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Comparative plastomics

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https://www.readbyqxmd.com/read/27899326/complete-plastid-genome-sequence-of-goosegrass-eleusine-indica-and-comparison-with-other-poaceae
#1
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...
November 26, 2016: 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
#2
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
#3
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
https://www.readbyqxmd.com/read/27808159/limited-mitogenomic-degradation-in-response-to-a-parasitic-lifestyle-in-orobanchaceae
#4
Weishu Fan, Andan Zhu, Melisa Kozaczek, Neethu Shah, Natalia Pabón-Mora, Favio González, Jeffrey P Mower
In parasitic plants, the reduction in plastid genome (plastome) size and content is driven predominantly by the loss of photosynthetic genes. The first completed mitochondrial genomes (mitogenomes) from parasitic mistletoes also exhibit significant degradation, but the generality of this observation for other parasitic plants is unclear. We sequenced the complete mitogenome and plastome of the hemiparasite Castilleja paramensis (Orobanchaceae) and compared them with additional holoparasitic, hemiparasitic and nonparasitic species from Orobanchaceae...
November 3, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27790830/strategies-for-complete-plastid-genome-sequencing
#5
Alex D Twyford, Rob W Ness
Plastid sequencing is an essential tool in the study of plant evolution. This high-copy organelle is one of the most technically accessible regions of the genome, and its sequence conservation makes it a valuable region for comparative genome evolution, phylogenetic analysis and population studies. Here, we discuss recent innovations and approaches for de novo plastid assembly that harness genomic tools. We focus on technical developments including low-cost sequence library preparation approaches for genome skimming, enrichment via hybrid baits and methylation sensitive capture, sequence platforms with higher read outputs and longer read lengths, and automated tools for assembly...
October 28, 2016: Molecular Ecology Resources
https://www.readbyqxmd.com/read/27790228/comparative-transcriptome-and-chloroplast-genome-analyses-of-two-related-dipteronia-species
#6
Tao Zhou, Chen Chen, Yue Wei, Yongxia Chang, Guoqing Bai, Zhonghu Li, Nazish Kanwal, Guifang Zhao
Dipteronia (order Sapindales) is an endangered genus endemic to China and has two living species, D.sinensis and D. dyeriana. The plants are closely related to the genus Acer, which is also classified in the order Sapindales. Evolutionary studies on Dipteronia have been hindered by the paucity of information on their genomes and plastids. Here, we used next generation sequencing to characterize the transcriptomes and complete chloroplast genomes of both Dipteronia species. A comparison of the transcriptomes of both species identified a total of 7814 orthologs...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27719665/plastid-molecular-pharming-ii-production-of-biopharmaceuticals-by-plastid-transformation
#7
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
https://www.readbyqxmd.com/read/27682170/plastid-genome-of-seseli-montanum-complete-sequence-and-comparison-with-plastomes-of-other-members-of-the-apiaceae-family
#8
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
https://www.readbyqxmd.com/read/27589600/chloroplast-genome-evolution-in-actinidiaceae-clpp-loss-heterogenous-divergence-and-phylogenomic-practice
#9
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
https://www.readbyqxmd.com/read/27488804/plastid-phylogenomic-study-of-species-within-the-genus-zea-rates-and-patterns-of-three-classes-of-microstructural-changes
#10
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
https://www.readbyqxmd.com/read/27452401/comparative-analysis-of-plastid-genomes-of-non-photosynthetic-ericaceae-and-their-photosynthetic-relatives
#11
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
https://www.readbyqxmd.com/read/27443299/understanding-the-evolution-of-holoparasitic-plants-the-complete-plastid-genome-of-the-holoparasite-cytinus-hypocistis-cytinaceae
#12
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
https://www.readbyqxmd.com/read/27412609/lineage-specific-reductions-of-plastid-genomes-in-an-orchid-tribe-with-partially-and-fully-mycoheterotrophic-species
#13
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
https://www.readbyqxmd.com/read/27401175/genes-translocated-into-the-plastid-inverted-repeat-show-decelerated-substitution-rates-and-elevated-gc-content
#14
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
https://www.readbyqxmd.com/read/27391235/the-complete-chloroplast-genome-of-ye-xing-ba-scrophularia-dentata-scrophulariaceae-an-alpine-tibetan-herb
#15
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
https://www.readbyqxmd.com/read/27375965/complete-plastid-genome-sequence-of-primula-sinensis-primulaceae-structure-comparison-sequence-variation-and-evidence-for-accd-transfer-to-nucleus
#16
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
https://www.readbyqxmd.com/read/27354172/analysis-of-transposable-elements-and-organellar-dna-in-male-and-female-genomes-of-a-species-with-a-huge-y-chromosome-reveals-distinct-y-centromeres
#17
Aretuza Sousa, Sidonie Bellot, Jörg Fuchs, Andreas Houben, Susanne S Renner
Few angiosperms have distinct Y chromosomes. Among those that do are Silene latifolia (Caryophyllaceae), Rumex acetosa (Polygonaceae) and Coccinia grandis (Cucurbitaceae), the latter having a male/female difference of 10% of the total genome (female individuals have a 0.85 pg genome, male individuals 0.94 pg), due to a Y chromosome that arose about 3 million years 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
https://www.readbyqxmd.com/read/27335389/drastic-reduction-of-plastome-size-in-the-mycoheterotrophic-thismia-tentaculata-relative-to-that-of-its-autotrophic-relative-tacca-chantrieri
#18
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
https://www.readbyqxmd.com/read/27297403/map-based-cloning-and-functional-analysis-of-ygl8-which-controls-leaf-colour-in-rice-oryza-sativa
#19
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
https://www.readbyqxmd.com/read/27192713/variable-presence-of-the-inverted-repeat-and-plastome-stability-in-erodium
#20
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
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