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Comparative plastomics

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https://www.readbyqxmd.com/read/29765380/the-complete-plastome-sequences-of-seven-species-in-gentiana-sect-kudoa-gentianaceae-insights-into-plastid-gene-loss-and-molecular-evolution
#1
Shan-Shan Sun, Peng-Cheng Fu, Xiao-Jun Zhou, Yan-Wei Cheng, Fa-Qi Zhang, Shi-Long Chen, Qing-Bo Gao
The chloroplast (cp) genome is useful in the study of phylogenomics, molecular dating, and molecular evolution. Gentiana sect. Kudoa is a predominantly alpine flowering plant that is valued for its contributions to medicine, ecology, and horticulture. Previous evolutionary studies showed that the plastid gene loss pattern and intra-sectional phylogenetics in sect. Kudoa are still unclear. In this study, we compared 11 Gentiana plastomes, including 7 newly sequenced plastomes from sect. Kudoa , to represent its three serious: ser...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29755486/organelle-genome-inheritance-in-deparia-ferns-athyriaceae-aspleniineae-polypodiales
#2
Li-Yaung Kuo, Te-Yen Tang, Fay-Wei Li, Huei-Jiun Su, Wen-Liang Chiou, Yao-Moan Huang, Chun-Neng Wang
Organelle genomes of land plants are predominately inherited maternally but in some cases can also be transmitted paternally or biparentally. Compared to seed plants (>83% genera of angiosperms and >12% genera of gymnosperms), plastid genome (plastome) inheritance has only been investigated in fewer than 2% of fern genera, and mitochondrial genome (mitogenome) from only one fern genus. We developed a new and efficient method to examine plastome and mitogenome inheritance in a fern species- Deparia lancea (Athyriaceae, Aspleniineae, Polypodiales), and found that plastid and mitochondrial DNAs were transmitted from only the maternal parentage to a next generation...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29747436/sequencing-characterization-and-comparative-analyses-of-the-plastome-of-caragana-rosea-var-rosea
#3
Mei Jiang, Haimei Chen, Shuaibing He, Liqiang Wang, Amanda Juan Chen, Chang Liu
To exploit the drought-resistant Caragana species, we performed a comparative study of the plastomes from four species: Caragana rosea , C. microphylla , C. kozlowii , and C. Korshinskii . The complete plastome sequence of the C. rosea was obtained using the next generation DNA sequencing technology. The genome is a circular structure of 133,122 bases and it lacks inverted repeat. It contains 111 unique genes, including 76 protein-coding, 30 tRNA, and four rRNA genes. Repeat analyses obtained 239, 244, 258, and 246 simple sequence repeats in C...
May 9, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29722901/organellar-phylogenomics-inform-systematics-in-the-green-algal-family-hydrodictyaceae-chlorophyceae-and-provide-clues-to-the-complex-evolutionary-history-of-plastid-genomes-in-the-green-algal-tree-of-life
#4
Hilary A McManus, Karolina Fučíková, Paul O Lewis, Louise A Lewis, Kenneth G Karol
PREMISE OF THE STUDY: Phylogenomic analyses across the green algae are resolving relationships at the class, order, and family levels and highlighting dynamic patterns of evolution in organellar genomes. Here we present a within-family phylogenomic study to resolve genera and species relationships in the family Hydrodictyaceae (Chlorophyceae), for which poor resolution in previous phylogenetic studies, along with divergent morphological traits, have precluded taxonomic revisions. METHODS: Complete plastome sequences and mitochondrial protein-coding gene sequences were acquired from representatives of the Hydrodictyaceae using next-generation sequencing methods...
May 3, 2018: American Journal of Botany
https://www.readbyqxmd.com/read/29694416/the-chloroplast-genome-sequence-of-bittersweet-solanum-dulcamara-plastid-genome-structure-evolution-in-solanaceae
#5
Ali Amiryousefi, Jaakko Hyvönen, Péter Poczai
Bittersweet (Solanum dulcamara) is a native Old World member of the nightshade family. This European diploid species can be found from marshlands to high mountainous regions and it is a common weed that serves as an alternative host and source of resistance genes against plant pathogens such as late blight (Phytophthora infestans). We sequenced the complete chloroplast genome of bittersweet, which is 155,580 bp in length and it is characterized by a typical quadripartite structure composed of a large (85,901 bp) and small (18,449 bp) single-copy region interspersed by two identical inverted repeats (25,615 bp)...
