林业科学 ›› 2021, Vol. 57 ›› Issue (9): 140-151.doi: 10.11707/j.1001-7488.20210914
彭欣1,王瀚棠1,郭春晖1,杨振德1,2,*,周静1,王雪1,丁芷柔1
收稿日期:
2020-12-24
出版日期:
2021-09-25
发布日期:
2021-11-29
通讯作者:
杨振德
基金资助:
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
摘要:
目的: 对入侵性致瘿害虫桉树枝瘿姬小蜂(膜翅目:姬小蜂科)进行EST-SSR引物开发和隐种鉴定,为桉树枝瘿姬小蜂种群遗传学研究及其防治提供理论依据。方法: 采用Illumina HiSeqTM 2000测序平台对3个地理种群的桉树枝瘿姬小蜂雌性成虫进行转录组测序,利用MISA和Primer Premier 3软件进行EST-SSR标记的搜索、挖掘和引物设计。选取400对EST-SSR引物,结合国外报道的14对多态性G-SSR引物,应用1%琼脂糖凝胶电泳检测扩增效率,并用8%变性聚丙烯酰胺凝胶电泳验证引物多态性。基于桉树枝瘿姬小蜂COI基因序列数据对我国14个地理种群320个桉树枝瘿姬小蜂雌性成虫样本进行隐种鉴定。结果: 1)共获得277 048 525条clean reads,包括82.86 G个核苷酸,组装后得到44 878个unigene,平均长度1 082.76 bp,N50为1 976 bp;利用MISA软件搜索到EST-SSR位点14 190个,其中主要重复类型是单核苷酸重复(占总EST-SSR的69.63%),其次是二核苷酸重复和三核苷酸重复(分别占总EST-SSR的16.17%、13.51%)。2)400对EST-SSR引物中有205对引物可有效扩增出目的片段,扩增效率51.25%,国外报道的14对G-SSR引物均能扩增出目的片段;3)用8%变性聚丙烯酰胺凝胶电泳验证SSR引物多态性,最终筛选出10对多态性良好的EST-SSR引物,国外报道的14对G-SSR引物中仅有LiSS2、LiSS5、LiSS13在我国桉树枝瘿姬小蜂样本中存在多态性;4)从我国14个桉树枝瘿姬小蜂地理种群中共获得320条605 bp的COI基因序列,基于桉树枝瘿姬小蜂COI基因序列构建的NJ系统发育树表明,我国仅存在A、B 2种类型的桉树枝瘿姬小蜂隐种,样本比例约为1:2。结论: 筛选出10对适合我国桉树枝瘿姬小蜂种群遗传学研究的EST-SSR引物。我国存在A、B 2种类型的桉树枝瘿姬小蜂隐种,其中隐种A首次在我国发现,桉树枝瘿姬小蜂的隐种鉴定可为该害虫在生物防治中采用正确的生物型提供依据。
中图分类号:
彭欣,王瀚棠,郭春晖,杨振德,周静,王雪,丁芷柔. 入侵性致瘿害虫桉树枝瘿姬小蜂(膜翅目: 姬小蜂科)EST-SSR开发及隐种鉴定[J]. 林业科学, 2021, 57(9): 140-151.
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.
表1
桉树枝瘿姬小蜂14个地理种群采样信息"
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 |
表2
桉树枝瘿姬小蜂转录组组装质量"
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 | — |
表3
桉树枝瘿姬小蜂不同类型EST-SSRs重复次数统计"
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 | — |
表4
桉树枝瘿姬小蜂EST-SSRs重复基元类型统计"
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 |
表5
桉树枝瘿姬小蜂10对多态性EST-SSRs与国外3对多态性G-SSRs引物信息①"
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 |
图1
桉树枝瘿姬小蜂c127471引物的变性聚丙烯酰胺凝胶电泳 M:DNA分子量标记DNA molecular weight marker;GXNN1:广西南宁1 Nanning 1, Guangxi;JXGZ:江西赣州Ganzhou, Jiangxi;FJSM:福建三明Sanming, Fujian;SCPZH:四川攀枝花Panzhihua, Sichuan;SCDY:四川德阳Deyang, Sichuan;GXWZ:广西梧州Wuzhou, Guangxi;GXNN2:广西南宁2 Nanning 2, Guangxi;GXFCG2:广西防城港2 Fangchenggang 2, Guangxi."
表6
桉树枝瘿姬小蜂隐种鉴定结果统计"
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%) |
表7
全球桉树枝瘿姬小蜂隐种比例统计"
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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