TN20

Gene Ortholog Familes of H. glycines and Globodera ellingtonae

Opscan (1) was used to call orthologous gene families between H. glycines V1 genome and Globodera ellingtonae (2).

Gene by gene format download: ellingtonaeiadhoretable.docx

 

Public gene models were not available at the time of the analysis, so genes were called using Braker.pl version 1.  The Globodera genome and the augustus.gff3 file obtained through alignments of SRR3162514 at NCBI.

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Gene Ortholog Familes of H. glycines and Globodera pallida

Opscan (1) was used to call orthologous gene families between H. glycines V1 genome and Globodera pallida (2).

 

1.  Drillon, Guénola, Alessandra Carbone, and Gilles Fischer. "SynChro: a fast and easy tool to reconstruct and visualize synteny blocks along eukaryotic chromosomes." PLoS One 9.3 (2014): e92621.

2.  Cotton, James A., et al. "The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode." Genome biology 15.3 (2014): R43.

  Read more about Gene Ortholog Familes of H. glycines and Globodera pallida

Gene Ortholog Familes of H. glycines and Globodera rostochiensis

Opscan (1) was used to call orthologous gene families between H. glycines V1 genome and Globodera rostochiensis (2).

 

1.  Drillon, Guénola, Alessandra Carbone, and Gilles Fischer. "SynChro: a fast and easy tool to reconstruct and visualize synteny blocks along eukaryotic chromosomes." PLoS One 9.3 (2014): e92621.

2. Eves-van den Akker, Sebastian, et al. "The genome of the yellow potato cyst nematode, Globodera rostochiensis, reveals insights into the basis of parasitism and virulence." Genome biology 17.1 (2016): 124. Read more about Gene Ortholog Familes of H. glycines and Globodera rostochiensis

Gene Ortholog Familes of H. glycines and Meloidogyne incognita

Opscan (1) was used to call orthologous gene families between H. glycines V1 genome and Meloidogyne incognita (2).

1.  Drillon, Guénola, Alessandra Carbone, and Gilles Fischer. "SynChro: a fast and easy tool to reconstruct and visualize synteny blocks along eukaryotic chromosomes." PLoS One 9.3 (2014): e92621.

2.  Abad, Pierre, et al. "Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita." Nature biotechnology 26.8 (2008): 909.

  Read more about Gene Ortholog Familes of H. glycines and Meloidogyne incognita

Gene Ortholog Familes of H. glycines and Bursephelenchus xylophilus

Opscan (1) was used to call orthologous gene families between H. glycines V1 genome and Bursaphelenchus xylophilus (2).

 

1.  Drillon, Guénola, Alessandra Carbone, and Gilles Fischer. "SynChro: a fast and easy tool to reconstruct and visualize synteny blocks along eukaryotic chromosomes." PLoS One 9.3 (2014): e92621.

2.  Kikuchi, Taisei, et al. "Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus." PLoS pathogens 7.9 (2011): e1002219. Read more about Gene Ortholog Familes of H. glycines and Bursephelenchus xylophilus

Gene Ortholog Familes of H. glycines and Meloidogyne hapla

Opscan (1) was used to call orthologous gene families between H. glycines V1 genome and Meloidogyne hapla (2).

1.  Drillon, Guénola, Alessandra Carbone, and Gilles Fischer. "SynChro: a fast and easy tool to reconstruct and visualize synteny blocks along eukaryotic chromosomes." PLoS One 9.3 (2014): e92621.

2.  Opperman, Charles H., et al. "Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism." Proceedings of the National Academy of Sciences (2008).

  Read more about Gene Ortholog Familes of H. glycines and Meloidogyne hapla

Repeat Explorer of TN20

RepeatExplorer is an online tool that can give a bioinformatician a grasp on what repeats are in a genome, as well as their relative abundance.  Here, I took TN20 reads from NCBI (SRR1800548), trimmed with trimmomatic, converted to fasta with the fastx-toolkit, and sorted and interlaced with seqtk.  200,000 reads were retained that maintained the maximum length (150bp) and had a full length mate. Classified repeats were also obtained from running RepeatModeler on the H. glycines genome [1]. Read more about Repeat Explorer of TN20

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