De novo genome assembly question: which assembly should I use?

[tarias]

I have sequenced two individuals and done three libraries per individual each with a different insert size (170, 500, 800).Using flow citometry I know this genome is 332MB. Also I know is diploid and the genetic variation is not to high. I have done different assemblies for a this plant genome and found this two were the best:

One Individual
3 libraries
Insert size 170, 500, 800
Number of clean reads 70,287,710
Number of contigs 134,557
Mean N50 length (bp) 5,050
BUSCO 78.54


Two Individuals
2 individuals
6 libraries
Insert size 170, 500, 800
Number of clean reads 209,022,970
Number of contigs 446,608
Mean N50 length (bp) 4,010.65
BUSCO 76.38

I then ran PEP_SCAFFOLDER in this two alignments and got this

One Individual
3 libraries

Main genome scaffold total: 136339
Main genome scaffold sequence total: 189.946 MB
Main genome contig N/L50: 17091/2.413 KB

Two Individuals
2 individuals
6 libraries

Main genome scaffold total: 444336
Main genome scaffold sequence total: 332.652 MB
Main genome contig N/L50: 83374/706

I have two questions:
1. Would you annotate any of these two genomes?
2. Which one would you annotate and why?

Thanks,
Tatiana

[ctseto]

Annotation may reveal what's not there, esp if you know from exp that a given gene is present (eg someone PCR/subcloned ). Guessing eukaryote and that you may have hit some contigs that are repeat heavy (eg contig is pure repeat), and perhaps that your library isn't traversing those repeats?