XENLA WorldCup

Information about Xenopus laevis gene annotation released on July, 2014.

Genome Browser

• You can see/search final gene model (UTA201407f) and all other sequences mentioned in this page at http://daudin.icmb.utexas.edu/XENLA_JGIv72/

• It should be noted that XENLA_JGIv72 is slightly modified version of JGI version 7.1 genome (ftp://ftp.xenbase.org/pub/Genomics/JGI/Xenla7.1/):
  1. assign chromosome name based on chromosome FISH data from NIG/Japan
  2. split mis-joint scaffolds (http://daudin.icmb.utexas.edu/XENLA_JGIv72/raw/Fucui201405_chimera.txt)
• ChIP-seq data is kindly contributed by following groups:
  • H3K27ac, H3K4me1, H3K4me3 - Rakhi Gupta/Julie Baker lab, Stanford University, USA
  • H3K27ac, H3K4me3, H3K4me2, E2f4, E2f4+Mci - Ian Quigley/Chris Kintner lab, Salk Institute, USA. E2f4 data is published here
  • H3K4me3 - Marta Teperek/John Gurdon lab, Cambridge, UK
  • Rfx2 - Mei-I Chung/John Wallingford lab, University of Texas at Austin, USA, published here

Raw materials

• Xenopus laevis Reference sequences - http://daudin.icmb.utexas.edu/xenopus-pub/ref/ (original) http://daudin.icmb.utexas.edu/xenopus-pub/tx/pub.201406 (processed)
  • mgEST_Xl4jul2012.fa - Michael Gilchrist's assembled transcript (2012 July version)
  • XENLA_XBv5_cdna.fa - XenBase NCBI mRNA sequences (2012 June version)
  • XENLA_UG94.fa - X. laevis UniGene (version 94)
  • XENLA_xb201405_mrna.fa - XenBase NCBI mRNA sequences (2014 May version)
  • XGI_022511_TC.fa - John Quackenbush's assembled ESTs (XGI 022511 version)
  • XENTR_UG52_uniq.fa - X. tropicalis UniGene (version 52).
  • XENTR_xb201405_mrna.fa - XenBase NCBI mRNA sequences (2014 May version)

• Reference species proteome sequence - http://daudin.icmb.utexas.edu/xenopus-pub/ens72/
  • CHICK_ens72_prot_annot_longest.fa - Chicken
  • DANRE_ens72_prot_annot_longest.fa - Zebrafish
  • MOUSE_ens72_prot_annot_longest.fa - Mouse
  • XENTR_ens72_prot_annot_longest.fa - X. tropicalis
  • HUMAN_ens72_prot_annot_longest.fa - Human

• JGI gene annotation data -http://daudin.icmb.utexas.edu/xenopus-pub/annot/JGI/ (original) http://daudin.icmb.utexas.edu/xenopus-pub/tx/pub.201406 (processed)
  • XENLA_JGIv10p_pub.fa.gz - JGI v1.0. ('XlaevisJGIv1.0.primaryTrs.fa' with a header like 'Xelaev10020581m')
  • XENLA_JGIv14pCDS_pub.fa.gz - JGI v1.4 ('XlaevisJGIv1.4.primaryTrs.fa' with a header like 'Xelaev14000002m')
  • XENLA_JGIv15_primTx_pub.fa.gz - JGI v1.5 ('XlaevisJGIv1.5.primaryTrs.fa' with a header like 'Xelaev15034936m')
  • XENLA_JGIv610pCDS_pub.fa.gz - ??? ('Xenopus_laevisJGIL6RMv1.0.primaryTrs.fa' with a header like XeXenL6RMv10000001m)
  • XENLA_JGIv16pa_pub.fa.gz - JGI v1.6. ('Xlaevisv1.6.primaryTrs.fa.gz' with a header like 'Xelaev16061684m')

