Population Genetic Structure Of Swamp Eel(Monopterus Albus)

Swamp eel(Monopterus albus)is a freshwater fish belonging to Actinopterygii Synbranchiformes Synbranchidae Monopterus.They have several physiological features,which are quite different from other fresh-water fishs,such as no scales and gills degradation.Most of them hibernate in the cold winter,while in the hot summer they can breathe out of the water in order to get more oxygen.They can survive with few water during long transportation,which endues the species spread in different locations.Nerverthless,population genetic structure of the eel remains to be explored.De-novo assembly of three kinds Monopterus albus gonad(Female,Intersex and Male)RNA-Seqs were made by trinity.Next,assembled RNAs were blasted with the reference genome,and INDELs and SNPs were obtained by Perl script.Finally,distributions of the these genetic markers were determined in the genome.Expression of genes with INDEL or SNP was also analyzed,which showed that the expression of genes with INDEL or SNP was higher than those without INDEL or SNP.To analyze genetic structure and diversity of Monopterus albus,the D-loop region was sequenced from samples of Yangtze River basin and cross-strait Monopterus albus,including Dazhou,Chongqing,Wuhan,Hefei,Nanjing,Sanming and Taiwan.Haplotype diversity(h)and nucleotide diversity(Pi)of D-loop were determined,which showed that h values of samples from Wuhan,Taiwan,Nanjing and Hefei were high while Pi values were low,both h and Pi values in Dazhou and Chongqing samples were low,and h value from Sanming was low while Pi was high.Genetic identity clustering analysis got the same conclusion.Monopterus albus populations from Wuhan,Taiwan,Nanjing,Hefei,Dazhou and Chongqing were belonging to haplogroup A-B,and Wuhan,Taiwan,Nanjing,Hefei groups' genetic structures were more similar,while Dazhou and Chongqing populations' genetic structures were similar to each other.In addition,Sanming group was belonging to haplogroup C-D,which was quite different from haplogroup A-B.However,I observed obvious gene purification of Monopterus albus groups based on the nuclear genome INDEL genotyping.Combined with the characteristics of Monopterus albus,I found that Monopterus albus could reproduce within a small population.The genetic diversities of Taiwan,Nanjing,Hefei,Dazhou,Chongqing and Sanming groups were low because long time mating in small groups make their nuclear gene purification and genetic diversity decrease while D-loop genetic diversity was not affected for maternal inheritance.A little higher of Wuhan group'nuclear genome diversity may be caused by frequent population communications.In conclusion,the De-novo RNA assembly based on RNA-Seq data was determined and the INDEL and SNP markers were obtained in genome coding regions.Combined with the expression anslysis,I found that genes with SNP or INDEL were highly expressed than those without SNP or INDEL.D-loop haplotyping showed that genetic diversity of Wuhan,Sanming,Hefei,Nanjing and Taiwan groups were high,while Dazhou and Chongqing group' genetic diversity were lower.Nuclear genome INDEL genetyping data showed that Monopterus albus could reproduce within a small population,which caused low genetic diversity in Sanming,Hefei,Nanjing,Taiwan,Dazhou and Chongqing groups.In addition,a little higher of genetic diversity in Wuhan group was probably caused by frequently communication among populations.