Conversation
Species: Brachydesmus stygivagus Taxa: Diplopoda Project: ERGA-BGE
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Hi @fcamara7, thanks for sending the EAR of Brachydesmus stygivagus. |
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Hi @additive3, do you agree to supervise this assembly? |
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Hi @JoannaCollins, do you agree to review this assembly? |
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yes |
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Thanks for agreeing! |
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Hi @fcamara7, Happy New Year! I have taken a look at this assembly and there are some regions to edit which i have listed below. Looking also at the mq10 map I also think there is evidence that instead of 10 chromosomes, this assembly may have a karyotype of 5 and the following arms pair up: SUPER's 1 and 9, 2 and 4, 8 and 3, 6 and 5, and 7 and 10. Some of the unassembled repeat scaffolds can be used to pull the arms together. I am working on a map where i have started to pull the repeats together for which i will send you a savestate. This is the list of internal fixes: SUPER_2: 22.68-23.03 goes in the gap @ 18.68. 28.05-28.71 goes in the gap @ 27.79. 27.80-28.05 flips and goes in the gap @ 29.81 and then 29.81-30.45 flips. Then there should be a break @ 28.71 and from here to 29.79 flips. Then you can break scaffold_18 @ 1.98 flip and add this onto the end of the chr. There are a number of other repetitive scaffolds that you then look to join. SUPER_3: flip 8.70-9.18, 16.57-17.14 flips and goes in the gap @ 13.58. Break @ 14.36 and although there is no gap here it looks to me that the region 13.59-14.36 flips and places best @ ~12.76. Break @ 17.74 and flip. Break @ 19.39-19.47, this region belongs on SUPER_2 in the gap @ 18.67. 20.91-21.10 flips. 23.42-23.91 goes in the gap @ 22.31. Then flip 22.31-23.42 and 23.91-24.46 as one chunk. 24.48 to end looks to be part of the repeat that belongs on the end of SUPER_4. I would add scaffold_94 @ ~457. Scaffold_57 1.24-1.36 flips and goes in the gap @ 2.50. SUPER_4: flip 0-790, then break @ 1.80 and flip 0-790 and 791-1.79 as one chunk. Remove dup @ ~2.61-2.70. I would add scaffold_67 then 156 into the gap @ 19.56. Unassign 19.57-19.66 as matches multiple locations. SUPER_5: 8.68-8.87 goes in the gap @ 4.11. 4.12-4.31 flips. SUPER_6: 10.74-10.80 needs to be removed from where it is, but it matches at multiple locations so i would leave as unassigned. 14.33-15.54 belongs in the gap @ 10.74. 15.55-15.75 is part of the centromeric region and sits within other repeat scaffolds within this region. Scaffolds_82 and 91 are also part of the centromere. SUPER_7: 14.42-14.62 flips and joins @ 15.57. Then scaffold 16 needs to break @ 3.26, this piece flips and joins the end of SUPER_7. SUPER_8: 1.14-1.25 flips 1.60-2.29 flips. 1.61-2.49 goes in the gap @ 1.26. ~5.42-5.46 places @ 7.96. 7.97-8.17 flips. 11.83-12.52 flips. SUPER_9: 1.24-1.79 flips and goes in the gap @ 2.21. 10.59-11.81 goes in the gap @ 5.68. 7.09-7.54 flips. 7.55-7.66 flips. 7.92-8.11 flips and goes in the gap @ 8.97. 8.12-8.17 belongs on SUPER_8 in the gap @ 1.60. The whole region from 7.66-8.96 now flips. Then this whole chunk along with 8.10-10.08 goes in the gap @ 11.78. Then the region 10.09-10.26 needs to move to the gap @ 6.49. I would add scaffolds 110 followed by 115 flipped onto the end. SUPER_10: 5.60-7.30 needs to be moved to the gap @ 3.36 Please let me know if you have any questions Best Wishes Jo |
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These Myriapoda are pretty tricky.. I'm sharing a savestate (it is not txt file) with scaffold rearrangements as some chromosomes have many changes.. I also had a play about with the assignment of the repeat tail, which is a large proportion of the genome! Take a look, no need to include the repeat scaffold additions :) qdBraStyg.scrubbed_mq0.extensions.pretext.savestate_jmdw.txt |
Happy new year and thanks a lot for the detailed analysis and help with this one! I agree that the karyotype might indeed be five but without your pointing it out I am not sure I could have seen it...I will start working on the fixes asap and thanks for your help in trying to put the putative chromosome arms together. Best, Francisco |
thanks a lot for your help. Not easy indeed! |
