Genome and transcriptome sequencing characterises the gene space of Macadamia integrifolia (Proteaceae)

Abstract

BackgroundThe large Gondwanan plant family Proteaceae is an early-diverging eudicot lineage renowned for its morphological, taxonomic and ecological diversity. Macadamia is the most economically important Proteaceae crop and represents an ancient rainforest-restricted lineage. The family is a focus for studies of adaptive radiation due to remarkable species diversification in Mediterranean-climate biodiversity hotspots, and numerous evolutionary transitions between biomes. Despite a long history of research, comparative analyses in the Proteaceae and macadamia breeding programs are restricted by a paucity of genetic information. To address this, we sequenced the genome and transcriptome of the widely grown Macadamia integrifolia cultivar 741.ResultsOver 95 gigabases of DNA and RNA-seq sequence data were de novo assembled and annotated. The draft assembly has a total length of 518 Mb and spans approximately 79% of the estimated genome size. Following annotation, 35,337 protein-coding genes were predicted of which over 90% were expressed in at least one of the leaf, shoot or flower tissues examined. Gene family comparisons with five other eudicot species revealed 13,689 clusters containing macadamia genes and 1005 macadamia-specific clusters, and provides evidence for linage-specific expansion of gene families involved in pathogen recognition, plant defense and monoterpene synthesis. Cyanogenesis is an important defense strategy in the Proteaceae, and a detailed analysis of macadamia gene homologues potentially involved in cyanogenic glycoside biosynthesis revealed several highly expressed candidate genes.ConclusionsThe gene space of macadamia provides a foundation for comparative genomics, gene discovery and the acceleration of molecular-assisted breeding. This study presents the first available genomic resources for the large basal eudicot family Proteaceae, access to most macadamia genes and opportunities to uncover the genetic basis of traits of importance for adaptation and crop improvement.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3272-3) contains supplementary material, which is available to authorized users.

Selecting for Nut Characteristics in Macadamia Using a Genome-wide Association Study

“…One limitation with our research was that there is currently no completely assembled macadamia genome, so our markers could not be easily mapped; however, multiple regression results suggest that several significant markers are detecting the same QTL. Research by Nock et al (2016) has sequenced 79% of the macadamia genome. When a more complete reference genome becomes available, the location of significant markers for macadamia NW, KW, and KR can be determined.…”

“…Macadamias (Macadamia integrifolia, Macadamia tetraphylla, and their hybrids) are grown commercially around the world for their high-quality nuts. The genus is from the ancient Proteaceae family and native to the east coast of Australia (Nock et al, 2016). Macadamia was first developed as an international commercial crop in Hawaii in the early 1920s (Hardner et al, 2009).…”

Global Macadamia Science: Overview of the Special Section

“…Nock et al, personal communication) using the Hawaiian cultivar 741 as a fundamental resource for future genetics and breeding studies. Genome and transcriptome sequence data were used to develop an annotated gene space released in 2016 (Nock et al, 2016). Currently, additional Illumina short-read and PacBio longread sequence data, a bioinformatics pipeline that incorporates transcriptome data in the de novo assembly process, and a dense linkage map are being used to improve anchoring and orientation of genome scaffolds.…”

Genome assembly and annotation of Macadamia tetraphylla

“…Mb to 780 Mb [17][18][19] , but research on the genome of macadamia was very few. In 2014, 2017 and 2018, the chloroplast genome of M. integrifolia, M. ternifolia and M. tetraphylla have been sequenced by Australian and Chinese researchers [20][21][22] , and in 2016, the darft genome and transcriptome of M. integrifolia cultivar 741 have been sequenced, a total length of 518 Mb have been assembly, which spans approximately 79% of the 3 estimated genome size 18 . But up to now, the genome sequencing of M. tetraphylla has not yet been reported.…”