Draft genome of a high value tropical timber tree, Teak (Tectona grandis L. f): insights into SSR diversity, phylogeny and conservation

Abstract

Teak (Tectona grandis L. f.) is one of the precious bench mark tropical hardwood having qualities of durability, strength and visual pleasantries. Natural teak populations harbour a variety of characteristics that determine their economic, ecological and environmental importance. Sequencing of whole nuclear genome of teak provides a platform for functional analyses and development of genomic tools in applied tree improvement. A draft genome of 317 Mb was assembled at 151× coverage and annotated 36, 172 protein-coding genes. Approximately about 11.18% of the genome was repetitive. Microsatellites or simple sequence repeats (SSRs) are undoubtedly the most informative markers in genotyping, genetics and applied breeding applications. We generated 182,712 SSRs at the whole genome level, of which, 170,574 perfect SSRs were found; 16,252 perfect SSRs showed in silico polymorphisms across six genotypes suggesting their promising use in genetic conservation and tree improvement programmes. Genomic SSR markers developed in this study have high potential in advancing conservation and management of teak genetic resources. Phylogenetic studies confirmed the taxonomic position of the genus Tectona within the family Lamiaceae. Interestingly, estimation of divergence time inferred that the Miocene origin of the Tectona genus to be around 21.4508 million years ago.

Nanopore sequencing: Review of potential applications in functional genomics

“…In the case of plant genomes such as the fastest-growing angiosperm (greater duckweed) or tropical timber trees (teak), HMW genomic DNA extraction has been successfully performed by a CTAB method (Hoang et al, 2018;Yasodha et al, 2018), following homogenization steps to break the cell wall, where grinding with liquid nitrogen is generally used to crush the cell wall while cellular enzymes remain inactivated. Therefore, homogenization and DNA extraction methods should be optimized for each species, especially for plants or arthropods that harbor thick cell walls and cuticular exoskeletons.…”

“…Therefore, homogenization and DNA extraction methods should be optimized for each species, especially for plants or arthropods that harbor thick cell walls and cuticular exoskeletons. In the case of plant genomes such as the fastest-growing angiosperm (greater duckweed) or tropical timber trees (teak), HMW genomic DNA extraction has been successfully performed by a CTAB method (Hoang et al, 2018;Yasodha et al, 2018), following homogenization steps to break the cell wall, where grinding with liquid nitrogen is generally used to crush the cell wall while cellular enzymes remain inactivated. After sufficient homogenization, samples are then resuspended in detergent-based extraction buffers containing cetyltrimethylammonium bromide (CTAB).…”

Ecotypes or phenotypic plasticity—The aquatic and terrestrial forms of Helosciadium repens (Apiaceae)

“…Using the polymerase chain reaction (PCR), with specific primer pairs flanking a specific microsatellite, it is possible to amplify and measure the exact bp length of a microsatellite. SSR markers are considered to be a reliable system for diversity studies as they are codominant and multiallelic (Baldwin, Pither-Joyce, Wright, Chen, & McCallum, 2012;Fu, Kong, Yingxiong, & Cameron, 2005;Geethanjali, Anitha Rukmani, & Rajakumar, 2018;Park, Lee, & Kim, 2009;Yasodha et al, 2018). They are neutral markers and are thus usually not subjected to natural selection (Holderegger, Kamm, & Gugerli, 2006;Kimura, 1983 (Table S2).…”

Analysis of NAC Domain Transcription Factor Genes of Tectona grandis L.f. Involved in Secondary Cell Wall Deposition

“…Teak's secondary xylem biosynthesis is a complex molecular process that involves several genes and environmental factors. Recent genomic and transcriptomic analyses of T. grandis have allowed to improve the understanding of the xylogenesis role in biomass increase and wood quality [35][36][37][38], even though T. grandis NAC transcription factors have not yet been identified. The identification and characterization of teak NAC TFs are fundamental to elucidate their regulation role in vascular tissue differentiation and wood formation, as well as future biotechnological studies aiming to improve biomass and wood quality.…”