The first symbiont-free genome sequence of marine red alga, Susabi-nori (Pyropia yezoensis).
Nori, a marine red alga, is one of the most profitable mariculture crops in the world. However, the biological properties of this macroalga are poorly understood at the molecular level. In this study, we determined the draft genome sequence of susabi-nori (Pyropia yezoensis) using next-generation se...
Guardado en:
| Autores principales: | , , , , , , , , , , , , , , , , , , , |
|---|---|
| Formato: | article |
| Lenguaje: | EN |
| Publicado: |
Public Library of Science (PLoS)
2013
|
| Materias: | |
| Acceso en línea: | https://doaj.org/article/6846861a15e94aad8f2e70b6b25f00ee |
| Etiquetas: |
Agregar Etiqueta
Sin Etiquetas, Sea el primero en etiquetar este registro!
|
| id |
oai:doaj.org-article:6846861a15e94aad8f2e70b6b25f00ee |
|---|---|
| record_format |
dspace |
| spelling |
oai:doaj.org-article:6846861a15e94aad8f2e70b6b25f00ee2021-11-18T07:54:02ZThe first symbiont-free genome sequence of marine red alga, Susabi-nori (Pyropia yezoensis).1932-620310.1371/journal.pone.0057122https://doaj.org/article/6846861a15e94aad8f2e70b6b25f00ee2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23536760/?tool=EBIhttps://doaj.org/toc/1932-6203Nori, a marine red alga, is one of the most profitable mariculture crops in the world. However, the biological properties of this macroalga are poorly understood at the molecular level. In this study, we determined the draft genome sequence of susabi-nori (Pyropia yezoensis) using next-generation sequencing platforms. For sequencing, thalli of P. yezoensis were washed to remove bacteria attached on the cell surface and enzymatically prepared as purified protoplasts. The assembled contig size of the P. yezoensis nuclear genome was approximately 43 megabases (Mb), which is an order of magnitude smaller than the previously estimated genome size. A total of 10,327 gene models were predicted and about 60% of the genes validated lack introns and the other genes have shorter introns compared to large-genome algae, which is consistent with the compact size of the P. yezoensis genome. A sequence homology search showed that 3,611 genes (35%) are functionally unknown and only 2,069 gene groups are in common with those of the unicellular red alga, Cyanidioschyzon merolae. As color trait determinants of red algae, light-harvesting genes involved in the phycobilisome were predicted from the P. yezoensis nuclear genome. In particular, we found a second homolog of phycobilisome-degradation gene, which is usually chloroplast-encoded, possibly providing a novel target for color fading of susabi-nori in aquaculture. These findings shed light on unexplained features of macroalgal genes and genomes, and suggest that the genome of P. yezoensis is a promising model genome of marine red algae.Yoji NakamuraNaobumi SasakiMasahiro KobayashiNobuhiko OjimaMotoshige YasuikeYuya ShigenobuMasataka SatomiYoshiya FukumaKoji ShiwakuAtsumi TsujimotoTakanori KobayashiIchiro NakayamaFuminari ItoKazuhiro NakajimaMotohiko SanoTokio WadaSatoru KuharaKiyoshi InouyeTakashi GojoboriKazuho IkeoPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 3, p e57122 (2013) |
| institution |
DOAJ |
| collection |
DOAJ |
| language |
EN |
| topic |
Medicine R Science Q |
| spellingShingle |
Medicine R Science Q Yoji Nakamura Naobumi Sasaki Masahiro Kobayashi Nobuhiko Ojima Motoshige Yasuike Yuya Shigenobu Masataka Satomi Yoshiya Fukuma Koji Shiwaku Atsumi Tsujimoto Takanori Kobayashi Ichiro Nakayama Fuminari Ito Kazuhiro Nakajima Motohiko Sano Tokio Wada Satoru Kuhara Kiyoshi Inouye Takashi Gojobori Kazuho Ikeo The first symbiont-free genome sequence of marine red alga, Susabi-nori (Pyropia yezoensis). |
| description |
Nori, a marine red alga, is one of the most profitable mariculture crops in the world. However, the biological properties of this macroalga are poorly understood at the molecular level. In this study, we determined the draft genome sequence of susabi-nori (Pyropia yezoensis) using next-generation sequencing platforms. For sequencing, thalli of P. yezoensis were washed to remove bacteria attached on the cell surface and enzymatically prepared as purified protoplasts. The assembled contig size of the P. yezoensis nuclear genome was approximately 43 megabases (Mb), which is an order of magnitude smaller than the previously estimated genome size. A total of 10,327 gene models were predicted and about 60% of the genes validated lack introns and the other genes have shorter introns compared to large-genome algae, which is consistent with the compact size of the P. yezoensis genome. A sequence homology search showed that 3,611 genes (35%) are functionally unknown and only 2,069 gene groups are in common with those of the unicellular red alga, Cyanidioschyzon merolae. As color trait determinants of red algae, light-harvesting genes involved in the phycobilisome were predicted from the P. yezoensis nuclear genome. In particular, we found a second homolog of phycobilisome-degradation gene, which is usually chloroplast-encoded, possibly providing a novel target for color fading of susabi-nori in aquaculture. These findings shed light on unexplained features of macroalgal genes and genomes, and suggest that the genome of P. yezoensis is a promising model genome of marine red algae. |
