| Oratosqilla oratoria belongs to phylum Arthropoda,class Crustacea,order Stomatopoda,family Squilidae,and genus Oratosquilla.It is widely distributed in the coastal waters of China.It is a kind of highly economic crustaceans.In recent years,however,with the influence of overfishing and environmental degradation,the resources of O.oratoria are dramatically declining,and the fishing catch is decreasing year by year,and the resource status is not optimistic.It is necessary that measures should be taken to protect the resources of O.oratoria.In this paper,the population samples of O.oratoria were broadly collected from the Northwestern Pacific Ocean.The genetic structure and genetic variation among populations were systematically analyzed and studied by investigating mitochondrial DNA control region and the transcriptomic sequencing.The population structure and adaptive evolution of different geographic populations were revealed.The results in this study laid the foundation for the study of O.oratoria germplasm resources,and provided basic data for fisheries management of O.oratoria resources in China.Firstly,in order to test the effects of the physical barrier formed by the Yangtze River fresh water on the genetic diversity of O.oratoria and the precise genetic structure across the populations.The mitochondrial DNA control region sequences were used to analyze the genetic structure of O.oratoria individuals sampled from the Yellow Sea,Bohai Sea,the East China Sea,the South China Sea and the Japanese seas.A total of 309 individuals from13 geographic populations were analyzed,and 308 haplotypes were defined.The average haplotype diversity was 1.0000±0.0003 and the average nucleotide diversity was0.1720±0.0817.The NJ tree showed that the O.oratoria was divided into two clades: the northern group and the southern group.However,a very interesting result was showed that the two clades of O.oratoria distributed sympatrically in Hokkaido and Hyogo.The results of AMOVA and Fs T showed that the genetic differentiation between the three groups(the northern group,southern group and Japanese group)was at a higher level,but there was no significant genetic differentiation across populations.Significant and positive values ofTajima’s D and Fu’s Fs tests indicated population expansion in O.oratoria populations.The mismatch distribution for all samples was unimodal,which also supported the population expansion.In this study,the genetic structure and genetic diversity of the 13 geographic populations in 4 different sea areas were analyzed,which provided effective molecular bases for the protection and rational utilization of the resources of O.oratoria.Secondly,in order to elucidate the population genetic variation of the O.oratoria,the RNA-seq technique was used to transcriptome sequencing,assembling and functional analyses,and to compare the differences of the transcriptome between different genetic lineages.In this study,the samples were collected from Qingdao and Zhoushan,and the transcriptome sequenced and analyzed by Illumina Hi Seq 2000 technique.After assembly of the transcriptome data,60223 unigenes were obtained,the average length was 897 NT,the Qingdao population obtained 121606 unigenes,and the Zhoushan population obtained157584 unigenes.A total of 41373 unigenes can successfully aligned with Nr,KEGG,COG and GO databases,the number of aligned hits was 34930,26052,15746 and 8990,respectively.The species with the higher ratio of alignment were Octopus bimaculoides,Zootermopsis nevadensis and Octopus nevadensis in the Nr dataset.Differential expression genes of two groups of O.oratoria was were 11391.The up-regulation genes was 6477 and the down-regulation genes was 4914.GO analysis and Pathway enrichment analysis of differentially expressed genes obtained 61 different GO functional classifications and 257 pathways,Including two classification of significant enrichment of GO function and 40 significant enrichment pathways.The transcriptome data of O.oratoria in the two populations were respectively analyzed by SNP.95810 SNP polymorphic loci were detected in Qingdao group,comprise 59,749 transitions and 36,061 transversions.A total of100,598 polymorphic loci were detected by O.oratoria in Zhoushan group.There were65178 transitions and 35420 transversions.Thirdly,in this paper,we use high-throughput sequencing technology to obtain the sequencing data of the O.oratoria transcriptome and filter and develop polymorphic SSR markers.A total of 67,657 microsatellite sites were obtained,of which mostly SSRs were Di-nucleotide repeats and Tri-nucleotide repeats,with 30,235 and 17,590,respectively.Atotal of 230 types of repetition were obtained.In Di-nucleotide SSR repeats,the most repeated type was AC/GT repetition(14064).In the Tri-nucleotide repeats of SSR,the repeated dominant type is AGG/CCT repetition(5344).The 50 pairs of microsatellite primers with high number of base repetitions were selected to synthesize.A total of 6 pairs of SSR markers with clear bands and polymorphisms were identified by using 24 samples from Beihai.Based on mitochondrial DNA control region and transcriptome sequencing,we assessed the genetic structure and genetic variation among different populations of mantis shrimp.The results of control region showed that sampled population can be divided into three groups(northern group,southern group and Japanese group),and the genetic differentiation among groups was significant,but the genetic differentiation within the population was not significant,and there was no obvious genetic structure.Three groups could be divided into three management units to manage the fishery resources.The results of the transcriptome sequence showed that there was a great difference in the expression of the two populations.This may be due to the different long-term environmental adaptability of the O.oratoria.Further studies are needed to discover the mechanisms of population differentiation among O.oratoria populations. |
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