南极红藻<i>Iridaea cordata</i>和<i>Curdiea racovitzae</i>转录组分析及其极端光环境适应相关基因的挖掘

刘晨临; 王秀良; 林学政

doi:10.3969/j.issn.0253-4193.2020.10.011

南极红藻Iridaea cordata和Curdiea racovitzae转录组分析及其极端光环境适应相关基因的挖掘

doi: 10.3969/j.issn.0253-4193.2020.10.011

刘晨临^{1, 3,},
王秀良^{2, 3},
林学政¹

1.
自然资源部第一海洋研究所，山东青岛 266061
2.
中国科学院海洋研究所，山东青岛 266071
3.
青岛海洋科学与技术试点国家实验室海洋生物学与生物技术实验室，山东青岛 266237

基金项目: 国家自然科学基金（41276203）；国家南极观测监测网运维与管理项目（JDKC0518013）。

详细信息

作者简介:
刘晨临(1974-)，女，山东省滨州市人，博士，主要从事藻类逆境分子生物学研究。E-mail：chenlinliu@fio.org.cn

中图分类号: S917.3
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出版历程
- 收稿日期: 2019-07-02
- 修回日期: 2019-11-18
- 网络出版日期: 2020-11-13
- 刊出日期: 2020-10-25

De nova transcriptome analysis and mining extreme light environments acclimation responding genes of Antarctic seaweed Iridaea cordata (Gigartinales, Rhodophyta) and Curdiea racovitzae (Gracilariaceae, Rhodophyta)

Liu Chenlin^{1, 3
,},
Wang Xiuliang^{2, 3},
Lin Xuezheng¹

1.
First Institute of Oceanography, Ministry of Natural Resources, Qingdao 266061, China
2.
Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China
3.
Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China

摘要

摘要: 南极红藻具有重要的生态学功能和开发利用价值。南极极端环境赋予了其独特的生理耐受机制，也是发现新基因和代谢途径的理想材料。我们测序分析了南极产胶红藻Iridaea cordata (Turner) Bory和Curdiea racovitzae Hariot的转录组序列，并与其常温近缘种进行了比较，同时挖掘了其与光限制和强紫外线辐射等光环境适应相关的基因。I. cordata和C. racovitzae的转录组序列分别拼接成了14055条和12006条非冗余基因，平均长度分别为1473 bp和1448 bp。在I. cordata转录组中发现多条与绿藻基因同源的捕光复合物LHC基因Lhca2、Lhca6和Lhcb，并且在两种南极红藻中都各发现了1条编码结合岩藻黄质和Chl a/c蛋白的Lhcf基因，目前尚未在其他红藻中发现这类基因。光裂解酶修复紫外线诱导DNA损伤，在I. cordata的转录组序列中发现了6−4光裂解酶，光裂解酶CPD I和CPD II基因，而C. racovitzae转录组序列中仅找到了光裂解酶CPD II基因。尽管南极红藻中这些特有基因的功能有待进一步的验证，但是本文为后续研究红藻的南极极端光环境适应机制提供了方向。
- 南极红藻 /
- 转录组 /
- 极端光环境适应 /
- Iridaea cordata /
- Curdiea racovitzae
Abstract: Antarctic red algae play important roles in the coastal ecosystems and industrial applications. Meanwhile, their unique physiological acclimation mechanisms to the extreme environments endow them to be ideal organisms for discovering new genes and new metabolic pathways. In this study, we sequenced the transcriptomes of Antarctic red algae Iridaea cordata (Turner) Bory and Curdiea racovitzae Hariot, and compared with their moderate temperature close relatives. The transcriptome sequences of I. cordata and C. racovitzae were assembled into 14055 and 12006 Unigenes, with an average length of 1473 bp and 1448 bp, respectively. The Lhca2, Lhca6 and Lhcb genes homologous to the green algae genes were found in I. cordata transcriptome while not in other red algae. Lhcf gene encoding fucoxanthine and Chl a/c binding protein presenting in brown algae and diatoms were identified in both I. cordata and C. racovitzae. Photolyase repairs UV-induced DNA damages. 6-4 photolyase, CPD I and CPD II genes were identified in the transcriptome of I. cordata, while only CPD II gene was found in the transcriptome of C. racovitzae. Although the functions of those specific genes in Antarctic red algae are expected further investigation, our study provides a foundation for the following researches on the acclimation mechanisms of seaweeds to the extreme light environments in Antarctica.
- Antarctic red algae /
- transcriptome /
- extreme light environmental acclimation /
- Iridaea cordata /
- Curdiea racovitzae

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图 1 南极红藻Iridaea cordata （a）和Curdiea racovitzae （b）的形态

Fig. 1 The morphology of Iridaea cordata (a) and Curdiea racovitzae (b)

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图 2 Iridaea cordata和Curdiea racovitzae转录组序列的EggNOG功能分类

Fig. 2 EggNOG function classification of Iridaea cordata and Curdiea racovitzae

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图 3 角叉菜Chondrus crispus与Iridaea cordata，龙须菜Gracilariopsis chorda与Curdiea racovitzae匹配基因数目的韦恩图

红色表示南极红藻，绿色表示常温红藻

Fig. 3 Diagram of the matching gene numbers between Chondrus crispus and Iridaea cordata, Gracilariopsis chorda and Curdiea racovitzae

Red represents the Antarctic red algae, green represents the normal temperate red algae

