Representation and High‐Quality Annotation of the <i>Physcomitrella patens</i> Transcriptome Demonstrates a High Proportion of Proteins Involved in Metabolism in Mosses

Plant Biology - Tập 7 Số 3 - Trang 238-250 - 2005
Daniel Lang1, Jochen Eisinger2, Ralf Reski1, Stefan A. Rensing1
1Plant Biotechnology, Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104, Freiburg, Germany
2Faculty of Applied Science, Chair of Computer Architecture, University of Freiburg, Georges-Koehler-Allee, Building 051, 79110 Freiburg, Germany

Tóm tắt

Abstract: To gain insight into the transcriptome of the well‐used plant model system Physcomitrella patens, several EST sequencing projects have been undertaken. We have clustered, assembled, and annotated all publicly available EST and CDS sequences in order to represent the transcriptome of this non‐seed plant. Here, we present our fully annotated knowledge resource for the Physcomitrella patens transcriptome, integrating annotation from the production process of the clustered sequences and from a high‐quality annotation pipeline developed during this study. Each transcript is represented as an entity containing full annotations and GO term associations. The whole production, filtering, clustering, and annotation process is being modelled and results in seven datasets, representing the annotated Physcomitrella transcriptome from different perspectives. We were able to annotate 63.4 % of the 26 123 virtual transcripts. The transcript archetype, as covered by our clustered data, is compared to a compilation based on all available Physcomitrella full length CDS. The distribution of the gene ontology annotations (GOA) for the virtual transcriptome of Physcomitrella patens demonstrates consistency in the ratios of the core molecular functions among the plant GOA. However, the metabolism subcategory is over‐represented in bryophytes as compared to seed plants. This observation can be taken as an indicator for the wealth of alternative metabolic pathways in moss in comparison to spermatophytes. All resources presented in this study have been made available to the scientific community through a suite of user‐friendly web interfaces via http:www.cosmoss.org and form the basis for assembly and annotation of the moss genome, which will be sequenced in 2005.

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Tài liệu tham khảo

10.1023/A:1026077825584

10.1093/nar/25.17.3389

10.1146/annurev.arplant.55.031903.141701

10.1093/nar/gkh131

10.1038/75556

10.1093/nar/gkh121

10.1093/nar/18.6.1517

10.1016/S0300-9084(01)01350-5

10.1101/gr.461403

10.1093/nar/gkh021

10.1007/s003440000031

Du X. M., 2001, [The production and scavenging of reactive oxygen species in plants], Sheng Wu Gong Cheng Xue Bao, 17, 121

10.1101/gr.8.3.186

10.1101/gr.8.3.175

10.1093/nar/28.14.2679

10.1002/biuz.19940240304

FujitaT. Shin‐iT. SekiM. KamiyaA. UchiyamaI. NishiyamaT. CarninciP. HayashizakiY. ShinozakiK. KoharaY. HasebeM. 82317 Genbank accessions. (2004).

10.1046/j.1365-313X.1998.00178.x

10.1093/nar/gkg548

10.1093/nar/gkh036

10.1002/elps.200305795

10.1073/pnas.93.16.8175

10.1007/s00114-002-0321-3

IseliC. JongeneelC. V. BucherP. ESTScan: a program for detecting evaluating and reconstructing potential coding regions in EST sequences. International Conference on Intelligent Systems for Molecular Biology (1999)138–148.

10.1016/S0168-9525(00)02093-X

10.1101/gr.992803

10.1038/sj.embor.7400238

KittsP. A. MaddenT. L. H. S. OstellJ. A. UniVec.http:www.ncbi.nlm.nih.govVecScreenUniVec.html.

10.1055/s-2003-44721

10.1074/jbc.M204971200

10.1007/s00299-004-0785-z

10.1093/nar/25.2.362

10.1093/bib/3.3.296

10.1093/jxb/erh140

Miller N. D., 1984, New Manual of Bryology, 1194

10.1093/nar/gkg046

10.1073/pnas.0932694100

10.1186/1471-2164-5-89

Patnaik D., 2001, Germins and germin like proteins: an overview, The Journal of Experimental Biology, 39, 191

10.1016/S0097-8485(96)80016-7

10.1093/nar/30.1.335

QuatranoR. BashiardesS. CoveD. CumingA. KnightC. CliftonS. MarraM. HillierL. PapeD. MartinJ. WylieT. UnderwoodK. TheisingB. AllenM. BowersY. PersonB. SwallerT. SteptoeM. GibbonsM. HarveyN. RitterE. JacksonY. McCannR. WaterstonR. WilsonR. Leeds/Wash U Moss EST Project 19538 Genbank accessions. (1999).

10.1023/A:1013726308559

Rensing S. A., 2005, Protein encoding genes in an ancient plant: analysis of codon usage, retained genes and splice sites in a moss, Physcomitrella patens., BMC Genomics, 10.1186/1471-2164-6-43

Rensing S. A., 2003, In silico prediction of UTR repeats using clustered EST data, 117

RensingS. A. RombautsS. HoheA. LangD. DuwenigE. RouzeP. van dePeerY. ReskiR. The transcriptome of the mossPhyscomitrella patens: Comparative analysis reveals a rich source of new genes.http:www.plantbiotech.netRensing_et_al_transcriptome2002.pdf. (2002a).

10.1016/S1360-1385(02)02363-4

10.1111/j.1438-8677.1998.tb00670.x

10.1007/s004250050563

10.1093/nar/gkg076

10.1016/S0378-1119(02)00583-8

10.1016/j.phytochem.2004.04.028

10.1016/S0076-6879(96)66012-1

SchweenG. EgenerT. FritzkowskyD. GranadoJ. GuittonM.‐C. HartmannN. HoheA. HoltorfH. LangD. LuchtJ. M. ReinhardC. RensingS. A. SchlinkK. SchulteJ. ReskiR. Large‐scale analysis of 73 329Physcomitrellaplants transformed with different gene disruption libraries: production parameters and mutant phenotypes.Plant Biology(2005) in press .

10.1101/gr.361602

10.1016/j.bbrc.2004.03.052

10.1046/j.1469-8137.2001.00089.x

10.1007/s00299-004-0754-6

Walczak R., 1996, A novel RNA structural motif in the selenocysteine insertion element of eukaryotic selenoprotein mRNAs, RNA, 2, 367

10.1093/nar/30.1.103

10.1093/nar/gkh073

10.1016/j.tplants.2003.10.012

10.1042/bj3220681

10.1046/j.1365-313X.2002.01354.x

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Plant Biology

Tập 7 Số 3

238-250

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