Journal of Marine Life Science (한국해양생명과학회지)

The Korean Society of Marine Life Science (한국해양생명과학회)
권호 표지
DOI QR코드

DOI QR Code

Chromosomal Assembly of Tegillarca granosa Genome using Third-generation DNA Sequencing and Hi-C Technology

3세대 DNA 염기서열 분석과 Hi-C기술을 이용한 꼬막 게놈의 유전체 연구

  • Kim, Jinmu (Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University) ;
  • Lee, Seung Jae (Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University) ;
  • Jo, Euna (Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University) ;
  • Choi, Eunkyung (Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University) ;
  • Cho, Minjoo (Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University) ;
  • Shin, So Ryung (Department of Aqualife Medicine, Chonnam National University) ;
  • Lee, Jung Sick (Department of Aqualife Medicine, Chonnam National University) ;
  • Park, Hyun (Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University)
  • 김진무 (고려대학교 생명공학과) ;
  • 이승재 (고려대학교 생명공학과) ;
  • 조은아 (고려대학교 생명공학과) ;
  • 최은경 (고려대학교 생명공학과) ;
  • 조민주 (고려대학교 생명공학과) ;
  • 신소령 (전남대학교 수산생명의학과) ;
  • 이정식 (전남대학교 수산생명의학과) ;
  • 박현 (고려대학교 생명공학과)
  • Received : 2021.11.18
  • Accepted : 2021.11.25
  • Published : 2021.12.15
Download PDF
⟨ Previous Next ⟩

Abstract

Tegillarca granosa, is one of the most important fishery resources throughout Asia. However, due to industrialization factories, marine environmental pollution, and global warming, the marine fishery production has drop sharply. In order to understand the genetic factors of the blood clam, which is a major fishery resource on the southern coast of Korea, the whole genome of blood clam was studied. The assembled genome of T. granosa was 915.4 Mb, and 19 chromosomes were identified. 25,134 genes were identified, and 22,745 genes were functionally annotated. As a result of performing gene gain and loss analysis between the blood clam genome and eight other types of shellfish, it was confirmed that 725 gene groups were expanded, and 479 gene groups were contracted. The homeobox gene cluster of blood clam showed a well-preserved genetic structure within lophotrochozoan ancestor. T. granosa genome showed high similarity between three hemoglobin genes with Scarpharca broughtonii. The blood clam genome will provide information for the genetic and physiological characteristics of blood clam adaptation, evolution, and the development of aquaculture industry.

꼬막은 해양 어업으로써 아시아 전 지역에 있어서 중요한 수산자원 중 하나이다. 하지만, 공장의 산업화, 해양 환경오염, 그리고 지구 온난화로 인해 해양 어업 생산량이 급격히 떨어졌다. 우리나라 남해안의 주요 수산자원인 꼬막의 유전적 특성을 파악하기 위하여 꼬막의 전장유전체를 해독하고 염색체 서열을 규명하였다. 915.4 Mb의 게놈을 조립하였고, 19개의 염색체 유전자 서열을 식별하였다. 꼬막의 유전체에서 25,134개의 유전자들을 확인하였고, 그 중에 22,745개의 유전자들에 대한 기능을 확인했으며, 4,014개의 유전자들에 대한 KEGG pathway를 분석하였다. 꼬막유전체와 8종의 다른 패류와 비교유전체 분석을 통하여 확장/감소(gene gain and loss) 분석을 수행한 결과, 725개의 유전자군의 확장과 479개의 유전자군의 감소를 확인하였다. 꼬막의 homeobox 유전자 클러스터는 촉수담륜동물 내에서 잘 보존된 유전자 구조를 보였다. 또한, 꼬막은 3개의 hemoglobin 유전자들이 피조개의 hemoglobin과 높은 유사성을 보였다. 꼬막의 전장유전체 정보를 통해 꼬막의 환경 적응과 진화의 유전적 특성과 생리적 특성뿐만 아니라, 꼬막 양식의 효율성을 높이는 양식산업에 널리 이용될 수 있는 유전적 정보를 제공할 것이다.

Keywords

Acknowledgement

이 논문은 2021년도 정부(해양수산부)의 재원으로 해양수산과학기술진흥원 포스트게놈다부처유전체사업의 지원을 받아 수행된 연구임(No. 20180430).

