JOURNAL OF SHANDONG UNIVERSITY(NATURAL SCIENCE) ›› 2020, Vol. 55 ›› Issue (11): 1-7.doi: 10.6040/j.issn.1671-9352.0.2020.231

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Comparative study on genetic structure of three color variants of the sea cucumber (Apostichopus japonicus) based on mitochondrial and ribosomal genes

Zhan-sheng GUO1(),Zhen WANG2,Xu-guang HOU1,Hai-tao ZHANG1,*()   

  1. 1. Marine College, Shandong University, Weihai 264209, Shandong, China
    2. Binzhou Institute of Scientific and Technical Information, Binzhou 256600, Shandong, China
  • Received:2020-05-19 Online:2020-11-20 Published:2020-11-17
  • Contact: Hai-tao ZHANG E-mail:guomarine@163.com;zhanghaitao201208@163.com
  • Supported by:
    威海市“十三五”海洋经济创新发展示范城市项目

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Abstract:

The sea cucumber Apostichopus japonicus is an important marine aquatic species in China. Selecting good breeding is a major issue for sea cucumber aquaculture, and body color is chosen as an important consideration. In order to explore the genetic structure and phylogenetic relationship of sea cucumber populations with different body color characteristics, 16S rRNA, COⅠ and 18S rRNA-ITS-28S rRNA sequences were amplified and sequenced. The results showed that the lengths of 16S rRNA, COⅠ and 18S rRNA-ITS-28S rRNA sequences were 812-830 bp, 877-915 bp and 1 536-1 572 bp, respectively. In the green, white and purple morphs of the sea cucumber, 4/5/5, 5/3/4, and 4/4/3 haplotypes were detected in 16S rRNA, COⅠ and 18S rRNA-ITS-28S rRNA sequences, respectively. The number of polymorphic loci in the COⅠ sequences was the highest, and that of 16S rRNA sequences was the smallest. The genetic distances of 16S rRNA, COⅠ and 18S rRNA-ITS-28S rRNA sequences among three color morphs were both small, ranging from 0-0.014 7, 0-0.021 2, and 0-0.010 3, respectively, and they did not reach the species differentiation level. The phylogenetic tree was constructed based on the COⅠ sequences, and Strongylocentrotus purpuratus was chose as the outgroup. The results showed that the white sea cucumbers were clustered into one branch, the purple and green sea cucumbers were cross-aggregated with each other and could not be distinguished.

Key words: Apostichopus japonicus, body color, 16S rRNA, COⅠ, 18S rRNA-ITS-28S rRNA, genetic structure

CLC Number: 

  • S917.4

Table 1

Primers of A.japonicus"

引物名称 序列(5′-3′) 退火温度/℃
16S-F CGCCGTTTATCAAAAACAT 50
16S-R CCGGTCTGAACTCAGATCACG
16S-COⅠ-F RAGTTTTGGTTGGGGCAACCGTG 60
16S-COⅠ-F CCCTCTTTCAACTCCTGCAGAG
COⅠ-F ATAATGATAGGAGGRTTTGG 46
COⅠ-R GCTCGTGTRTCTACRTCCAT
ITS-F ACGAGATGGAGCAATAACAGG 53
ITS-R AAATCCAGCGGGTAATCTCAT

Table 2

Sequence informations in three color of A.japonicus"

序列名称 物种名称 序列长度/bp 序列碱基组成/%
T C A G A+T
B1—B5 812~828 27.11 20.15 32.67 20.08 59.78
16S rRNA W1—W5 826~829 27.50 20.40 32.17 19.94 59.67
P1—P5 826~830 27.67 20.26 32.19 19.87 59.86
平均值 824.20 27.43 20.27 32.34 19.96 59.77
B1—B5 877~913 31.45 21.03 27.48 20.04 58.93
COⅠ W1—W5 898~915 31.45 20.71 27.89 19.94 59.34
P1—P5 889~911 31.69 20.79 27.51 20.01 59.20
平均值 902.40 31.53 20.84 27.63 20.00 59.16
18S B1—B5 1 557~1 572 19.43 30.52 18.83 31.22 38.26
rRNA-ITS-28S W1—W5 1 547~1 566 19.42 30.42 18.78 31.37 38.20
rRNA P1—P5 1 536~1 566 19.35 30.37 18.78 31.50 38.13
平均值 1 557.40 19.40 30.44 18.80 31.36 38.20

Table 3

The genetic diversity indices in different color of A.japonicus"

