Transcriptome analysis of metamorphosis stage of Holothuria leucospilota
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摘要:
海参幼苗发育需要经历耳状幼体、樽形幼体、五触手幼体及幼苗阶段,而从浮游幼体变态发育至附着幼苗阶段的高死亡率是热带海参繁育中的共性问题,目前有关热带海参变态发育的调控机制仍不清楚。以玉足海参 (Holothuria leucospilota) 为研究对象,采集小耳幼体 (A)、中耳幼体 (B)、大耳幼体 (C) 和樽形幼体 (D) 4个时期样品进行高通量转录组测序分析,以探究其变态发育的分子机制。结果显示,共产生83.6 GB Raw reads,拼接获得93 528个Unigenes。对4个组测序文库的相邻组间 (A_vs_B, B_vs_C, C_vs_D) 进行两两比较,A_vs_B、B_vs_C和C_vs_D的差异表达基因数目分别为17 732、11 757和11 319 个。GO功能富集显示,差异基因主要富集于分子功能、催化活性等与细胞成长相关的GO功能。此外对KEGG通路进行了分析,结果显示差异基因显著富集于PI3K-Akt、细胞周期、癌症途径等与细胞分化增殖、凋亡相关的信号通路中,其中在幼体由浮游的大耳状幼体变态至附着的樽形幼体过程中,癌症途径的富集频率显著上升,表明其在幼体生长发育模式转换上发挥了关键作用。筛选的差异表达基因及预测的功能信息可为热带海参生长发育调控机制研究、人工繁育及分子改良应用提供参考。
Abstract:Development of sea cucumber larvae needs to go through stages of auricularia, doliolaria, pentactula and juvenile. High mortality rate from metamorphosis and development of planktonic larvae to attachment stage of seedlings is a common problem in tropical sea cucumbers breeding. However, the gene regulation mechanism underlying the metamorphosis development of tropical sea cucumber is still unclear. In this study, we chose larval Holothuria leucospilota from four periods of early auricularia (A), mid auricularia (B), late auricularia (C) and doliolaria (D) as samples for high-throughput transcriptome sequencing to investigate the molecular mechanism underlying its metamorphosis development. The results show that a total of 83.6 GB Raw reads were generated, and 93 528 Unigenes were obtained by splicing. Pairwise comparisons between adjacent groups of the four sequencing libraries show that the number of genes with significant differential expression in A_vs_B, B_vs_C and C_vs_D were 17 732, 11 757 and 11 319, respectively. GO function enrichment shows that differential genes were mainly enriched in GO functions related to cell growth, such as molecular function and catalytic activity. In addition, KEGG pathways were analyzed, and the results show that the differential genes were significantly enriched in pathways related to cell differentiation, proliferation and apoptosis, such as PI3K-Akt, cell cycle and cancer pathways. Among them, the enrichment frequency of the pathway in cancer significantly increased during the metamorphosis process, which indicates a key role in the transformation of larval growth and development mode. The screened differentially expressed genes and predicted functional information can lay a foundation for the research on the regulatory mechanism of growth and development, artificial breeding and molecular improvement application of H. leucospilota.
