This week we have worked on the annotation of genes and their expression (transcriptomics).

Based on the information from the genome publication article:

(a) What strategies were used to annotate the genome? Was any ab initio search performed? What program(s) was/were used? Were there any searches for homology with a nearby species? Which one? Were expression data used? What type? If expression data were obtained, which developmental stages of the organism were analyzed? Which tissues? Do you think the results obtained provide a complete picture of the species’ transcriptional expression?

(b) Based on the annotation strategy followed, which functional regions of genes (e.g., coding exons, UTRs, etc.) do you think are annotated in the genome, and which ones are not?

(c) Was an attempt made to determine the function of the annotated genes or some of them? How was it done?

(d) Were non-coding genes annotated? What type? How many were detected?

(e) Were attempts made to determine the transcription factor binding sites?

(f) Is this genome available for graphical consultation in a genome browser? If so, indicate which one and provide the corresponding link.

(g) Based on what you know about your genome, do you think gene annotation was difficult? What level of confidence do you have in the obtained result? Justify your answer.