The Chromosome-Scale Reference Genome of Macadamia tetraphylla Provides Insights Into Fatty Acid Biosynthesis.

Macadamia is an evergreen tree belonging to the Proteaceae family. The two commercial macadamia species, Macadamia integrifolia and M. tetraphylla, are highly prized for their edible kernels. The M. integrifolia genome was recently sequenced, but the genome of M. tetraphylla has to date not been published, which limits the study of biological research and breeding in this species. This study reports a high-quality genome sequence of M. tetraphylla based on the Oxford Nanopore Technologies technology and high-throughput chromosome conformation capture techniques (Hi-C). An assembly of 750.87 Mb with 51.11 Mb N50 length was generated, close to the 740 and 758 Mb size estimates by flow cytometry and k-mer analysis, respectively. Genome annotation indicated that 61.42% of the genome is composed of repetitive sequences and 34.95% is composed of long terminal repeat retrotransposons. Up to 31,571 protein-coding genes were predicted, of which 92.59% were functionally annotated. The average gene length was 6,055 bp. Comparative genome analysis revealed that the gene families associated with defense response, lipid transport, steroid biosynthesis, triglyceride lipase activity, and fatty acid metabolism are expanded in the M. tetraphylla genome. The distribution of fourfold synonymous third-codon transversion showed a recent whole-genome duplication event in M. tetraphylla. Genomic and transcriptomic analysis identified 187 genes encoding 33 crucial oil biosynthesis enzymes, depicting a comprehensive map of macadamia lipid biosynthesis. Besides, the 55 identified WRKY genes exhibited preferential expression in root as compared to that in other tissues. The genome sequence of M. tetraphylla provides novel insights for breeding novel varieties and genetic improvement of agronomic traits.

The complete chloroplast genome of Passiflora caerulea, a tropical fruit with a distinctive aroma.

Passiflora caerulea is native to brazil. In recent years, the edible, medicinal, and ornamental value of P. caerulea has stimulated its wide cultivation in Southeast Asian countries, especially China. Because the chloroplast genome is rich with information about the species evolution as well as its genetic relationship to other species, the P. caerulea chloroplast genome was sequenced, assembled, and annotated in this study. The P. caerulea chloroplast genome is 151,362 bp in total with an overall GC content of 37.03%. It has a quadripartite structure, includes a large single-copy region (LSC, 85,623 bp), a small single-copy region (SSC, 13,397 bp), and two inverted repeat regions (IRa and IRb, 26,180 bp combined). There are 131 genes in the P. caerulea chloroplast genome, including 79 protein-coding genes, 37 tRNA genes, 8 rRNA genes, and 7 pseudogenes. Phylogenetic analysis of 29 Passiflora spp. showed that P. caerulea is most closely related to P. edulis. These results provide a considerable foundation for P. caerulea conservation genetics research.

Complete chloroplast genome of Synsepalum dulcificum D.: a magical plant that modifies sour flavors to sweet.

Synsepalum dulcificum D. belongs to the Sapotaceae family, which is an evergreen shrub native to tropical West Africa. It is a kind of magical plant that has the unique characteristic of modifying sour flavors to sweet. In this study, the chloroplast genome of S. dulcificum was sequenced, assembled, and annotated firstly. Chloroplast genome size of S. dulcificum is 158,463 bp, the circular chloroplast genome consists of four regions: a large single-copy region of 88,256 bp, two inverted repeat regions of 25,958 bp, and a small single-copy region of 18,669 bp, with the GC content of 36.87%. A total of 133 genes were annotated in the S. dulcificum chloroplast genome, of which 88 were protein-coding genes (PCGs), 37 were transfer RNA (tRNA) genes, and eight were ribosomal RNA (rRNA) genes. Phylogenetic analysis showed that Pouteria campechiana was most closely related to S. dulcificum. The study provides important genomic data for further utilization and breeding of S. dulcificum.

The Chromosome-Based Rubber Tree Genome Provides New Insights into Spurge Genome Evolution and Rubber Biosynthesis.

The rubber tree, Hevea brasiliensis, produces natural rubber that serves as an essential industrial raw material. Here, we present a high-quality reference genome for a rubber tree cultivar GT1 using single-molecule real-time sequencing (SMRT) and Hi-C technologies to anchor the ∼1.47-Gb genome assembly into 18 pseudochromosomes. The chromosome-based genome analysis enabled us to establish a model of spurge chromosome evolution, since the common paleopolyploid event occurred before the split of Hevea and Manihot. We show recent and rapid bursts of the three Hevea-specific LTR-retrotransposon families during the last 10 million years, leading to the massive expansion by ∼65.88% (∼970 Mbp) of the whole rubber tree genome since the divergence from Manihot. We identify large-scale expansion of genes associated with whole rubber biosynthesis processes, such as basal metabolic processes, ethylene biosynthesis, and the activation of polysaccharide and glycoprotein lectin, which are important properties for latex production. A map of genomic variation between the cultivated and wild rubber trees was obtained, which contains ∼15.7 million high-quality single-nucleotide polymorphisms. We identified hundreds of candidate domestication genes with drastically lowered genomic diversity in the cultivated but not wild rubber trees despite a relatively short domestication history of rubber tree, some of which are involved in rubber biosynthesis. This genome assembly represents key resources for future rubber tree research and breeding, providing novel targets for improving plant biotic and abiotic tolerance and rubber production.

The complete chloroplast genome of Theobroma grandiflorum, an important tropical crop.

