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Comparative plastomics

Henrik Aronsson, Petter Larsson, Sandra Bains
Higher plants have been used in medicine throughout human history. While traditional medicinal uses relied on compounds produced naturally by plants, recent advances have enabled the use of plant-based factories to produce diverse agents including pharmaceuticals, antibiotics, and vaccines. The genes responsible for the production of these substances can be either transiently expressed in plants or integrated into their nuclear genome or plastid genome (plastome) by genetic transformation. This review focuses on the application of plastid transformation of higher plants to produce biopharmaceuticals for human applications that are neither antibiotics nor vaccines...
October 4, 2016: Mini Reviews in Medicinal Chemistry
T H Samigullin, M D Logacheva, E I Terenteva, G V Degtjareva, C M Vallejo-Roman
This work reports the complete plastid (pt) DNA sequence of Seseli montanum L. of the Apiaceae family, determined using next-generation sequencing technology. The complete genome sequence has been deposited in GenBank with accession No. KM035851. The S. montanum plastome is 147,823 bp in length. The plastid genome has a typical structure for angiosperms and contains a large single-copy region (LSC) of 92,620 bp and a small single-copy region (SSC) of 17,481 bp separated by a pair of 18,861 bp inverted repeats (IRa and IRb)...
September 2016: Biochemistry. Biokhimii︠a︡
Wen-Cai Wang, Si-Yun Chen, Xian-Zhi Zhang
Actinidiaceae is a well-known economically important plant family in asterids. To elucidate the chloroplast (cp) genome evolution within this family, here we present complete genomes of three species from two sister genera (Clematoclethra and Actinidia) in the Actinidiaceae via genome skimming technique. Comparative analyses revealed that the genome structure and content were rather conservative in three cp genomes in spite of different inheritance pattern, i.e.paternal in Actinidia and maternal in Clematoclethra...
2016: PloS One
Lauren M Orton, Sean V Burke, William P Wysocki, Melvin R Duvall
This project examines the relationships within the genus Zea using complete plastid genomes (plastomes). While Zea mays has been well studied, congeneric species have yet to be as thoroughly examined. For this study four complete plastomes and a fifth nearly complete plastome were sequenced in the five species (Zea diploperennis, Zea perennis, Zea luxurians, Zea nicaraguensis, and Zea mays subsp. huehuetenangensis) by Sanger or next-generation methods. An analysis of the microstructural changes, such as inversions, insertion or deletion mutations (indels) and determination of their frequencies were performed for the complete plastomes...
August 3, 2016: Current Genetics
Maria D Logacheva, Mikhail I Schelkunov, Victoria Y Shtratnikova, Maria V Matveeva, Aleksey A Penin
Although plastid genomes of flowering plants are typically highly conserved regarding their size, gene content and order, there are some exceptions. Ericaceae, a large and diverse family of flowering plants, warrants special attention within the context of plastid genome evolution because it includes both non-photosynthetic and photosynthetic species with rearranged plastomes and putative losses of "essential" genes. We characterized plastid genomes of three species of Ericaceae, non-photosynthetic Monotropa uniflora and Hypopitys monotropa and photosynthetic Pyrola rotundifolia, using high-throughput sequencing...
2016: Scientific Reports
Cristina Roquet, Éric Coissac, Corinne Cruaud, Martí Boleda, Frédéric Boyer, Adriana Alberti, Ludovic Gielly, Pierre Taberlet, Wilfried Thuiller, Jérémie Van Es, Sébastien Lavergne
BACKGROUND AND AIMS: Plant plastid genomes are highly conserved in size, gene content and structure; however, parasitic plants are a noticeable exception to this evolutionary stability. Although the evolution of parasites could help to better understand plastome evolution in general, complete plastomes of parasites have been sequenced only for some lineages so far. Here we contribute to filling this gap by providing and analysing the complete plastome sequence of Cytinus hypocistis, the first parasite sequenced for Malvales and a species suspected to have an extremely small genome...
July 21, 2016: Annals of Botany
Yan-Lei Feng, Susann Wicke, Jian-Wu Li, Yu Han, Choun-Sea Lin, De-Zhu Li, Ting-Ting Zhou, Wei-Chang Huang, Lu-Qi Huang, Xiao-Hua Jin
The plastid genome (plastome) of heterotrophic plants like mycoheterotrophs and parasites shows massive gene losses in consequence to the relaxation of functional constraints on photosynthesis. To understand the patterns of this convergent plastome reduction syndrome in heterotrophic plants, we studied 12 closely related orchids of three different lifeforms from the tribe Neottieae (Orchidaceae). We employ a comparative genomics approach to examine structural and selectional changes in plastomes within Neottieae...
