The chloroplast genome of the hexaploid Spartina maritima (Poaceae, Chloridoideae): Comparative analyses and molecular dating

Rousseau‐Gueutin, Mathieu; Bellot, Sidonie; Martin, Guillaume; Boutte, Julien; Chelaifa, Houda; Lima, Oscar; Michon-Coudouel, Sophie; Naquin, Delphine; Salmon, Armel; Ainouche, Kader; Aïnouche, Malika L.

doi:10.1016/j.ympev.2015.06.013

Cited by 65 publications

(67 citation statements)

References 88 publications

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“…The de novo assembly was performed using Velvet version 1.2.10 [11] with the following settings: k = 151, scaffolding = no, exp_cov = auto, -cov_cutoff = 10, -max_coverage = 500, and -min_contig_lgth = 2000. All resulting contigs were used as the query to run TBLASTX [12, 13] searches against the complete chloroplast genome of Spartina maritima [14] with the following cutoff: e-value = 10 −15 and sequence identity = 0.8. A total of 15 putative chloroplast contigs were identified and used as the first version of the draft assembly for further improvement until the complete chloroplast genome sequence was obtained.…”

Section: Methodsmentioning

confidence: 99%

“…To improve the assembly, the complete chloroplast genome of Spartina maritima [14] was used as a guide for scaffolding. In each round of our iterative process, all Illumina raw reads were mapped to the draft assembly using BWA version 0.7.12 [15], programmatically checked using the MPILEUP program in SAMTOOLS package version 1.2 [16], and visually inspected using IGV version 2.3.41 [17].…”

Section: Methodsmentioning

confidence: 99%

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Complete chloroplast genome sequence of common bermudagrass (Cynodon dactylon (L.) Pers.) and comparative analysis within the family Poaceae

et al. 2017

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Common bermudagrass (Cynodon dactylon (L.) Pers.) belongs to the subfamily Chloridoideae of the Poaceae family, one of the most important plant families ecologically and economically. This grass has a long connection with human culture but its systematics is relatively understudied. In this study, we sequenced and investigated the chloroplast genome of common bermudagrass, which is 134,297 bp in length with two single copy regions (LSC: 79,732 bp; SSC: 12,521 bp) and a pair of inverted repeat (IR) regions (21,022 bp). The annotation contains a total of 128 predicted genes, including 82 protein-coding, 38 tRNA, and 8 rRNA genes. Additionally, our in silico analyses identified 10 sets of repeats longer than 20 bp and predicted the presence of 36 RNA editing sites. Overall, the chloroplast genome of common bermudagrass resembles those from other Poaceae lineages. Compared to most angiosperms, the accD gene and the introns of both clpP and rpoC1 genes are missing. Additionally, the ycf1, ycf2, ycf15, and ycf68 genes are pseudogenized and two genome rearrangements exist. Our phylogenetic analysis based on 47 chloroplast protein-coding genes supported the placement of common bermudagrass within Chloridoideae. Our phylogenetic character mapping based on the parsimony principle further indicated that the loss of the accD gene and clpP introns, the pseudogenization of four ycf genes, and the two rearrangements occurred only once after the most recent common ancestor of the Poaceae diverged from other monocots, which could explain the unusual long branch leading to the Poaceae when phylogeny is inferred based on chloroplast sequences.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Complete chloroplast genome sequence of common bermudagrass (Cynodon dactylon (L.) Pers.) and comparative analysis within the family Poaceae

et al. 2017

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“…While these findings show novel patterns of response to hydrocarbon stress, and our experimental results support a role for SUVH5 and ATTPS21 in regulating the response to crude oil, the divergence between S. alterniflora, B. distachyon and A. thaliana limits the conclusions that we can draw. The Spartina genus (Chloridoideae subfamily) diverged from Brachypodium (Pooideae subfamily) more than 40 Ma (Rousseau-Gueutin et al, 2015) and from Arabidopsis 150 Ma (Kumar, Stecher, Suleski, & Hedges, 2017). During that time, the Spartina genus has undergone several hybridization and polyploidization events (Ainouche, Baumel, Salmon, & Yannic, 2003) that have increased chromosome number and ploidy level from 2n = 4x = 40 (tetraploid) to 2n = 12x = 120-124 (dodecaploid).…”