References

  1. Abbas Alkarkhi FM, Ismail N, Easa AM. 2008. "Assessment of arsenic and heavy metal contents in cockles (Anadara granosa) using multivariate statistical techniques". Journal of Hazardous Materials 150: 783-789. https://doi.org/10.1016/j.jhazmat.2007.05.035
  2. Bai CM, Xin LS, Rosani U, Wu B, Wang QC, Duan XK, Liu ZH, Wang CM. 2019. "Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-C". Gigascience 8.
  3. Bao Y, Wang Q, Lin Z. 2011. "Hemoglobin of the bloody clam Tegillarca granosa (Tg-HbI) is involved in the immune response against bacterial infection". Fish & Shellfish Immunology 31: 517-523. https://doi.org/10.1016/j.fsi.2011.05.029
  4. Bao Z, Eddy SR. 2002. "Automated de novo identification of repeat sequence families in sequenced genomes". Genome Res 12: 1269-1276. https://doi.org/10.1101/gr.88502
  5. Barton HJ, Zeng K. 2019. "The Impact of Natural Selection on Short Insertion and Deletion Variation in the Great Tit Genome". Genome Biol Evol 11: 1514-1524. https://doi.org/10.1093/gbe/evz068
  6. Barucca M, Olmo E, Canapa A. 2003. "Hox and paraHox genes in bivalve molluscs". Gene 317: 97-102. https://doi.org/10.1016/S0378-1119(03)00657-7
  7. Belton JM, McCord RP, Gibcus JH, Naumova N, Zhan Y, Dekker J. 2012. "Hi-C: a comprehensive technique to capture the conformation of genomes". Methods 58: 268-276. https://doi.org/10.1016/j.ymeth.2012.05.001
  8. Canesi L, Gallo G, Gavioli M, Pruzzo C. 2002. "Bacteria-hemocyte interactions and phagocytosis in marine bivalves". Microsc Res Tech 57: 469-476. https://doi.org/10.1002/jemt.10100
  9. Cantarel BL, Korf I, Robb SM, Parra G, Ross E, Moore B, Holt C, Sanchez Alvarado A, Yandell M. 2008. "MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes". Genome Res 18: 188-196. https://doi.org/10.1101/gr.6743907
  10. Chin CS, Peluso P, Sedlazeck FJ, Nattestad M, Concepcion GT, Clum A, Dunn C, O'Malley R, Figueroa-Balderas R, Morales-Cruz A, Cramer GR, Delledonne M, Luo C, Ecker JR, Cantu D, Rank DR, Schatz MC. 2016. "Phased diploid genome assembly with single-molecule real-time sequencing". Nat Methods 13: 1050-1054. https://doi.org/10.1038/nmeth.4035
  11. Dudchenko O, Batra SS, Omer AD, Nyquist SK, Hoeger M, Durand NC, Shamim MS, Machol I, Lander ES, Aiden AP, Aiden EL. 2017. "De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds". Science 356: 92-95. https://doi.org/10.1126/science.aal3327
  12. Emms DM, Kelly S. 2019. "OrthoFinder: phylogenetic orthology inference for comparative genomics". Genome Biol 20: 238. https://doi.org/10.1186/s13059-019-1832-y
  13. Gotz S, Garcia-Gomez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talon M, Dopazo J, Conesa A. 2008. "High-throughput functional annotation and data mining with the Blast2GO suite". Nucleic Acids Res 36: 3420-3435. https://doi.org/10.1093/nar/gkn176
  14. Hajirnis N, Mishra RK. 2021. "Homeotic Genes: Clustering, Modularity, and Diversity". Front Cell Dev Biol 9: 718308. https://doi.org/10.3389/fcell.2021.718308
  15. Jiang N, Tan NS, Ho B, Ding JL. 2007. "Respiratory protein-generated reactive oxygen species as an antimicrobial strategy". Nat Immunol 8: 1114-1122. https://doi.org/10.1038/ni1501
  16. Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K. 2017. "KEGG: new perspectives on genomes, pathways, diseases and drugs". Nucleic Acids Res 45: 353-361. https://doi.org/10.1093/nar/gkw1115
  17. Kim J, Lee SJ, Jo E, Choi E, Kim HJ, Lee JS, Park H. 2021. "Genome Survey and Microsatellite Marker Selection of Tegillarca granosa". Journal of Marine Life Science 6: 38-46. https://doi.org/10.23005/KSMLS.2021.6.1.38
  18. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. 2009. "Circos: an information aesthetic for comparative genomics". Genome Res 19: 1639-1645. https://doi.org/10.1101/gr.092759.109
  19. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018. "MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms". Mol Biol Evol 35: 1547-1549. https://doi.org/10.1093/molbev/msy096
  20. Kumar S, Stecher G, Suleski M, Hedges SB. 2017. "TimeTree: A Resource for Timelines, Timetrees, and Divergence Times". Mol Biol Evol 34: 1812-1819. https://doi.org/10.1093/molbev/msx116
  21. Liu B, Teng S, Shao Y, Chai X, Xiao G, Fang J, Zhang J, Wang C. 2017. "A Genetic Linkage Map of Blood Clam (Tegillarca granosa) Based on Simple Sequence Repeat and Amplified Fragment Length Polymorphism Markers". Journal of Shellfish Research 36: 31-40. https://doi.org/10.2983/035.036.0105
  22. Manni M, Berkeley MR, Seppey M, Simao FA, Zdobnov EM. 2021. "BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes". Mol Biol Evol 38: 4647-4654. https://doi.org/10.1093/molbev/msab199
  23. Marcais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A. 2018. "MUMmer4: A fast and versatile genome alignment system". PLoS Comput Biol 14: e1005944. https://doi.org/10.1371/journal.pcbi.1005944
  24. Wang S, Yu X, Zhang S, Jin H, Chen Z, Lin Z, Bao Y. 2021. "Cu2+ Inhibits the Peroxidase and Antibacterial Activity of Homodimer Hemoglobin From Blood Clam Tegillarca granosa by Destroying Its Heme Pocket Structure". Frontiers in Marine Science 8: 2296-7745.