2015
DOI: 10.1016/j.margen.2015.05.014
|View full text |Cite
|
Sign up to set email alerts
|

De novo transcriptome of the European brittle star Amphiura filiformis pluteus larvae

Help me understand this report

Search citation statements

Order By: Relevance

Paper Sections

Select...
2
1
1
1

Citation Types

3
22
1

Year Published

2016
2016
2024
2024

Publication Types

Select...
7
1

Relationship

2
6

Authors

Journals

citations
Cited by 26 publications
(26 citation statements)
references
References 84 publications
(112 reference statements)
3
22
1
Order By: Relevance
“…In this sense, the lack of homology with known proteins could be explained by biological reasons such as: i) the lack of annotated protein sequences of phylogenetically close species; ii) sequences from untranslated regions (UTR) of mRNA; iii) long noncoding RNA; and iv) orphan proteins38. These results are congruent to those reported for the transcriptome of the sea urchin S. intermedius 39, the sea star Acanthaster planci 14 and the brittle star Amphiura filiformis 40.…”
Section: Discussionsupporting
confidence: 63%
“…In this sense, the lack of homology with known proteins could be explained by biological reasons such as: i) the lack of annotated protein sequences of phylogenetically close species; ii) sequences from untranslated regions (UTR) of mRNA; iii) long noncoding RNA; and iv) orphan proteins38. These results are congruent to those reported for the transcriptome of the sea urchin S. intermedius 39, the sea star Acanthaster planci 14 and the brittle star Amphiura filiformis 40.…”
Section: Discussionsupporting
confidence: 63%
“…It shows a decreasing number of transcripts with longer sequences. A high percentage of short transcripts (>299 bp) is present but seems unavoidable, as it is the case for other transcriptome assemblies too (Du et al, 2012;Delroisse et al, 2015). The graph representing the length distribution of unigenes presents the same pattern (not shown).…”
Section: Discussionmentioning
confidence: 75%
“…From these unigenes, 60,439 (~34%) were blasted to known proteins in the public databases NCBI (nr) and UniProt (Swiss‐Prot and TrEMBL), while 116,446 (~66%) had no matches and may represent: (1) specific unigenes of M. franciscanus with unknown function; (2) sequences with low similarity to those compared in public databases; and/or (3) chimeric sequences. Although the percentage of unigenes with a BLAST‐hit may appear to be relatively low, we found that the number of unigenes with significant alignments (≤1 e −5 ) to known proteins in M. franciscanus is higher than those reported in other studies with nonmodel echinoderms (Delroisse et al., 2015; Dilly et al., 2015; Gaitán‐Espitia, et al, 2016; Gillard, Garama, & Brown, 2014; Pérez‐Portela, Turon, & Riesgo, 2016; Stewart, Stewart, & Rivera‐Posada, 2015; Vaughn, Garnhardt, Garey, Thomas, & Livingston, 2012; Zhou et al., 2014). Most of the annotated unigenes hit against the purple sea urchin Strongylocentrotus purpuratus (88.4%), followed by the acorn worm Saccoglossus kowalevskii (1.5%), and the Pacific oyster Crassostrea gigas (<1%; Fig.…”
Section: Resultsmentioning
confidence: 99%
“…However , thanks to the advances in next‐generation sequencing (NGS) technologies, the ability to sequence the entire transcriptome of a given tissue or life‐history stage in a matter of days is providing new opportunities to explore the complexity of developmental GRNs in other echinoderms (Delroisse, Ortega‐Martinez, Dupont, Mallefet, & Flammang, 2015; Dilly, Gaitán‐Espitia, & Hofmann, 2015; Dylus et al., 2016; Gildor, Malik, Sher, Avraham, & Ben‐Tabou de‐Leon, 2015; Tulin, Aguiar, Istrail, & Smith, 2013) and marine invertebrates (Jackson & Degnan, 2016; Layden, Rentzsch, & Röttinger, 2016). As changes in gene expression may underlie many of the phenotypic differences between species (Brawand et al., 2011), studying transcriptomic divergence of sympatric species may shed light upon the initial genetic targets of natural selection in speciation events (Filteau, Pavey, St‐Cyr, & Bernatchez, 2013).…”
Section: Introductionmentioning
confidence: 99%