Phylogeny And DNA Barcodes Of 15 Species In Penaeidae

By PCR amplification and sequencing,the cytochrome c oxidase submit I(COI)partial gene of 15 species in penaied were acquired and used to study its potentiality as DNA barcodes to distinguish shrimps.The two nuclear Protein-coding genes PEPCK and NaK are used to study the phylogenetic relationships of 15 penaeid shrimps(Penaeidae).The main results are shown as follows:1:In 137 samples of 15 species in penaieid shrimps(Penaeidae),the 634bp COI partial sequence contains 324 Variable sites,and 235 are parsimony sites.DNA barcodes based on mitochondrail COI gene sequences were developed to classify the species in Penaeidae family.The average Kimura-2-parameter(K2P)distance of pairwise-species reached to 0.223 which was 12 times as much as those of instra-species(0.0185).The result of phylogenetic tree confirmed that the DNA barcode could be used in species classification and identification in Penaeidae.2:The length of PEPCK genes of 15 species in penaeid shrimps is 549bp,Insertion and deletion are existed in the sequence,there are 204 Variable sites,and 163 are parsimony sites.The topology of MP.ML and NJ phylogenetic tree based on PEPCK gene are similar.Different samples of the same species are cluster together by clear boundary.9 genus shrimps can be divided into 3 clades.In the first clade,P.monodon of Genus Penaeus cluster with P.semisulcatus of Genus Penaeus,and then it cluster with F.penicillatus of Genus Fenneropenaeus and L.vannamei of Genus Litopenaeus gradually,on the other hand,M.latisulcatus of Genus Melicertus are cluster with M.japonicus of Genus Marsupenaeus as a clade,this two clade finally cluster together as the first clade.In the second clade,M.joyneri of Genus Metapenaeus cluster with M.ensis of Genus Metapenaeus as a clade,moreover,P.cornuta of Genus Parapen.aeopsis are cluster with P.sinica of Genus Parapenaeopsis,and then it cluster with T.curvirostris of Genus Trachypenaeus formed a clade,this two clade cluster together formed the second clade.third clade is formed by shrimps of Genus Metapenaeopsis,at first M.dalei cluster with M.barbata,and then it cluster with M.lamellata,finally,it cluster with M.stridulans formed the third clade.The results of this study support presumption that divided Penaeidae into three group suggested by Burkenroad in 1983.3.The length of NaK gene of 15 species in penaeid shrimps is 465bp,Insertion and deletion are existed in the sequence,there are 114 Variable sites,and 102 are parsimony sites.The topology of MP、ML and NJ phylogenetic tree based on NaK gene are similar,except the position of Genus Metapenaeus in MP phylogenetic tree are different with it’s position in ML and NJ phylogenetic tree.Different samples of the same species are cluster together by clear boundary,the phylogenetic realtionship are consistent with the taxonomic relationship based on morphology.Except Genus Metapenaeus,the other 8 genus shrimps can be divided into 3 clades.The topology of the first clade is:P.monodon of Genus Penaeus and F.penicillatus of Genus Fenneropenaeus are cluster into a clade,and then it cluster with P.semisulcatus of Genus Penaeus and L.vannamei of Genus Litopenaeus gradually.moreover,M.latisulcatus of Genus Melicertus are cluster with Mjaponicus of Genus Marsupenaeus as a clade.the two clade finally cluster into the first clade.The topology of the second clade is:P.cornuta of Genus Parapenaeopsis are cluster with P.sinica of Genus Parapenaeopsis,and then it cluster with T.curvirostris of Genus Trachypenaeus formed the second clade.The third clade consist of shrimps from Genus Metapenaeopsis,the topology in ML and MP phylogenetic tree are same:M.barbata cluster with M.stridulans,M.dalei cluster with M.lamellata,the two branch formed the third clade.While the topology in the NJ phylogenetic tree share some difference:M.barbata cluster with M.stridulans,and then it cluster with M.lamellata,finally,it cluster with M.dalei and formed the third clade.The position of Genus Metapenaaeus are different in MP、ML and NJ phylogentic tree,in the ML and NJ tree,it is at the root of the phylogenetic tree,while in the MP phylogenetic tree,Genus Metapenaeus and Genus Penaeus、Fenneropenaeus、Litopenaeus、Melicertus and Marsupenaeus formed the first clade.The results of this study support presumption that divided Penaeidae into three group suggested by Burkenroad in 1983.