序列片段 样本 单倍型数H 单倍型多样性Hd 多态性位点数S 平均核苷酸差异数K 核苷酸多样性指数Pi
16S rRNA B1—B5 4 0.900 3 1.400 0.001 73
P1—P5 5 1.000 12 6.200 0.007 53
W1—W5 5 1.000 8 4.500 0.005 45
总体 6 0.705 7 1.333 0.001 65
COⅠ B1—B5 5 1.000 13 6.400 0.007 31
P1—P5 3 0.800 11 5.200 0.005 85
W1—W5 4 0.900 4 2.100 0.002 34
总体 9 0.886 21 4.990 0.005 75
ITS B1—B5 4 0.900 9 3.800 0.002 45
P1—P5 4 0.900 3 1.400 0.000 91
W1—W5 3 0.700 5 2.200 0.001 43
总体 8 0.848 15 2.610 0.001 71

Table 4

The genetic distances in three color of A.japonicus (16S/COⅠ/18S-ITS-28S)"

B1 B2 B3 B4 B5 P1 P2 P3 P4 P5 W1 W2 W3 W4 W5
B1
B2 5.0/9.2/1.3
B3 2.5/11.3/0.0 2.5/4.6/0.0
B4 1.2/4.5/0.6 3.7/10.4/0.6 1.2/12.4/0.6
B5 2.5/6.7/4.5 6.2/9.2/4.5 6.2/10.1/4.5 2.5/7.8/5.2
P1 2.5/5.7/5.1 3.7/5.7/5.1 0.0/3.4/5.1 1.2/5.7/5.8 8.5/3.4/6.5
P2 1.2/4.5/0.7 4.9/10.4/0.7 1.2/10.1/0.7 0.0/6.7/1.3 7.3/17.9/5.2 2.4/4.5/0.7
P3 2.5/10.1/5.2 8.7/17.4/5.8 8.7/18.1/4.5 4.9/11.2/5.2 11.0/20.1/5.9 14.7/11.4/1.3 12.2/19.0/0.7
P4 1.2/3.4/5.8 6.2/10.4/6.5 4.9/10.1/5.2 2.5/4.5/5.8 8.5/9.0/5.2 9.8/4.5/1.9 7.3/3.0/1.3 7.3/12.4/0.6
P5 2.5/9.0/0.7 4.9/5.7/0.7 3.7/7.8/0.7 3.7/10.1/1.3 7.3/7.8/6.5 7.3/0.0/2.6 8.5/9.0/0.0 11.0/15.8/2.6 3.6/7.9/3.3
W1 1.2/4.5/3.2 6.2/11.5/3.2 4.9/11.3/3.2 2.5/5.6/3.9 6.1/5.6/7.2 8.5/5.7/5.8 6.1/6.7/2.6 8.5/13.5/5.9 3.6/3.4/6.5 6.1/9.0/2.6
W2 1.2/6.7/1.3 4.9/11.5/1.3 4.9/12.4/1.3 1.2/7.8/1.9 3.6/16.6/5.2 9.8/5.7/3.2 7.3/12.2/0.0 6.1/20.0/1.9 2.4/6.7/2.6 4.9/6.7/0.7 1.2/3.3/3.2
W3 1.2/6.7/9.6 4.9/11.5/9.7 1.2/12.4/9.6 1.2/9.0/10.3 8.5/13.3/10.4 2.4/5.7/8.4 0.0/12.2/1.3 13.4/21.2/1.9 7.3/6.7/2.6 8.5/10.1/3.3 6.1/3.3/5.2 7.3/11.0/7.1
W4 1.2/5.6/0.6 4.9/11.5/0.6 3.7/11.3/0.6 1.2/6.7/1.3 4.9/11.1/4.5 7.3/5.7/2.6 6.1/11.1/0.0 8.5/16.7/0.7 2.4/4.5/1.3 1.2/10.1/0.0 3.6/1.1/2.6 2.4/8.8/0.0 6.1/3.3/5.8
W5 1.2/5.6/0.6 4.9/11.5/0.6 4.9/11.3/0.6 1.2/6.7/1.3 3.6/14.4/5.2 9.8/5.7/3.2 8.5/12.2/0.0 9.8/16.7/1.3 7.3/4.5/1.9 6.1/10.1/0.0 4.9/1.1/2.6 2.4/9.9/0.0 9.7/9.9/5.8 3.6/4.4/0.0

Fig.1

ML phylogenetic tree of A.japonicus based on COⅠ gene"

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