Signatures of selection in recently domesticated macadamia

Abstract

Macadamia is a high value nut crop that is recently domesticated, ideal for testing the effect of artificial selection. Here, we sequence the genome of Hawaiian cultivar ‘Kau’ and assemble into 794 Mb in 14 pseudo-chromosomes with 37,728 genes. Genome analysis reveals a whole-genome duplication event, occurred 46.8 million years ago. Gene expansions occurred in gene families involves in fatty acid biosynthesis. Gene duplication of MADS-Box transcription factors in proanthocyanidin biosynthesis are relevant for seed coat development. Genome re-sequencing of 112 accessions reveals the origin of Hawaiian cultivars from Mount Bauple in southeast Queensland in Australia. Selective sweeps are detected in macadamia cultivars, including genes involved in fatty acid biosynthesis, seed coat development, and heat stress response. Such strong effects of artificial selection in few generations reveals the genomic basis for ‘one-step operation’ for clonal crop domestication. The knowledge gained could accelerate domestication of new crops from wild species.

Assembly and comparative analysis of the complete mitochondrial genome of three Macadamia species (M. integrifolia, M. ternifolia and M. tetraphylla)

“…Most of them are distributed in Oceania and South Africa, while a few are produced in East Asia and South America. Notably, more than 100 species in the Proteaceae family produce flowers that are traded internationally [ 3 ]. Besides, the species grown in the northeastern part of Oceania are also rich in nuts.…”

Macadamia germplasm and genomic database (MacadamiaGGD): A comprehensive platform for germplasm innovation and functional genomics in Macadamia

“…In the expression module of MacadamiaGGD, a total of 89.28 Gb of raw RNA-seq data were collected from tissues of young leaves, shoots, and flowers from the cultivar ‘Mauka’ ( Nock et al., 2020 ); tissues of leaves, stems, flowers, and roots from the cultivar ‘Kau’; and shells and kernels at five different development stages from cultivar ‘Hinde’ ( Lin et al., 2022 ). By mapping the transcriptome data to the reference genome and using transcripts per million (TPM) for calculation, we acquired the expression matrix of the annotated genes of macadamia.…”

“…The genome of M. jansenii has been improved by Hi-C assembly (219 scaffolds, N50 = 52 Mb, 758 Mb) ( Sharma et al., 2021c ) and was further updated by the latest hifiasm assembly (779 contigs, N50 = 46 Mb, 826 Mb) ( Sharma et al., 2021b ). Recently, the genome of the cultivar HAES 344 was sequenced and assembled into 14 pseudochromosomes by the use of Illumina NovaSeq and PacBio Sequel II sequencing (5387 contigs, N50 = 281 kb, 794 Mb) ( Lin et al., 2022 ). A chromosome-scale genome assembly of M. tetraphylla has also been constructed from long-read Oxford Nanopore Technologies (ONT) sequencing data (1059 scaffolds, N50 = 51 Mb, 751 Mb) ( Niu et al., 2022a ).…”

Chất thải rắn từ quá trình khí hóa vỏ mắc-ca: Tiềm năng sử dụng làm vật liệu hấp phụ

“…Mắc-ca là một loại cây thân gỗ có nguồn gốc ở ven biển phía bắc New South Wales và phía nam Queensland của nước Úc [1]. Hạt mắc-ca gồm hai loại vỏ, lớp vỏ cứng bên trong và vỏ mềm bọc bên ngoài lớp vỏ cứng và nhân, Mắcca được công nhận là loại hạt cao cấp trên thế giới do hàm lượng và chất lượng dầu cao và hương vị đặc biệt [2]. Tổng sản lượng mắc-ca toàn cầu năm 2020 đạt gần 63000 tấn.…”