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Comparative plastomics

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
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
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
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 29, 2016: Genome Biology and Evolution
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
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
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
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
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
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
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
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
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
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