| format |
article |
| author |
Yoji Nakamura Naobumi Sasaki Masahiro Kobayashi Nobuhiko Ojima Motoshige Yasuike Yuya Shigenobu Masataka Satomi Yoshiya Fukuma Koji Shiwaku Atsumi Tsujimoto Takanori Kobayashi Ichiro Nakayama Fuminari Ito Kazuhiro Nakajima Motohiko Sano Tokio Wada Satoru Kuhara Kiyoshi Inouye Takashi Gojobori Kazuho Ikeo |
| author_facet |
Yoji Nakamura Naobumi Sasaki Masahiro Kobayashi Nobuhiko Ojima Motoshige Yasuike Yuya Shigenobu Masataka Satomi Yoshiya Fukuma Koji Shiwaku Atsumi Tsujimoto Takanori Kobayashi Ichiro Nakayama Fuminari Ito Kazuhiro Nakajima Motohiko Sano Tokio Wada Satoru Kuhara Kiyoshi Inouye Takashi Gojobori Kazuho Ikeo |
| author_sort |
Yoji Nakamura |
| title |
The first symbiont-free genome sequence of marine red alga, Susabi-nori (Pyropia yezoensis). |
| title_short |
The first symbiont-free genome sequence of marine red alga, Susabi-nori (Pyropia yezoensis). |
| title_full |
The first symbiont-free genome sequence of marine red alga, Susabi-nori (Pyropia yezoensis). |
| title_fullStr |
The first symbiont-free genome sequence of marine red alga, Susabi-nori (Pyropia yezoensis). |
| title_full_unstemmed |
The first symbiont-free genome sequence of marine red alga, Susabi-nori (Pyropia yezoensis). |
| title_sort |
first symbiont-free genome sequence of marine red alga, susabi-nori (pyropia yezoensis). |
| publisher |
Public Library of Science (PLoS) |
| publishDate |
2013 |
| url |
https://doaj.org/article/6846861a15e94aad8f2e70b6b25f00ee |
| work_keys_str_mv |
AT yojinakamura thefirstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT naobumisasaki thefirstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT masahirokobayashi thefirstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT nobuhikoojima thefirstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT motoshigeyasuike thefirstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT yuyashigenobu thefirstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT masatakasatomi thefirstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT yoshiyafukuma thefirstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT kojishiwaku thefirstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT atsumitsujimoto thefirstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT takanorikobayashi thefirstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT ichironakayama thefirstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT fuminariito thefirstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT kazuhironakajima thefirstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT motohikosano thefirstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT tokiowada thefirstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT satorukuhara thefirstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT kiyoshiinouye thefirstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT takashigojobori thefirstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT kazuhoikeo thefirstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT yojinakamura firstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT naobumisasaki firstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT masahirokobayashi firstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT nobuhikoojima firstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT motoshigeyasuike firstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT yuyashigenobu firstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT masatakasatomi firstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT yoshiyafukuma firstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT kojishiwaku firstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT atsumitsujimoto firstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT takanorikobayashi firstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT ichironakayama firstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT fuminariito firstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT kazuhironakajima firstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT motohikosano firstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT tokiowada firstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT satorukuhara firstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT kiyoshiinouye firstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT takashigojobori firstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis AT kazuhoikeo firstsymbiontfreegenomesequenceofmarineredalgasusabinoripyropiayezoensis |
| _version_ |
1718422783447269376 |