Theobroma grandiflorum (Willd. ex Spreng.) K. Schum., an economically important tree in the family Malvaceae, is native to the Amazonian region of South America and it is widely cultivated as a tropical crop. Herein, we report the complete chloroplast genome of T. grandiflorum. The size of the complete chloroplast genome of T. grandiflorum is 160,606 bp with 36.88% GC content, which includes a pair of inverted repeat regions (IRs) of 25,496 bp separated by a large single-copy region (LSC) of 89,429 bp and a small single copy (SSC) region of 20,185 bp. A total of 126 genes were annotated, of which 82 were protein-coding genes, 36 were transfer RNA (tRNA) genes, and 8 were ribosomal RNA (rRNA) genes. A maximum-likelihood (ML) analysis supported a close relationship between T. grandiflorum and T. cacao. This study will provide useful information for further phylogenetic and evolutionary analysis of Malvaceae.

Chloroplast genome of tropical and sub-tropical fruit tree Clausena lansium (Rutaceae).

The Clausena lansium, originally native to the southern part of China and has a long history of cultivation, is a tree member of the family Rutaceae. Chloroplast genome sequences play a significant role in the development of molecular markers in plant phylogenetic and population genetic studies. In this study, we report the complete chloroplast genome sequence of C. lansium for the first time (accession number of MH047377). The chloroplast genome is 159,284 bp long and includes 113 genes. It's LSC, SSC, and IR regions are 88,634, 18,896, and 25,877 bp long, respectively. Phylogenetic tree analysis exhibited that C. lansium was clustered with other Rutaceae species with high bootstrap values.

Chloroplast genome of tropical and sub-tropical fruit tree Syzygium samarangense (Myrtaceae).

Syzygium samarangense is an important fruit of Myrtaceae family and commercially planted in tropical areas of the world. Chloroplast genome sequences play a significant role in the development of molecular markers in plant phylogenetic and population genetic studies. In this study, we report the complete chloroplast genome sequence of S. samarangense for the first time (accession number of MH371141). The chloroplast genome is 159,109 bp long and includes 113 genes. Its LSC, SSC and IR regions are 88,533, 18,882, and 25,847 bp long, respectively. Phylogenetic tree analysis exhibited that S. samarangense was clustered with other Myrtaceae species with 100% bootstrap values.

The whole chloroplast genome sequence of Macadamia tetraphylla (Proteaceae).

Macadamia tetraphylla (Proteaceae) is one of the two macadamia plants that are edible and of cultivated value. Only two chloroplast genomes were reported in Proteaceae so far. In this study, we report the complete chloroplast genome sequence of M. tetraphylla, which is the third reported chloroplast genome in Proteaceae. The chloroplast genome is 159,195 bp long and includes 113 genes. Its LSC, SSC and IR regions are 87,951, 18,748 and 26,248 bp long, respectively. Phylogenetic analysis indicates that M. tetraphylla was clustered with other two species of Proteaceae, the M. integrifoia and M. ternifolia.

The complete chloroplast genome of tropical and sub-tropical fruit tree Lucuma nervosa (Sapotaceae).

The Lucuma nervosa, native to Western Ghats of India, Malaysia and south-eastern Asia, is a tree member of the mulberry family (Sapotaceae). Chloroplast genome sequences play an significant role in the development of molecular markers in plant phylogenetic and population genetic studies. In this study, we report the complete chloroplast genome sequence of L. nervosa for the first time. The chloroplast genome is 157,920 bp long and includes 113 genes. Its LSC, SSC, and IR regions are 88,123, 18,861, and 25,468 bp long, respectively. Phylogenetic tree analysis exhibited that L. nervosa was clustered with other Sapotaceae species with high bootstrap values.

Complete chloroplast genome of a subtropical fruit tree Macadamia ternifolia (Proteaceae).

Macadamia ternifolia is a subtropical fruit tree of the family Proteaceae. Chloroplast genome sequences play a significant role in the development of molecular markers in plant phylogenetic and population genetic studies. In this study, we report the complete chloroplast genome sequence of M. ternifolia. The chloroplast genome is 159,669 bp long and includes 113 genes. Its LSC, SSC, and IR regions are 88,072, 18,801, and 26,408 bp long, respectively. Sequence comparison of M. ternifolia and M. integrifolia indicates large sequence conservation between these two species, only few sequence variations including single nucleotide polymorphisms (SNPs) and inserts/deletes (InDels) were detected.

The complete chloroplast genome of Artocarpus heterophyllus (Moraceae).

The Artocarpus heterophyllus, native to Western Ghats of India, Malaysia and south-eastern Asia, is a tree member of the mulberry family (Moraceae). Chloroplast genome sequences play a significant role in the development of molecular markers in plant phylogenetic and population genetic studies. In this study, we report the complete chloroplast genome sequence of A. heterophyllus for the first time. The chloroplast genome is 160,387 bp long and includes 113 genes. Its LSC, SSC and IR regions are 88,422, 18,869 and 26,548 bp long, respectively. Phylogenetic tree analysis exhibited that A. heterophyllus was clustered with other Moraceae species with high bootstrap values.

The complete pineapple (Ananas comosus; Bromeliaceae) varieties F153 chloroplast genome sequence.

This study reported the complete nucleotide sequence of the pineapple varieties F153 chloroplast (cp) genome. The cpDNA was 159,521 bp in length and contained 131 genes (77 protein-encoding genes, 30 tRNA genes and four rRNA genes). The phylogenetic relationship of the pineapple varieties F153 plastid was consistent with previous report.