Complete mitochondrial genome sequence and phylogenetic analysis of Procambarus clarkii and Cambaroides dauricus from China
Autor(a) principal: | |
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Data de Publicação: | 2023 |
Outros Autores: | , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/10400.1/19910 |
Resumo: | To enhance the management and protection of crayfish genetic diversity and germplasm resources in <i>Cambaroides dauricus</i> (<i>C. dauricus</i>), a common species of <i>Procambarus clarkii</i> (<i>P. clarkii</i>) was used as a control group to compare the whole mitochondrial genome sequence using Illumina sequencing technology. This study found that the mitochondrial genome of <i>C. dauricus</i> is 15580 bp in length, with a base composition of A (31.84%), G (17.66%), C (9.42%), and T (41.08%) and a C + G content of 27.08%. The C + G in the D-loop is rich in 17.06%, indicating a significant preference. The mitochondrial genome of <i>C. dauricus</i> contains 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes, with most of the genes labeled in the negative direction, except for a few genes that are labeled in the positive direction. The start codons of the ten coding sequences are ATG, and the quintessential TAA and TAG are the stop codons. This study also found that the Ka/Ks ratios of most protein-coding genes in the mitochondria of both shrimps are lower than 1, indicating weak natural selection, except for nad 2, nad 5, and cox 1. The Ka/Ks ratio of cox 3 is the lowest (less than 0.1), indicating that this protein-coding gene bears strong natural selection pressure and functional constraint in the process of mitochondrial genetic evolution of both shrimps. Furthermore, we constructed phylogenetic analyses based on the entire sequence, which effectively distinguishes the high body from other shrimp species of the genus based on the mitochondrial genome. This study provides molecular genetic data for the diversity investigation and protection of fishery resources with Chinese characteristics and a scientific reference for the evolutionary study of Procambarus. |
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Complete mitochondrial genome sequence and phylogenetic analysis of Procambarus clarkii and Cambaroides dauricus from ChinaProcambarus clarkiiCambaroides dauricusMitogenomePhylogenetic relationshipTo enhance the management and protection of crayfish genetic diversity and germplasm resources in <i>Cambaroides dauricus</i> (<i>C. dauricus</i>), a common species of <i>Procambarus clarkii</i> (<i>P. clarkii</i>) was used as a control group to compare the whole mitochondrial genome sequence using Illumina sequencing technology. This study found that the mitochondrial genome of <i>C. dauricus</i> is 15580 bp in length, with a base composition of A (31.84%), G (17.66%), C (9.42%), and T (41.08%) and a C + G content of 27.08%. The C + G in the D-loop is rich in 17.06%, indicating a significant preference. The mitochondrial genome of <i>C. dauricus</i> contains 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes, with most of the genes labeled in the negative direction, except for a few genes that are labeled in the positive direction. The start codons of the ten coding sequences are ATG, and the quintessential TAA and TAG are the stop codons. This study also found that the Ka/Ks ratios of most protein-coding genes in the mitochondria of both shrimps are lower than 1, indicating weak natural selection, except for nad 2, nad 5, and cox 1. The Ka/Ks ratio of cox 3 is the lowest (less than 0.1), indicating that this protein-coding gene bears strong natural selection pressure and functional constraint in the process of mitochondrial genetic evolution of both shrimps. Furthermore, we constructed phylogenetic analyses based on the entire sequence, which effectively distinguishes the high body from other shrimp species of the genus based on the mitochondrial genome. This study provides molecular genetic data for the diversity investigation and protection of fishery resources with Chinese characteristics and a scientific reference for the evolutionary study of Procambarus.This research was funded by the Natural Science Foundation of Heilongjiang Province (NO. LH2023C058) and the Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences (NO. 2020TD56)MDPISapientiaLuo, LiangXu, YueWang, ShihuiZhang, RuiGuo, KunXu, WeiZhao, Zhigang2023-08-01T15:05:12Z2023-07-102023-07-28T12:21:44Z2023-07-10T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10400.1/19910engInternational Journal of Molecular Sciences 24 (14): 11282 (2023)1422-006710.3390/ijms241411282info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-08-09T02:01:18Zoai:sapientia.ualg.pt:10400.1/19910Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T20:10:26.413793Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Complete mitochondrial genome sequence and phylogenetic analysis of Procambarus clarkii and Cambaroides dauricus from China |
