I should have clarified. The part of the genome we were annotating was on the right, so I focused more on that, but there are also gaps in the middle and on the left.
Possibly due to a shared evolutionary history and the selective pressure of needing to survive and infect the same host. These ncRNAs could have provided tools to help do that. Of course, more investigation would be necessary to prove any of that, which is what we would need the RNA-Seq and such for.
Just an evolutionary need. ncRNAs serve various necessary roles, like structure and translational roles. Another really important set of roles is post-transcriptional gene regulation via splicing and even degradation if something goes wrong, so I suppose necessity is the mother of evolution ¯_(ツ)_/¯
curesymposium.org 
Why do you think all the gaps were on the right-hand side of the genome?
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I should have clarified. The part of the genome we were annotating was on the right, so I focused more on that, but there are also gaps in the middle and on the left.
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What do you think is likely the reason that this ncRNA sequence was conserved in these 3 subclusters?
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Possibly due to a shared evolutionary history and the selective pressure of needing to survive and infect the same host. These ncRNAs could have provided tools to help do that. Of course, more investigation would be necessary to prove any of that, which is what we would need the RNA-Seq and such for.
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What causes these ncRNA’s to evolve separately from normal RNA’s?
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Just an evolutionary need. ncRNAs serve various necessary roles, like structure and translational roles. Another really important set of roles is post-transcriptional gene regulation via splicing and even degradation if something goes wrong, so I suppose necessity is the mother of evolution ¯_(ツ)_/¯
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