Development of a transcriptomic database for 14 species of scleractinian corals
Abstract Background Scleractinian corals are important reef builders, but around the world they are under the threat of global climate change as well as local stressors. Molecular resources are critical for understanding a species’ stress responses and resilience to the changing environment, but suc...
Main Authors: | , , , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
BMC
2019-05-01
|
Series: | BMC Genomics |
Subjects: | |
Online Access: | http://link.springer.com/article/10.1186/s12864-019-5744-8 |
id |
doaj-c3c013ad466442539ae2cfa9faac0c12 |
---|---|
record_format |
Article |
spelling |
doaj-c3c013ad466442539ae2cfa9faac0c122020-11-25T02:18:53ZengBMCBMC Genomics1471-21642019-05-012011910.1186/s12864-019-5744-8Development of a transcriptomic database for 14 species of scleractinian coralsYanjie Zhang0Qian Chen1James Y. Xie2Yip Hung Yeung3Baohua Xiao4Baoling Liao5Jianliang Xu6Jian-Wen Qiu7HKBU Institute of Research and Continuing Education, Virtual University ParkDepartment of Computer Science, Hong Kong Baptist UniversityDepartment of Biology, Hong Kong Baptist UniversityDepartment of Biology, Hong Kong Baptist UniversityShenzhen Institute of Guangdong Ocean UniversityShenzhen Institute of Guangdong Ocean UniversityDepartment of Computer Science, Hong Kong Baptist UniversityHKBU Institute of Research and Continuing Education, Virtual University ParkAbstract Background Scleractinian corals are important reef builders, but around the world they are under the threat of global climate change as well as local stressors. Molecular resources are critical for understanding a species’ stress responses and resilience to the changing environment, but such resources are unavailable for most scleractinian corals, especially those distributed in the South China Sea. We therefore aimed to provide transcriptome resources for 14 common species, including a few structure forming species, in the South China Sea. Description We sequenced the transcriptome of 14 species of scleractinian corals using high-throughput RNA-seq and conducted de novo assembly. For each species, we produced 7.4 to 12.0 gigabases of reads, and assembled them into 271 to 762 thousand contigs with a N50 value of 629 to 1427 bp. These contigs included 66 to 114 thousand unigenes with a predicted open reading frame, and 74.3 to 80.5% of the unigenes were functionally annotated. In the azooxanthelate species Tubastraea coccinea, 41.5% of the unigenes had at least a best-hit sequence from corals. In the other thirteen species, 20.2 to 48.9% of the annotated unigenes had best-hit sequences from corals, and 28.3 to 51.6% from symbiotic algae belonging to the family Symbiodinaceae. With these resources, we developed a transcriptome database (CoralTBase) which features online BLAST and keyword search for unigenes/functional terms through a user friendly Internet interface. Short conclusion We developed comprehensive transcriptome resources for 14 species of scleractinian corals and constructed a publicly accessible database (www.comp.hkbu.edu.hk/~db/CoralTBase). CoralTBase will facilitate not only functional studies using these corals to understand the molecular basis of stress responses and adaptation, but also comparative transcriptomic studies with other species of corals and more distantly related cnidarians.http://link.springer.com/article/10.1186/s12864-019-5744-8CoralCoral reefDatabaseScleractiniaSymbiotic algaeTranscriptome |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Yanjie Zhang Qian Chen James Y. Xie Yip Hung Yeung Baohua Xiao Baoling Liao Jianliang Xu Jian-Wen Qiu |
spellingShingle |
Yanjie Zhang Qian Chen James Y. Xie Yip Hung Yeung Baohua Xiao Baoling Liao Jianliang Xu Jian-Wen Qiu Development of a transcriptomic database for 14 species of scleractinian corals BMC Genomics Coral Coral reef Database Scleractinia Symbiotic algae Transcriptome |
author_facet |
Yanjie Zhang Qian Chen James Y. Xie Yip Hung Yeung Baohua Xiao Baoling Liao Jianliang Xu Jian-Wen Qiu |
author_sort |
Yanjie Zhang |
title |
Development of a transcriptomic database for 14 species of scleractinian corals |
title_short |
Development of a transcriptomic database for 14 species of scleractinian corals |
title_full |
Development of a transcriptomic database for 14 species of scleractinian corals |
title_fullStr |
Development of a transcriptomic database for 14 species of scleractinian corals |
title_full_unstemmed |
Development of a transcriptomic database for 14 species of scleractinian corals |
title_sort |
development of a transcriptomic database for 14 species of scleractinian corals |
publisher |
BMC |
series |
BMC Genomics |
issn |
1471-2164 |
publishDate |
2019-05-01 |
description |
Abstract Background Scleractinian corals are important reef builders, but around the world they are under the threat of global climate change as well as local stressors. Molecular resources are critical for understanding a species’ stress responses and resilience to the changing environment, but such resources are unavailable for most scleractinian corals, especially those distributed in the South China Sea. We therefore aimed to provide transcriptome resources for 14 common species, including a few structure forming species, in the South China Sea. Description We sequenced the transcriptome of 14 species of scleractinian corals using high-throughput RNA-seq and conducted de novo assembly. For each species, we produced 7.4 to 12.0 gigabases of reads, and assembled them into 271 to 762 thousand contigs with a N50 value of 629 to 1427 bp. These contigs included 66 to 114 thousand unigenes with a predicted open reading frame, and 74.3 to 80.5% of the unigenes were functionally annotated. In the azooxanthelate species Tubastraea coccinea, 41.5% of the unigenes had at least a best-hit sequence from corals. In the other thirteen species, 20.2 to 48.9% of the annotated unigenes had best-hit sequences from corals, and 28.3 to 51.6% from symbiotic algae belonging to the family Symbiodinaceae. With these resources, we developed a transcriptome database (CoralTBase) which features online BLAST and keyword search for unigenes/functional terms through a user friendly Internet interface. Short conclusion We developed comprehensive transcriptome resources for 14 species of scleractinian corals and constructed a publicly accessible database (www.comp.hkbu.edu.hk/~db/CoralTBase). CoralTBase will facilitate not only functional studies using these corals to understand the molecular basis of stress responses and adaptation, but also comparative transcriptomic studies with other species of corals and more distantly related cnidarians. |
topic |
Coral Coral reef Database Scleractinia Symbiotic algae Transcriptome |
url |
http://link.springer.com/article/10.1186/s12864-019-5744-8 |
work_keys_str_mv |
AT yanjiezhang developmentofatranscriptomicdatabasefor14speciesofscleractiniancorals AT qianchen developmentofatranscriptomicdatabasefor14speciesofscleractiniancorals AT jamesyxie developmentofatranscriptomicdatabasefor14speciesofscleractiniancorals AT yiphungyeung developmentofatranscriptomicdatabasefor14speciesofscleractiniancorals AT baohuaxiao developmentofatranscriptomicdatabasefor14speciesofscleractiniancorals AT baolingliao developmentofatranscriptomicdatabasefor14speciesofscleractiniancorals AT jianliangxu developmentofatranscriptomicdatabasefor14speciesofscleractiniancorals AT jianwenqiu developmentofatranscriptomicdatabasefor14speciesofscleractiniancorals |
_version_ |
1724880182010970112 |