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斑节对虾(Penaeus monodon)是世界重要的养殖对虾品种之一,国内外有许多关于斑节对虾的研究报道[1-4]。中国南方早在20世纪80年代末就开展斑节对虾的人工育苗[5]和养殖研究[6]工作。斑节对虾亲虾在性腺发育期间,卵巢质量能在1周内增加4~8倍[7-8],显然,这个过程进行了很活跃的营养代谢,发生了大量的营养积累。因此,研究亲虾在性腺发育期间肝胰腺、性腺等的生化组成及其变化很有必要。
有关斑节对虾蛋白质、氨基酸的研究报道很多,如斑节对虾亲虾肌肉和成熟卵巢的氨基酸组成[1];斑节对虾不同生长阶段肌肉氨基酸组成[9];斑节对虾对精氨酸(Arg)、蛋氨酸(Met)、苯丙氨酸(Phe)、色氨酸(Trp)的需求量[10]等。斑节对虾在卵巢发育过程中,卵巢和肝胰腺的脂肪酸组成研究已有报道[2],但未见有关氨基酸组成的报道。笔者收集了海南岛南部海域的野生斑节对虾,测定了卵巢发育不同阶段的全虾、肝胰腺和卵巢的氨基酸组成,为斑节对虾亲虾人工培育技术的优化及其人工饵料研制提供参考依据。
1. 材料与方法
1.1 材料
2011年10月至12月,从海南省陵水、三亚和乐东附近海区的渔获物中选购活体斑节对虾雌虾,根据黄建华等[11-12]的卵巢发育分期方法,把Ⅰ期和Ⅵ期作为卵巢发育初级阶段,Ⅱ、Ⅲ、Ⅳ期作为中级阶段,Ⅴ期作为高级阶段。3个阶段的雌虾各选购45尾,充氧包装,运回实验室。测量头胸甲长、体长和体质量,每阶段样品解剖30尾,分离出肝胰腺和卵巢,分别称取质量并记录(精确到0.01 g),同阶段肝胰腺和卵巢样品用研钵分别混合捣碎,同阶段全虾样品分别用绞肉机混合绞碎。样品放在75 ℃烘箱中烘干至恒质量,塑料袋密封包装,置干燥箱中备用。
1.2 方法
烘烤去水分后的样品用盐酸水解测定17种氨基酸,用甲氧酸水解法测定色氨酸,处理后在日产835-50型氨基酸自动分析仪上分析,每个样品分析3次。分析条件为离子交换柱2.6 mm×150 mm,交换柱型号No.2619,柱温53 ℃,泵流速0.225 mL · min-1,泵压力90 kg · cm-2,进样体积50 mL,分析时间72 min。
1.3 计算公式
肝胰腺指数(HSI)=肝胰腺质量/体质量×100
性腺指数(GSI)=性腺质量/体质量×100
1.4 数据处理
采用Excel 2003软件对数据进行统计分析并作图,数值用平均数±标准误差(x±SD)表示,并进行Duncan′s多重比较,P<0.05表示差异显著。
2. 结果
2.1 肝胰腺指数与性腺指数
野生斑节对虾卵巢发育的初级、中级和高级阶段,HSI有差异但不显著(P>0.05);GSI差异显著(P<0.05),中级阶段为初级阶段的2倍,高级阶段约为初级阶段的6倍。表明卵巢在发育过程中发生了大量的营养积累,卵巢质量不断增加,Ⅴ期达到最大值(图 1)。
2.2 全虾氨基酸
随着卵巢的发育,野生斑节对虾全虾氨基酸总量逐渐增加,但差异不显著(P>0.05)。必需氨基酸总量略呈“V”型变化趋势,差异不显著(P>0.05)。3个阶段样品中,谷氨酸(Glu)含量均最高,占氨基酸总量的15%;其次是门冬氨酸(Asp),占9.5%;含量最少的是胱氨酸(Cys),占氨基酸总量的0.5%(表 1)。牛磺酸(Tau)含量以中级阶段为最高,高级阶段次之,初级阶段最低(表 1),各阶段Tau含量差异显著(P<0.05)。表明卵巢发育中级阶段Tau代谢活跃。
表 1 野生斑节对虾卵巢发育过程中全虾的氨基酸质量分数Table 1. Amino acid (AA) contents of whole body of wild female P.monodon during ovary developmentmg·g-1 氨基酸amino acid 初级阶段primary stage 中级阶段medium stage 高级阶段the highest stage 门冬氨酸Asp 57.4±0.8 59.5±1.0 60.4±2.1 酪氨酸Tyr 19.3±0.1 19.6±0.7 19.7±0.6 丝氨酸Ser 20.5±0.2 21.5±1.1 21.7±0.6 谷氨酸Glu 90.4±3.8 90.9±4.3 91.0±4.8 脯氨酸Pro 24.1±1.2 24.5±1.0 24.4±1.4 甘氨酸Gly 41.2±1.6 43.8±1.4 43.2±2.6 丙氨酸Ala 38.8±1.0 38.6±0.9 39.3±1.1 胱氨酸Cys 3.0±0 3.2±0 3.1±0 缬氨酸* Val 30.3±0.9 30.5±0.7 30.8±1.2 蛋氨酸* Met 14.9±0.3 15.6±0.2 15.0±0.2 异亮氨酸* Ile 27.6±0.2 25.5±0.1 28.2±0.3 亮氨酸* Leu 44.3±2.0 42.1±2.1 45.0±1.8 