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@fcamara7 @JoannaCollins |
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I have also got a savestate where i have tried to pull together as much a repeat as i can to try and span the arms. Its still quite messy through the repeats though. As such i think once you are happy with the assembly it will be worthwhile adding something to the comments section of the EAR detailing the span of the regions on each chromosome where order and orientation of scaffolds is unsure. qdBraStyg.scrubbed_mq0.extensions.pretext.savestate_1_jcc.txt |
Thanks a lot for the save_states and for the suggestions @JoannaCollins @additive3 . I will use @JoannaCollins save_state for now and make any further changes as suggested. I also agree with adding some extra information to the EAR report in this case... |
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@JoannaCollins thanks for the extensive modifications you made on the original save_state. I have had to put together chromosome arms for a beetle a few months ago also based on an mq10 map but in this case it was much harder to see the connections. I only did notice a signal when I joined some of the SUPER scaffolds on the mq10 as suggested by you. As for the save_state you shared with me, I sincerely was not so sure how to improve on it. I have tentatively moved most of the repeats to the first painted scaffold's centromeric region, but I guess I might as well have put them on other painted scaffold centromeres? |
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Good Morning @fcamara7, No problem re the modifications, glad it was useful :-). As Jo said this is a really tricky one. I took a look at the latest savestate you sent and it looks good, there were a few more small changes to make which i have made on the savestate attached and then marked with a waymarker so you can see what the change was. Re assigning repeats to the chrs to span the arms, this is difficult due to the nature of the sequence and the ambigous HIC signal. What you already had in your savestate I think looked fine for painted chrs 2-5, unfortunately it's impossible to refine these regions as much as we would like but i think what is placed is reasonable and gives you some representation of the repeat thats exists between the chromosome arms. As mentioned before definitely detail these regions as as regions of uncertainty in the EAR report. I spent a while playing about with and grouping the repeat scaffolds that had been placed in the centromeric region of the first painted scaffold. However having done this and placing what I could on this chr and other chrs I am not confident there is enough evidence to place all of the remaining data on this on this chr so you will see on the savestate attached that I have moved most of it out to be left as unassigned. Does this sound ok to you @additive3? If you are reasonably happy with what we have I think the next step would be to make the curated map and see what it all looks like in that to see if any further changes are required. Please ask if you have any further questions Best, Jo qdBraStyg.scrubbed_mq0.extensions.pretext.savestate_jcc_20_01_26.txt |
Thanks a lot for the extensive work you have put on this @JoannaCollins . I think there is no chance w would have been able to move forward with this one...Interestingly I will soon be submitting another diplopoda (Typhloglomeris coeca) that assembled extremely well...Anyway, I will be waiting for @additive3 comments before moving on with this one. Thanks again for your help! Best, Francisco |
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Do you have an update to the assembly?... new contact map or savestate and I can happily look @fcamara7 :) |
Hi @additive3 !, we currently have @JoannaCollins latest save_state (shared above). I have put it in the folder I point to in the EAR report. The changes made look good to me and I have not dared change it any further. |
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Ping @additive3, |
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I'll try to take a look at the updates tomorrow and see if we can sign this off |
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I would proceed with the jcc_20_01_26 savestate and remake the assembly, I think can sign off this assembly once done |
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Assembly review request