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Comparative plastomics

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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
#1
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
https://www.readbyqxmd.com/read/29095905/the-complete-chloroplast-genome-sequence-of-the-cam-epiphyte-spanish-moss-tillandsia-usneoides-bromeliaceae-and-its-comparative-analysis
#2
Péter Poczai, Jaakko Hyvönen
Spanish moss (Tillandsia usneoides) is an epiphytic bromeliad widely distributed throughout tropical and warm temperate America. This plant is highly adapted to extreme environmental conditions. Striking features of this species include specialized trichomes (scales) covering the surface of its shoots aiding the absorption of water and nutrients directly from the atmosphere and a specific photosynthesis using crassulacean acid metabolism (CAM). Here we report the plastid genome of Spanish moss and present the comparison of genome organization and sequence evolution within Poales...
2017: PloS One
https://www.readbyqxmd.com/read/29046685/comparative-analysis-of-the-complete-plastomes-of-apostasia-wallichii-and-neuwiedia-singapureana-apostasioideae-reveals-different-evolutionary-dynamics-of-ir-ssc-boundary-among-photosynthetic-orchids
#3
Zhitao Niu, Jiajia Pan, Shuying Zhu, Ludan Li, Qingyun Xue, Wei Liu, Xiaoyu Ding
Apostasioideae, consists of only two genera, Apostasia and Neuwiedia, which are mainly distributed in Southeast Asia and northern Australia. The floral structure, taxonomy, biogeography, and genome variation of Apostasioideae have been intensively studied. However, detailed analyses of plastome composition and structure and comparisons with those of other orchid subfamilies have not yet been conducted. Here, the complete plastome sequences of Apostasia wallichii and Neuwiedia singapureana were sequenced and compared with 43 previously published photosynthetic orchid plastomes to characterize the plastome structure and evolution in the orchids...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28985306/plastome-evolution-in-the-sole-hemiparasitic-genus-laurel-dodder-cassytha-and-insights-into-the-plastid-phylogenomics-of-lauraceae
#4
Chung-Shien Wu, Ting-Jen Wang, Chia-Wen Wu, Ya-Nan Wang, Shu-Miaw Chaw
To date, little is known about the evolution of plastid genomes (plastomes) in Lauraceae. As one of the top five largest families in tropical forests, the Lauraceae contain many species that are important ecologically and economically. Lauraceous species also provide wonderful materials to study the evolutionary trajectory in response to parasitism because they contain both non-parasitic and parasitic species. This study compared the plastomes of nine Lauraceous species, including the sole hemiparasitic and herbaceous genus Cassytha (laurel dodder; here represented by Cas...
September 6, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28957463/evolutionary-comparisons-of-the-chloroplast-genome-in-lauraceae-and-insights-into-loss-events-in-the-magnoliids
#5
Yu Song, Wen-Bin Yu, Yunhong Tan, Bing Liu, Xin Yao, Jianjun Jin, Michael Padmanaba, Jun-Bo Yang, Richard T Corlett
Available plastomes of the Lauraceae show similar structure and varied size, but there has been no systematic comparison across the family. In order to understand the variation in plastome size and structure in the Lauraceae and related families of magnoliids, we here compare 47 plastomes, 15 newly sequenced, from 27 representative genera. We reveal that the two shortest plastomes are in the parasitic Lauraceae genus Cassytha, with lengths of 114,623 (C. filiformis) and 114,963 bp (C. capillaris), and that they have lost NADH dehydrogenase (ndh) genes in the large single-copy region and one entire copy of the inverted repeat (IR) region...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28935841/light-and-plastid-signals-regulate-different-sets-of-genes-in-the-albino-mutant-pap7-1
#6
Björn Grübler, Livia Merendino, Sven O Twardziok, Morgane Mininno, Guillaume Allorent, Fabien Chevalier, Monique Liebers, Robert Blanvillain, Klaus F X Mayer, Silva Lerbs-Mache, Stéphane Ravanel, Thomas Pfannschmidt
Plants possessing dysfunctional plastids due to defects in pigment biosynthesis or translation are known to repress photosynthesis-associated nuclear genes via retrograde signals from the disturbed organelles toward the nucleus. These signals are thought to be essential for proper biogenesis and function of the plastid. Mutants lacking plastid-encoded RNA polymerase-associated proteins (PAPs) display a genetic arrest in eoplast-chloroplast transition leading to an albino phenotype in the light. Retrograde signaling in these mutants, therefore, could be expected to be similar as under conditions inducing plastid dysfunction...
