High-Density Genetic Linkage Map of the Southern Blue-ringed Octopus (Octopodidae: <i>Hapalochlaena maculosa</i>)
Genetic linkage maps provide a useful resource for non-model genomes and can aid in genome reassembly to form more contiguous pseudo-chromosomes. We present the first linkage map of any cephalopod, <i>H. maculosa</i>, composed of 47 linkage groups (LG). A total of 2166 single nucleotide...
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MDPI AG
2022-12-01
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| Online Access: | https://www.mdpi.com/1424-2818/14/12/1068 |
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| author | Brooke L. Whitelaw David B. Jones Jarrod Guppy Peter Morse Jan M. Strugnell Ira R. Cooke Kyall Zenger |
| author_facet | Brooke L. Whitelaw David B. Jones Jarrod Guppy Peter Morse Jan M. Strugnell Ira R. Cooke Kyall Zenger |
| author_sort | Brooke L. Whitelaw |
| collection | DOAJ |
| description | Genetic linkage maps provide a useful resource for non-model genomes and can aid in genome reassembly to form more contiguous pseudo-chromosomes. We present the first linkage map of any cephalopod, <i>H. maculosa</i>, composed of 47 linkage groups (LG). A total of 2166 single nucleotide polymorphisms and 2455 presence–absence variant loci were utilised by Lep-Map3 in linkage map construction. The map length spans 2016.62 cM with an average marker distance of 0.85 cM. Integration of the recent <i>H. maculosa</i> genome allowed 1151 scaffolds comprising 34% of the total genomic sequence to be orientated and/or placed using 1278 markers across all 47 LG. The linkage map generated provides a new perspective on HOX gene distribution in octopods. In the <i>H. maculosa</i> linkage map three (SCR, LOX4 and POST1) of six identified HOX genes (HOX1/LAB, SCR, LOX2, LOX4, LOX5, POST1) were located within the same LG (LG 9). The generation of a linkage map for <i>H. maculosa</i> has provided a valuable resource for understanding the evolution of cephalopod genomes and will provide a base for future work. |
| first_indexed | 2024-03-09T17:07:23Z |
| format | Article |
| id | doaj.art-691ef26fc0eb4431b321851096f8caca |
| institution | Directory Open Access Journal |
| issn | 1424-2818 |
| language | English |
| last_indexed | 2024-03-09T17:07:23Z |
| publishDate | 2022-12-01 |
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| spelling | doaj.art-691ef26fc0eb4431b321851096f8caca2023-11-24T14:23:01ZengMDPI AGDiversity1424-28182022-12-011412106810.3390/d14121068High-Density Genetic Linkage Map of the Southern Blue-ringed Octopus (Octopodidae: <i>Hapalochlaena maculosa</i>)Brooke L. Whitelaw0David B. Jones1Jarrod Guppy2Peter Morse3Jan M. Strugnell4Ira R. Cooke5Kyall Zenger6Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD 4811, AustraliaCentre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD 4811, AustraliaCentre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD 4811, AustraliaCentre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD 4811, AustraliaCentre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD 4811, AustraliaCollege of Public Health, Medical and Vet Sciences, James Cook University, Townsville, QLD 4811, AustraliaCentre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD 4811, AustraliaGenetic linkage maps provide a useful resource for non-model genomes and can aid in genome reassembly to form more contiguous pseudo-chromosomes. We present the first linkage map of any cephalopod, <i>H. maculosa</i>, composed of 47 linkage groups (LG). A total of 2166 single nucleotide polymorphisms and 2455 presence–absence variant loci were utilised by Lep-Map3 in linkage map construction. The map length spans 2016.62 cM with an average marker distance of 0.85 cM. Integration of the recent <i>H. maculosa</i> genome allowed 1151 scaffolds comprising 34% of the total genomic sequence to be orientated and/or placed using 1278 markers across all 47 LG. The linkage map generated provides a new perspective on HOX gene distribution in octopods. In the <i>H. maculosa</i> linkage map three (SCR, LOX4 and POST1) of six identified HOX genes (HOX1/LAB, SCR, LOX2, LOX4, LOX5, POST1) were located within the same LG (LG 9). The generation of a linkage map for <i>H. maculosa</i> has provided a valuable resource for understanding the evolution of cephalopod genomes and will provide a base for future work.https://www.mdpi.com/1424-2818/14/12/1068enetic linkageHapalochlaenagenome evolutioncephalopodsHOX genes |
| spellingShingle | Brooke L. Whitelaw David B. Jones Jarrod Guppy Peter Morse Jan M. Strugnell Ira R. Cooke Kyall Zenger High-Density Genetic Linkage Map of the Southern Blue-ringed Octopus (Octopodidae: <i>Hapalochlaena maculosa</i>) Diversity enetic linkage Hapalochlaena genome evolution cephalopods HOX genes |
| title | High-Density Genetic Linkage Map of the Southern Blue-ringed Octopus (Octopodidae: <i>Hapalochlaena maculosa</i>) |
| title_full | High-Density Genetic Linkage Map of the Southern Blue-ringed Octopus (Octopodidae: <i>Hapalochlaena maculosa</i>) |
| title_fullStr | High-Density Genetic Linkage Map of the Southern Blue-ringed Octopus (Octopodidae: <i>Hapalochlaena maculosa</i>) |
| title_full_unstemmed | High-Density Genetic Linkage Map of the Southern Blue-ringed Octopus (Octopodidae: <i>Hapalochlaena maculosa</i>) |
| title_short | High-Density Genetic Linkage Map of the Southern Blue-ringed Octopus (Octopodidae: <i>Hapalochlaena maculosa</i>) |
| title_sort | high density genetic linkage map of the southern blue ringed octopus octopodidae i hapalochlaena maculosa i |
| topic | enetic linkage Hapalochlaena genome evolution cephalopods HOX genes |
| url | https://www.mdpi.com/1424-2818/14/12/1068 |
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