Submission TODO list

[KamilSJaron]

writing

• [x] write a cover letter
• [x] update reference list for figure 1
• [x] adjust gene loss section accoring to the comments in the doc
• [x] correct the analysis or explain in the text
• [x] figure cryptobiosis in ref33 (fix p34, comment by reviewer # 4)
• [x] integrate reviwers comments to TEs section
• [x] update references (the reference placeholder is {cit} with a pointer in the comment)
• [x] regenerate Supplementary figure 4 (TEs vs cellular mechanism)
• [x] polish Heterozygosity Structure section
• [x] remove the Panadrolaimus strains
• [x] fix box 2 figure or text. (central / terminal fusion are messy and reverted terminal... it's not clear at all... We should focus on consequences of inheritance)
• [x] polish the first Result paragraph (explanation why we have this strange hybrid between a review and research paper)
• [x] integrate reviwers comments to Palindrome section
• [x] S4 text - bdelloid rotifer genomics
• [x] update numbering for supplementary figures (they all shift by one; the main text needs to be adjusted appropriately)

computing

• [ ] linked HGT with SwissProt database
• [x] update all supplementary tables
• [x] figure out what is going to with A. ricciae dnaPipeTE analysis (#22 )
• [x] get dnaPipeTE of P. fallax (running)
• [x] regenerate Figure 4: TEs
• [x] redo dnaPipeTE of Mbel1 (#18)
• [x] get dnaPipeTE estimates of three honeybee genomes (#19 running)
• [x] tardigrade GenomeScope on filtered reads
• [x] est. number of palindromes in Mbel1 (me) (#18)

[KamilSJaron]

I just reordered the supplementary sections by the appearance in the text! I triple check every reference, but if you would spot something odd, don't hesitate to report it.