Complete sequences of organelle genomes from the medicinal plant Rhazya stricta(Apocynaceae) and contrasting patterns of mitochondrial genome evolution across asterids

Park, Seongjun; Ruhlman, Tracey A.; Sabir, Jamal S. M.; Mutwakil, Mohammed H. Z.; Baeshen, Mohammed N.; Sabir, Meshaal J.; Baeshen, Nabih A.; Jansen, Robert K.

doi:10.1186/1471-2164-15-405

Cited by 72 publications

(59 citation statements)

References 81 publications

(108 reference statements)

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“…To isolate mitochondrial sequences from the original Illumina reads, a BLAT (BLAST‐like alignment tool v36) search of forward and reverse reads against a reference database including 41 protein‐coding genes and two rDNA mitochondrial gene regions from the two Gentianales taxa Asclepias syriaca L. (NC_022796) and Rhazya stricta Decne. (NC_024293) was conducted (Straub et al, 2013; Park et al, 2014). Forward and reverse reads were both saved if either showed at least 70% similarity to any of the Gentianales reference sequences.…”

Section: Methodsmentioning

confidence: 99%

Conflicting results from mitochondrial genomic data challenge current views of Rubiaceae phylogeny

Rydin

Wikström

Bremer

2017

American J of Botany

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Today, about 30 years aft er the beginning of the "molecular revolution" of systematics, we have relatively good knowledge of angiosperm evolution and interrelationships among major groups ( APG III, 2009 ). Th ere are, however, still unanswered phylogenetic questions and unresolved nodes. Furthermore, contemporary knowledge of plant phylogeny typically derives from plastid data, which have been widely used for resolving evolutionary relationships. Early phylogenetic studies based on analysis of the rubisco gene rbcL ( Olmstead et al., 1992 ;Chase et al., 1993 ;Bremer et al., 1995 ) inspired, and the availability of universal primers (e.g., Zurawski and Clegg, 1987 ;Taberlet et al., 1991 ) enhanced molecular laboratory work, resulting in numerous phylogenetic studies on land plants during the subsequent decades. Typically, these studies were single-gene or multigene studies, i.e., they were based on one to several gene regions. Following recent developments, new sequencing techniques permit time-and cost-effi cient production of much more data, e.g., entire genomes, but it is nevertheless still not fully clear to what extent phylogenomics can signifi cantly increase our understanding of land plant phylogeny.While it was early recognized that data from the nuclear and mitochondrial genomes are desirable, such data have been much less used for the purpose of resolving evolutionary relationships in plants than have plastid data. Using nuclear genes may pose biological challenges associated with, for example, allelic variation and paralogy, as well as methodological problems with availability of general primers and requirements of fresh plant material (see e.g., Zimmer and Wen, 2012 ). The exception is nuclear ribosomal DNA, which is present in many copies that are assumed to be PREMISE OF THE STUDY:Reconstruction of plant phylogeny has heavily relied on single-gene or multigene plastid data. New sequencing methods have led to an increasing number of studies based on data from the entire plastid, but the mitochondrion has rarely been used to infer plant phylogeny because of an assumed information poverty and demonstrated lateral transfer of mitochondrial gene regions between distantly related species. METHODS:We explored phylogenetic information from the plant mitochondrion using 57 representatives of the species-rich coff ee family as study system and assessed consistency with previous results based (mostly) on plastid data. KEY RESULTS:We showed that the mitochondrial genome can provide structured and statistically signifi cant information on plant phylogeny. While most of our results are consistent with those based on plastid data, some surprising and statistically signifi cant confl icts emerge, and our study demonstrates with striking clarity that the phylogeny of Rubiaceae is far from resolved.CONCLUSIONS: It appears unlikely that confl icts between results retrieved from the diff erent genomic compartments would be restricted to Rubiaceae. Rather, they are probably a general phenomenon and an important facto...

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Section: Methodsmentioning

confidence: 99%

Conflicting results from mitochondrial genomic data challenge current views of Rubiaceae phylogeny

Rydin

Wikström

Bremer

2017

American J of Botany

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“…We used minimap2 to map the enriched PacBio reads against these four sequences, with the expectation that reads spanning the repeat and flanking regions of the alternative configurations with robust mapping quality (MQ > 50) represent actual structural variations present within the sequenced individual tree (e.g. Park et al 2014; Skippington et al 2015; Cole et al 2018; Dong et al 2018).…”

Section: Methodsmentioning

confidence: 99%

The mitogenome of Norway spruce and a reappraisal of mitochondrial recombination in plants

