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Comparative plastomics

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https://www.readbyqxmd.com/read/28533973/plastomes-of-the-green-algae-hydrodictyon-reticulatum-and-pediastrum-duplex-sphaeropleales-chlorophyceae
#1
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
#2
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
#3
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
#4
Kasey Khanh Pham, Andrew L Hipp, Paul S Manos, Richard C Cronn
Due 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
#5
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
#6
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 10, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28376717/fossils-matter-improved-estimates-of-divergence-times-in-pinus-reveal-older-diversification
#7
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
#8
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...
February 27, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28294981/the-complete-chloroplast-genome-sequences-of-six-rehmannia-species
#9
Shuyun Zeng, Tao Zhou, Kai Han, Yanci Yang, Jianhua Zhao, Zhan-Lin Liu
Rehmannia is a non-parasitic genus in Orobanchaceae including six species mainly distributed in central and north China. Its phylogenetic position and infrageneric relationships remain uncertain due to potential hybridization and polyploidization. In this study, we sequenced and compared the complete chloroplast genomes of six Rehmannia species using Illumina sequencing technology to elucidate the interspecific variations. Rehmannia plastomes exhibited typical quadripartite and circular structures with good synteny of gene order...
March 15, 2017: Genes
https://www.readbyqxmd.com/read/28286710/the-complete-chloroplast-genome-sequence-of-morus-cathayana-and-morus-multicaulis-and-comparative-analysis-within-genus-morus-l
#10
Wei Qing Kong, Jin Hong Yang
Trees in the Morus genera belong to the Moraceae family. To better understand the species status of genus Morus and to provide information for studies on evolutionary biology within the genus, the complete chloroplast (cp) genomes of M. cathayana and M. multicaulis were sequenced. The plastomes of the two species are 159,265 bp and 159,103 bp, respectively, with corresponding 83 and 82 simple sequence repeats (SSRs). Similar to the SSRs of M. mongolica and M. indica cp genomes, more than 70% are mononucleotides, ten are in coding regions, and one exhibits nucleotide content polymorphism...
2017: PeerJ
https://www.readbyqxmd.com/read/28265281/chloroplast-genome-analysis-of-resurrection-tertiary-relict-haberlea-rhodopensis-highlights-genes-important-for-desiccation-stress-response
#11
Zdravka Ivanova, Gaurav Sablok, Evelina Daskalova, Gergana Zahmanova, Elena Apostolova, Galina Yahubyan, Vesselin Baev
Haberlea rhodopensis is a paleolithic tertiary relict species, best known as a resurrection plant with remarkable tolerance to desiccation. When exposed to severe drought stress, H. rhodopensis shows an ability to maintain the structural integrity of its photosynthetic apparatus, which re-activates easily upon rehydration. We present here the results from the assembly and annotation of the chloroplast (cp) genome of H. rhodopensis, which was further subjected to comparative analysis with the cp genomes of closely related species...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28186635/diversification-of-rosaceae-since-the-late-cretaceous-based-on-plastid-phylogenomics
#12
Shu-Dong Zhang, Jian-Jun Jin, Si-Yun Chen, Mark W Chase, Douglas E Soltis, Hong-Tao Li, Jun-Bo Yang, De-Zhu Li, Ting-Shuang Yi
Phylogenetic relationships in Rosaceae have long been problematic because of frequent hybridisation, apomixis and presumed rapid radiation, and their historical diversification has not been clarified. With 87 genera representing all subfamilies and tribes of Rosaceae and six of the other eight families of Rosales (outgroups), we analysed 130 newly sequenced plastomes together with 12 from GenBank in an attempt to reconstruct deep relationships and reveal temporal diversification of this family. Our results highlight the importance of improving sequence alignment and the use of appropriate substitution models in plastid phylogenomics...
February 10, 2017: New Phytologist
https://www.readbyqxmd.com/read/28182646/complete-chloroplast-genomes-from-apomictic-taraxacum-asteraceae-identity-and-variation-between-three-microspecies
#13
Rubar Hussein M Salih, Ľuboš Majeský, Trude Schwarzacher, Richard Gornall, Pat Heslop-Harrison
Chloroplast DNA sequences show substantial variation between higher plant species, and less variation within species, so are typically excellent markers to investigate evolutionary, population and genetic relationships and phylogenies. We sequenced the plastomes of Taraxacum obtusifrons Markl. (O978); T. stridulum Trávniček ined. (S3); and T. amplum Markl. (A978), three apomictic triploid (2n = 3x = 24) dandelions from the T. officinale agg. We aimed to characterize the variation in plastomes, define relationships and correlations with the apomictic microspecies status, and refine placement of the microspecies in the evolutionary or phylogenetic context of the Asteraceae...
