Scientia Silvae Sinicae ›› 2021, Vol. 57 ›› Issue (9): 140-151.doi: 10.11707/j.1001-7488.20210914
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Xin Peng1,Hantang Wang1,Chunhui Guo1,Zhende Yang1,2,*,Jing Zhou1,Xue Wang1,Zhirou Ding1
Received:
2020-12-24
Online:
2021-09-25
Published:
2021-11-29
Contact:
Zhende Yang
CLC Number:
Xin Peng,Hantang Wang,Chunhui Guo,Zhende Yang,Jing Zhou,Xue Wang,Zhirou Ding. EST-SSR Development and Cryptic Species Identification of the Invasive Gall-Causing Pest Leptocybe invasa (Hymenopetra: Eulophidae)[J]. Scientia Silvae Sinicae, 2021, 57(9): 140-151.
Table 1
Sampling information of 14 geographic populations of L. invasa"
种群代码 Population code | 采集地 Sample sites | 经纬度 Longitude and latitude | 海拔 Elevation/m | 采样时间 Sample time |
SCDY | 四川德阳Deyang, Sichuan | 104°17′E,31°10′N | 512.3 | 2019-12 |
SCPZH | 四川攀枝花Panzhihua, Sichuan | 101°75′E, 26°49′N | 1 137.2 | 2018-07 |
JXGZ | 江西赣州Ganzhou, Jiangxi | 114°43′E, 25°36′N | 195.6 | 2016-07 |
FJSM | 福建三明Sanming, Fujian | 117°57′E, 26°30′N | 177.6 | 2019-09 |
HNDZ | 海南儋州Danzhou, Hainan | 108°56′E, 18°09′N | 24.6 | 2017-07 |
YNKM | 云南昆明Kunming, Yunnan | 103°10′E, 26°06′N | 1 846.5 | 2019-07 |
GXFCG1 | 广西防城港1 Fangchenggang 1, Gaungxi | 108°1′E, 22°14′N | 250.0 | 2019-07 |
GXFCG2 | 广西防城港2 Fangchenggang 2, Gaungxi | 107°47′E, 21°57′N | 220.0 | 2019-10 |
GXNN1 | 广西南宁1 Nanning 1, Guangxi | 108°17′E, 22°51′N | 143.3 | 2019-06 |
GXNN2 | 广西南宁2 Nanning 2, Guangxi | 108°17′E, 22°50′N | 156.4 | 2019-06 |
GXWZ | 广西梧州Wuzhou, Guangxi | 111°03′E, 23°03′N | 76.2 | 2016-07 |
GXLB | 广西来宾Laibin, Guangxi | 108°24′E, 23°16′N | 361.3 | 2020-06 |
GXYL | 广西玉林Yulin, Guangxi | 110°01′E, 22°30′N | 150.5 | 2019-08 |
GXQZ | 广西钦州Qinzhou, Guangxi | 109°12′E, 21°52′N | 45.3 | 2020-07 |
Table 2
Transcriptome assembly quality of L. invasa"
项目Item | 转录本 Transcripts | 独立基因 Unigenes | ||||
数量Number | 百分比Percentage(%) | 数量Number | 百分比Percentage(%) | |||
长度范围 Sequence length | 300~500 bp | 24 604 | 31.95 | 21 646 | 48.23 | |
500~1 000 bp | 15 989 | 20.76 | 10 931 | 24.36 | ||
1 000~2 000 bp | 14 026 | 18.21 | 6 272 | 13.98 | ||
>2 000 bp | 22 390 | 29.07 | 6 029 | 13.43 | ||
总数Total number | 77 009 | 100.00 | 44 878 | 100.00 | ||
总长度Total length/bp | 140 690 637 | — | 48 592 158 | — | ||
N50长度N50 length/bp | 3 568 | — | 1 976 | — | ||
平均长度Mean length/bp | 1 826.94 | — | 1 082.76 | — |
Table 3
Repeated number statistics of EST-SSRs of different types in L. invasa"
