Satellitome Analysis of Adalia bipunctata (Coleoptera): Revealing Centromeric Turnover and Potential Chromosome Rearrangements in a Comparative Interspecific Study
Abstract
:1. Introduction
2. Results and Discussion
2.1. Adalia bipunctata Satellitome Description
2.2. SatDNA Location in Adalia bipunctata Chromosomes by FISH and CHRISMAPP
2.3. Satellitome Representation in the Adalia bipunctata Genome Assembly
2.4. Comparative Analysis with Adalia decempunctata
3. Materials and Methods
3.1. Insects, Preparation of Chromosome Spreads, and C-Banding
3.2. Satellitome Analysis
3.3. Cytogenetic Mapping by Fluorescence In Situ Hybridization (FISH) and by Chromosome In Silico Mapping (CHRISMAPP) and Synteny Analysis
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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SatDNA Families | % A+T | Illumina Reads | Genome Assembly | ||
---|---|---|---|---|---|
Genome (%) | Divergence (Kimura-2p) | Chromosomes (%) | Chromosomes + Unplaced Scaffolds (%) | ||
AbipSat01-187 | 70.1 | 9.9808 | 7.91 | 3.2895 | 7.0636 |
AbipSat02-497 | 64.8 | 1.6789 | 15.99 | 1.8672 | 1.7659 |
AbipSat03-8 | 87.5 | 0.3864 | 2.57 | 0.2758 | 0.5723 |
AbipSat04-193 | 55.4 | 0.2678 | 6.62 | 0.2257 | 0.2134 |
AbipSat05-258 | 65.9 | 0.2383 | 6.91 | 0.2325 | 0.2199 |
AbipSat06-176 | 74.4 | 0.2328 | 7.01 | 0.0019 | 0.1960 |
AbipSat07-579 | 63.4 | 0.1054 | 6.22 | 0.1396 | 0.1323 |
AbipSat08-316 | 64.9 | 0.1017 | 8.56 | 0.1349 | 0.1276 |
AbipSat09-473 | 68.7 | 0.0916 | 18.10 | 0.1705 | 0.1613 |
AbipSat10-1902 | 57.1 | 0.0874 | 1.52 | 0.1012 | 0.1100 |
AbipSat11-151 | 62.3 | 0.0816 | 9.31 | 0.1029 | 0.0976 |
AbipSat12-233 | 62.2 | 0.0810 | 2.16 | 0.0268 | 0.0254 |
AbipSat13-1767 | 66.3 | 0.0799 | 7.13 | 0.1924 | 0.1823 |
AbipSat14-53 | 73.6 | 0.0751 | 3.25 | 0.0001 | 0.0008 |
AbipSat15-179 | 65.4 | 0.0712 | 17.93 | 0.0957 | 0.0905 |
AbipSat16-443 | 56.7 | 0.0660 | 10.05 | 0.0946 | 0.0920 |
AbipSat17-86 | 69.8 | 0.0642 | 22.80 | 0.0826 | 0.0781 |
AbipSat18-14 | 64.3 | 0.0636 | 6.85 | 0.0664 | 0.0641 |
AbipSat19-1237 | 63.3 | 0.0618 | 3.28 | 0.1174 | 0.1110 |
AbipSat20-176 | 61.9 | 0.0550 | 10.94 | 0.0540 | 0.0543 |
AbipSat21-1899 | 65.4 | 0.0537 | 8.61 | 0.0796 | 0.0759 |
AbipSat22-148 | 57.4 | 0.0527 | 4.00 | 0.0455 | 0.0431 |
AbipSat23-376 | 58.8 | 0.0474 | 11.11 | 0.1068 | 0.1024 |
AbipSat24-5-TEL | 60.0 | 0.0434 | 3.63 | 0.0068 | 0.0137 |
AbipSat25-176 | 63.6 | 0.0416 | 18.96 | 0.0369 | 0.0349 |
AbipSat26-2235 | 60.1 | 0.0398 | 3.47 | 0.0549 | 0.0544 |
AbipSat27-84 | 61.9 | 0.0352 | 23.48 | 0.0007 | 0.0006 |
