The third de novo sequenced genome in our series Whose genome has been sequenced? is the “living fossil” Latimera chalumnae.
The most difficult part for this de novo genome sequencing approach was to get enough starting material. The authors even reported that their first approach was to use the Sanger technology, but is simply was not enough DNA available. Therefore they had to wait until the next generation sequencing techniques were stable enough to risk the sequencing (BioTechniques). Here are the sequencing facts of this study (Amemiya et al.):
What was sequenced?
A blood sample from an adult African coelacanth
De novo sequencing strategy:
- Libraries: shotgun library 61-fold coverage; 3 kb jumping library – 88-fold coverage, 40 kb fosmid library 1-fold coverage
- Illumina HiSeq 2000 (paired-end module)
- De novo genome assembly using the software ALLPATHS-LG
- RNA sequencing
RNA-Seq sequencing strategy:
- 4 cDNA libraries (1x mRNA-Seq library, 3x strand specific dUTP libraries from brain, gonad/kidney, gut/liver tissue) were sequenced using a HiSeq
- Data output: mRNA-Seq library ~ 210M paired-end reads; dUTP libarires ~ 3-4 Gb of sequence/tissue
- Assembly was performed using Trinity
The genome sequencing helped to understand the possibility of this prehistoric fish to thrive on dry land and the phenotype that is so similar to 300 million year old fossils (BioTechniques).
Read the complete publication here.
Earlier published genomes: Goat genome (Capra hircus); Chickpea plant (Cicer arietinum)