Sullivan

Eldfjell

Schiffthaler

et al. 2019

Preprint

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27Plant mitogenomes can be difficult to assemble because they are structurally dynamic and prone 28 to intergenomic DNA transfers, leading to the unusual situation where an organelle genome is far 29 outnumbered by its nuclear counterparts. As a result, comparative mitogenome studies are in 30 their infancy and some key aspects of genome evolution are still known mainly from pre-31 genome, qualitative methods. To help address these limitations, we combined machine learning 32 and in silico enrichment of mitochondrial-like long reads to assemble the bacterial-sized 33 mitogenome of Norway spruce (Pinaceae: Picea abies). We conducted comparative analyses of 34 repeat abundance, intergenomic transfers, substitution and rearrangement rates, and estimated 35 repeat-by-repeat homologous recombination rates. Prompted by our discovery of highly 36 recombinogenic small repeats in P. abies, we assessed the genomic support for the prevailing 37 hypothesis that intramolecular recombination is predominantly driven by repeat length, with 38 larger repeats facilitating DNA exchange more readily. Overall, we found mixed support for this 39 view: recombination dynamics were heterogeneous across vascular plants and highly active 40 small repeats (ca. 200 bp) were present in about a third of studied mitogenomes. As in previous 41 studies, we did not observe any robust relationships among commonly-studied genome 42 attributes, but we identify variation in recombination rates as a underinvestigated source of plant 43 mitogenome diversity. 44 45 forest tree, Norway spruce (Pinaceae: Picea abies), from whole-genome shotgun sequencing 77 reads. The P. abies mitogenome helps to fill a phylogenetic gap in comparative analyses, and to 78 that end we analyzed gene repertoires; sources of genome size heterogeneity; intraspecific 79 variation; and mutation, recombination, and rearrangement rates in gymnosperms. Prompted by 80 the detection of highly recombinogenic small repeats in P. abies, we reevaluated published 81 recombination rates in seed plants. Despite early recognition of recombination as a factor in 82 generating the diversity of eukaryotic mitogenomes (Palmer & Herbon 1988; Gray et al. 1999), 83 surprisingly little attention has been given to recombinational dynamics as a source of 84 mitogenomic diversity within plants. As in previous studies, we found no clear relationship 85 between mitogenome traits and potential mechanisms infor example, genome size and the 86 proportion of intergenomically transferred DNAbut the role of recombination as a driver of 87 mitogenomic diversity within plants merits further scrutiny. 88 Results and Discussion 89Mitogenome assembly 90 We combined machine learning, in silico enrichment of long sequencing reads, and assembly 91 reconciliation to produce a highly contiguous P. abies draft mitogenome (Fig. 1). First, we 92 developed a support vector machine (SVM) to identify mitochondrial-like scaffolds from the P. 93 abies v. 1.0 genome assembly (Nystedt et al. 2013). Training the SVM classifier...

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“…A recent study found that R. stricta extracts promoted apoptosis induction in breast cancer cells, suggesting its potential as an achemo-preventive or therapeutic agent [18,19]. However, currently there have been no genomic resources for R. stricta to facilitate the development of this species for therapeutic applications using a genomic approach on natural product [20][21][22].…”

Section: Introductionmentioning

confidence: 99%

Genetic Variation of Harmal (Peganum Harmala L. and Rhazya Stricta Decne) Based on Polymorphism in Protein Profile, Soil Analysis and Internode Anatomy

Abd-Elgawad¹,

Alotaibi²

2017

Nano BioMed ENG

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The vernacular name 'harmal' is applied to Peganum harmala L. and another noxious weed Rhazya stricta Decne. The study aimed to clarify the genetic relationships among different populations of harmal by employing ecological, anatomical characters and a pattern of leaf protein analysis. The soil and plant samples were collected from three regions of Saudi Arabia for each species. Soil texture of the harmal populations was characterized by loamy sand and sandy. Soil type had a significant effect on the internode anatomical characters of the soil textures of both hamal populations. The anatomical characters were observed in the cuticle layer on the stem. Similarly, compact epidermis, wide cortex and many water storing tissues were observed. In the present study, it was also observed that plants have numerous cortical cells to store large amount of water, so as to fight against the dry environment. This interaction between the soil type and the plant anatomical characters was found to be well adapted to the environment of different habitats. The sodium dodecylsulphate polyacrylamide gel electrophoresis (SDS-PAGE) analysis of pattern profiles showed limited variations between the two species of harmal, which indicated the genetic similarity among populations of both species at different habitats. These variations were considered as successful adaptations leading to tolerance.

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Complete sequences of organelle genomes from the medicinal plant Rhazya stricta(Apocynaceae) and contrasting patterns of mitochondrial genome evolution across asterids

Cited by 72 publications

References 81 publications

Conflicting results from mitochondrial genomic data challenge current views of Rubiaceae phylogeny

Conflicting results from mitochondrial genomic data challenge current views of Rubiaceae phylogeny

The mitogenome of Norway spruce and a reappraisal of mitochondrial recombination in plants

Genetic Variation of Harmal (Peganum Harmala L. and Rhazya Stricta Decne) Based on Polymorphism in Protein Profile, Soil Analysis and Internode Anatomy

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