AbipSat28-165 | 67.9 | 0.0330 | 16.69 | 0.0432 | 0.0408 |
AbipSat29-174 | 64.9 | 0.0282 | 23.19 | 0.0369 | 0.0349 |
AbipSat30-212 | 59.0 | 0.0278 | 21.05 | 0.0047 | 0.0057 |
AbipSat31-145 | 63.4 | 0.0241 | 8.06 | 0.0353 | 0.0335 |
AbipSat32-163 | 60.1 | 0.0237 | 8.55 | 0.0310 | 0.0321 |
AbipSat33-284 | 62.7 | 0.0228 | 11.54 | 0.0339 | 0.0322 |
AbipSat34-137 | 70.1 | 0.0223 | 10.47 | 0.0354 | 0.0337 |
AbipSat35-141 | 56.0 | 0.0218 | 4.68 | 0.0167 | 0.0158 |
AbipSat36-157 | 47.8 | 0.0194 | 4.49 | 0.0364 | 0.0345 |
AbipSat37-297 | 65.3 | 0.0153 | 11.24 | 0.0221 | 0.0209 |
AbipSat38-2435 | 58.2 | 0.0141 | 4.60 | 0.0210 | 0.0204 |
AbipSat39-159 | 60.4 | 0.0132 | 6.50 | 0.0103 | 0.0097 |
AbipSat40-152 | 61.8 | 0.0131 | 11.87 | 0.0109 | 0.0105 |
AbipSat41-69 | 53.6 | 0.0117 | 4.52 | 0.0069 | 0.0067 |
AbipSat42-21 | 61.9 | 0.0116 | 18.70 | 0.0330 | 0.0313 |
AbipSat43-282 | 69.9 | 0.0111 | 7.37 | 0.0086 | 0.0092 |
AbipSat44-148 | 56.8 | 0.0110 | 8.71 | 0.0138 | 0.0130 |
AbipSat45-307 | 64.5 | 0.0109 | 5.95 | 0.0088 | 0.0083 |
AbipSat46-126 | 50.8 | 0.0089 | 2.36 | 0.0061 | 0.0058 |
AbipSat47-399 | 60.7 | 0.0080 | 5.88 | 0.0162 | 0.0153 |
AbipSat48-18 | 50.0 | 0.0080 | 7.15 | ND | ND |
AbipSat49-148 | 60.8 | 0.0075 | 8.48 | 0.0091 | 0.0086 |
AbipSat50-199 | 55.8 | 0.0072 | 12.04 | 0.0042 | 0.0040 |
AbipSat51-128 | 60.9 | 0.0071 | 4.80 | 0.0055 | 0.0052 |
AbipSat52-177 | 66.7 | 0.0064 | 8.37 | 0.0089 | 0.0084 |
AbipSat53-22 | 50.0 | 0.0059 | 15.97 | 0.0035 | 0.0033 |
AbipSat54-271 | 65.3 | 0.0058 | 6.28 | 0.0002 | 0.00350 |
AbipSat55-145 | 62.1 | 0.0054 | 4.12 | 0.0085 | 0.0082 |
AbipSat56-30 | 46.7 | 0.0051 | 9.38 | ND | ND |
AbipSat57-144 | 58.3 | 0.0049 | 14.89 | 0.0040 | 0.0039 |
AbipSat58-518 | 60.0 | 0.0047 | 7.88 | 0.0060 | 0.0062 |
AbipSat59-105 | 55.2 | 0.0039 | 1.37 | 0.0030 | 0.0026 |
AbipSat60-160 | 60.0 | 0.0038 | 3.13 | 0.0020 | 0.0020 |
AbipSat61-175 | 68.0 | 0.0038 | 8.32 | 0.0070 | 0.0064 |
AbipSat62-144 | 55.6 | 0.0037 | 2.52 | 0.0020 | 0.0019 |
AbipSat63-186 | 61.8 | 0.0031 | 4.08 | 0.0020 | 0.0017 |
AbipSat64-201 | 62.2 | 0.0031 | 5.24 | 0.0020 | 0.0023 |
AbipSat65-286 | 59.1 | 0.0029 | 5.91 | 0.0040 | 0.0036 |
AbipSat66-169 | 62.1 | 0.0028 | 1.26 | ND | ND |
AbipSat67-304 | 67.8 | 0.0027 | 2.01 | 0.0020 | 0.0019 |
AbipSat68-237 | 54.9 | 0.0025 | 6.66 | 0.0006 | 0.0006 |
AbipSat69-438 | 63.5 | 0.0025 | 2.03 | 0.0020 | 0.0019 |
AbipSat70-168 | 56.0 | 0.0024 | 3.23 | 0.0009 | 0.0008 |
AbipSat71-438 | 61.9 | 0.0023 | 1.93 | 0.0012 | 0.0011 |
AbipSat72-426 | 64.1 | 0.0022 | 2.45 | 0.0019 | 0.0018 |
