The Lungfish Transcriptome: A Glimpse into Molecular Evolution Events at the Transition from Water to Land.
Maria Assunta Biscotti,Marco Gerdol,Adriana Canapa,Mariko Forconi,Ettore Olmo,Alberto Pallavicini,Marco Barucca,Manfred Schartl +7 more
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TLDR
It is indicated that lungfish, not coelacanths, are the closest relatives to land-adapted vertebrates and transposable elements appear to be active and show high diversity, suggesting a role for them in the remarkable expansion of the lungfish genome.Abstract:
Lungfish and coelacanths are the only living sarcopterygian fish. The phylogenetic relationship of lungfish to the last common ancestor of tetrapods and their close morphological similarity to their fossil ancestors make this species uniquely interesting. However their genome size, the largest among vertebrates, is hampering the generation of a whole genome sequence. To provide a partial solution to the problem, a high-coverage lungfish reference transcriptome was generated and assembled. The present findings indicate that lungfish, not coelacanths, are the closest relatives to land-adapted vertebrates. Whereas protein-coding genes evolve at a very slow rate, possibly reflecting a “living fossil” status, transposable elements appear to be active and show high diversity, suggesting a role for them in the remarkable expansion of the lungfish genome. Analyses of single genes and gene families documented changes connected to the water to land transition and demonstrated the value of the lungfish reference transcriptome for comparative studies of vertebrate evolution.read more
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Evolution and Diversity of Transposable Elements in Vertebrate Genomes.
TL;DR: The current understanding of vertebrate TE diversity and evolution is reviewed and the current bottleneck in genome analyses lies in the proper annotation of TEs and examples where superficial analyses led to misleading conclusions about genome evolution are provided.
Journal ArticleDOI
Transposons, Genome Size, and Evolutionary Insights in Animals.
TL;DR: The current situation represents a balance between insertion and amplification of transposons and the mechanisms responsible for their deletion or for decreasing their activity, and methylation and the silencing action of small RNAs likely represent the most frequent mechanisms.
Journal ArticleDOI
Rapid de novo assembly of the European eel genome from nanopore sequencing reads
Hans J. Jansen,Michael Liem,Susanne Jong-Raadsen,Sylvie Dufour,Finn-Arne Weltzien,W. Swinkels,Alex Koelewijn,Arjan P. Palstra,Bernd Pelster,Herman P. Spaink,Guido van den Thillart,Ron P. Dirks,Christiaan V. Henkel,Christiaan V. Henkel +13 more
TL;DR: The genome of the endangered European eel is sequenced using the MinION by Oxford Nanopore and assembled using a novel algorithm specifically designed for large eukaryotic genomes, improving on a previous draft based on short reads only.
Journal ArticleDOI
African lungfish genome sheds light on the vertebrate water-to-land transition.
Kun Wang,Jun Wang,Chenglong Zhu,Liandong Yang,Yandong Ren,Yandong Ren,Jue Ruan,Guangyi Fan,Jiang Hu,Wenjie Xu,X. J. Bi,Y. H. Zhu,Yue Song,Huatao Chen,Tiantian Ma,Ruoping Zhao,Haifeng Jiang,Bin Zhang,Chenguang Feng,Yuan Yuan,Xiaoni Gan,Yongxin Li,H.R. Zeng,Qun Liu,Yaolei Zhang,Feng Shao,Shijie Hao,He Zhang,Xun Xu,Xin Liu,De-Peng Wang,Min Zhu,Guojie Zhang,Wenming Zhao,Qiang Qiu,Shunping He,Wen Wang,Wen Wang +37 more
TL;DR: In this paper, the authors reported a 40-Gb chromosome-level assembly of the African lungfish (Protopterus annectens) genome, which is the largest genome assembly ever reported and has a contig and chromosome N50 of 1.60 mb and 2.81 Gb, respectively.
References
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