2018: PloS One
https://www.readbyqxmd.com/read/29675939/markers-in-time-and-space-a-review-of-the-last-decade-of-plant-phylogeographic-approaches
#6
Ashley B Morris, Joey Shaw
Plant studies comprise a relatively small proportion of the phylogeographic literature, likely as a consequence of the fundamental challenges posed by the complex genomic structures and life history strategies of these organisms. Comparative plastomics (i.e., comparisons of mutation rates within and among regions of the chloroplast genome) across plant lineages has led to an increased understanding of which markers are likely to provide the most information at low taxonomic levels. However, the extent to which the results of such work have influenced the literature have not been fully assessed, nor has the extent to which plant phylogeographers explicitly analyze markers in time and space, both of which are integral components of the field...
April 19, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29619041/comparative-chloroplast-genomics-of-gossypium-species-insights-into-repeat-sequence-variations-and-phylogeny
#7
Ying Wu, Fang Liu, Dai-Gang Yang, Wei Li, Xiao-Jian Zhou, Xiao-Yu Pei, Yan-Gai Liu, Kun-Lun He, Wen-Sheng Zhang, Zhong-Ying Ren, Ke-Hai Zhou, Xiong-Feng Ma, Zhong-Hu Li
Cotton is one of the most economically important fiber crop plants worldwide. The genus Gossypium contains a single allotetraploid group (AD) and eight diploid genome groups (A-G and K). However, the evolution of repeat sequences in the chloroplast genomes and the phylogenetic relationships of Gossypium species are unclear. Thus, we determined the variations in the repeat sequences and the evolutionary relationships of 40 cotton chloroplast genomes, which represented the most diverse in the genus, including five newly sequenced diploid species, i...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29608731/genome-reports-contracted-genes-and-dwarfed-plastome-in-mycoheterotrophic-sciaphila-thaidanica-triuridaceae-pandanales
#8
Gitte Petersen, Athanasios Zervas, Henrik Æ Pedersen, Ole Seberg
With a reduced need for photosynthesis, the plastome of parasitic and mycoheterotrophic plants degrades. In the tiny, fully mycoheterotrophic plant Sciaphila thaidanica, we find one of the smallest plastomes yet encountered. Its size is just 12,780 bp and it contains only 20 potentially functional housekeeping genes. Thus S. thaidanica fits the proposed model of gene loss in achlorophyllous plants. The most astonishing feature of the plastome is its extremely compact nature, with more than half of the genes having overlapping reading frames...
March 1, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29541088/optimized-method-of-extracting-rice-chloroplast-dna-for-high-quality-plastome-resequencing-and-de-novo-assembly
#9
Takeshi Takamatsu, Marouane Baslam, Takuya Inomata, Kazusato Oikawa, Kimiko Itoh, Takayuki Ohnishi, Tetsu Kinoshita, Toshiaki Mitsui
Chloroplasts, which perform photosynthesis, are one of the most important organelles in green plants and algae. Chloroplasts maintain an independent genome that includes important genes encoding their photosynthetic machinery and various housekeeping functions. Owing to its non-recombinant nature, low mutation rates, and uniparental inheritance, the chloroplast genome (plastome) can give insights into plant evolution and ecology and in the development of biotechnological and breeding applications. However, efficient methods to obtain high-quality chloroplast DNA (cpDNA) are currently not available, impeding powerful sequencing and further functional genomics research...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29532923/total-duplication-of-the-small-single-copy-region-in-the-angiosperm-plastome-rearrangement-and-inverted-repeat-instability-in-asarum
#10
Brandon T Sinn, Dylan D Sedmak, Lawrence M Kelly, John V Freudenstein
PREMISE OF THE STUDY: As more plastomes are assembled, it is evident that rearrangements, losses, intergenic spacer expansion and contraction, and syntenic breaks within otherwise functioning plastids are more common than was thought previously, and such changes have developed independently in disparate lineages. However, to date, the magnoliids remain characterized by their highly conserved plastid genomes (plastomes). METHODS: Illumina HiSeq and MiSeq platforms were used to sequence the plastomes of Saruma henryi and those of representative species from each of the six taxonomic sections of Asarum...
