Diploid and tetraploid genomes of Acorus and the evolution of monocots.

Monocots are a major taxon within flowering plants, have unique morphological traits, and show an extraordinary diversity in lifestyle. To improve our understanding of monocot origin and evolution, we generate chromosome-level reference genomes of the diploid Acorus gramineus and the tetraploid Ac. calamus, the only two accepted species from the family Acoraceae, which form a sister lineage to all other monocots. Comparing the genomes of Ac. gramineus and Ac. calamus, we suggest that Ac. gramineus is not a potential diploid progenitor of Ac. calamus, and Ac. calamus is an allotetraploid with two subgenomes A, and B, presenting asymmetric evolution and B subgenome dominance. Both the diploid genome of Ac. gramineus and the subgenomes A and B of Ac. calamus show clear evidence of whole-genome duplication (WGD), but Acoraceae does not seem to share an older WGD that is shared by most other monocots. We reconstruct an ancestral monocot karyotype and gene toolkit, and discuss scenarios that explain the complex history of the Acorus genome. Our analyses show that the ancestors of monocots exhibit mosaic genomic features, likely important for that appeared in early monocot evolution, providing fundamental insights into the origin, evolution, and diversification of monocots.

The Euscaphis japonica genome and the evolution of malvids.

Malvids is one of the largest clades of rosids, includes 58 families and exhibits remarkable morphological and ecological diversity. Here, we report a high-quality chromosome-level genome assembly for Euscaphis japonica, an early-diverging species within malvids. Genome-based phylogenetic analysis suggests that the unstable phylogenetic position of E. japonica may result from incomplete lineage sorting and hybridization event during the diversification of the ancestral population of malvids. Euscaphis japonica experienced two polyploidization events: the ancient whole genome triplication event shared with most eudicots (commonly known as the γ event) and a more recent whole genome duplication event, unique to E. japonica. By resequencing 101 samples from 11 populations, we speculate that the temperature has led to the differentiation of the evergreen and deciduous of E. japonica and the completely different population histories of these two groups. In total, 1012 candidate positively selected genes in the evergreen were detected, some of which are involved in flower and fruit development. We found that reddening and dehiscence of the E. japonica pericarp and long fruit-hanging time promoted the reproduction of E. japonica populations, and revealed the expression patterns of genes related to fruit reddening, dehiscence and abscission. The key genes involved in pentacyclic triterpene synthesis in E. japonica were identified, and different expression patterns of these genes may contribute to pentacyclic triterpene diversification. Our work sheds light on the evolution of E. japonica and malvids, particularly on the diversification of E. japonica and the genetic basis for their fruit dehiscence and abscission.

Chromosome-scale assembly of the Dendrobium chrysotoxum genome enhances the understanding of orchid evolution.

As one of the largest families of angiosperms, the Orchidaceae family is diverse. Dendrobium represents the second largest genus of the Orchidaceae. However, an assembled high-quality genome of species in this genus is lacking. Here, we report a chromosome-scale reference genome of Dendrobium chrysotoxum, an important ornamental and medicinal orchid species. The assembled genome size of D. chrysotoxum was 1.37 Gb, with a contig N50 value of 1.54 Mb. Of the sequences, 95.75% were anchored to 19 pseudochromosomes. There were 30,044 genes predicted in the D. chrysotoxum genome. Two whole-genome polyploidization events occurred in D. chrysotoxum. In terms of the second event, whole-genome duplication (WGD) was also found to have occurred in other Orchidaceae members, which diverged mainly via gene loss immediately after the WGD event occurred; the first duplication was found to have occurred in most monocots (tau event). We identified sugar transporter (SWEET) gene family expansion, which might be related to the abundant medicinal compounds and fleshy stems of D. chrysotoxum. MADS-box genes were identified in D. chrysotoxum, as well as members of TPS and Hsp90 gene families, which are associated with resistance, which may contribute to the adaptive evolution of orchids. We also investigated the interplay among carotenoid, ABA, and ethylene biosynthesis in D. chrysotoxum to elucidate the regulatory mechanisms of the short flowering period of orchids with yellow flowers. The reference D. chrysotoxum genome will provide important insights for further research on medicinal active ingredients and breeding and enhances the understanding of orchid evolution.

