PMID- 37016293
OWN - NLM
STAT- MEDLINE
DCOM- 20230406
LR  - 20230411
IS  - 1471-2164 (Electronic)
IS  - 1471-2164 (Linking)
VI  - 24
IP  - 1
DP  - 2023 Apr 4
TI  - GelFAP v2.0: an improved platform for Gene functional analysis in Gastrodia 
      elata.
PG  - 164
LID - 10.1186/s12864-023-09260-1 [doi]
LID - 164
AB  - BACKGROUND: Gastrodia elata (tianma), a well-known medicinal orchid, is widely 
      used to treat various kinds of diseases with its dried tuber. In recent years, 
      new chromosome-level genomes of G.elata have been released in succession, which 
      offer an enormous resource pool for understanding gene function. Previously we 
      have constructed GelFAP for gene functional analysis of G.elata. As genomes are 
      updated and transcriptome data is accumulated, collection data in GelFAP cannot 
      meet the need of researchers. RESULTS: Based on new chromosome-level genome and 
      transcriptome data, we constructed co-expression network of G. elata, and then we 
      annotated genes by aligning with sequences from NR, TAIR, Uniprot and Swissprot 
      database. GO (Gene Ontology) and KEGG (Kyoto Encylopaedia of Genes and Genomes) 
      annotations were predicted by InterProScan and GhostKOALA software. Gene families 
      were further predicted by iTAK (Plant Transcription factor and Protein kinase 
      Identifier and Classifier), HMMER (hidden Markov models), InParanoid. Finally, we 
      developed an improved platform for gene functional analysis in G. elata (GelFAP 
      v2.0) by integrating new genome, transcriptome data and processed functional 
      annotation. Several tools were also introduced to platform including BLAST (Basic 
      Local Alignment Search Tool), GSEA (Gene Set Enrichment Analysis), Heatmap, 
      JBrowse, Motif analysis and Sequence extraction. Based on this platform, we found 
      that the flavonoid biosynthesis might be regulated by transcription factors (TFs) 
      such as MYB, HB and NAC. We also took C4H and GAFP4 as examples to show the usage 
      of our platform. CONCLUSION: An improved platform for gene functional analysis in 
      G. elata (GelFAP v2.0, www.gzybioinformatics.cn/Gelv2 ) was constructed, which 
      provides better genome data, more transcriptome resources and more analysis 
      tools. The updated platform might be preferably benefit researchers to carry out 
      gene functional research for their project.
CI  - (c) 2023. The Author(s).
FAU - Yang, Jiaotong
AU  - Yang J
AD  - Resource Institute for Chinese and Ethnic Materia Medica, Guizhou University of 
      Traditional Chinese Medicine, Guizhou, 550025, China.
FAU - Li, Pengfei
AU  - Li P
AD  - Resource Institute for Chinese and Ethnic Materia Medica, Guizhou University of 
      Traditional Chinese Medicine, Guizhou, 550025, China.
FAU - Li, Yuping
AU  - Li Y
AD  - Resource Institute for Chinese and Ethnic Materia Medica, Guizhou University of 
      Traditional Chinese Medicine, Guizhou, 550025, China.
FAU - Xiao, Qiaoqiao
AU  - Xiao Q
AD  - Resource Institute for Chinese and Ethnic Materia Medica, Guizhou University of 
      Traditional Chinese Medicine, Guizhou, 550025, China. xqqiao2021@163.com.
LA  - eng
GR  - 32160139/National Natural Science Foundation of China/
GR  - 32260140/National Natural Science Foundation of China/
GR  - (2019)141/Ph.D. Startup Foundation of Guizhou University of Traditional Chinese 
      Medicine/
GR  - (2020)32/Ph.D. Startup Foundation of Guizhou University of Traditional Chinese 
      Medicine/
PT  - Journal Article
DEP - 20230404
PL  - England
TA  - BMC Genomics
JT  - BMC genomics
JID - 100965258
SB  - IM
MH  - *Gastrodia/genetics
MH  - Phenotype
PMC - PMC10074892
OTO - NOTNLM
OT  - Analysis tools
OT  - Functional annotation
OT  - Gastrodia elata
OT  - Platform
COIS- The authors declare that there are no competing interests.
EDAT- 2023/04/05 06:00
MHDA- 2023/04/06 10:16
PMCR- 2023/04/04
CRDT- 2023/04/04 23:43
PHST- 2022/09/23 00:00 [received]
PHST- 2023/03/20 00:00 [accepted]
PHST- 2023/04/06 10:16 [medline]
PHST- 2023/04/04 23:43 [entrez]
PHST- 2023/04/05 06:00 [pubmed]
PHST- 2023/04/04 00:00 [pmc-release]
AID - 10.1186/s12864-023-09260-1 [pii]
AID - 9260 [pii]
AID - 10.1186/s12864-023-09260-1 [doi]
PST - epublish
SO  - BMC Genomics. 2023 Apr 4;24(1):164. doi: 10.1186/s12864-023-09260-1.