Multi-Omics Driven Assembly and Annotation of the Sandalwood (Santalum album) Genome

Abstract

Indian sandalwood () is an important tropical evergreen tree known for its fragrant heartwood-derived essential oil and its valuable carving wood. Here, we applied an integrated genomic, transcriptomic, and proteomic approach to assemble and annotate the Indian sandalwood genome. Our genome sequencing resulted in the establishment of a draft map of the smallest genome for any woody tree species to date (221 Mb). The genome annotation predicted 38,119 protein-coding genes and 27.42% repetitive DNA elements. In-depth proteome analysis revealed the identities of 72,325 unique peptides, which confirmed 10,076 of the predicted genes. The addition of transcriptomic and proteogenomic approaches resulted in the identification of 53 novel proteins and 34 gene-correction events that were missed by genomic approaches. Proteogenomic analysis also helped in reassigning 1,348 potential noncoding RNAs as bona fide protein-coding messenger RNAs. Gene expression patterns at the RNA and protein levels indicated that peptide sequencing was useful in capturing proteins encoded by nuclear and organellar genomes alike. Mass spectrometry-based proteomic evidence provided an unbiased approach toward the identification of proteins encoded by organellar genomes. Such proteins are often missed in transcriptome data sets due to the enrichment of only messenger RNAs that contain poly(A) tails. Overall, the use of integrated omic approaches enhanced the quality of the assembly and annotation of this nonmodel plant genome. The availability of genomic, transcriptomic, and proteomic data will enhance genomics-assisted breeding, germplasm characterization, and conservation of sandalwood trees.

Genome- wide characterization, expression profile analysis of WRKY family genes in Santalum album and functional identification of their role in abiotic stress

“…4) generated using these expression values exhibited different expression patterns for all the identified SaWRKY genes except for SaWRKY1 in the five tissues, indicating that they may perform diversified functions in plant development or in response to stress. SaWRKY12, 30,31,39, and 42 shared similarly high expression levels in all the tested tissues (Fig. 4), indicating that these genes may play essential roles in S. album SaWRKY genes that were identified showed higher tissue-specific expression patterns, i.e., SaWRKY2, 15,20,22,27,32 and 44, which were preferentially expressed in wood tissue (sapwood, transition zone and heartwood) (Fig.…”

“…As far as we are aware, there is scarce knowledge on WRKY TFs in S. album. Large-scale available RNA-seq data sets [26,28,29] and genomic data generated recently in S. album [30] might offer additional insight about WRKY family genes.…”

Systematic Multi-Omics Integration (MOI) Approach in Plant Systems Biology

“…These reports integrated transcriptome and metabolome data sets into manually reconstructed terpenoid and sesquiterpenoid biosynthetic pathways specifically for this non-model plant ( Rahnamaie-Tajadod et al., 2017 ; Rahnamaie-Tajadod et al., 2019 ). Additionally, santalol (sesquiterpene) biosynthesis from sandalwood ( Santalum album ) was also successfully reconstructed using multi-omics annotation to available KEGG database ( Mahesh et al., 2018 ). These studies suggest that manual pathway reconstruction using available pathway databases is possible for pathway-based MOI, albeit time-consuming.…”

Integrated omics approach to understand Pistacia - aphid gall development

“…SSR markers were identi ed from the assembled sequences using MIcroSAtellite tool (MISA) (http://pgrc.ipkgatersleben.de/misa/) as per the protocol described by Kuravadi et al (25). AUGUSTUS software was used for gene prediction (26). Functional annotation of genes was carried out using Uniprot database.…”