The Phoebe genome sheds light on the evolution of magnoliids.

Lauraceae includes the genus Phoebe, and the family is linked to the evolution of magnoliids. We sequenced the genome of Phoebe bournei Nanmu. The assembled genome size was 989.19 Mb, with a contig N50 value of 2.05 Mb. A total of 28,198 protein-coding genes were annotated in P. bournei. Whole-genome duplication (WGD) analysis showed that Lauraceae has experienced two WGD events; the older WGD event occurred just before the divergence of Lauraceae and Magnoliales, and the more recent WGD was shared by all lineages of Lauraceae. The phylogenetic tree showed that magnoliids form a sister clade to monocots and eudicots. We also identified 63 MADS-box genes, including AGL12-like genes that may be related to the regulation of P. bournei roots and FIN219-like genes encoding GH3 proteins, which are involved in photomorphogenesis. SAUR50-like genes involved in light signal-mediated pedicel or stem development were also identified. Four ATMYB46- and three PtrEPSP-homologous genes related to lignin biosynthesis were identified. These genes may be associated with the formation of straight trunks in P. bournei. Overall, the P. bournei reference genome provides insight into the origin, evolution, and diversification of Phoebe and other magnoliids.

Chromosome-scale assembly of the Kandelia obovata genome.

The mangrove Kandelia obovata (Rhizophoraceae) is an important coastal shelterbelt and landscape tree distributed in tropical and subtropical areas across East Asia and Southeast Asia. Herein, a chromosome-level reference genome of K. obovata based on PacBio, Illumina, and Hi-C data is reported. The high-quality assembled genome size is 177.99 Mb, with a contig N50 value of 5.74 Mb. A large number of contracted gene families and a small number of expanded gene families, as well as a small number of repeated sequences, may account for the small K. obovata genome. We found that K. obovata experienced two whole-genome polyploidization events: one whole-genome duplication shared with other Rhizophoreae and one shared with most eudicots (γ event). We confidently annotated 19,138 protein-coding genes in K. obovata and identified the MADS-box gene class and the RPW8 gene class, which might be related to flowering and resistance to powdery mildew in K. obovata and Rhizophora apiculata, respectively. The reference K. obovata genome described here will be very useful for further molecular elucidation of various traits, the breeding of this coastal shelterbelt species, and evolutionary studies with related taxa.

The complete chloroplast genome sequence of Euscaphis japonica (Staphyleaceae).

Euscaphis japonica is not only an ideal ornamental plant, but also a traditional medicinal plant, which is an extremely valuable species to study. We determined the complete chloroplast genome sequence for E. japonica using Illumina sequencing technology. The complete chloroplast sequence is 160,467 bp in length, including a large single-copy (LSC) region of 88,716 bp, a small single-copy (SSC) region of 18,614 bp, and a pair of invert repeats (IR) regions of 26,568 bp. Plastid genome contains 142 genes, 46 protein-coding genes, 39 tRNA genes, and eight rRNA genes. Phylogenetic analysis base on 14 chloroplast genomes indicates that E. japonica forms an isolated clade and sisters to Glycosmis-Gossypium clade with strong support.

The complete chloroplast genome sequence of Ludisia discolor from Hainan of China.

Ludisia discolor is one of the most important ornamental and medicinal orchids. To improve our understanding of the evolution of chloroplast, we resequenced complete chloroplast (cp) genome of L. discolor from Hainan, China. The cp genome sequence of L. discolor of Hainan was 153,324 bp in length, with a large single-copy (LSC) region of 82,922 bp, a small single-copy (SSC) region of 17,258 bp, and a pair of inverted repeats (IR) regions of 26,572 bp. Complete chloroplast genome contain 132 genes, there were 86 protein-coding genes, 38 tRNA genes and eight rRNA genes. The phylogenetic tree showed that L. discolor of Hainan is sister to L. discolor (unknown distributed region). Their cp genomes have same gene number but different in length of genome, indicating high conserved among them.