2016: Genome Biology and Evolution
Fay-Wei Li, Li-Yaung Kuo, Kathleen M Pryer, Carl J Rothfels
Plant chloroplast genomes (plastomes) are characterized by an inverted repeat (IR) region and two larger single copy (SC) regions. Patterns of molecular evolution in the IR and SC regions differ, most notably by a reduced rate of nucleotide substitution in the IR compared to the SC region. In addition, the organization and structure of plastomes is fluid, and rearrangements through time have repeatedly shuffled genes into and out of the IR, providing recurrent natural experiments on how chloroplast genome structure can impact rates and patterns of molecular evolution...
2016: Genome Biology and Evolution
Lianghong Ni, Zhili Zhao, Gaawe Dorje, Mi Ma
Scrophularia dentata is an important Tibetan medicinal plant and traditionally used for the treatment of exanthema and fever in Traditional Tibetan Medicine (TTM). However, there is little sequence and genomic information available for S. dentata. In this paper, we report the complete chloroplast genome sequence of S. dentata and it is the first sequenced member of the Sect. Tomiophyllum within Scrophularia (Scrophulariaceae). The gene order and organization of the chloroplast genome of S. dentata are similar to other Lamiales chloroplast genomes...
2016: PloS One
Tong-Jian Liu, Cai-Yun Zhang, Hai-Fei Yan, Lu Zhang, Xue-Jun Ge, Gang Hao
Species-rich genus Primula L. is a typical plant group with which to understand genetic variance between species in different levels of relationships. Chloroplast genome sequences are used to be the information resource for quantifying this difference and reconstructing evolutionary history. In this study, we reported the complete chloroplast genome sequence of Primula sinensis and compared it with other related species. This genome of chloroplast showed a typical circular quadripartite structure with 150,859 bp in sequence length consisting of 37...
2016: PeerJ
Aretuza Sousa, Sidonie Bellot, Jörg Fuchs, Andreas Houben, Susanne S Renner
Few angiosperms have distinct Y-chromosomes, among them Silene latifolia (Caryophyllaceae), Rumex acetosa (Polygonaceae), and Coccinia grandis (Cucurbitaceae), the latter with a male/female difference of 10% of the total genome (female individuals have a 0.85 pg, male individuals 0.94 pg), due to a Y chromosome that arose ca. 3 my ago. We compared the sequence composition of male and female C. grandis plants and determined the chromosomal distribution of repetitive and organellar DNA with probes developed from 21 types of repetitive DNA including 16 mobile elements...
June 29, 2016: Plant Journal: for Cell and Molecular Biology
Gwynne S Lim, Craig F Barrett, Chun-Chiu Pang, Jerrold I Davis
PREMISE OF THE STUDY: Heterotrophic angiosperms tend to have reduced plastome sizes relative to those of their autotrophic relatives because genes that code for proteins involved in photosynthesis are lost. However, some plastid-encoded proteins may have vital nonphotosynthetic functions, and the plastome therefore may be retained after the loss of photosynthesis. METHODS: We sequenced the plastome of the mycoheterotrophic species Thismia tentaculata and a representative of its sister genus, Tacca chantrieri, using next-generation technology, and we compared sequences and structures of genes and genomes of these species...
June 2016: American Journal of Botany
Xiaoyan Zhu, Shuang Guo, Zhongwei Wang, Qing Du, Yadi Xing, Tianquan Zhang, Wenqiang Shen, Xianchun Sang, Yinghua Ling, Guanghua He
BACKGROUND: As the indispensable part of plant, leaf blade mainly functions as the production workshops where organic substance is produced by photosynthesis. Leaf colour mutation is a genetic phenomenon that has a high frequency and is easily identified. The mutations always exhibit negative impact on the development of plants in any of the different stages of growth. Up to now, numerous genes involved in leaf colour mutations have been cloned. RESULTS: In this study, a yellow-green leaf mutant, yellow-green leaf 8 (ygl8), with stable genetic phenotype, has been screened out in the progeny of an excellent indica restorer line Jinhui 10 with seeds treated by EMS...
2016: BMC Plant Biology
John C Blazier, Robert K Jansen, Jeffrey P Mower, Madhu Govindu, Jin Zhang, Mao-Lun Weng, Tracey A Ruhlman
BACKGROUND AND AIMS: Several unrelated lineages such as plastids, viruses and plasmids, have converged on quadripartite genomes of similar size with large and small single copy regions and a large inverted repeat (IR). Except for Erodium (Geraniaceae), saguaro cactus and some legumes, the plastomes of all photosynthetic angiosperms display this structure. The functional significance of the IR is not understood and Erodium provides a system to examine the role of the IR in the long-term stability of these genomes...