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图 4 捕光复合物的系统进化树

进化树由来自几种主要红藻的基因组或转录组中的所有LHC基因编码的蛋白序列，以及褐藻、绿藻和硅藻的部分LHC蛋白序列组成。5种类型的LHC用不同颜色的方框区分。LHCR为红藻型捕光复合物，LHCF是硅藻和褐藻中主要的天线蛋白，LHCa2、LHCa6和LHCb主要来自绿藻。IcoTRINITY和CraTRINITY分别表示Iridaea cordata和Curdiea racovitzae的蛋白编码序列。进化树经MEGA-X软件用邻接法构建，得到1 000次检验一致性的系统树，自举值在相应的节点标示

Fig. 4 Phylogenetic tree of the light harvesting complex superfamily

All of LHC sequences from the genome or transcriptome of several red algae species, and some LHCs from brown algae, green algae and diatoms are shown in the tree. Five LHC branches are represented by different color boxes. LHCR is from red algae, LHCf is mainly from diatom and brown algae, LHCa2, LHCa6 and LHCb are mainly from green algae. IcoTRINITY and CraTRINITY represent the sequences from Iridaea cordata and Curdiea racovitzae, respectively. The phylogenetic tree is obtained using Neighbor-Joining (NJ) method by MEGA-X software. Bootstrap values referred to 1 000 replicates are shown at the nodes

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图 5 Iridaea cordata的Lhca2、Lhca6和Lhcb基因编码的蛋白序列与绿藻LHC序列的比较

3种LHC序列用绿色线段区分，*表示参考莱茵衣藻序列中的叶绿素分子结合位点。Ath：拟南芥；Cin：衣藻；Cre：莱茵衣藻；Csu：胶球藻；Cva：小球藻；Dsa：杜氏盐藻；Ico：南极红藻；Ota：绿藻；Vca：团藻

Fig. 5 Alignment of Lhca2, Lhca6 and Lhcb of Iridaea cordata with homologous LHCs in green algae

Three LHC groups are distinguished with green lines; *marks amino acid residues that binding chlorophylls in Chlamydomonas reinhardtii sequences. Ath: Arabidopsis thaliana; Cin: Chlamydomonas incerta; Cre: Chlamydomonas reinhardtii; Csu: Coccomyxa subellipsoidea; Cva: Chlorella variabilis; Dsa: Dunaliella salina; Ico: Iridaea cordata; Ota: Ostreococcus tauri; Vca: Volvox carteri f. nagariensis

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图 6 光裂解酶/隐花色素超家族的系统进化树

进化树中序列的物种包括红藻（红色标记），绿藻和高等植物（绿色标记）以及褐藻和硅藻（褐色标记）。两株南极红藻用红线框标记。聚类的6个分支用不同颜色的边线表示，包括环丁烷嘧啶二聚体光裂解酶CPDI和CPDII，6−4嘧啶酮光裂解酶，隐花色素Cry，Cry-DASH和Cry-DASH II。1 000次检验一致性的系统树经MEGA-X软件用邻接法构建，自举值在相应的节点标示。Ath: 拟南芥; Ccr: 皱波角叉菜; Cme: 红藻; Cra: 南极红藻; Cre: 莱茵衣藻; Esi: 长囊水云; Gch: 绳状龙须菜; Ico: 南极红藻; Gsu: 红藻; Ptr: 三角褐指藻; Tps: 伪矮海链藻

Fig. 6 Phylogenetic tree of the cryptochrome/photolyase family

Species in the evolutionary tree include red algae (red marker), green algae and higher plants (green marker), and brown algae and diatoms (brown marker). Two Antarctic red algae are labeled with red frame. The six clusters are represented by different color lines, including photolyase CPD I and CPD II, 6−4 photolyase, and cryptochromes Cry, Cry-DASH and Cry-DASH II. The phylogenetic tree is constructed using Neighbor-Joining (NJ) method by MEGA-X. Bootstrap values referred to 1000 replicates are shown at the nodes. Taxonomic abbreviations: Ath: Arabidopsis thaliana; Ccr: Chondrus crispus; Cme: Cyanidioschyzon merolae; Cra: Curdiea racovitzae; Cre: Chlamydomonas reinhardtii; Esi: Ectocarpus siliculosus; Gch: Gracilariopsis chorda; Ico: Iridaea cordata; Gsu: Galdieria sulphuraria; Ptr: Phaeodactylum tricornutum; Tps: Thalassiosira pseudonana

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表 1 南极红藻Iridaea cordata和Curdiea racovitzae转录本和非冗余基因

Tab. 1 The contigs and unigenes of Iridaea cordata and Curdiea racovitzae

	Iridaea cordata		Curdiea racovitzae
	重叠群	非冗余基因	重叠群	非冗余基因
总长度/bp	23957720	20707433	19982213	17378947
序列数目	32395	14055	26226	12006
最大序列长度/bp	24631	24418	27865	26227
平均序列长度/bp	740	1473	762	1448
N50/bp	2724	3133	3256	3673
N50 序列数	2329	1901	1635	1307
N90/bp	199	537	210	457
N90 序列数	15816	7637	12822	6213
GC%	53.82	53.29	47.28	46.88

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表 2 Iridaea cordata和Curdiea racovitzae转录组序列在各个数据库的注释结果

Tab. 2 The annotation results of Iridaea cordata and Curdiea racovitzae transcriptome

数据库	Iridaea cordata		Curdiea racovitzae
数据库	数目	百分比	数目	百分比
NR	4788	34.07	4468	37.21
GO	1806	12.85	1838	15.31
KEGG	2024	14.40	1903	15.85
EggNOG	4523	32.18	4238	35.3
Swissprot	4864	34.61	4938	41.13
全部数据库	972	6.92	947	7.89

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