ArticleBMC genomics2013
Analysis of the transcriptome of the Indonesian coelacanth Latimeria menadoensis.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
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- A bioinformatic approach to characterize the vitellogenin receptor and the low density lipoprotein receptor superfamily in the newt Cynops orientalis.Scientific reports · 2025Article
- Investigation of the activity of transposable elements and genes involved in their silencing in the newt Cynops orientalis, a species with a giant genome.Scientific reports · 2021Article
- The transcriptome of the newt Cynops orientalis provides new insights into evolution and function of sexual gene networks in sarcopterygians.Scientific reports · 2020Article
- Identification of circRNAs in the Liver of Whitespotted Bamboo Shark (Frontiers in genetics · 2020Article
- A Comparison of the Innate and Adaptive Immune Systems in Cartilaginous Fish, Ray-Finned Fish, and Lobe-Finned Fish.Frontiers in immunology · 2019Review
- A Comparative View on Sex Differentiation and Gametogenesis Genes in Lungfish and Coelacanths.Genome biology and evolution · 2018Article
- Transcriptome of Pterospermum kingtungense provides implications on the mechanism underlying its rapid vegetative growth and limestone adaption.Scientific reports · 2017Article
- The small non-coding RNA processing machinery of two living fossil species, lungfish and coelacanth, gives new insights into the evolution of the Argonaute protein family.Genome biology and evolution · 2017Article
- Transcriptome sequencing and de novo characterization of Korean endemic land snail, Koreanohadra kurodana for functional transcripts and SSR markers.Molecular genetics and genomics : MGG · 2016Article
- The Lungfish Transcriptome: A Glimpse into Molecular Evolution Events at the Transition from Water to Land.Scientific reports · 2016Article
- De Novo Transcriptome Sequencing of Olea europaea L. to Identify Genes Involved in the Development of the Pollen Tube.TheScientificWorldJournal · 2016Article
- Transcriptome sequencing, annotation and polymorphism detection in the hop bush, Dodonaea viscosa.BMC genomics · 2015Article
- A De novo Transcriptomic Approach to Identify Flavonoids and Anthocyanins "Switch-Off" in Olive (Olea europaea L.) Drupes at Different Stages of Maturation.Frontiers in plant science · 2015Article
- circBase: a database for circular RNAs.RNA (New York, N.Y.) · 2014Article
- De novo transcriptome of Ischnura elegans provides insights into sensory biology, colour and vision genes.BMC genomics · 2014Article
- Genome complexity in the coelacanth is reflected in its adaptive immune system.Journal of experimental zoology. Part B, Molecular and developmental evolution · 2014Article
- De novo assembly and characterization of the transcriptome in the desiccation-tolerant moss Syntrichia caninervis.BMC research notes · 2014Article
- Interspecies insertion polymorphism analysis reveals recent activity of transposable elements in extant coelacanths.PloS one · 2014Article
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Authors and funding
15 authors.
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Abstract
backgroundLatimeria menadoensis is a coelacanth species first identified in 1997 in Indonesia, at 10,000 Km of distance from its African congener. To date, only six specimens have been caught and just a very limited molecular data is available. In the present work we describe the de novo transcriptome assembly obtained from liver and testis samples collected from the fifth specimen ever caught of this species.
resultsThe deep RNA sequencing performed with Illumina technologies generated 145,435,156 paired-end reads, accounting for ~14 GB of sequence data, which were de novo assembled using a Trinity/CLC combined strategy. The assembly output was processed and filtered producing a set of 66,308 contigs, whose quality was thoroughly assessed. The comparison with the recently sequenced genome of the African congener Latimeria chalumnae and with the available genomic resources of other vertebrates revealed a good reconstruction of full length transcripts and a high coverage of the predicted full coelacanth transcriptome.
conclusionGiven the high genomic affinity between the two coelacanth species, the here described de novo transcriptome assembly can be considered a valuable support tool for the improvement of gene prediction within the genome of L. chalumnae and a valuable resource for investigation of many aspects of tetrapod evolution.
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