenetic position within Nolinoideae (Asparagaceae)

Complete chloroplast genome of Reineckia carnea and its implications for the phylogenetic position within Nolinoideae (Asparagaceae)

The Complete Chloroplast Genome Sequence of the Speirantha gardenii: Comparative and Adaptive Evolutionary Analysis

The Impact of Ecologic Factors on Growth and Development of Two Polygonatum Species

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