November 2017: Plant Physiology
https://www.readbyqxmd.com/read/28855622/multiple-origins-of-endosymbionts-in-chlorellaceae-with-no-reductive-effects-on-the-plastid-or-mitochondrial-genomes
#7
Weishu Fan, Wenhu Guo, James L Van Etten, Jeffrey P Mower
Ancient endosymbiotic relationships have led to extreme genomic reduction in many bacterial and eukaryotic algal endosymbionts. Endosymbionts in more recent and/or facultative relationships can also experience genomic reduction to a lesser extent, but little is known about the effects of the endosymbiotic transition on the organellar genomes of eukaryotes. To understand how the endosymbiotic lifestyle has affected the organellar genomes of photosynthetic green algae, we generated the complete plastid genome (plastome) and mitochondrial genome (mitogenome) sequences from three green algal endosymbionts (Chlorella heliozoae, Chlorella variabilis and Micractinium conductrix)...
August 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28829825/the-complete-chloroplast-genome-sequences-of-three-adenophora-species-and-comparative-analysis-with-campanuloid-species-campanulaceae
#8
Kyeong-Sik Cheon, Kyung-Ah Kim, Ki-Oug Yoo
We report the complete chloroplast genomes of three Adenophora species, and analyzed these compared them to five published Campanuloid plastomes. The total genome length of Adenophora divaricata, Adenophora erecta, and Adenophora stricta ranged from 159,759 to 176,331 bp. Among the eight Campanuloid species, many inversions were found to be only in the LSC region. IR contraction was also identified in the plastid genome of Adenophora stricta. Phylogenetic analyses based on 76 protein coding genes showed that Campanuloids are monophyletic, and are composed of two major groups: Campanula s...
2017: PloS One
https://www.readbyqxmd.com/read/28809950/characterization-of-the-complete-chloroplast-genome-of-arabis-stellari-and-comparisons-with-related-species
#9
Gurusamy Raman, Veronica Park, Myounghai Kwak, Byoungyoon Lee, SeonJoo Park
Arabis stellari var. japonica is an ornamental plant of the Brassicaceae family, and is widely distributed in South Korea. However, no information is available about its molecular biology and no genomic study has been performed on A. stellari. In this paper, the authors report the complete chloroplast genome sequence of A. stellari. The plastome of A. stellari was 153,683 bp in length with 36.4% GC and included a pair of inverted repeats (IRs) of 26,423 bp that separated a large single-copy (LSC) region of 82,807 bp and a small single-copy (SSC) region of 18,030 bp...
2017: PloS One
https://www.readbyqxmd.com/read/28793854/complete-plastome-sequencing-of-both-living-species-of-circaeasteraceae-ranunculales-reveals-unusual-rearrangements-and-the-loss-of-the-ndh-gene-family
#10
Yanxia Sun, Michael J Moore, Nan Lin, Kole F Adelalu, Aiping Meng, Shuguang Jian, Linsen Yang, Jianqiang Li, Hengchang Wang
BACKGROUND: Among the 13 families of early-diverging eudicots, only Circaeasteraceae (Ranunculales), which consists of the two monotypic genera Circaeaster and Kingdonia, lacks a published complete plastome sequence. In addition, the phylogenetic position of Circaeasteraceae as sister to Lardizabalaceae has only been weakly or moderately supported in previous studies using smaller data sets. Moreover, previous plastome studies have documented a number of novel structural rearrangements among early-divergent eudicots...
