<it>De novo</it> sequencing and analysis of the <it>Ulva linza</it> transcriptome to discover putative mechanisms associated with its successful colonization of coastal ecosystems
<p>Abstract</p> <p>Background</p> <p>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 <it>Ulva</it> species are also highly...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2012-10-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/13/565 |
| _version_ | 1818347359453577216 |
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| author | Zhang Xiaowen Ye Naihao Liang Chengwei Mou Shanli Fan Xiao Xu Jianfang Xu Dong Zhuang Zhimeng |
| author_facet | Zhang Xiaowen Ye Naihao Liang Chengwei Mou Shanli Fan Xiao Xu Jianfang Xu Dong Zhuang Zhimeng |
| author_sort | Zhang Xiaowen |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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 <it>Ulva</it> 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. <it>Ulva linza</it> 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 <it>U. linza</it> 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.</p> <p>Results</p> <p><it>De novo</it> 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 <it>U. linza</it> and 18 conserved in land plants. In addition, a specific photoprotective mechanism based on both <it>Lhc</it>SR and <it>Psb</it>S proteins and a C4-like carbon-concentrating mechanism were found, which may help <it>U. linza</it> 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 <it>U. linza</it> under stress conditions.</p> <p>Conclusions</p> <p>The transcriptome of <it>U. linza</it> 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 <it>Lhc</it>SR and <it>Psb</it>S; 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.</p> |
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| spelling | doaj.art-baa8b6d2829141f48e622b4266ec93152022-12-21T23:37:00ZengBMCBMC Genomics1471-21642012-10-0113156510.1186/1471-2164-13-565<it>De novo</it> sequencing and analysis of the <it>Ulva linza</it> transcriptome to discover putative mechanisms associated with its successful colonization of coastal ecosystemsZhang XiaowenYe NaihaoLiang ChengweiMou ShanliFan XiaoXu JianfangXu DongZhuang Zhimeng<p>Abstract</p> <p>Background</p> <p>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 <it>Ulva</it> 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. <it>Ulva linza</it> 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 <it>U. linza</it> 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.</p> <p>Results</p> <p><it>De novo</it> 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 <it>U. linza</it> and 18 conserved in land plants. In addition, a specific photoprotective mechanism based on both <it>Lhc</it>SR and <it>Psb</it>S proteins and a C4-like carbon-concentrating mechanism were found, which may help <it>U. linza</it> 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 <it>U. linza</it> under stress conditions.</p> <p>Conclusions</p> <p>The transcriptome of <it>U. linza</it> 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 <it>Lhc</it>SR and <it>Psb</it>S; 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.</p>http://www.biomedcentral.com/1471-2164/13/565 |
| spellingShingle | Zhang Xiaowen Ye Naihao Liang Chengwei Mou Shanli Fan Xiao Xu Jianfang Xu Dong Zhuang Zhimeng <it>De novo</it> sequencing and analysis of the <it>Ulva linza</it> transcriptome to discover putative mechanisms associated with its successful colonization of coastal ecosystems BMC Genomics |
| title | <it>De novo</it> sequencing and analysis of the <it>Ulva linza</it> transcriptome to discover putative mechanisms associated with its successful colonization of coastal ecosystems |
| title_full | <it>De novo</it> sequencing and analysis of the <it>Ulva linza</it> transcriptome to discover putative mechanisms associated with its successful colonization of coastal ecosystems |
| title_fullStr | <it>De novo</it> sequencing and analysis of the <it>Ulva linza</it> transcriptome to discover putative mechanisms associated with its successful colonization of coastal ecosystems |
| title_full_unstemmed | <it>De novo</it> sequencing and analysis of the <it>Ulva linza</it> transcriptome to discover putative mechanisms associated with its successful colonization of coastal ecosystems |
| title_short | <it>De novo</it> sequencing and analysis of the <it>Ulva linza</it> transcriptome to discover putative mechanisms associated with its successful colonization of coastal ecosystems |
| title_sort | it de novo it sequencing and analysis of the it ulva linza it transcriptome to discover putative mechanisms associated with its successful colonization of coastal ecosystems |
| url | http://www.biomedcentral.com/1471-2164/13/565 |
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