The information from the Neem Genome Portal is intended to enable research in the areas of biology, evolution and genetic relationship of the members of the Meliaceae family, bulk production of bioactive compounds through microbial engineering and increase the understanding of the diverse pathways and enzymes involved in the synthesis of the terpenoids.
This version (v2.0) of the portal uses data and annotations published on the 2nd draft genome (1), and earlier data on the published draft genome and the transcriptomes (2,3).
The Neem Genome Portal was created using Gbrowse 2.0 (4).
Genome: We used multiple Illumina paired-end libraries for contiging and multiple Illumina mate pair libraries only for scaffolding. In addition to the Illumina reads, we also used the error-corrected PacBio reads for assembly (1). The assembled scaffolds were annotated using standalone blast (2.2.26+) using the blastn program. The blastout file was converted to GFF3 for use in the Genome Portal. The gi IDs in blastout GFF3 file were appended with their gene names/descriptions, to make the browser searchable using keywords.
Transcriptomes: RNA-seq libraries from five organs of the neem tree (flower, fruit, leaf, root, stem) were combined and assembled to produce a representative transcriptome assembly. For this, Trinity_r20140717 was used with trimming. The assembled transcripts were aligned to the genome scaffolds using PASA_r20140417 (GMAP), after cleaning the transcripts using the seqclean utility in the PASA package.
The browser currently displays all annotations of the scaffolds based on sequence homology with the sequences in the 'nt' blast database. The 6-frame translation can be displayed, as can restriction sites for various enzymes (built-in capabilities). Wherever available, the 'Assembled Transcripts' track displays de novo assembled transcripts detected in that region of the genome assembly.
The genome is searchable using gene names and displays all possible locations where a gene of interest can be found in the genome.
1. Krishnan NM et al., (2016). doi:10.1534/g3.116.03005
2. Krishnan NM et al., (2011), 101, 1553-1561 test.ias.ac.in/cs/Volumes/101/12/1553.pdf
3. Krishnan NM et al., (2012). doi:10.1186/1471-2164-13-464
4. Stein LD. (2013). doi: 10/1093/bib/bbt001