AbipSat73-396 | 71.0 | 0.0020 | 7.27 | 0.0012 | 0.0011 |
AbipSat74-344 | 61.0 | 0.0019 | 7.28 | 0.0023 | 0.0022 |
AbipSat75-471 | 61.6 | 0.0019 | 7.51 | 0.0011 | 0.0011 |
AbipSat76-140 | 76.4 | 0.0018 | 4.76 | 0.0006 | 0.0005 |
AbipSat77-155 | 54.8 | 0.0018 | 4.58 | 0.0024 | 0.0022 |
AbipSat78-399 | 63.9 | 0.0017 | 4.18 | 0.0021 | 0.0020 |
AbipSat79-309 | 67.0 | 0.0017 | 1.39 | 0.0034 | 0.0032 |
AbipSat80-337 | 57.3 | 0.0016 | 3.51 | 0.0019 | 0.0018 |
AbipSat81-258 | 66.7 | 0.0016 | 3.95 | 0.0006 | 0.0005 |
AbipSat82-291 | 59.8 | 0.0014 | 2.87 | 0.0009 | 0.0008 |
AbipSat83-191 | 64.9 | 0.0012 | 0.93 | 0.0009 | 0.0008 |
AbipSat84-169 | 52.7 | 0.0011 | 0.57 | 0.0005 | 0.0004 |
AbipSat85-284 | 65.1 | 0.0011 | 5.45 | 0.0010 | 0.0009 |
AbipSat86-294 | 61.9 | 0.0009 | 3.25 | 0.0016 | 0.0015 |
Satellite proportion | 14.6677 | 8.1351 | 12.1966 |
SatDNA Family | Oligonucleotide Name | Sequence |
---|---|---|
AbipSat01-187 | Abip-CL1-F | ACTGCTGTGAATAATCGG |
Abip-CL1-R | GACTTTTTGATCTGAGGG | |
AbipSat02-497 | Abip-CL4-F | AATATGGTGTTTTTGGGG |
Abip-CL4-R | TTTCACCTGTCAAATGGC | |
AbipSat03-8 | AbipCL-13 | GTCAAATGTCATCTGTCAAA |
AbipSat04-193 | Abip-CL46-F | CAAATTTTTTCTCTTCGC |
Abip-CL46-R | ACCATGCATGCTGTATTG | |
AbipSat05-258 | Abip-CL42-F | TTTCGAAAAATTATATTCC |
Abip-CL42-R | CTTTGTAGCTCAATTGTTC | |
AbipSat06-176 | Abip-CL46-RE2-F | AACGAATTCCACCAAGGG |
Abip-CL46-RE2-R | TCGTTCAAGTAGCCGAGC |
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Mora, P.; Rico-Porras, J.M.; Palomeque, T.; Montiel, E.E.; Pita, S.; Cabral-de-Mello, D.C.; Lorite, P. Satellitome Analysis of Adalia bipunctata (Coleoptera): Revealing Centromeric Turnover and Potential Chromosome Rearrangements in a Comparative Interspecific Study. Int. J. Mol. Sci. 2024, 25, 9214. https://doi.org/10.3390/ijms25179214
Mora P, Rico-Porras JM, Palomeque T, Montiel EE, Pita S, Cabral-de-Mello DC, Lorite P. Satellitome Analysis of Adalia bipunctata (Coleoptera): Revealing Centromeric Turnover and Potential Chromosome Rearrangements in a Comparative Interspecific Study. International Journal of Molecular Sciences. 2024; 25(17):9214. https://doi.org/10.3390/ijms25179214
Chicago/Turabian StyleMora, Pablo, José M. Rico-Porras, Teresa Palomeque, Eugenia E. Montiel, Sebastián Pita, Diogo C. Cabral-de-Mello, and Pedro Lorite. 2024. "Satellitome Analysis of Adalia bipunctata (Coleoptera): Revealing Centromeric Turnover and Potential Chromosome Rearrangements in a Comparative Interspecific Study" International Journal of Molecular Sciences 25, no. 17: 9214. https://doi.org/10.3390/ijms25179214