苏氨酸* Thr 22.9±0.1 23.1±0.2 23.5±1.0 苯丙氨酸* Phe 26.7±0.5 26.0±0.3 28.7±0.4 赖氨酸* Lys 42.1±0.3 42.6±1.2 43.1±2.0 组氨酸* His 10.2±0.1 9.6±0.2 11.0±0.1 色氨酸* Trp 5.0±0 5.1±0 5.7±0 精氨酸* Arg 54.3±3.3 55.5±4.8 55.7±3.9 牛磺酸Tau 9.8±0.1a 13.1±0.2b 11.1±0.1c 氨基酸总量total AA 600.8±23.2a 606.6±30.5a 618.0±31.1a 必需氨基酸总量total EAA 278.3±11.3a 275.6±9.6a 286.0±12.0a 注:同行数据中不同上标字母者差异显著(P<0.05);*.必需氨基酸;后表同此
Note:Values in same row with different superscript letters are significantly different from each other (P<0.05);*. essential amino acid;The same case in the following table.2.3 肝胰腺与卵巢的氨基酸
在初级、中级和高级3个发育阶段的野生斑节对虾肝胰腺及卵巢中,肝胰腺和卵巢氨基酸总量呈倒“V”型,差异不显著(P>0.05)(表 2);肝胰腺中的必需氨基酸总量也略呈倒“V”型,卵巢的必需氨基酸总量呈增加的趋势,但各阶段之间差异不显著(P>0.05)(表 2)。中级阶段卵巢有5种氨基酸处于峰值,分别是天门冬氨酸(Asp)、谷氨酸(Glu)、脯氨酸(Pro)、酪氨酸(Tyr)和赖氨酸(Lys)(表 2)。
表 2 野生斑节对虾卵巢发育过程中肝胰腺与卵巢的氨基酸质量分数Table 2. Amino acid (AA) contents of hepatopancreas and ovary of wild female P.monodon during ovary developmentmg·g-1 氨基酸amino acid 肝胰腺hepatopancreas 卵巢ovary 初级阶段primary stage 中级阶段medium stage 高级阶段the highest stage 初级阶段primary stage 中级阶段medium stage 高级阶段the highest stage 天门冬氨酸Asp 38.0±0.4 43.4±2.0 38.5±0.9 47.7±3.4 48.2±4.2 23.7±2.3 谷氨酸Glu 49.3±0.8 52.5±1.8 48.9±3.2 69.9±4.2 74.5±3.8 67.6±4.6 丝氨酸Ser 16.5±0.2 18.7±0.3 16.7±0.3 21.0±0.7 22.2±1.2 23.1±1.2 甘氨酸Gly 23.2±0.5 25.0±0.3 23.1±0.4 29.9±0.8 28.1±1.0 27.0±0.8 丙氨酸Ala 24.8±0.9 25.4±0.7 22.6±0.6 29.5±1.3 25.9±2.5 34.6±1.8 脯氨酸Pro 17.0±0.5 17.1±0.3 16.8±0.6 17.2±0.7 19.4±0.8 1.91±0.1 酪氨酸Tyr 15.3±0.2 18.0±0.4 15.2±0.5 17.4±0.6 19.7±0.9 19.4±0.5 胱氨酸Cys 2.6±0 2.3±0.1 2.1±0.01 2.0±0 2.2±0.1 2.3±0.1 苏氨酸* Thr 18.0±0.2 19.3±0.4 18.0±0.3 32.5±0.6 27.1±2.3 28.8±1.1 组氨酸* His 7.1±0.1 7.3±0.2 6.5±0.1 9.3±0.4 11.5±0.4 11.6±0.9 精氨酸* Arg 28.4±1.0 28.5±0.9 25.1±1.0 26.3±2.2 24.8±2.4 24.4±1.7 缬氨酸* Val 23.3±0.6 26.5±0.7 23.2±0.9 25.9±1.1 23.3±0.6 33.2±1.0 蛋氨酸* Met 8.7±0.1 8.2±0.3 8.0±0.3 10.4±0.4 11.6±0.3 12.0±0.4 异亮氨酸* Ile 18.9±1.0 23.5±0.6 19.0±0.5 20.9±1.4 25.8±0.6 27.6±1.2 苯丙氨酸* Phe 18.1±0.8 21.0±0.7 17.6±1.0 20.5±2.2 22.5±1.3 23.8±0.8 亮氨酸* Leu 31.4±1.1 25.8±1.0 30.6±2.4 34.0±2.8 37.2±2.0 38.7±1.8 色氨酸* Trp 4.5±0.1 4.8±0.2 4.3±0.3 4.1±0.2 4.3±0.3 4.8±0.2 赖氨酸* Lys 27.4±0.3 28.3±0.4 26.6±0.8 32.5±1.1 35.9±2.2 33.7±1.6 氨基酸总量total AA 372.5±18.4a 395.6±20.3ab 362.8±24.1bc 451.0±24.3a 464.2±35.5a 455.4±28.1a 必需氨基酸总量total EAA 185.8±13.3a 193.2±12.6a 178.9±15.2a 216.4±14.6a 224.0±14.1ab 238.6±11.3bc 3. 讨论