January 2018: American Journal of Botany
https://www.readbyqxmd.com/read/29494552/the-complete-plastome-sequence-of-an-antarctic-bryophyte-sanionia-uncinata-hedw-loeske
#11
Mira Park, Hyun Park, Hyoungseok Lee, Byeong-Ha Lee, Jungeun Lee
Organellar genomes of bryophytes are poorly represented with chloroplast genomes of only four mosses, four liverworts and two hornworts having been sequenced and annotated. Moreover, while Antarctic vegetation is dominated by the bryophytes, there are few reports on the plastid genomes for the Antarctic bryophytes. Sanionia uncinata (Hedw.) Loeske is one of the most dominant moss species in the maritime Antarctic. It has been researched as an important marker for ecological studies and as an extremophile plant for studies on stress tolerance...
March 1, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29494509/complete-chloroplast-genome-sequences-of-four-meliaceae-species-and-comparative-analyses
#12
Malte Mader, Birte Pakull, Céline Blanc-Jolivet, Maike Paulini-Drewes, Zoéwindé Henri-Noël Bouda, Bernd Degen, Ian Small, Birgit Kersten
The Meliaceae family mainly consists of trees and shrubs with a pantropical distribution. In this study, the complete chloroplast genomes of four Meliaceae species were sequenced and compared with each other and with the previously published Azadirachta indica plastome. The five plastomes are circular and exhibit a quadripartite structure with high conservation of gene content and order. They include 130 genes encoding 85 proteins, 37 tRNAs and 8 rRNAs. Inverted repeat expansion resulted in a duplication of rps19 in the five Meliaceae species, which is consistent with that in many other Sapindales, but different from many other rosids...
March 1, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29479365/plastid-genome-evolution-in-the-early-diverging-legume-subfamily-cercidoideae-fabaceae
#13
Yin-Huan Wang, Susann Wicke, Hong Wang, Jian-Jun Jin, Si-Yun Chen, Shu-Dong Zhang, De-Zhu Li, Ting-Shuang Yi
The subfamily Cercidoideae is an early-branching legume lineage, which consists of 13 genera distributed in the tropical and warm temperate Northern Hemisphere. A previous study detected two plastid genomic variations in this subfamily, but the limited taxon sampling left the overall plastid genome (plastome) diversification across the subfamily unaddressed, and phylogenetic relationships within this clade remained unresolved. Here, we assembled eight plastomes from seven Cercidoideae genera and conducted phylogenomic-comparative analyses in a broad evolutionary framework across legumes...
2018: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29409454/gene-loss-and-genome-rearrangement-in-the-plastids-of-five-hemiparasites-in-the-family-orobanchaceae
#14
Daniel C Frailey, Srinivasa R Chaluvadi, Justin N Vaughn, Caroline G Coatney, Jeffrey L Bennetzen
BACKGROUND: The chloroplast genomes (plastome) of most plants are highly conserved in structure, gene content, and gene order. Parasitic plants, including those that are fully photosynthetic, often contain plastome rearrangements. These most notably include gene deletions that result in a smaller plastome size. The nature of gene loss and genome structural rearrangement has been investigated in several parasitic plants, but their timing and contributions to the adaptation of these parasites requires further investigation, especially among the under-studied hemi-parasites...
February 6, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/29333694/chemical-composition-fractionation-of-olefin-plastomers-elastomers-by-solvent-and-thermal-gradient-interaction-chromatography
#15
Anthony Ndiripo, Andreas Albrecht, Benjamin Monrabal, Jingbo Wang, Harald Pasch
Olefin plastomers/elastomers are typically copolymers with high comonomer contents and low crystallinities. Therefore, the fractionation of these materials with crystallization-based methods is not feasible. On the other hand, solvent and temperature gradient interaction chromatography (SGIC and TGIC, respectively) are suitable techniques for the separation of olefin copolymers with regard to their chemical composition. In this study, the application ranges of both techniques are investigated and compared for ethylene-propylene (EP) copolymers...