2017: PloS One
https://www.readbyqxmd.com/read/28042043/first-plastid-phylogenomic-study-reveals-potential-cyto-nuclear-discordance-in-the-evolutionary-history-of-ficus-l-moraceae
#14
Sam Bruun-Lund, Wendy L Clement, Finn Kjellberg, Nina Rønsted
Standard Sanger chloroplast markers provide limited information to resolve species level relationships within plants, in particular within large genera. Figs (Ficus L., Moraceae) compose one of the 50 largest genera of angiosperms with ∼750 species occurring in the tropics and subtropics worldwide. Figs, in addition to being a keystone food resource in rainforests, are well-known for the mutualistic interactions with their pollinating wasps. It is regarded as a model system for understanding co-evolution dating back more than 75million years...
December 29, 2016: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28039231/large-scale-comparative-analysis-reveals-the-mechanisms-driving-plastomic-compaction-reduction-and-inversions-in-conifers-ii-cupressophytes
#15
Chung-Shien Wu, Shu-Miaw Chaw
Conifers II (cupressophytes), comprising about 400 tree species in five families, are the most diverse group of living gymnosperms. Their plastid genomes (plastomes) are highly variable in size and organization, but such variation has never been systematically studied. In this study, we assessed the potential mechanisms underlying the evolution of cupressophyte plastomes. We analyzed the plastomes of 24 representative genera in all of the five cupressophyte families, focusing on their variation in size, noncoding DNA content, and nucleotide substitution rates...
December 1, 2016: Genome Biology and Evolution
https://www.readbyqxmd.com/read/27965698/analysis-of-complete-chloroplast-genome-sequences-improves-phylogenetic-resolution-in-paris-melanthiaceae
#16
Yuling Huang, Xiaojuan Li, Zhenyan Yang, Chengjin Yang, Junbo Yang, Yunheng Ji
The genus Paris in the broad concept is an economically important group in the monocotyledonous family Melanthiaceae (tribe Parideae). The phylogeny of Paris was controversial in previous morphology-based classification and molecular phylogeny. Here, the complete cp genomes of eleven Paris taxa were sequenced, to better understand the evolutionary relationships among these plants and the mutation patterns in their chloroplast (cp) genomes. Comparative analyses indicated that the overall cp genome structure among the Paris taxa is quite similar...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27917315/the-first-complete-plastid-genomes-of-melastomataceae-are-highly-structurally-conserved
#17
Marcelo Reginato, Kurt M Neubig, Lucas C Majure, Fabian A Michelangeli
BACKGROUND: In the past three decades, several studies have predominantly relied on a small sample of the plastome to infer deep phylogenetic relationships in the species-rich Melastomataceae. Here, we report the first full plastid sequences of this family, compare general features of the sampled plastomes to other sequenced Myrtales, and survey the plastomes for highly informative regions for phylogenetics. METHODS: Genome skimming was performed for 16 species spread across the Melastomataceae...
2016: PeerJ
https://www.readbyqxmd.com/read/27899326/complete-plastid-genome-sequence-of-goosegrass-eleusine-indica-and-comparison-with-other-poaceae
#18
COMPARATIVE STUDY
Hui Zhang, Nathan Hall, J Scott McElroy, Elijah K Lowe, Leslie R Goertzen
Eleusine indica, also known as goosegrass, is a serious weed in at least 42 countries. In this paper we report the complete plastid genome sequence of goosegrass obtained by de novo assembly of paired-end and mate-paired reads generated by Illumina sequencing of total genomic DNA. The goosegrass plastome is a circular molecule of 135,151bp in length, consisting of two single-copy regions separated by a pair of inverted repeats (IRs) of 20,919 bases. The large (LSC) and the small (SSC) single-copy regions span 80,667 bases and 12,646 bases, respectively...
February 5, 2017: Gene
https://www.readbyqxmd.com/read/27898825/complete-chloroplast-genome-sequence-of-corroborates-structural-heterogeneity-of-inverted-repeats-in-wild-progenitors-of-cultivated-bananas-and-plantains
#19
Santoshkumar M Shetty, Maria Ulfa Md Shah, Kavyashree Makale, Yusmin Mohd-Yusuf, Norzulaani Khalid, Rofina Yasmin Othman
Complete genome sequencing of cytoplasmically inherited chloroplast DNA provides novel insights into the origins of clonally propagated crops such as banana and plantain ( spp.). This study describes the structural organization of the chloroplast genome of Colla and its phylogenetic relationship with other wild progenitors of the domesticated banana cultivars. The chloroplast genome was sequenced using Illumina HiSeq 2000 platform, followed by a combination of de novo short-read assembly and reference-guided mapping of contigs to generate complete plastome sequence...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27856583/complete-plastome-sequence-of-ludwigia-octovalvis-onagraceae-a-globally-distributed-wetland-plant
#20
Shih-Hui Liu, Christine Edwards, Peter C Hoch, Peter H Raven, Janet C Barber
Here, we present the first plastome of Ludwigia octovalvis (Onagraceae, Myrtales) as well as the first plastome in the subfamily Ludwigioideae. This genome is notable for its contracted inverted repeat regions and an expanded small single-copy region compared to other species in the orders Myrtales and Geraniales.
November 17, 2016: Genome Announcements
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