De novo sequencing and analysis of the Ulva linza transcriptome to discover putative mechanisms associated with its successful colonization of coastal ecosystems.
De novo sequencing and analysis of the Ulva linza transcriptome to discover putative mechanisms associated with its successful colonization of coastal ecosystems.
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DOI：
10.1186/1471-2164-13-565
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发表时间：
2012-10-25
期刊：
影响因子：
4.4
通讯作者：
Zhuang Z
中科院分区：
文献类型：
--
作者：
Zhang X;Ye N;Liang C;Mou S;Fan X;Xu J;Xu D;Zhuang Z
绿藻属石莼属（石莼科、石莼目、绿藻门）以其广泛分布于世界各地的海洋、淡水和咸水环境中而闻名。石莼物种还对盐度、温度和辐照度的变化具有高度耐受性，是绿潮的主要原因，绿潮可能产生有害的生态影响。然而，目前这种非模式且具有重要生态意义的物种的基因组信息有限。石莼是一种栖息在中低潮间带基岩中的物种，是生物污垢的主要贡献者。在这里，我们使用罗氏 GS FLX Titanium 平台展示了 U. linza 转录组的全局特征，旨在揭示沿海生态系统快速成功定植的基因组机制。 382,884 个读数的从头组装生成了 13,426 个重叠群，平均长度为 1,000 个碱基。连续序列进一步组装成 10,784 个 isotig，平均长度为 1,515 个碱基。 BLAST名义上鉴定了总共304,101个读数； 4,368 个 isotig 被用 13,550 个 GO 术语进行功能注释，2,404 个具有酶委员会 (EC) 编号的 isotig 被分配到 262 个 KEGG 通路。与其他四种全测序绿藻相比，在 U. linza 中发现了 3,457 种独特的 isotig，在陆地植物中发现了 18 种。此外，还发现了基于 LhcSR 和 PsbS 蛋白的特定光保护机制以及类似 C4 的碳浓缩机制，这可能有助于 U. linza 在应激条件下生存。至少 19 个必需无机营养物质（即氮、磷和硫）的转运蛋白决定了其吸收无机营养物质的能力，而至少 25 个真核细胞色素 P450（数量比其他藻类中的数量要高）可能与其强烈的化感作用有关。应激相关蛋白的多来源，例如谷氨酸脱氢酶、超氧化物歧化酶、抗坏血酸过氧化物酶、过氧化氢酶和热休克蛋白，也可能有助于U. linza在应激条件下的定殖。 U. linza 的转录组揭示了一些潜在的基因组机制，这些机制可能解释其快速、成功地殖民沿海生态系统的能力，包括陆地特异性基因；基于LhcSR和PsbS的特殊光保护机制；开发类似C4的碳浓缩机制；必需无机营养素的多源转运蛋白；多个复杂的 P450；以及与抗应激相关的谷氨酸脱氢酶、超氧化物歧化酶、抗坏血酸过氧化物酶、过氧化氢酶和热休克蛋白。
The green algal genus Ulva Linnaeus (Ulvaceae, Ulvales, Chlorophyta) is well known for its wide distribution in marine, freshwater, and brackish environments throughout the world. The Ulva species are also highly tolerant of variations in salinity, temperature, and irradiance and are the main cause of green tides, which can have deleterious ecological effects. However, limited genomic information is currently available in this non-model and ecologically important species. Ulva linza is a species that inhabits bedrock in the mid to low intertidal zone, and it is a major contributor to biofouling. Here, we presented the global characterization of the U. linza transcriptome using the Roche GS FLX Titanium platform, with the aim of uncovering the genomic mechanisms underlying rapid and successful colonization of the coastal ecosystems. De novo assembly of 382,884 reads generated 13,426 contigs with an average length of 1,000 bases. Contiguous sequences were further assembled into 10,784 isotigs with an average length of 1,515 bases. A total of 304,101 reads were nominally identified by BLAST; 4,368 isotigs were functionally annotated with 13,550 GO terms, and 2,404 isotigs having enzyme commission (EC) numbers were assigned to 262 KEGG pathways. When compared with four other full sequenced green algae, 3,457 unique isotigs were found in U. linza and 18 conserved in land plants. In addition, a specific photoprotective mechanism based on both LhcSR and PsbS proteins and a C4-like carbon-concentrating mechanism were found, which may help U. linza survive stress conditions. At least 19 transporters for essential inorganic nutrients (i.e., nitrogen, phosphorus, and sulphur) were responsible for its ability to take up inorganic nutrients, and at least 25 eukaryotic cytochrome P450s, which is a higher number than that found in other algae, may be related to their strong allelopathy. Multi-origination of the stress related proteins, such as glutamate dehydrogenase, superoxide dismutases, ascorbate peroxidase, catalase and heat-shock proteins, may also contribute to colonization of U. linza under stress conditions. The transcriptome of U. linza uncovers some potential genomic mechanisms that might explain its ability to rapidly and successfully colonize coastal ecosystems, including the land-specific genes; special photoprotective mechanism based on both LhcSR and PsbS; development of C4-like carbon-concentrating mechanisms; muti-origin transporters for essential inorganic nutrients; multiple and complex P450s; and glutamate dehydrogenase, superoxide dismutases, ascorbate peroxidase, catalase, and heat-shock proteins that are related to stress resistance.
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影响因子：
3.4
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