重复类型 Repeat type | 重复次数Repeated number | 合计 Total | 比例 Ratio(%) | ||||||||
4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | ≥12 | |||
单核苷酸Mononucleotide | — | — | — | — | — | — | 3 526 | 1 867 | 4 488 | 9 881 | 69.63 |
二核苷酸Dinucleotide | — | — | 795 | 548 | 426 | 313 | 166 | 45 | 2 | 2 295 | 16.17 |
三核苷酸Trinucleotide | — | 1 005 | 632 | 272 | 8 | 0 | 0 | 0 | 0 | 1 917 | 13.51 |
四核苷酸Tetranucleotide | 0 | 75 | 10 | 2 | 0 | 0 | 1 | 0 | 0 | 88 | 0.62 |
五核苷酸Pentanucleotide | 0 | 3 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 5 | 0.04 |
六核苷酸Hexanucleotide | 0 | 1 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 4 | 0.03 |
总计Total | 0 | 1 084 | 1 438 | 824 | 435 | 313 | 1 968 | 981 | 7 147 | 14 190 | 100.00 |
比例Ratio(%) | 0 | 7.64 | 10.13 | 5.81 | 3.07 | 2.21 | 13.87 | 6.91 | 50.37 | 100.00 | — |
Table 4
Statistics on repeat motifs type of EST-SSRs in L. invasa"
重复基元类型 Repeat motifs type | 数量(百分比) Number(percentage) | 占总SSR比率 Percentage in total SSR(%) | 重复基元类型 Repeat motifs type | 数量(百分比) Number(percentage) | 占总SSR比率 Percentage in total SSR(%) | |
单核苷酸Mononucleotide | 三核苷酸Trinucleotide | |||||
A/T | 9 686(98.03%) | TGC/GCA | 262(13.67%) | |||
C/G | 195(1.97%) | CAG/CTG | 240(12.52%) | |||
合计Subtotal | 9 881(100%) | 69.63 | AGC/GCT | 192(10.02%) | ||
二核苷酸Dinucleotide | TCG/CGA | 104(5.43%) | ||||
GA/TC | 603(26.27%) | AAT/ATT | 91(4.75%) | |||
AG/CT | 531(23.14%) | GCG/CGC | 89(4.64%) | |||
AT/AT | 244(10.63%) | GAC/GTC | 84(4.38%) | |||
AC/GT | 232(10.11%) | GGC/GCC | 82(4.28%) | |||
CA/TG | 232(10.11%) | 其他Others | 773(40.31%) | |||
TA/TA | 218(9.50%) | 合计Subtotal | 1 917(100%) | 13.51 | ||
GC/GC | 121(5.27%) | 四、五、六核苷酸Tetra-, penta-and hexa-nucleotide | 97(100%) | 0.69 | ||
CG/CG | 114(4.97%) | |||||
合计Subtotal | 2 295(100%) | 16.17 | 总计Total | 14 190(100%) | 100 |
Table 5
Information of 10 polymorphic EST-SSRs and 3 polymorphic G-SSRs primers of L. invasa"
编号 ID | 引物序列 Primers(5′-3′) | 重复基元 Reapeat motifs | Ta | NA | 等位基因大小 Alleles size/bp | |
c120771 | F: AGCCAAAAGGGGTTTGTTCT | R: ACTCAGCAACAGGTGTCACG | (AG)6 | 56 | 2 | 248、252 |
c125483 | F: AGCGTTCAACCGAAAAGAGA | R: TAAGTCGCTCGCTGTGTGTC | (TC)8 | 56 | 4 | 213、215、217、219 |
c124062 | F: CGTCTGTTCAGTCCTCCTCC | R: CATTGCAAGCTACAGTCCGA | (CG)7 | 58 | 2 | 145、155 |
c120888 | F: GCGCGCGTCTATATACTTCC | R: TACGCGCACGAGTTGTATGT | (CT)6 | 57 | 2 | 233、239 |
c121460 | F: CGCTCTCACGAGGAGAGACT | R: ACATCCGCGACAACTTCTCT | (ATA)7 | 58 | 3 | 196、199、217 |
