TY - JOUR
T1 - Genome-wide discovery of single nucleotide polymorphisms (SNPs) and single nucleotide variants (SNVs) in deep-sea mussels
T2 - Potential use in population genomics and cross-species application
AU - Xu, Ting
AU - Sun, Jin
AU - Lv, Jia
AU - Kayama Watanabe, Hiromi
AU - Li, Tianqi
AU - Zou, Weiwen
AU - Rouse, Greg W.
AU - Wang, Shi
AU - Qian, Pei Yuan
AU - Bao, Zhenmin
AU - Qiu, Jian Wen
N1 - Funding Information:
This study was supported by Hong Kong Baptist University (Ph.D. studentship to T.X and Grant number FRG2/14-15/002 to J.W.Q.), the Strategic Priority Research Program of Chinese Academy of Sciences (Grant no. XDB06010102 to P.Y.Q.), the State Key Program of National Natural Science of China (Grant no. 31130054 to Z.B.), and the Trans-crustal Advection and In situ Biogeochemical Processes of the Global Sub-seafloor Aquifer (TAIGA) Project, Grant-in-Aid for Scientific Research on Innovative Areas (KAKENHI, No. 20109004) from the Ministry of Education, Culture, Sports, Science and Technology (MEXT), and the Canon Foundation to H.W., and a InterRidge Fellowship to J.S. We thank Dr. Xinxin You from the Beijing Genomics Institute (Shenzhen, China) for her helpful comments on our data analyses.
Funding Information:
This study was supported by Hong Kong Baptist University (Ph.D. studentship to T.X and Grant number FRG2/14-15/002 to J.W.Q.), the Strategic Priority Research Program of Chinese Academy of Sciences (Grant no. XDB06010102 to P.Y.Q.), the State Key Program of National Natural Science of China (Grant no. 31130054 to Z.B.), and the Trans-crustal Advection and In situ Biogeochemical Processes of the Global Sub-seafloor Aquifer (TAIGA) Project, Grant-in-Aid for Scientific Research on Innovative Areas (KAKENHI, No. 20109004) from the Ministry of Education, Culture, Sports, Science and Technology (MEXT), and the Canon Foundation to H.W., and a InterRidge Fellowship to J.S. We thank Dr. Xinxin You from the Beijing Genomics Institute (Shenzhen, China) for her helpful comments on our data analyses.
PY - 2017/3/1
Y1 - 2017/3/1
N2 - The present study aimed to generate genome-wide single nucleotide polymorphisms (SNPs) for the deep-sea mussel Bathymodiolus platifrons via a combination of genome survey sequencing and the type IIB endonuclease restriction-site associated DNA (2b-RAD) sequencing, assess the potential use of SNPs in detecting fine-sale population genetic structure and signatures of divergent selection, as well as their cross-species application in other bathymodioline mussels. Genome survey sequencing was conducted for one individual of B. platifrons. De novo assembly resulted in 781,720 sequences with a scaffold N50 of 2.9 kb. Using these sequences as a reference, 9307 genome-wide SNPs were identified by 2b-RAD for 28 B. platifrons individuals collected from a seep and a vent population. Among these SNPs, nine outliers showed significant evidence for divergent selection, and their positions in the genes or scaffolds were identified. The FST estimated based on the putative neutral SNPs was low (0.0126) indicating the two B. platifrons populations having a high genetic connectivity. However, the permutation test detected significant differences (P<0.00001), indicating the two populations having clearly detectable genetic differentiation. The Bayesian clustering analyses and principle component analyses (PCA) performed based on either the putative neutral or outlier SNPs also showed that these two populations were genetically differentiated. In addition, 2b-RAD was also conducted to detect 10,199, 6429, and 3811 single nucleotide variants (SNVs) respectively in the bathymodioline mussels Bathymodiolus japonicus, Bathymodiolus aduloides and Idas sp. with different phylogenetic distances from B. platifrons. Overall, our study has demonstrated the feasibility and effectiveness of combining genome survey sequencing and 2b-RAD to rapidly generate genomic resources for use in fine-scale population genetic studies, and various cross-species applications.
AB - The present study aimed to generate genome-wide single nucleotide polymorphisms (SNPs) for the deep-sea mussel Bathymodiolus platifrons via a combination of genome survey sequencing and the type IIB endonuclease restriction-site associated DNA (2b-RAD) sequencing, assess the potential use of SNPs in detecting fine-sale population genetic structure and signatures of divergent selection, as well as their cross-species application in other bathymodioline mussels. Genome survey sequencing was conducted for one individual of B. platifrons. De novo assembly resulted in 781,720 sequences with a scaffold N50 of 2.9 kb. Using these sequences as a reference, 9307 genome-wide SNPs were identified by 2b-RAD for 28 B. platifrons individuals collected from a seep and a vent population. Among these SNPs, nine outliers showed significant evidence for divergent selection, and their positions in the genes or scaffolds were identified. The FST estimated based on the putative neutral SNPs was low (0.0126) indicating the two B. platifrons populations having a high genetic connectivity. However, the permutation test detected significant differences (P<0.00001), indicating the two populations having clearly detectable genetic differentiation. The Bayesian clustering analyses and principle component analyses (PCA) performed based on either the putative neutral or outlier SNPs also showed that these two populations were genetically differentiated. In addition, 2b-RAD was also conducted to detect 10,199, 6429, and 3811 single nucleotide variants (SNVs) respectively in the bathymodioline mussels Bathymodiolus japonicus, Bathymodiolus aduloides and Idas sp. with different phylogenetic distances from B. platifrons. Overall, our study has demonstrated the feasibility and effectiveness of combining genome survey sequencing and 2b-RAD to rapidly generate genomic resources for use in fine-scale population genetic studies, and various cross-species applications.
KW - Bathymodioline
KW - Bathymodiolus
KW - Bivalve
KW - Population genetics
KW - RAD-seq
KW - Restriction site-associated DNA
UR - http://www.scopus.com/inward/record.url?scp=84964664675&partnerID=8YFLogxK
U2 - 10.1016/j.dsr2.2016.03.011
DO - 10.1016/j.dsr2.2016.03.011
M3 - Journal article
AN - SCOPUS:84964664675
SN - 0967-0645
VL - 137
SP - 318
EP - 326
JO - Deep-Sea Research Part II: Topical Studies in Oceanography
JF - Deep-Sea Research Part II: Topical Studies in Oceanography
ER -