Introduction to Maize GDB database Bioinformatics The Maize Genetics and Genomics Database. The Community Resource for Access to Diverse Maize Data1 Carolyn J. Lawrence, Trent E. Seigfried, and Volker Brendel* Department of Genetics, Development and Cell Biology (C.J.L., V.B.), and ...
14ZmPME/PMEIgenes specifically expressed in anthers,ZmPME24(not including in the maize microarray data) andZmPME30(expressed low in all tissues) were selected for conducting semiq-RT-PCR. Semiq-RT-PCR was performed with total RNA isolated from the roots, leaves, ears, immature tassels, pollen...
b. The remaining genes (3) did not have available expression data across the four leaf stages or for the vegetative meristem in the database. Genes GRMZM2G033413, GRMZM5G813007, GRMZM2G031352, AC210013.4_FG014, GRMZM2G061602, GRMZM2G164787, GRMZM2G031584, and GRMZM2G313737 exhibited...
thaliana were subjected to Blastp searches against the genomic database in Zea mays (http://www.maizegdb.org/), Sorghum bicolor (http:// www.plantgdb.org/SbGDB/) and the Chromatin Database (http://chromdb.org/). Conserved domain analysis was performed using CDD program (http://www.ncbi...
The B73, W22 and PE0075 genome can be downloaded in Maize GDB (https://www.maizegdb.org/). The LT2357 genome was unpublished data from Beijing Lantron Seed and was uploaded to the NCBI database (PRJNA894302). The datasets generated and/or analyzed during the current study are available ...
concentration and data amount required. After removing the adaptor and low-quality sequences with Trimmomatic v0.39, Bowtie2 v2.1.0 was used to eliminate the host-derived sequences by mapping the clean data to the maize genome (B73 RedGen_v4 from maize GDB). The high-quality reads were ass...
thaliana were subjected to Blastp searches against the genomic database in Zea mays (http://www.maizegdb.org/), Sorghum bicolor (http:// www.plantgdb.org/SbGDB/) and the Chromatin Database (http://chromdb.org/). Conserved domain analysis was performed using CDD program (http://www.ncbi...
Clean paired-end reads were aligned to the B73 maize genome v5.0, which was downloaded from maize GDB, using Hisat2v 2.0.5 [76]. StringTie v 2.2.1 [77] was used to count the number of reads mapped to each gene, and the fragments per kilobase of transcript per million mapped reads...
Candidate genes model entries were queried on Mai- zeGDB (www.maizegdb.org) for classical names and best sequence homologues in A. thaliana and O. sativa. Genes without classical names were queried against a maximum likelihood protein sequence tree (ensembl.gramene.org). Protein domains were ...
and RNA-seq) analysis was employed by using the PASA65and EVM66pipeline. The predicted gene models from EVM66were then updated by PASA65assembly alignments. Gene functions were assigned according to the best alignment using BLASTP67(Evalue < 10−5) to the UniProt database68. InterProSca...