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. 2017 Jan 1:2017:bax032.
doi: 10.1093/database/bax032.

Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community

Surya Saha  1 , Prashant S Hosmani  1 , Krystal Villalobos-Ayala  2 , Sherry Miller  3 , Teresa Shippy  3 , Mirella Flores  1 , Andrew Rosendale  4 , Chris Cordola  2 , Tracey Bell  2 , Hannah Mann  2 , Gabe DeAvila  2 , Daniel DeAvila  2 , Zachary Moore  4 , Kyle Buller  4 , Kathryn Ciolkevich  4 , Samantha Nandyal  4 , Robert Mahoney  4 , Joshua Van Voorhis  4 , Megan Dunlevy  4 , David Farrow  4 , David Hunter  3 , Taylar Morgan  3 , Kayla Shore  3 , Victoria Guzman  3 , Allison Izsak  5 , Danielle E Dixon  1   6 , Andrew Cridge  7 , Liliana Cano  7 , Xiaolong Cao  8 , Haobo Jiang  9 , Nan Leng  10 , Shannon Johnson  11 , Brandi L Cantarel  12 , Stephen Richards  13   14 , Adam English  13   14 , Robert G Shatters  15 , Chris Childers  15 , Mei-Ju Chen  16 , Wayne Hunter  17 , Michelle Cilia  18   19 , Lukas A Mueller  1   20 , Monica Munoz-Torres  21 , David Nelson  22 , Monica F Poelchau  15 , Joshua B Benoit  4 , Helen Wiersma-Koch  2 , Tom D'Elia  2 , Susan J Brown  3
Affiliations

Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community

Surya Saha et al. Database (Oxford). .

Erratum in

  • Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community.
    Saha S, Hosmani PS, Villalobos-Ayala K, Miller S, Shippy T, Flores M, Rosendale A, Cordola C, Bell T, Mann H, DeAvila G, DeAvila D, Moore Z, Buller K, Ciolkevich K, Nandyal S, Mahoney R, Voorhis JV, Dunlevy M, Farrow D, Hunter D, Morgan T, Shore K, Guzman V, Izsak A, Dixon DE, Cridge A, Cano L, Cao X, Jiang H, Leng N, Johnson S, Cantarel BL, Richards S, English A, Shatters RG, Childers C, Chen MJ, Hunter W, Cilia M, Mueller LA, Munoz-Torres M, Nelson D, Poelchau MF, Benoit JB, Wiersma-Koch H, D'Elia T, Brown SJ. Saha S, et al. Database (Oxford). 2019 Jan 1;2019:baz035. doi: 10.1093/database/baz035. Database (Oxford). 2019. PMID: 30820572 Free PMC article. No abstract available.

Abstract

https://citrusgreening.org/.

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Figures

Figure 1.
Figure 1.
BUSCO completeness comparison for D. citri datasets using the Hemiptera markers based on ORTHODBv9.1 orthologs (nine species and n = 3350 genes). Diaphorina citri MCOT v1.0 has the most complete single-copy orthologs (92.9%, largest blue bar) and fewer missing orthologs (7%, smaller red bar) compared to Adult, Egg and Nymph Transcriptomes v0.9, NCBI v100 and Maker v1.1 sets.
Figure 2.
Figure 2.
Annotation edit distance (AED) plot comparing NCBI v100 annotation (20 996), the mapped MCOT v1.0 annotation (19 744), Maker v1.1 (18 205) and curated genes (530) generated from a genome-guided transcriptome assembly based upon the NCBI-Diaci1.1 genome. AED cumulative fraction of transcripts plot shows that genes in the NCBI v100 annotation have more expression evidence support compared to MCOT v1.0 mapped set. Curated genes show better evidence support compared to any other automated prediction pipelines.
Figure 3.
Figure 3.
Workflow followed by student annotators for the structural curation of gene models using i5k Apollo. The OGS was created at the end of the annotation cycle along with gene reports included as Supplementary Notes 1–39. The dark colored boxes denote processes with multiple steps.
Figure 4.
Figure 4.
Phylogeny of P450 genes with insect orthologs. Neighbor-joining midpoint rooted tree of P450s from R. prolixus (red), A. pisum (green) and D. citri (blue) was generated using CLUSTAL Omega and drawn in Figtree. Four clans of P450s, CYP2 (orange), CYP3 (green), CYP4 (red) and mito (blue) clan are shown in the phylogenetic tree. Arc A, B and C are described in the main body of text. Excluding some partial genes, a total of 189 P450s were used to generate this phylogenetic tree.
See this image and copyright information in PMC

References

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