c121011 | F: TGAAGACGGCGAAGAGAAGT | R: ATACAGGTTACGCGCGAGAG | (CA)9 | 57 | 2 | 123、127 |
c69914 | F: ATCGAATGGCCGTATTTCAA | R: CTTGCGGAGAAATCAAGGAG | (TA)10 | 54 | 4 | 198、200、202、204 |
c121749 | F: GTATACGAGGGGGAGGGAAA | R: ACAGTTGCTGCTGTACGTGG | (CAG)6 | 58 | 2 | 249、258 |
c127471 | F: ATGTCGAAGGGCAATTTCTG | R: ACTCGGAATTCAATCAACGC | (TGT)7 | 56 | 2 | 220、229 |
c123946 | F: GTGTCGATTGGCGCTATTGT | R: CGTGTGTGAGAGTGCGAAAT | (GCT)5 | 56 | 4 | 237、240、246、249 |
LiSS2 | F: CCATATTGGGTCCACCTACC | R: ACCGTCCTTGCGTATACAGG | (AC)12 or (AC)20 | 56 | 9 | 189、191、193、211、213、215、217、243、245 |
LiSS5 | F: TCGTGTTTACCACCTGACCA | R: AGAGTGCTCAGGCTCGACAT | (AGC)9 | 56 | 2 | 351、354 |
LiSS13 | F: TGGTACAAATCCCGTCTATGG | R: CGCAACGGTACAGAAATTCA | (ACGC)7 | 54 | 2 | 141、149 |
Table 6
Statistical of L. invasa cryptic species identification result"
种群代码 Population code | 样本量 Samples | 隐种A数量(比例) Cryptic species A number(Ratio) | 隐种B数量(比例) Cryptic species B number(Ratio) | 隐种C数量(比例) Cryptic species C number(Ratio) |
SCDY | 32 | 0(0.00%) | 32(100.00%) | 0(0.00%) |
SCPZH | 32 | 11(34.38%) | 21(65.62%) | 0(0.00%) |
JXGZ | 32 | 30(93.75%) | 2(6.25%) | 0(0.00%) |
FJSM | 32 | 0(0.00%) | 32(100.00%) | 0(0.00%) |
HNDZ | 4 | 0(0.00%) | 4(100.00%) | 0(0.00%) |
YNKM | 3 | 0(0.00%) | 3(100.00%) | 0(0.00%) |
GXFCG1 | 32 | 30(93.75%) | 2(6.25%) | 0(0.00%) |
GXFCG2 | 32 | 1(3.12%) | 31(96.88%) | 0(0.00%) |
GXNN1 | 32 | 2(6.25%) | 30(93.75%) | 0(0.00%) |
GXNN2 | 32 | 1(3.12%) | 31(96.88%) | 0(0.00%) |
GXWZ | 32 | 29(84.38%) | 3(15.62%) | 0(0.00%) |
GXLB | 16 | 0(0.00%) | 16(100.00%) | 0(0.00%) |
GXYL | 3 | 0(0.00%) | 3(100.00%) | 0(0.00%) |
GXQZ | 6 | 0(0.00%) | 6(100.00%) | 0(0.00%) |
总计Total | 320 | 104(32.50%) | 216(67.50%) | 0(0.00%) |
Table 7
Statistics on the proportion of cryptic species of L. invasa in the world"
国外种群 Foreign population | 样本量 Sample | 隐种数量(比例)Cryptic species (Ratio) | mtDNA COI基因序列的GenBank登录号 GenBank accession numbers for mtDNA COI gene sequences | ||
A | B | C | |||
加纳Ghana | 8 | 0(0.00%) | 8(100.00%) | 0(0.00%) | MH093117—MH093119, MH093168—MH093172 |
肯尼亚Kenya | 49 | 49(100.00%) | 0(0.00%) | 0(0.00%) | MH093190—MH093193, MH093226—MH093228, MH093410—MH093426, MH092440—MH093445 MH093446—MH093451, MH093427—MH093439 |
莫桑比克 Mozambique | 36 | 36(100.00%) | 0(0.00%) | 0(0.00%) | MH093197—MH093199, MH093234—MH093238, MH093305—MH093309, MH093453—MH094375 |
南非 South Africa | 38 | 34(89.47%) | 4(10.53%) | 0(0.00%) | MH093310—MH093324, MH093186, MH093241—MH093243, MH093325—MH093339, MH093111, MH093112, MH093180, MH093181 |
