TY - JOUR
T1 - The chromosome-scale genome assembly for the West Nile vector Culex quinquefasciatus uncovers patterns of genome evolution in mosquitoes
AU - Ryazansky, Sergei S.
AU - Chen, Chujia
AU - Potters, Mark
AU - Naumenko, Anastasia N.
AU - Lukyanchikova, Varvara
AU - Masri, Reem A.
AU - Brusentsov, Ilya I.
AU - Karagodin, Dmitriy A.
AU - Yurchenko, Andrey A.
AU - dos Anjos, Vitor L.
AU - Haba, Yuki
AU - Rose, Noah H.
AU - Hoffman, Jinna
AU - Guo, Rong
AU - Menna, Theresa
AU - Kelley, Melissa
AU - Ferrill, Emily
AU - Schultz, Karen E.
AU - Qi, Yumin
AU - Sharma, Atashi
AU - Deschamps, Stéphane
AU - Llaca, Victor
AU - Mao, Chunhong
AU - Murphy, Terence D.
AU - Baricheva, Elina M.
AU - Emrich, Scott
AU - Fritz, Megan L.
AU - Benoit, Joshua B.
AU - Sharakhov, Igor V.
AU - McBride, Carolyn S.
AU - Tu, Zhijian
AU - Sharakhova, Maria V.
N1 - Publisher Copyright:
© 2024, The Author(s).
PY - 2024/12
Y1 - 2024/12
N2 - Background: Understanding genome organization and evolution is important for species involved in transmission of human diseases, such as mosquitoes. Anophelinae and Culicinae subfamilies of mosquitoes show striking differences in genome sizes, sex chromosome arrangements, behavior, and ability to transmit pathogens. However, the genomic basis of these differences is not fully understood. Methods: In this study, we used a combination of advanced genome technologies such as Oxford Nanopore Technology sequencing, Hi-C scaffolding, Bionano, and cytogenetic mapping to develop an improved chromosome-scale genome assembly for the West Nile vector Culex quinquefasciatus. Results: We then used this assembly to annotate odorant receptors, odorant binding proteins, and transposable elements. A genomic region containing male-specific sequences on chromosome 1 and a polymorphic inversion on chromosome 3 were identified in the Cx. quinquefasciatus genome. In addition, the genome of Cx. quinquefasciatus was compared with the genomes of other mosquitoes such as malaria vectors An. coluzzi and An. albimanus, and the vector of arboviruses Ae. aegypti. Our work confirms significant expansion of the two chemosensory gene families in Cx. quinquefasciatus, as well as a significant increase and relocation of the transposable elements in both Cx. quinquefasciatus and Ae. aegypti relative to the Anophelines. Phylogenetic analysis clarifies the divergence time between the mosquito species. Our study provides new insights into chromosomal evolution in mosquitoes and finds that the X chromosome of Anophelinae and the sex-determining chromosome 1 of Culicinae have a significantly higher rate of evolution than autosomes. Conclusion: The improved Cx. quinquefasciatus genome assembly uncovered new details of mosquito genome evolution and has the potential to speed up the development of novel vector control strategies.
AB - Background: Understanding genome organization and evolution is important for species involved in transmission of human diseases, such as mosquitoes. Anophelinae and Culicinae subfamilies of mosquitoes show striking differences in genome sizes, sex chromosome arrangements, behavior, and ability to transmit pathogens. However, the genomic basis of these differences is not fully understood. Methods: In this study, we used a combination of advanced genome technologies such as Oxford Nanopore Technology sequencing, Hi-C scaffolding, Bionano, and cytogenetic mapping to develop an improved chromosome-scale genome assembly for the West Nile vector Culex quinquefasciatus. Results: We then used this assembly to annotate odorant receptors, odorant binding proteins, and transposable elements. A genomic region containing male-specific sequences on chromosome 1 and a polymorphic inversion on chromosome 3 were identified in the Cx. quinquefasciatus genome. In addition, the genome of Cx. quinquefasciatus was compared with the genomes of other mosquitoes such as malaria vectors An. coluzzi and An. albimanus, and the vector of arboviruses Ae. aegypti. Our work confirms significant expansion of the two chemosensory gene families in Cx. quinquefasciatus, as well as a significant increase and relocation of the transposable elements in both Cx. quinquefasciatus and Ae. aegypti relative to the Anophelines. Phylogenetic analysis clarifies the divergence time between the mosquito species. Our study provides new insights into chromosomal evolution in mosquitoes and finds that the X chromosome of Anophelinae and the sex-determining chromosome 1 of Culicinae have a significantly higher rate of evolution than autosomes. Conclusion: The improved Cx. quinquefasciatus genome assembly uncovered new details of mosquito genome evolution and has the potential to speed up the development of novel vector control strategies.
KW - Annotation
KW - Genome assembly
KW - Genome evolution
KW - Mosquito
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UR - http://www.scopus.com/inward/citedby.url?scp=85183001740&partnerID=8YFLogxK
U2 - 10.1186/s12915-024-01825-0
DO - 10.1186/s12915-024-01825-0
M3 - Article
C2 - 38273363
AN - SCOPUS:85183001740
SN - 1741-7007
VL - 22
JO - BMC Biology
JF - BMC Biology
IS - 1
M1 - 16
ER -