Using Apollo to Browse and Edit Genome Annotations

Misra, Sima; Harris, Nomi L.

doi:10.1002/0471250953.bi0905s12

Cited by 49 publications

(37 citation statements)

References 7 publications

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“…Alternative browsers can be used: for example Argo[Engels et al, 2006] is a convenient browser for smaller genomes which can be run on a desktop machine without complicated setup. Other browsers include Ensembl, CisGenome [Ji et al, 2008], Apollo [Misra and Harris, 2006], Gene-Track [Albert et al, 2008], EagleView [Huang and Marth, 2008] and Gbrowse [Stein et al, 2002]. .…”

Section: Discussionmentioning

confidence: 99%

Genomic location analysis by ChIP‐Seq

Barski

Zhao

2009

J of Cellular Biochemistry

143

117

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The interaction of a multitude of transcription factors and other chromatin proteins with the genome can influence gene expression and subsequently cell differentiation and function. Thus systematic identification of binding targets of transcription factors is key to unraveling gene regulation networks. The recent development of ChIP-Seq has revolutionized mapping of DNA-protein interactions. Now protein binding can be mapped in a truly genome-wide manner with extremely high resolution. This review discusses ChIP-Seq technology, its possible pitfalls, data analysis and several early applications of the ChIP-Seq technology.

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Section: Discussionmentioning

confidence: 99%

Genomic location analysis by ChIP‐Seq

Barski

Zhao

2009

J of Cellular Biochemistry

143

117

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“…Meanwhile, tRNA genes were identified using tRNAscan-SE 31 and ARAGORN 32 . Manual corrections on the positions of the start and stop codons, and for the intron/exon boundaries were performed based on the entries in the Chloroplast Genome Database 33 using the Apollo program 34 . Moreover, the circular chloroplast genome map of A. membranaceus was drawn using OrganellarGenomeDRAW 35 .…”

Section: Methodsmentioning

confidence: 99%

Intraspecific and heteroplasmic variations, gene losses and inversions in the chloroplast genome of Astragalus membranaceus

Liu

DaPeng

Wang

et al. 2016

Sci Rep

100

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Astragalus membranaceus is an important medicinal plant in Asia. Several of its varieties have been used interchangeably as raw materials for commercial production. High resolution genetic markers are in urgent need to distinguish these varieties. Here, we sequenced and analyzed the chloroplast genome of A. membranaceus (Fisch.) Bunge var. mongholicus (Bunge) P.K. Hsiao using the next generation DNA sequencing technology. The genome was assembled using Abyss and then subjected to gene prediction using CPGAVAS and repeat analysis using MISA, Tandem Repeats Finder, and REPuter. Finally, the genome was subjected phylogenetic and comparative genomic analyses. The complete genome is 123,582 bp long, containing only one copy of the inverted repeat. Gene prediction revealed 110 genes encoding 76 proteins, 30 tRNAs, and four rRNAs. Five intra-specific hypermutation loci were identified, three of which are heteroplasmic. Furthermore, three gene losses and two large inversions were identified. Comparative genomic analyses demonstrated the dynamic nature of the Papilionoideae chloroplast genomes, which showed occurrence of numerous hypermutation loci, frequent gene losses, and fragment inversions. Results obtained herein elucidate the complex evolutionary history of chloroplast genomes and have laid the foundation for the identification of genetic markers to distinguish A. membranaceus varieties.

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“…Geseq was then used to con rm the annotation results [66]. Furthermore, the annotations with problems were manually edited by using Apollo [67]. The genome maps were drawn by OGDRAW [68].…”

Section: Genome Assembly and Annotationmentioning

confidence: 99%

Comparative Chloroplast Genomics of Four Pilea Species (Urticaceae): High Levels of Sequences Divergence Provides New Insight into Interspecific Diversity in Pilea

Li¹,

Tang²,

Zeng³

et al. 2020

Preprint

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Background Pilea is a genus of perennial herbs from the family Urticaceae, which are used for courtyard ornamental. For some species, they are used as medicinal plants in traditional Chinese medicine as well. The morphological characteristics of medicinal species from Pilea are similar, and it is difficult to accurately distinguish them based only on morphological characteristics. Besides, the species classification of Pilea are still controversial. The classification of many species are still in an unresolved state. At present, there is no information about the chloroplast genomes of Pilea, which limits our further understanding of this genus. Here, we first reported 4 chloroplast genomes of Pilea taxa (P. mollis, P. glauca, P. peperomioides and P. serpyllacea), and performed comprehensive comparative analysis. Results The four chloroplast genomes have similar structural characteristics and gene order with other angiosperms. These genomes all have a typical quartile structure, which contains 113 unique genes, including 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes. Besides, we detected SSRs and repeat sequences, and analyzed the expansion/contraction of IR regions. In particular, the comparative analysis showed a rather level of sequence divergence in the non-coding regions, even in the protein-coding regions of the four genome sequences, suggesting a high level of genetic diversity in Pilea. Moreover, we identified eight hypervariable regions, including petN-psbM; psbZ-trnG-GCC; trnT-UGU-trnL-UAA; accD-psbI; ndhF-rpl32; rpl32-trnL-UAG; ndhA-intron and ycf1, are proposed for use as DNA barcode regions. Phylogenetic analysis showed that four Pilea species form a monophyletic cluster with a 100% bootstrap value. Conclusion The results obtained here could provide abundant information for the phylogenetic position of Pilea and further species identification. High levels of sequences divergence promote our understanding of the interspecific diversity of this genus, also provide reference for the rational classification of unsolved species in the future.

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Using Apollo to Browse and Edit Genome Annotations

Cited by 49 publications

References 7 publications

Genomic location analysis by ChIP‐Seq

Genomic location analysis by ChIP‐Seq

Intraspecific and heteroplasmic variations, gene losses and inversions in the chloroplast genome of Astragalus membranaceus

Comparative Chloroplast Genomics of Four Pilea Species (Urticaceae): High Levels of Sequences Divergence Provides New Insight into Interspecific Diversity in Pilea

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