突尼斯Tunisia | 3 | 3(100.00%) | 0(0.00%) | 0(0.00%) | KP233982— KP233984 |
乌干达Uganda | 23 | 23(100.00%) | 0(0.00%) | 0(0.00%) | MH093194—MH093196, MH093239, MH093240, MH093246, MH093252—MH093259, MH093394—MH093402 |
津巴布韦Zimbabwe | 1 | 1(100.00%) | 0(0.00%) | 0(0.00%) | MH093476 |
非洲总计 Africa total | 158 | 146(92.41%) | 12(7.59%) | 0(0.00%) | — |
中国江西赣州 Ganzhou, Jiangxi,China | 15 | 0(0.00%) | 15(100.00%) | 0(0.00%) | KP233985— KP233988, KP233990—KP233993, JQ289999—JQ280005 |
以色列Israel | 33 | 33(100.00%) | 0(0.00%) | 0(0.00%) | MH093187—MH093189, MH093207—MH093210, MH093218—MH093223, MH093260—MH093279 |
老挝Laos | 38 | 31(81.58%) | 7(18.42%) | 0(0.00%) | MH093200—MH093204, MH093280—MH093289, MH093452, MH093146, MH093147, MH093149—MH093152, MH093355, MH093148, MH093349—MH093354, MH093345—MH093348, MH093340—MH093343 |
马来西亚Malaysia | 9 | 0(0.00%) | 9(100.00%) | 0(0.00%) | MH093113—MH093116, MH093175—MH093179 |
越南Vietnam | 10 | 1(10.00%) | 9(90.00%) | 0(0.00%) | MH093139—MH093145, MH093173, MH093174, MH093344 |
泰国Thailand | 65 | 31(47.69%) | 34(52.31%) | 0(0.00%) | MH093120—MH093138, MH093153—MH093167, MH093211, MH093212, MH093217, MH093245, MH093247—MH093251, MH093372—MH093393 |
亚洲总计 Asia total | 170 | 96(56.47%) | 74(43.53%) | 0(0.00%) | — |
澳大利亚Australia | 114 | 0(0.00%) | 109(95.61%) | 5(4.39%) | MH093063, MH093048—MH093052, MH093053, MH093064—MH093074, MH093054, MH093055, MH093182—MH093185, MH093056, MH093075— MH093078, MH093082—MH093086, MH093087, MH093088, MH093057—MH093062, MH093010—MH093042, MH093001—MH093005, MH093006—MH093009, MH093043—MH093047, MH093094, MH093095, MH093079, MH093089— MH093093, MH093080, MH093081, MH093096—MH093110 |
大洋洲总计 Australasia total | 114 | 0(0.00%) | 109(95.61%) | 5(4.39%) | — |
意大利Italy | 38 | 38(100.00%) | 0(0.00%) | 0(0.00%) | MH093205, MH093206, MH093224, MH093225, MH093290—MH093304, MH093361—MH093371, KP233972— KP233979 |
土耳其Turkey | 1 | 1(100.00%) | 0(0.00%) | 0(0.00%) | KP233954 |
欧洲总计 Europe total | 39 | 39(100.00%) | 0(0.00%) | 0(0.00%) | — |
巴西Brazil | 27 | 27(100.00%) | 0(0.00%) | 0(0.00%) | MH093213—MH093216, MH093229—MH093233, MH093244, MH093403—MH093409, MH093356— MH093360, MH093477—MH093481, |
阿根廷Argentina | 3 | 3(100.00%) | 0(0.00%) | 0(0.00%) | KP233979—KP233981 |
美洲总计 America total | 30 | 30(100.00%) | 0(0.00%) | 0(0.00%) | — |
总计Total | 511 | 311(60.86%) | 195(38.16%) | 5(0.98%) | — |
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