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Robert J Henry - One of the best experts on this subject based on the ideXlab platform.

  • Chloroplast Genome sequence confirms distinctness of australian and asian wild rice
    Ecology and Evolution, 2012
    Co-Authors: Daniel Le Waters, Catherine J Nock, Nicole F Rice, Robert J Henry, Ryuji Ishikawa
    Abstract:

    Cultivated rice (Oryza sativa) is an AA Genome Oryza species that was most likely domesticated from wild populations of O. rufipogon in Asia. O. rufipogon and O. meridionalis are the only AA Genome species found within Australia and occur as widespread populations across northern Australia. The Chloroplast Genome sequence of O. rufipogon from Asia and Australia and O. meridionalis and O. australiensis (an Australian member of the genus very distant from O. sativa) was obtained by massively parallel sequencing and compared with the Chloroplast Genome sequence of domesticated O. sativa. Oryza australiensis differed in more than 850 sites single nucleotide polymorphism or indel from each of the other samples. The other wild rice species had only around 100 differences relative to cultivated rice. The Chloroplast Genomes of Australian O. rufipogon and O. meridionalis were closely related with only 32 differences. The Asian O. rufipogon Chloroplast Genome (with only 68 differences) was closer to O. sativa than the Australian taxa (both with more than 100 differences). The Chloroplast sequences emphasize the genetic distinctness of the Australian populations and their potential as a source of novel rice germplasm. The Australian O. rufipogon may be a perennial form of O. meridionalis.

  • Chloroplast Genome sequences from total dna for plant identification
    Plant Biotechnology Journal, 2011
    Co-Authors: Catherine J Nock, Daniel Le Waters, Mark A Edwards, Stirling Bowen, Nicole F Rice, Giovanni M Cordeiro, Robert J Henry
    Abstract:

    Chloroplast DNA sequence data are a versatile tool for plant identification or barcoding and establishing genetic relationships among plant species. Different Chloroplast loci have been utilized for use at close and distant evolutionary distances in plants, and no single locus has been identified that can distinguish between all plant species. Advances in DNA sequencing technology are providing new cost-effective options for Genome comparisons on a much larger scale. Universal PCR amplification of Chloroplast sequences or isolation of pure Chloroplast fractions, however, are nontrivial. We now propose the analysis of Chloroplast Genome sequences from massively parallel sequencing (MPS) of total DNA as a simple and cost-effective option for plant barcoding, and analysis of plant relationships to guide gene discovery for biotechnology. We present Chloroplast Genome sequences of five grass species derived from MPS of total DNA. These data accurately established the phylogenetic relationships between the species, correcting an apparent error in the published rice sequence. The Chloroplast Genome may be the elusive single-locus DNA barcode for plants.

Gaawe Dorje - One of the best experts on this subject based on the ideXlab platform.

Xiaogai Hou - One of the best experts on this subject based on the ideXlab platform.

  • Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Paeonia ostii
    Molecules, 2018
    Co-Authors: Shuai Guo, Lili Guo, Wei Zhao, Li Yuying, Xiaoyan Zhang, Xiaofeng Shen, Xiaogai Hou
    Abstract:

    Paeonia ostii, a common oil-tree peony, is important ornamentally and medicinally. However, there are few studies on the Chloroplast Genome of Paeonia ostii. We sequenced and analyzed the complete Chloroplast Genome of P. ostii. The size of the P. ostii Chloroplast Genome is 152,153 bp, including a large single-copy region (85,373 bp), a small single-copy region (17,054 bp), and a pair of inverted repeats regions (24,863 bp). The P. ostii Chloroplast Genome encodes 111 genes, including 77 protein-coding genes, four ribosomal RNA genes, and 30 transfer RNA genes. The Genome contains forward repeats (22), palindromic repeats (28), and tandem repeats (24). The presence of rich simple-sequence repeat loci in the Genome provides opportunities for future population genetics work for breeding new varieties. A phylogenetic analysis showed that P. ostii is more closely related to Paeonia delavayi and Paeonia ludlowii than to Paeonia obovata and Paeonia veitchii. The results of this study provide an assembly of the whole Chloroplast Genome of P. ostii, which may be useful for future breeding and further biological discoveries. It will provide a theoretical basis for the improvement of peony yield and the determination of phylogenetic status.

Xiaoxiao Feng - One of the best experts on this subject based on the ideXlab platform.

  • complete Chloroplast Genome sequences of mongolia medicine artemisia frigida and phylogenetic relationships with other plants
    PLOS ONE, 2013
    Co-Authors: Yue Liu, Naxin Huo, Lingli Dong, Yi Wang, Shuixian Zhang, Hugh A Young, Xiaoxiao Feng
    Abstract:

    Background: Artemisia frigida Willd. is an important Mongolian traditional medicinal plant with pharmacological functions of stanch and detumescence. However, there is little sequence and genomic information available for Artemisia frigida, which makes phylogenetic identification, evolutionary studies, and genetic improvement of its value very difficult. We report the complete Chloroplast Genome sequence of Artemisia frigida based on 454 pyrosequencing. Methodology/Principal Findings: The complete Chloroplast Genome of Artemisia frigida is 151,076 bp including a large single copy (LSC) region of 82,740 bp, a small single copy (SSC) region of 18,394 bp and a pair of inverted repeats (IRs) of 24,971 bp. The Genome contains 114 unique genes and 18 duplicated genes. The Chloroplast Genome of Artemisia frigida contains a small 3.4 kb inversion within a large 23 kb inversion in the LSC region, a unique feature in Asteraceae. The gene order in the SSC region of Artemisia frigida is inverted compared with the other 6 Asteraceae species with the Chloroplast Genomes sequenced. This inversion is likely caused by an intramolecular recombination event only occurred in Artemisia frigida. The existence of rich SSR loci in the Artemisia frigida Chloroplast Genome provides a rare opportunity to study population genetics of this Mongolian medicinal plant. Phylogenetic analysis demonstrates a sister relationship between Artemisia frigida and four other species in Asteraceae, including Ageratina adenophora, Helianthus annuus, Guizotia abyssinica and Lactuca sativa, based on 61 protein-coding sequences. Furthermore, Artemisia frigida was placed in the tribe Anthemideae in the subfamily Asteroideae (Asteraceae) based on ndhF and trnL-F sequence comparisons. Conclusion: The Chloroplast Genome sequence of Artemisia frigida was assembled and analyzed in this study, representing the first plastid Genome sequenced in the Anthemideae tribe. This complete Chloroplast Genome sequence will be useful for molecular ecology and molecular phylogeny studies within Artemisia species and also within the Asteraceae family.

Haifei Yan - One of the best experts on this subject based on the ideXlab platform.