March 2018: Macromolecular Rapid Communications
https://www.readbyqxmd.com/read/29297348/comparative-analysis-of-inverted-repeats-of-polypod-fern-polypodiales-plastomes-reveals-two-hypervariable-regions
#16
Maria D Logacheva, Anastasiya A Krinitsina, Maxim S Belenikin, Kamil Khafizov, Evgenii A Konorov, Sergey V Kuptsov, Anna S Speranskaya
BACKGROUND: Ferns are large and underexplored group of vascular plants (~ 11 thousands species). The genomic data available by now include low coverage nuclear genomes sequences and partial sequences of mitochondrial genomes for six species and several plastid genomes. RESULTS: We characterized plastid genomes of three species of Dryopteris, which is one of the largest fern genera, using sequencing of chloroplast DNA enriched samples and performed comparative analysis with available plastomes of Polypodiales, the most species-rich group of ferns...
December 28, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/29216844/comparative-analyses-of-plastid-genomes-from-fourteen-cornales-species-inferences-for-phylogenetic-relationships-and-genome-evolution
#17
Chao-Nan Fu, Hong-Tao Li, Richard Milne, Ting Zhang, Peng-Fei Ma, Jing Yang, De-Zhu Li, Lian-Ming Gao
BACKGROUND: The Cornales is the basal lineage of the asterids, the largest angiosperm clade. Phylogenetic relationships within the order were previously not fully resolved. Fifteen plastid genomes representing 14 species, ten genera and seven families of Cornales were newly sequenced for comparative analyses of genome features, evolution, and phylogenomics based on different partitioning schemes and filtering strategies. RESULTS: All plastomes of the 14 Cornales species had the typical quadripartite structure with a genome size ranging from 156,567 bp to 158,715 bp, which included two inverted repeats (25,859-26,451 bp) separated by a large single-copy region (86,089-87,835 bp) and a small single-copy region (18,250-18,856 bp) region...
December 8, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29206296/comparative-plastome-genomics-and-phylogenomics-of-brachypodium-flowering-time-signatures-introgression-and-recombination-in-recently-diverged-ecotypes
#18
Rubén Sancho, Carlos P Cantalapiedra, Diana López-Alvarez, Sean P Gordon, John P Vogel, Pilar Catalán, Bruno Contreras-Moreira
Few pan-genomic studies have been conducted in plants, and none of them have focused on the intraspecific diversity and evolution of their plastid genomes. We address this issue in Brachypodium distachyon and its close relatives B. stacei and B. hybridum, for which a large genomic data set has been compiled. We analyze inter- and intraspecific plastid comparative genomics and phylogenomic relationships within a family-wide framework. Major indel differences were detected between Brachypodium plastomes. Within B...
December 5, 2017: New Phytologist
https://www.readbyqxmd.com/read/29172252/prospects-on-the-evolutionary-mitogenomics-of-plants-a-case-study-on-the-olive-family-oleaceae
#19
Céline Van de Paer, Olivier Bouchez, Guillaume Besnard
The mitogenome is rarely used to reconstruct the evolutionary history of plants, contrary to nuclear and plastid markers. Here, we evaluate the usefulness of mitochondrial DNA for molecular evolutionary studies in Oleaceae, in which cases of cytoplasmic male sterility (CMS) and of potentially contrasted organelle inheritance are known. We compare the diversity and the evolution of mitochondrial and chloroplast genomes by focusing on the olive complex and related genera. Using high-throughput techniques, we reconstructed complete mitogenomes (ca...
November 24, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29140976/independent-degradation-in-genes-of-the-plastid-ndh-gene-family-in-species-of-the-orchid-genus-cymbidium-orchidaceae-epidendroideae
#20
Hyoung Tae Kim, Mark W Chase
In this paper, we compare ndh genes in the plastid genome of many Cymbidium species and three closely related taxa in Orchidaceae looking for evidence of ndh gene degradation. Among the 11 ndh genes, there were frequently large deletions in directly repeated or AT-rich regions. Variation in these degraded ndh genes occurs between individual plants, apparently at population levels in these Cymbidium species. It is likely that ndh gene transfers from the plastome to mitochondrial genome (chondriome) occurred independently in Orchidaceae and that ndh genes in the chondriome were also relatively recently transferred between distantly related species in Orchidaceae...
2017: PloS One
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