• De novo assembled transcripts from RNA-seq - http://daudin.icmb.utexas.edu/xenopus-pub/tx/pub.201406
  • Amin201106_XENLA.cdna_pub.fa - Frank Conlon lab, University of North Carolina, USA
  • Audic201207_XENLA.cdna_pub.fa - Yann Audic, Université de RENNES I, France
  • Blower201306_XENLAab.cdna_pub.fa, Blower201306_XENLAcap.cdna_pub.fa, Blower201306_XENLApA.cdna_pub.fa - Michael Blower lab, Harvard Medical School, USA (published here)
  • Chang2013_XENLA.cdna_pub.fa - Chenbei Chang lab, University of Alabama, USA
  • Chung201110_XENLA.cdna_pub.fa - Mei-I Chung/John Wallingford lab, University of Texas at Austin, USA
  • Ismailoglu201203_XENLA.cdna_pub.fa - Ali Brivanlou lab, Rockefeller University, USA]
  • Park201106_XENLA.cdna_pub.fa - Tae Joo Park lab, UNIST, Republic of Korea
  • Quigley201112_XENLA.cdna_pub.fa, Quigley201207_XENLA.cdna_pub.fa, Quigley201212_XENLA.cdna_pub.fa, Quigley201307_XENLA.cdna_pub.fa - Ian Quigley/Chris Kintner lab, Salk Institute, USA
  • Taira201203_XENLA_stage.cdna_pub.fa, Taira201203_XENLA_tissue.cdna_pub.fa - Masanori Taira/Naoto Ueno/Shuji Takahashi (genome consortium)
  • TeperekTkacz201202_XENLA.cdna_pub.fa, TeperekTkacz201205_XENLA.cdna_pub.fa, TeperekTkacz201206_XENLA.cdna_pub.fa - Marta Teperek/John Gurdon lab, Cambridge, UK
  • TXGP201107_XENLA.cdna_pub.fa - John Wallingford/Edward Marcotte lab (genome consortium)
  • Ueno201210_XENLA_stage.cdna_pub.fa, Ueno201210_XENLA_tissue.cdna_pub.fa, Ueno201302_XENLA_stage.cdna_pub.fa - Masanori Taira/Naoto Ueno/Shuji Takahashi (genome consortium)

First merging

http://daudin.icmb.utexas.edu/xenopus-pub/annot/201407_WorldCup/XENLA_UTA201407f_raw.fa.gz

1. Map on JGI ver 7.1 genome with GMAP (default setting).
2. Sort all transcripts based on CDS length identified by GMAP (from longest to shortest). For transcripts with identical CDS length, sort them based on exon length also identified by GMAP (from shortest to longest; when I did this second sorting in opposite way, there were so many fused genes produced so I decide to sacrifice long UTRs instead).
3. Choose longest transcripts per give genome scaffold region and direction of transcription.

Translation

1. Translate non-redundant transcripts into all possible 6 frames, with standard codon usage table.
2. Search it against Reference species proteome (human, mouse, zebrafish, chicken, X. tropicalis; EnsEMBL ver. 72)
3. Determine the translation frame.

Gene name assignment based on phylogeny

http://daudin.icmb.utexas.edu/xenopus-pub/annot/201407_WorldCup/XENLA_UTA201407f.names

• Mapping reference proteins (EnsEMBL + XenBase) to EggNOG database (v4)
  • Use median length sequences of each orthogroup defined at opiNOG (orthogroup of Opisthoknots) - http://daudin.icmb.utexas.edu/xenopus-pub/eggnog/eggnogv4_opiNOG_pep.fa.gz
  • Report hits with E-value < 1.0
• Mapping query proteins to same database.
• Group queries and references into each NOG.
  • If NOG does not have more than two reference sequences, discard it.
  • If NOG does not have a query, discard it.
• Do multiple sequence alignment per orthogroup using muscle, and construct a phylogenetic tree with neighbor-joining (using Kimura distance as a measure of distance).
• Calculate the distance from a query to
  • Closest X. tropicalis gene (either EnsEMBL or XenBase)
  • Closest human gene (EnsEMBL)
  • Closest reference gene
  • Those distances should be less than maximum distance in each orthogroup.
• Cleaning Xenopus gene name to compatible to HGNC name: Remove ‘XXX-a/-b’, or ‘YYY.1/2/3’
• If human_name == trop_name, take that name.
• If human_name != trop_name,
  • If human_name is ‘NA’, take trop name
  • If trop_name is ‘unnamed’, take human name
  • If they have different ‘actual’ name, look at the distance from the query, and take the name of closest gene.

Second merging

• Assign gene name
  • http://daudin.icmb.utexas.edu/xenopus-pub/annot/201407_WorldCup/XENLA_UTA201407f_cdna_all.fa.gz
  • http://daudin.icmb.utexas.edu/xenopus-pub/annot/201407_WorldCup/XENLA_UTA201407f_prot_all.fa.gz

• Re-examine sequences with rules same as first merging step.
• If there is sequences overlapped, and assigned with same gene name, choose a sequence having longer CDS.
  • http://daudin.icmb.utexas.edu/xenopus-pub/annot/201407_WorldCup/XENLA_UTA201407f_cdna_longest.fa.gz
  • http://daudin.icmb.utexas.edu/xenopus-pub/annot/201407_WorldCup/XENLA_UTA201407f_prot_longest.fa.gz