3.1 性腺发育过程的采样
亲虾的卵巢发育是一个连续过程,大多学者根据卵巢发育形态、组织学观察或化学成分分析分为6期[2, 11-13],这些分期方法较细但工作量大且费时,笔者通过简单的肉眼判断将卵巢发育分为初级阶段(对光看不到性腺,即Ⅰ和Ⅵ期)、中级阶段(对光看清性腺,即Ⅱ、Ⅲ和Ⅳ期)和高级阶段(对光性腺极度膨大,即Ⅴ期),测定的GSI差异极显著。因此,笔者认为此研究采用该分期方法简便可行。
3.2 卵巢发育中全虾的氨基酸和Tau质量分数
该试验中,斑节对虾全虾样品质量分数最高是Glu,约占总氨基酸的15%;最低为Cys,约占0.5%。与斑节对虾成虾肌肉中w(Glu)最高(约14%)、w(Cys)最低(约0.6%)[14]的结果相似。全虾氨基酸总量和必需氨基酸总量略有差异,但不显著。卵巢发育过程中肝胰腺和卵巢氨基酸代谢活跃,这可能是全虾氨基酸略有差异的主要原因。但是,w(Tau)差异显著(P<0.05),中级阶段最高,初级阶段最低。Tau是一种含硫的非蛋白结构氨基酸,影响动物的繁殖性能[15],对脂肪代谢发挥重要的生理作用[16],能显著提高雄性大鼠血清睾丸酮水平[17],明显提高鸡蛋质量[18],促进黄鸡性腺组织发育[19],对鱼类繁殖成功同样起到促进作用[20]。尚未见Tau对对虾繁殖性能的研究报道,原因可能是还没有适宜亲虾的配合饲料。对虾是无脊椎动物,比前述实验动物低等,其卵巢发育表现在卵黄积累,Tau可能加速卵黄积累,导致性腺成熟,但其作用机理有待进一步研究。
3.3 卵巢发育中肝胰腺和卵巢氨基酸质量分数
该试验中肝胰腺氨基酸总量和必需氨基酸总量随着卵巢发育而逐渐上升,至临产(Ⅴ期)时下降。中国对虾(P.chinensis)亲虾肝胰腺的消化酶活性随卵巢发育逐渐上升,至临产卵时(Ⅴ期)活性下降[13];消化酶是一种蛋白质,由氨基酸构成,可以理解为中国对虾氨基酸总量随性腺发育而逐渐上升。一些鱼类也有类似的现象[21-22];斑节对虾卵巢发育期间需要消化更多食物才能快速积累营养,氨基酸水平上升可能是消化酶活性增加所致。摘除眼柄是促使对虾卵巢发育的典型方法,但摘除眼柄后中华绒螯蟹(Eriocheir sinensis)肝脏氨基酸略有下降[23],摘除眼柄无助于诱导中华绒螯蟹卵巢的成熟[24]。这从肝胰腺氨基酸变化可以得到旁证。
该试验中随着卵巢发育,野生斑节对虾卵巢的氨基酸总量逐渐上升,临产时(Ⅴ期)下降,而必需氨基酸总量逐渐上升。哈氏仿对虾(Parapenaeopsis hardwickii)卵巢发育时蛋白质发生了积累[25];成熟凡纳滨对虾(P.vannamei)卵巢蛋白质含量增加[26];随着性腺发育,野生和养殖褐牙鲆(Paralichthys olivaceus)亲鱼卵巢中氨基酸含量也发生类似的变化[19]。对虾卵巢发育需要积累大量卵黄蛋白,即氨基酸水平会上升。但临产(Ⅴ期)时卵巢氨基酸水平会下降,其原因有待深入研究。
笔者研究结果显示,卵巢中级阶段野生斑节对虾卵巢的Asp、Glu、Pro、Tyr和Lys质量分数达到极大值,总和占总氨基酸的42.5%。实际生产中为了促使对虾卵巢发育,多投喂沙蚕、乌贼、牡蛎等,其中以沙蚕的效果最好。这可能与饵料中富含Asp、Glu、Pro、Tyr和Lys有关。据报道,长吻沙蚕(Glycera chirori)中上述几种氨基酸总量占36.8%[27],近江牡蛎(Crassostrea rivularis)占37.0%[27],杜氏枪乌贼(Loligo duvancelii)占37.7%[27]。饲料蛋白质的氨基酸不平衡会降低蛋白质效率[28]。笔者研究结果提示人工配制亲虾饵料时要考虑Asp、Glu、Pro、Tyr和Lys等这几种氨基酸总量要求(约为氨基酸总量的37%)及它们之间的平衡关系,并添加适量的Tau,但适宜的添加水平有待于进一步研究。
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图 5 相邻组间差异表达基因火山图
注:A_vs_B. B期以A期为参照基准比较;B_vs_C. C期以B期为参照基准比较;C_vs_D. D期以C期为参照基准比较。后图同此。
Figure 5. Volcano map of differentially expressed genes between adjacent groups