August 9, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28754764/plastome-sequences-of-an-ancient-fern-lineage-reveal-remarkable-changes-in-gene-content-and-architecture
#11
Paulo H Labiak, Kenneth G Karol
PREMISE OF THE STUDY: Comparative analyses of plastid genomes have suggested that gene order and content are relatively stable across the main groups of land plants, with significant changes rarely reported. We examine plastome organization and RNA editing in ferns and report changes that add valuable information on plastome evolution in land plants. METHODS: Using next-generation sequencing methods, we fully sequenced plastomes from three species of Schizaeaceae, and compared their plastomes with other groups of land plants to study changes in gene composition, plastome architecture, and putative RNA editing sites...
July 28, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28743759/anatolian-origins-and-diversification-of-aethionema-the-sister-lineage-of-the-core-brassicaceae
#12
Setareh Mohammadin, Kim Peterse, Sara J van de Kerke, Lars W Chatrou, Ali A Dönmez, Klaus Mummenhoff, J Chris Pires, Patrick P Edger, Ihsan A Al-Shehbaz, M Eric Schranz
PREMISE OF THE STUDY: The Irano-Turanian region harbors three biodiversity hotspots and ∼25% of Brassicaceae species are endemic to the region. Aethionema (∼61 species) is the sister lineage to the core Brassicaceae and occurs mainly in the Irano-Turanian region. The evolutionary important position of Aethionema makes it an ideal reference for broader comparative genetics and genomics. To understand the evolution of Aethionema, and for a broader understanding of crucifer evolution, a time-calibrated phylogenetic tree and biogeographical history of the genus is needed...
July 25, 2017: American Journal of Botany
https://www.readbyqxmd.com/read/28533973/plastomes-of-the-green-algae-hydrodictyon-reticulatum-and-pediastrum-duplex-sphaeropleales-chlorophyceae
#13
Hilary A McManus, Daniel J Sanchez, Kenneth G Karol
BACKGROUND: Comparative studies of chloroplast genomes (plastomes) across the Chlorophyceae are revealing dynamic patterns of size variation, gene content, and genome rearrangements. Phylogenomic analyses are improving resolution of relationships, and uncovering novel lineages as new plastomes continue to be characterized. To gain further insight into the evolution of the chlorophyte plastome and increase the number of representative plastomes for the Sphaeropleales, this study presents two fully sequenced plastomes from the green algal family Hydrodictyaceae (Sphaeropleales, Chlorophyceae), one from Hydrodictyon reticulatum and the other from Pediastrum duplex...
2017: PeerJ
https://www.readbyqxmd.com/read/28522861/comparative-analysis-of-dendrobium-plastomes-and-utility-of-plastomic-mutational-hotspots
#14
Niu Zhitao, Zhu Shuying, Pan Jiajia, Li Ludan, Sun Jing, Ding Xiaoyu
Dendrobium is one of the largest genera in Orchidaceae, comprising about 800-1500 species mainly distributed in tropical Asia, Australasia, and Australia. There are 74 species and two varieties of this genus in China. Because of their ornamental and commercial value, Dendrobium orchids have been studied at low taxonomic levels. However, structural changes and effective mutational hotspots of Dendrobium plastomes have rarely been documented. Here, 30 Dendrobium plastomes were compared, comprising 25 newly sequenced in this study and five previously published...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28515737/the-complete-plastome-sequences-of-four-orchid-species-insights-into-the-evolution-of-the-orchidaceae-and-the-utility-of-plastomic-mutational-hotspots
#15
Zhitao Niu, Qingyun Xue, Shuying Zhu, Jing Sun, Wei Liu, Xiaoyu Ding
Orchidaceae (orchids) is the largest family in the monocots, including about 25,000 species in 880 genera and five subfamilies. Many orchids are highly valued for their beautiful and long-lasting flowers. However, the phylogenetic relationships among the five orchid subfamilies remain unresolved. The major dispute centers on whether the three one-stamened subfamilies, Epidendroideae, Orchidoideae, and Vanilloideae, are monophyletic or paraphyletic. Moreover, structural changes in the plastid genome (plastome) and the effective genetic loci at the species-level phylogenetics of orchids have rarely been documented...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28445658/a-time-and-a-place-for-everything-phylogenetic-history-and-geography-as-joint-predictors-of-oak-plastome-phylogeny
#16
Kasey K Pham, Andrew L Hipp, Paul S Manos, Richard C Cronn
Owing to high rates of introgressive hybridization, the plastid genome is poorly suited to fine-scale DNA barcoding and phylogenetic studies of the oak genus (Quercus, Fagaceae). At the tips of the oak plastome phylogeny, recent gene migration and reticulation generally cause topology to reflect geographic structure, while deeper branches reflect lineage divergence. In this study, we quantify the simple and partial effects of geographic proximity and nucleome-inferred phylogenetic history on oak plastome phylogeny at different evolutionary scales...
