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+[[!meta title="Maternal and zygotic transcriptomes in the appendicularian, Oikopleura dioica: novel protein-encoding genes, intra-species sequence variations, and trans-spliced RNA leader."]]
+[[!tag Oikopleura trans-splicing]]
+
+Wang K, Omotezako T, Kishi K, Nishida H, Onuma TA.
+
+Dev Genes Evol. 2015 Jun;225(3):149-59. doi:10.1007/s00427-015-0502-7
+
+Maternal and zygotic transcriptomes in the appendicularian, Oikopleura dioica: novel protein-encoding genes, intra-species sequence variations, and trans-spliced RNA leader.
+
+[[!pmid 26032664 desc="Only one splice leader was found and it was identical to the one reported by Ganot. “Samples were prepared from cohorts of a single pair.” “The transcript sequences showed a high degree of variability between the Japanese and Norwegian O. dioica populations. The average degrees of nucleotide and amino acid sequence conservation were 91.0 and 94.8 %, respectively.” “In the present analysis, the SL was observed in 40.8 % of mRNA species. It showed preferential linkage to adenine at the 5′ ends of the downstream exons. Intriguingly, the trans-splicing occurs more frequently in eggs than in larvae.” “Among the 12,311 assembled transcripts, 63 and 99 % were detected in eggs and larvae, respectively. Thus, the mRNAs of most of genes are present at the developing larval stage. In this quick developer, it is most probable that residual maternal mRNAs are still preserved in 8 hpf larvae.” “The raw data were deposited in the National Center for Biotechnology Information (NCBI) Short Read Archive (SRP accession number: SRP050571, run accession numbers are SRR1693762, SRR1693765, SRR1693766, and SRR1693767) and Gene Expression Omnibus (GEO accession: GSE64421).”"]]

diff --git a/tags/Oikopleura.mdwn b/tags/Oikopleura.mdwn
index 9eca5a9916ee6e70cdb5f0be01f35faef59b6d42..970284980e9f30d58d8e5e64c00135cd613e1b43 100644 (file)
--- a/tags/Oikopleura.mdwn
+++ b/tags/Oikopleura.mdwn
@@ -105,6 +105,9 @@ Genome
    “Spots of sequence ultraconservation are almost systematically located
    in non coding regions, including introns that are larger than average
    in such genes than in others.” ([[Denoeud et al., 2010|biblio/21097902]]).
+ - Transcriptome comparisons between Atlantic and Pacific strains showed
+   nucleotide and amino acid sequence similarities of 91.0 and 94.8 %,
+   respectively ([[Wang and coll., 2015|biblio/26032664]]).
 
 
 Genes and pathways
@@ -134,6 +137,7 @@ Genes and pathways
    ([[Torres-Águila and coll., 2018|biblio/30272001]]).
  - _O. dioica_ has 83 homeobox genes, according to [[Edvardsen and coll., 2005|biblio/15649342]].
 
+
 Transcriptome
 -------------
 
@@ -142,8 +146,12 @@ Transcriptome
    The SL gene is found downstream of the 5S RNA gene, which is repeated multiple
    times in the genome.  The 3′ acceptor site has a strong UUU(C/U/A)AG consensus
    ([[Ganot et al., 2004|biblio/15314184]]).
+ - The splice leader found in the Norwegian strain by ([[Ganot et al., 2004|biblio/15314184]])
+   was found indentical in a Japanese strain by ([[Wang and coll., 2015|biblio/26032664]]).
  - A study using CAGE found that 39% of annotated gene models are trans-spliced with the
    SL and that 42% of SL transcripts are monocistronic ([[Danks et al., 2015|biblio/25525214]]).
+ - Embryonic RNAs are more trans-spliced than larval RNAs ([[Danks et al., 2015|biblio/25525214]],
+   [[Wang and coll., 2015|biblio/26032664]]).
  - A `TCTAGA` promoter element is found in 73.5% of the non-trans-spliced genes detected with
    CAGE in testis ([[Danks et al, 2018|biblio/29482522]]).
  - Introns are very small (peak at 47 base pairs, 2.4% > 1 kb, [[Denoeud et