June 2016: Annals of Botany
Sharof S Egamberdiev, Sukumar Saha, Ilkhom Salakhutdinov, Johnie N Jenkins, Dewayne Deng, Ibrokhim Y Abdurakhmonov
The importance of the cytoplasmic genome for many economically important traits is well documented in several crop species, including cotton. There is no report on application of cotton chloroplast specific SSR markers as a diagnostic tool to study genetic diversity among improved Upland cotton lines. The complete plastome sequence information in GenBank provided us an opportunity to report on 17 chloroplast specific SSR markers using a cost-effective data mining strategy. Here we report the comparative analysis of genetic diversity among a set of 42 improved Upland cotton lines using SSR markers specific to chloroplast and nuclear genome, respectively...
June 2016: Genetica
Birgit Kersten, Patricia Faivre Rampant, Malte Mader, Marie-Christine Le Paslier, Rémi Bounon, Aurélie Berard, Cristina Vettori, Hilke Schroeder, Jean-Charles Leplé, Matthias Fladung
Complete Populus genome sequences are available for the nucleus (P. trichocarpa; section Tacamahaca) and for chloroplasts (seven species), but not for mitochondria. Here, we provide the complete genome sequences of the chloroplast and the mitochondrion for the clones P. tremula W52 and P. tremula x P. alba 717-1B4 (section Populus). The organization of the chloroplast genomes of both Populus clones is described. A phylogenetic tree constructed from all available complete chloroplast DNA sequences of Populus was not congruent with the assignment of the related species to different Populus sections...
2016: PloS One
Sidonie Bellot, Susanne S Renner
The 23 species of mycoheterotrophic or exoparasitic land plants (from 15 genera and 6 families) studied so far all retain a minimal set of 17 of the normally 116 plastome genes. Only Rafflesia lagascae, an endoparasite concealed in its host except when flowering, has been reported as perhaps lacking a plastome, although it still possesses plastid-like compartments. We analyzed two other endoparasites, the African Apodanthaceae Pilostyles aethiopica and the Australian Pilostyles hamiltonii, both living inside Fabaceae...
December 12, 2015: Genome Biology and Evolution
Diana V Dugas, David Hernandez, Erik J M Koenen, Erika Schwarz, Shannon Straub, Colin E Hughes, Robert K Jansen, Madhugiri Nageswara-Rao, Martijn Staats, Joshua T Trujillo, Nahid H Hajrah, Njud S Alharbi, Abdulrahman L Al-Malki, Jamal S M Sabir, C Donovan Bailey
The Leguminosae has emerged as a model for studying angiosperm plastome evolution because of its striking diversity of structural rearrangements and sequence variation. However, most of what is known about legume plastomes comes from few genera representing a subset of lineages in subfamily Papilionoideae. We investigate plastome evolution in subfamily Mimosoideae based on two newly sequenced plastomes (Inga and Leucaena) and two recently published plastomes (Acacia and Prosopis), and discuss the results in the context of other legume and rosid plastid genomes...
2015: Scientific Reports
Monika Szczecińska, Jakub Sawicki
BACKGROUND: The European continent is presently colonized by nine species of the genus Pulsatilla, five of which are encountered only in mountainous regions of southwest and south-central Europe. The remaining four species inhabit lowlands in the north-central and eastern parts of the continent. Most plants of the genus Pulsatilla are rare and endangered, which is why most research efforts focused on their biology, ecology and hybridization. The objective of this study was to develop genomic resources, including complete plastid genomes and nuclear rRNA clusters, for three sympatric Pulsatilla species that are most commonly found in Central Europe...
2015: International Journal of Molecular Sciences
Yu Song, Wenpan Dong, Bing Liu, Chao Xu, Xin Yao, Jie Gao, Richard T Corlett
Machilus is a large (c. 100 sp.) genus of trees in the family Lauraceae, distributed in tropical and subtropical East Asia. Both molecular species identification and phylogenetic studies of this morphologically uniform genus have been constrained by insufficient variable sites among frequently used biomarkers. To better understand the mutation patterns in the chloroplast genome of Machilus, the complete plastomes of two species were sequenced. The plastomes of Machilus yunnanensis and M. balansae were 152, 622 and 152, 721 bp, respectively...
2015: Frontiers in Plant Science
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