April 26, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28431152/insights-into-the-existence-of-isomeric-plastomes-in-cupressoideae-cupressaceae
#17
Xiao-Jian Qu, Chung-Shien Wu, Shu-Miaw Chaw, Ting-Shuang Yi
The cypress family (Cupressaceae) possesses highly rearranged plastomes that lack a pair of large inverted repeats typically found in land plants. A few cypress species have been reported to contain isomeric plastomes, but whether the existence of isomeric plastomes is ubiquitous in the family remains to be investigated with a broader taxon sampling. In this study, we sequenced the complete plastomes of ten species in Cupressoideae, the largest cypress subfamily. Cupressoideae showed relatively accelerated rates of substitutions at both nonsynonymous and synonymous sites as compared with other subfamilies of Cupressaceae...
April 14, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28397003/plastome-wide-nucleotide-substitution-rates-reveal-accelerated-rates-in-papilionoideae-and-correlations-with-genome-features-across-legume-subfamilies
#18
Erika N Schwarz, Tracey A Ruhlman, Mao-Lun Weng, Mohammad A Khiyami, Jamal S M Sabir, Nahid H Hajarah, Njud S Alharbi, Samar O Rabah, Robert K Jansen
This study represents the most comprehensive plastome-wide comparison of nucleotide substitution rates across the three subfamilies of Fabaceae: Caesalpinioideae, Mimosoideae, and Papilionoideae. Caesalpinioid and mimosoid legumes have large, unrearranged plastomes compared with papilionoids, which exhibit varying levels of rearrangement including the loss of the inverted repeat (IR) in the IR-lacking clade (IRLC). Using 71 genes common to 39 legume taxa representing all the three subfamilies, we show that papilionoids consistently have higher nucleotide substitution rates than caesalpinioids and mimosoids, and rates in the IRLC papilionoids are generally higher than those in the IR-containing papilionoids...
April 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28376717/fossils-matter-improved-estimates-of-divergence-times-in-pinus-reveal-older-diversification
#19
Bianca Saladin, Andrew B Leslie, Rafael O Wüest, Glenn Litsios, Elena Conti, Nicolas Salamin, Niklaus E Zimmermann
BACKGROUND: The taxonomy of pines (genus Pinus) is widely accepted and a robust gene tree based on entire plastome sequences exists. However, there is a large discrepancy in estimated divergence times of major pine clades among existing studies, mainly due to differences in fossil placement and dating methods used. We currently lack a dated molecular phylogeny that makes use of the rich pine fossil record, and this study is the first to estimate the divergence dates of pines based on a large number of fossils (21) evenly distributed across all major clades, in combination with applying both node and tip dating methods...
April 4, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28338826/the-evolutionary-fate-of-the-chloroplast-and-nuclear-rps16-genes-as-revealed-through-the-sequencing-and-comparative-analyses-of-four-novel-legume-chloroplast-genomes-from-lupinus
#20
COMPARATIVE STUDY
J Keller, M Rousseau-Gueutin, G E Martin, J Morice, J Boutte, E Coissac, M Ourari, M Aïnouche, A Salmon, F Cabello-Hurtado, A Aïnouche
The Fabaceae family is considered as a model system for understanding chloroplast genome evolution due to the presence of extensive structural rearrangements, gene losses and localized hypermutable regions. Here, we provide sequences of four chloroplast genomes from the Lupinus genus, belonging to the underinvestigated Genistoid clade. Notably, we found in Lupinus species the functional loss of the essential rps16 gene, which was most likely replaced by the nuclear rps16 gene that encodes chloroplast and mitochondrion targeted RPS16 proteins...
August 1, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
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