A nice review of my 2015 Coffee Beetle paper in GenomeWeb today.
My genome had 163 million bases and 19,222 predicted protein-coding genes. I am very pleased to learn that a revised version of the draft genome sequence (from a group in Columbia) contains 160 million bases and 22,000 gene models. They also confirm the 12 horizontally transferred genes that I identified.
Coffee Pest, Plant Genomes Presented at PAG Conference
Researchers from the USDA's Agricultural Research Service, New York
University, King Abdullah University of Science and Technology, and
elsewhere published information on a 163 million base draft genome for the coffee berry borer in the journal Scientific Reports in 2015.
genome assembly, produced with Illumina HiSeq 2000 reads, housed
hundreds of small RNAs and an estimated 19,222 protein-coding genes,
including enzymes, receptors, and transporters expected to contribute to
coffee plant predation, pesticide response, and defense against
potential pathogens. It also provided evidence of horizontal gene
transfer involving not only mannanase, but several other bacterial genes
At the annual Plant and Animal Genomes meeting here this week, National
Center for Coffee Research (Cenicafe) scientist Lucio Navarro provided
an update on efforts to sequence and interpret the coffee berry borer
genome during a session on coffee genomics. For their own recent analyses, Navarro and his
colleagues upgraded an earlier version of a coffee berry borer genome
that had been generated by Roche 454 FLX sequencing, using Illumina
short reads from male and female coffee berry borers to produce a
consensus assembly spanning around 160 million bases. The assembly is
believed to represent roughly 96 percent of the insect's genome.
addition to producing a genome with improved contiguity levels, he
reported, members of that team also combined 454 and Illumina reads to
get consensus transcriptomes for the beetle. With these and other data,
they identified almost 22,000 gene models, novel transposable element
families, and their own evidence of horizontal gene transfer.
Choice of workflow leads to wide variation in gene expression results - RNA-Seq has supplanted microarrays as the preferred method of transcriptome-wide identification of differentially expressed genes. However, RNA-Seq analysi...
12 hours ago