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This is a de novo assembly and annotation of a complete mitochondrial genome from Pyrus pyrifolia in the family Rosaceae. The complete mitochondrial genome of P. pyrifolia was assembled from PacBio RSII P6-C4 sequencing reads. The circular genome was 458,873 bp in length, containing 39 protein-coding genes, 23 tRNA genes and three rRNA genes. The nucleotide composition was A (27.5%), T (27.3%), G (22.6%) and C (22.6%) with GC content of 45.2%. Most of protein-coding genes use the canonical start codon ATG, whereas nad1, cox1, matR and rps4 use ACG, mttB uses ATT, rpl16 and rps19 uses GTG. The stop codon is also common in all mitochondrial genes. The phylogenetic analysis showed that P. pyrifolia was clustered with the Malus of Rosaceae family. Maximum-likelihood analysis suggests a clear relationship of Rosids and Asterids, which support the traditional classification. [ABSTRACT FROM AUTHOR]

The complete chloroplast genome of Wonwhang (BioSample SAMN05196235), Pyrus pyrifolia, was assembled and analyzed by de novo assembly using whole-genome sequencing data. The accession NC_015996 was used as a reference sequence in this study. The total chloroplast genome size of the Wonwhang was 159,922 bp in length, including a pair of inverted repeat regions (IRs) of 26,392 bp that are separated by a large single-copy region of 72,023 bp and a small single-copy region of 19,235 bp. A total of 132 genes, including 93 protein-coding genes, 31 tRNA genes and eight rRNA genes, were predicted from the chloroplast genomes. Among them, 18 genes occur in IRs, containing nine protein-coding genes, five tRNA genes and four rRNA genes. The GC content of Wonwhang chloroplast genome is 36.6%. The phylogenetic analysis with nine Rosids species and three other species revealed that Wonwhang was clustered with Malus genus. [ABSTRACT FROM AUTHOR]

This is a de novo assembly and annotation of a complete mitochondrial genome from Pyrus pyrifolia in the family Rosaceae. The complete mitochondrial genome of P. pyrifolia was assembled from PacBio RSII P6-C4 sequencing reads. The circular genome was 458,873 bp in length, containing 39 protein-coding genes, 23 tRNA genes and three rRNA genes. The nucleotide composition was A (27.5%), T (27.3%), G (22.6%) and C (22.6%) with GC content of 45.2%. Most of protein-coding genes use the canonical start codon ATG, whereas nad1 , cox1 , matR and rps4 use ACG, mttB uses ATT, rpl16 and rps19 uses GTG. The stop codon is also common in all mitochondrial genes. The phylogenetic analysis showed that P. pyrifolia was clustered with the Malus of Rosaceae family. Maximum-likelihood analysis suggests a clear relationship of Rosids and Asterids, which support the traditional classification., Competing Interests: The authors declare no conflicts of interest., (© 2017 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

The complete chloroplast genome of Wonwhang (BioSample SAMN05196235), Pyrus pyrifolia , was assembled and analyzed by de novo assembly using whole-genome sequencing data. The accession NC_015996 was used as a reference sequence in this study. The total chloroplast genome size of the Wonwhang was 159,922 bp in length, including a pair of inverted repeat regions (IRs) of 26,392 bp that are separated by a large single-copy region of 72,023 bp and a small single-copy region of 19,235 bp. A total of 132 genes, including 93 protein-coding genes, 31 tRNA genes and eight rRNA genes, were predicted from the chloroplast genomes. Among them, 18 genes occur in IRs, containing nine protein-coding genes, five tRNA genes and four rRNA genes. The GC content of Wonwhang chloroplast genome is 36.6%. The phylogenetic analysis with nine Rosids species and three other species revealed that Wonwhang was clustered with Malus genus., Competing Interests: The authors declare no conflicts of interest., (© 2017 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

Background: Geminivirus AC2 is a multifunctional protein that acts as a pathogenicity factor. Transcriptional regulation by AC2 appears to be mediated through interaction with a plant specific DNA binding protein, PEAPOD2 (PPD2), that specifically binds to sequences known to mediate activation of the CP promoter of Cabbage leaf curl virus (CaLCuV) and Tomato golden mosaic virus (TGMV). Suppression of both basal and innate immune responses by AC2 in plants is mediated through inactivation of SnRK1.2, an Arabidopsis SNF1 related protein kinase, and adenosine kinase (ADK). An indirect promoter targeting strategy, via AC2-host dsDNA binding protein interactions, and inactivation of SnRK1.2-mediated defense responses could provide the opportunity for geminiviruses to alter host gene expression and in turn, reprogram the host to support virus infection. The goal of this study was to identify changes in the transcriptome of Arabidopsis induced by the transcription activation function of AC2 and the inactivation of SnRK1.2., Results: Using full-length and truncated AC2 proteins, microarray analyses identified 834 genes differentially expressed in response to the transcriptional regulatory function of the AC2 protein at one and two days post treatment. We also identified 499 genes differentially expressed in response to inactivation of SnRK1.2 by the AC2 protein at one and two days post treatment. Network analysis of these two sets of differentially regulated genes identified several networks consisting of between four and eight highly connected genes. Quantitative real-time PCR analysis validated the microarray expression results for 10 out of 11 genes tested., Conclusions: It is becoming increasingly apparent that geminiviruses manipulate the host in several ways to facilitate an environment conducive to infection, predominantly through the use of multifunctional proteins. Our approach of identifying networks of highly connected genes that are potentially co-regulated by geminiviruses during infection will allow us to identify novel pathways of co-regulated genes that are stimulated in response to pathogen infection in general, and virus infection in particular.