Section: Conclusion Smentioning

confidence: 99%

Transcriptome response of the foundation plant Spartina alterniflora to the Deepwater Horizon oil spill

et al. 2018

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Despite the severe impacts of the Deepwater Horizon oil spill, the foundation plant species Spartina alterniflora proved resilient to heavy oiling, providing an opportunity to identify mechanisms of response to the anthropogenic stress of crude oil exposure. We assessed plants from oil-affected and unaffected populations using a custom DNA microarray to identify genomewide transcription patterns and gene expression networks that respond to crude oil exposure. In addition, we used T-DNA insertion lines of the model grass Brachypodium distachyon to assess the contribution of four novel candidate genes to crude oil response. Responses in S. alterniflora to hydrocarbon exposure across the transcriptome as well as xenobiotic specific response pathways had little overlap with those previously identified in the model plant Arabidopsis thaliana. Among T-DNA insertion lines of B. distachyon, we found additional support for two candidate genes, one (ATTPS21) involved in volatile production, and the other (SUVH5) involved in epigenetic regulation of gene expression, that may be important in the response to crude oil. The architecture of crude oil response in S. alterniflora is unique from that of the model species A. thaliana, suggesting that xenobiotic response may be highly variable across plant species. In addition, further investigations of regulatory networks may benefit from more information about epigenetic response pathways.

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“…This proposal, however, presents major disadvantages including not only the creation of an extremely large genus that encompasses highly divergent clades (e.g., Spartina diverged from its sister clade sometimes 12–20 million years ago; Rousseau‐Gueutin et al. ), but also overlooking the long and well‐rooted history of scientific, cultural and socioeconomic relevance implicit in the name Spartina . The important criterion for rejection or conservation of botanical names is to avoid “disadvantageous nomenclatural changes” (McNeill et al.…”

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confidence: 99%

“…The authors argued that conserving the name Sporobolus would avoid taxonomic destabilization, noting that shifting all names to the senior name Spartina would necessitate many new binomial combinations and heterotypic synonyms. This proposal, however, presents major disadvantages including not only the creation of an extremely large genus that encompasses highly divergent clades (e.g., Spartina diverged from its sister clade sometimes 12-20 million years ago; Rousseau-Gueutin et al 2015), but also overlooking the long and well-rooted history of scientific, cultural and socioeconomic relevance implicit in the name Spartina. The important criterion for rejection or conservation of botanical names is to avoid Article e02863; page 2 ALEJANDRO BORTOLUS ET AL.…”

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confidence: 99%

SupportingSpartina: Interdisciplinary perspective showsSpartinaas a distinct solid genus

Bortolus

Adam

Adams

et al. 2019

Ecology

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In 2014, a DNA‐based phylogenetic study confirming the paraphyly of the grass subtribe Sporobolinae proposed the creation of a large monophyletic genus Sporobolus, including (among others) species previously included in the genera Spartina, Calamovilfa, and Sporobolus. Spartina species have contributed substantially (and continue contributing) to our knowledge in multiple disciplines, including ecology, evolutionary biology, molecular biology, biogeography, experimental ecology, biological invasions, environmental management, restoration ecology, history, economics, and sociology. There is no rationale so compelling to subsume the name Spartina as a subgenus that could rival the striking, global iconic history and use of the name Spartina for over 200 yr. We do not agree with the subjective arguments underlying the proposal to change Spartina to Sporobolus. We understand the importance of both the objective phylogenetic insights and of the subjective formalized nomenclature and hope that by opening this debate we will encourage positive feedback that will strengthen taxonomic decisions with an interdisciplinary perspective. We consider that the strongly distinct, monophyletic clade Spartina should simply and efficiently be treated as the genus Spartina.

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The chloroplast genome of the hexaploid Spartina maritima (Poaceae, Chloridoideae): Comparative analyses and molecular dating

Cited by 65 publications

References 88 publications

Complete chloroplast genome sequence of common bermudagrass (Cynodon dactylon (L.) Pers.) and comparative analysis within the family Poaceae

Complete chloroplast genome sequence of common bermudagrass (Cynodon dactylon (L.) Pers.) and comparative analysis within the family Poaceae

Transcriptome response of the foundation plant Spartina alterniflora to the Deepwater Horizon oil spill

SupportingSpartina: Interdisciplinary perspective showsSpartinaas a distinct solid genus

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