Note: A_vs_B. Stage B was compared with Stage A; B_vs_C. Stage C was compared with Stage B; C_vs_D. Stage D was compared with Stage C. The same case in following figures.
表 1 引物信息
Table 1 Primer information
基因 ID
Gene ID正向引物
Forward primer反向引物
Reverse primerU_57660 CACTCACGCAGAAGATGT CCAGCAATTCCAAGTTCAAT U_166100 CCTCATCCTTGCTGCTATT GTCACTCCAACACCAACA U_10254 AGTCACAGAACAGAGGTAAT CGAACGGTCCACATATCA U_21303 ACACCGAACACAGGAATC CCGTTAAGGAGTAAGAGTCA U_27749 TCATTGTTCGGATTGATTGC AACTGCTGACATTGACCAT U_179808 GGATGGCAAGATGAATACTG CGTCGCTATTAAGATTAGGAG β-Actin GTCAGGTCATCACTATCGGCAAT AGAGGTCTTTACGGATGTCAACGT 表 2 转录本组装结果统计分析
Table 2 Statistics analysis of transcript assembly results
项目类型
Item type数量
Number总序列数 Total sequence number 93 528 碱基总数 Total base 287 791 031 最长转录本长度 Maximum transcript length 9 920 最短转录本长度 Minimum transcript length 133 转录本平均长度 Average transcript length 3 077.06 N50 长度 N50 length 3 608 E90N50 长度 E90N50 length 3 575 GC 百分比 GC percent 38.67% Mapped 率 Mapped percent 73.71% 表 3 相邻组间差异表达基因 GO 富集分析 (前 5)
Table 3 GO enrichment analysis of differentially expressed genes between adjacent groups (Top five)
相邻组间
IntergroupGO ID GO 分类
GO Term频率
FrequencyP 值
P value类型
TypeA _vs _B GO: 0071840 细胞成分组织或生物发生
Cellular component organization or biogenesis0.072 0.091 233 GO: 0016043 细胞成分组织
Cellular component organization0.068 0.303 803 GO: 0044281 小分子代谢过程
Small molecule metabolic process0.066 0.000 836 生物过程
Biological processGO: 0007017 基于微管的过程
Microtubule-based process0.039 0.000 702 GO: 0019752 羧酸代谢过程
Carboxylic acid metabolic process0.037 0.000 818 GO: 0005575 细胞组分
Cellular_component0.661 0.081 363 GO: 0110165 细胞解构实体
Cellular anatomical entity0.594 0.061 953 GO: 0005576 细胞外区
Extracellular region0.053 0.000 702 细胞组分
Cellular componentGO: 0042995 细胞投影
Cell projection0.031 0.000 858 GO: 0099080 超分子复合物
Supramolecular complex0.030 0.001 038 GO: 0043167 离子结合
Ion binding0.325 0.014 108 GO: 0016787 水解酶活性
Hydrolase activity0.170 0.000 939 GO: 0036094 小分子结合
Small molecule binding0.163 0.000 962 分子功能
Molecular functionGO: 1901265 核苷磷酸结合
Nucleoside phosphate binding0.151 0.001 825 GO: 0000166 核苷酸结合
