Genetic Diversity Of Feneropenaeus Chinensis And Marsupenaeus Japonicus And Molecular Phylogeny Of Penaeidae

In this study,the genetic diversity and evolutionary demography ofFeneropenaeus chinensis and Marsupenaeus japonicus were studied by mtDNAmarkers.We discussed the role of Pleistocene ice ages and present environmentalfactors in shaping the phylogeographic pattern and genetic structures of the twospecies.In addition,ITS1,mt genome sequences and Numts were used as molecularmarkers for studying the phylogenetic relationships among species of penaeid shrimps.1,Genetic structure and demographic history ofFeneropenaeus chinensis wasexamined using sequence data of partial mitochondrial cytochrome oxidase I (COI)gene and the complete mitochondrial control region (CR).Samples of 93 individualswere collected from 5 localities over most of the species' range in the Yellow Sea andthe Bohai Sea.For COI data,atotal of 20 nucleotide sites were detected variable,defining 20 haplotypes.The variation level was low,with H=0.4816±0.0639 and=0.0846±0.0711 (%),respectively.For CR data,there are 84 variable sites defining68 haplotypes.Haplotype diversity levels were very high (0.95±0.03-0.99±0.02),while that ofnucleotide diversitywere at moderate to low level (0.66±0.36%-0.84±0.46%).Analysis of molecular variance and the conventional population statisticFST revealed no significant genetic structure throughout the range of F.chinensis.However,Isolation with Migration (IM) coalescence results based on CR data suggestF.chinensis distributed along the coasts of northern China and Korean Peninsula(about 1000 km apart) diverged recently,and the estimated split time was 12,800 (7,400-18,600) years ago.Both mismatch distribution analyses and neutrality testsbased on COI data and CR data suggested a late Pleistocene or Holocene populationexpansion (12,100-28,500 years ago) for F.chinensis,which was consistent withthe geological period of formation of the Bohai Sea and the Yellow Sea.These results indicated that F.chinensis in the Bohai Sea and the Yellow Sea might have undergonea genetic bottleneck or founder event during the late Pleistocene globle glacial period.2,DNA sequencing is very useful for the genetic diversity analysis at molycular level.Mitochondrial COI gene fragments of kuruma shrimp Marsupenaeus japonicus wereamplified via polymerase chain reaction (PCR),the PCR products were sequenced for85 individuals,5 population of China.858 base-pair nucleotide sequences wereexamined and analyzed for genetic polymorphism.Resultant sequences data analysisshowed that all 85 sequences were grouped into 58 haplotypes and there were 106variable nucleotide positions in this gene fragment.The genetic diversity indexesincluding S (polymorphic sites),π(nucleotide diversity) and H (haplotype diversity)were calculated and the results indicated that Guangxi population showed morevariation than others and more differences to others.Based on the mitochondrial DNAsequence data,the shrimps were separated into two distinct clades.Analyses ofmolecular variance and the population statistic FST revealed significant geneticstructure.Both mismatch distribution analyses and neutrality tests based suggested aPleistocene population expansion for Marsupenaeus japonicus.3,The ribosomal DNA internal transcribed spacer 1 (ITS1) of Fenneropenaeuschinensis was cloned and sequenced.The objective of the present study is to estimatephylogenies and explore the feasibility of using ITS1 as a molecular marker forstudying the interspecific and intraspecific genetic variations among penaeid shrimps.Inter-and intraindividual polymorphisms of ITS 1 were clearly observed in F.chinensis.The length of the ITS1 ranged from 637 to 652bp,with a GC content of 66.9%.Repeats of microsatellite loci of ITS 1 plays an important role in length heteroplasmyat both between-and within-individual levels in this species.Eight microsatellite lociwere found in the ITS1 sequence of F.chinensis.According to existing data,somemicrosatellites were found in only one specie,(CAGC) 2-4 in F.chinensis,(GCGA)4in P.semisalcatus and (CGGA)4-9 in P.monodon.The DNA data of the penaeidshrimps were processed in neighbor-joining (NJ) methods to build phylogeneticrelationships within the family of Penaeidae.According to the NJ tree,differentindividuals of the same species,different species of the same genus were grouped together,in consistence with the morphological taxonomy.The genetic distancesamong different genus ranged from 0.313 to 0.977 and the average was 0.633,exceeding those estimated with COI and partial 16S rRNAgene sequences,and beingtherefore larger than the value among subgenera.The results of the present studyindicated that Fenneropenaeus,Litopenaeus,Farfanatepenaeus,Marsupenaeus andPenaeus are at a higher phylogenetic level than subgenus,which supports the opinionof the elevation of phylogenetic status of the four subgenera to genus level.Theseresults show that ITS 1 is highly divergent among different penaeid shrimps and couldbe an appropriate marker for molecular systematic studies at the species levels,although the presence of intragenomic variation needs to be taken into consideration.4,Mt genome sequences have provided useful markers for investigating populationgenetic structures,systematics and phylogenetics of organisms.In this study,mtgenome sequences and Numts were used as molecular markers for studying the phylogeneticrelationships among species of penaeid shrimps.Phylogenetic analyses based onconcatenated amino acid and nucleic acid sequences of the 13 mt protein-codinggenes strongly support the monophyly of the Decapoda and Penaeidae.However,relationships among species within the Penaeidae based on the 13 mt protein-codinggenes and Numts could not be resolved,and further studies were necessary to becarried out based.on the increasing number of mitochondrial genome sequences,inorder to better understand the relationships among species of Penaeidae.