title |
Complete mitochondrial genome sequence and phylogenetic analysis of Procambarus clarkii and Cambaroides dauricus from China |
spellingShingle |
Complete mitochondrial genome sequence and phylogenetic analysis of Procambarus clarkii and Cambaroides dauricus from China Luo, Liang Procambarus clarkii Cambaroides dauricus Mitogenome Phylogenetic relationship |
title_short |
Complete mitochondrial genome sequence and phylogenetic analysis of Procambarus clarkii and Cambaroides dauricus from China |
title_full |
Complete mitochondrial genome sequence and phylogenetic analysis of Procambarus clarkii and Cambaroides dauricus from China |
title_fullStr |
Complete mitochondrial genome sequence and phylogenetic analysis of Procambarus clarkii and Cambaroides dauricus from China |
title_full_unstemmed |
Complete mitochondrial genome sequence and phylogenetic analysis of Procambarus clarkii and Cambaroides dauricus from China |
title_sort |
Complete mitochondrial genome sequence and phylogenetic analysis of Procambarus clarkii and Cambaroides dauricus from China |
author |
Luo, Liang |
author_facet |
Luo, Liang Xu, Yue Wang, Shihui Zhang, Rui Guo, Kun Xu, Wei Zhao, Zhigang |
author_role |
author |
author2 |
Xu, Yue Wang, Shihui Zhang, Rui Guo, Kun Xu, Wei Zhao, Zhigang |
author2_role |
author author author author author author |
dc.contributor.none.fl_str_mv |
Sapientia |
dc.contributor.author.fl_str_mv |
Luo, Liang Xu, Yue Wang, Shihui Zhang, Rui Guo, Kun Xu, Wei Zhao, Zhigang |
dc.subject.por.fl_str_mv |
Procambarus clarkii Cambaroides dauricus Mitogenome Phylogenetic relationship |
topic |
Procambarus clarkii Cambaroides dauricus Mitogenome Phylogenetic relationship |
description |
To enhance the management and protection of crayfish genetic diversity and germplasm resources in <i>Cambaroides dauricus</i> (<i>C. dauricus</i>), a common species of <i>Procambarus clarkii</i> (<i>P. clarkii</i>) was used as a control group to compare the whole mitochondrial genome sequence using Illumina sequencing technology. This study found that the mitochondrial genome of <i>C. dauricus</i> is 15580 bp in length, with a base composition of A (31.84%), G (17.66%), C (9.42%), and T (41.08%) and a C + G content of 27.08%. The C + G in the D-loop is rich in 17.06%, indicating a significant preference. The mitochondrial genome of <i>C. dauricus</i> contains 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes, with most of the genes labeled in the negative direction, except for a few genes that are labeled in the positive direction. The start codons of the ten coding sequences are ATG, and the quintessential TAA and TAG are the stop codons. This study also found that the Ka/Ks ratios of most protein-coding genes in the mitochondria of both shrimps are lower than 1, indicating weak natural selection, except for nad 2, nad 5, and cox 1. The Ka/Ks ratio of cox 3 is the lowest (less than 0.1), indicating that this protein-coding gene bears strong natural selection pressure and functional constraint in the process of mitochondrial genetic evolution of both shrimps. Furthermore, we constructed phylogenetic analyses based on the entire sequence, which effectively distinguishes the high body from other shrimp species of the genus based on the mitochondrial genome. This study provides molecular genetic data for the diversity investigation and protection of fishery resources with Chinese characteristics and a scientific reference for the evolutionary study of Procambarus. |
publishDate |
2023 |
dc.date.none.fl_str_mv |
2023-08-01T15:05:12Z 2023-07-10 2023-07-28T12:21:44Z 2023-07-10T00:00:00Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10400.1/19910 |
url |
http://hdl.handle.net/10400.1/19910 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
International Journal of Molecular Sciences 24 (14): 11282 (2023) 1422-0067 10.3390/ijms241411282 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
MDPI |
publisher.none.fl_str_mv |
MDPI |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
instname_str |
Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
instacron_str |
RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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1799133354072735744 |