Nucleotide binding0.151 0.001 825 B_vs_C GO: 0044281 小分子代谢过程
Small molecule metabolic process0.063 0.097 450 GO: 0005975 碳水化合物代谢过程
Carbohydrate metabolic process0.030 0.000 614 GO: 0019637 有机磷代谢过程
Organophosphate metabolic process0.026 0.289 465 生物过程
Biological processGO: 0044283 小分子生物合成过程
Small molecule biosynthetic process0.021 0.076 630 GO: 0006091 前体代谢物和能量的产生
Generation of precursor metabolites and energy0.018 0.011 235 GO: 0005575 细胞组分
Cellular_component0.676 0.001 002 GO: 0110165 细胞解构实体
Cellular anatomical entity0.597 0.085 132 GO: 0031224 膜的内在成分
Intrinsic component of membrane0.307 0.071 058 细胞组分
Cellular componentGO: 0016021 膜的组成部分
Integral component of membrane0.306 0.087 041 GO: 000557 6 细胞外区
Extracellular region0.067 0.000 566 GO: 0043169 阳离子结合
Cation binding0.204 0.134 971 GO: 0046872 金属离子结合
Metal ion binding0.204 0.121 753 GO: 0016491 氧化还原酶活性
Oxidoreductase activity0.090 0.002 897 分子功能
Molecular functionGO: 0005215 转运蛋白活性
Transporter activity0.075 0.029 888 GO: 0005509 钙离子结合
Calcium ion binding0.073 0.000 626 C_ vs _D GO: 0005975 碳水化合物代谢过程
Carbohydrate metabolic process0.025 0.162 444 GO: 0044283 小分子生物合成过程
Small molecule biosynthetic process0.023 0.022 217 GO: 0007166 细胞表面受体信号通路
Cell surface receptor signaling pathway0.022 0.113 132 生物过程
Biological processGO: 0006790 硫化合物代谢过程
Sulfur compound metabolic process0.021 0.000 184 GO: 0032259 甲基化
Methylation0.020 0.014 144 GO: 0031224 膜的内在成分
Intrinsic component of membrane0.325 0.000 333 GO: 0016021 膜的组成部分
Integral component of membrane0.325 0.000 332 GO: 0005576 细胞外区
Extracellular region0.063 0.000 185 细胞组分
Cellular componentGO: 0005581 胶原蛋白三聚体
Collagen trimer0.031 0.000 184 GO: 0005615 细胞外空间
Extracellular space0.019 0.000 207 GO: 0003674 分子功能
Molecular_function0.820 0.000 312 GO: 0043169 阳离子结合
Cation binding0.214 0.000 417 GO: 0046872 金属离子结合
Metal ion binding0.214 0.000 382 分子功能
Molecular functionGO: 0140096 催化活性,作用于蛋白质
Catalytic activity, acting on a protein0.113 0.020 871 GO: 0016491 氧化还原酶活性
Oxidoreductase activity0.095 0.000 247 -
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