As Charles Darwin anticipated, living fossils provide excellent opportunities to study evolutionary questions related to extinction, competition, and adaptation. Ginkgo (Ginkgo biloba L.) is one of the oldest living plants and a fascinating example of how people have saved a species from extinction and assisted its resurgence. By resequencing 545 genomes of ginkgo trees sampled from 51 populations across the world, we identify three refugia in China and detect multiple cycles of population expansion and reduction along with glacial admixture between relict populations in the southwestern and southern refugia. We demonstrate multiple anthropogenic introductions of ginkgo from eastern China into different continents. Further analyses reveal bioclimatic variables that have affected the geographic distribution of ginkgo and the role of natural selection in ginkgo’s adaptation and resilience. These investigations provide insights into the evolutionary history of ginkgo trees and valuable genomic resources for further addressing various questions involving living fossil species.

BackgroundJapanese quail (Coturnix japonica), a recently domesticated poultry species, is important not only as an agricultural product, but also as a model bird species for genetic research. However, most of the biological questions concerning genomics, phylogenetics, and genetics of some important economic traits have not been answered. It is thus necessary to complete a high-quality genome sequence as well as a series of comparative genomics, evolution, and functional studies.ResultsHere, we present a quail genome assembly spanning 1.04 Gb with 86.63% of sequences anchored to 30 chromosomes (28 autosomes and 2 sex chromosomes Z/W). Our genomic data have resolved the long-term debate of phylogeny among Perdicinae (Japanese quail), Meleagridinae (turkey), and Phasianinae (chicken). Comparative genomics and functional genomic data found that four candidate genes involved in early maturation had experienced positive selection, and one of them encodes follicle stimulating hormone beta (FSHβ), which is correlated with different FSHβ levels in quail and chicken. We re-sequenced 31 quails (10 wild, 11 egg-type, and 10 meat-type) and identified 18 and 26 candidate selective sweep regions in the egg-type and meat-type lines, respectively. That only one of them is shared between egg-type and meat-type lines suggests that they were subject to an independent selection. We also detected a haplotype on chromosome Z, which was closely linked with maroon/yellow plumage in quail using population resequencing and a genome-wide association study. This haplotype block will be useful for quail breeding programs.ConclusionsThis study provided a high-quality quail reference genome, identified quail-specific genes, and resolved quail phylogeny. We have identified genes related to quail early maturation and a marker for plumage color, which is significant for quail breeding. These results will facilitate biological discovery in quails and help us elucidate the evolutionary processes within the Phasianidae family.

Tulipa L. (Liliaceae) is among the world's most beloved and economically important ornamental bulbs. Here, we reported the first chloroplast genome sequence of Tulipa. The plastome of T. altaica is 146,887 bp in length, including a large single-copy (LSC) of 78,433 bp, a small single-copy (SSC) of 16,628 bp, and a pair of inverted repeat regions (IRa and IRb) of 25,913 bp. It contains 111 unique genes consisting of 77 protein-coding genes, 30 tRNA genes, and four rRNA genes. The phylogenetic analysis revealed that Tulipa is sister to the clade formed by Erythronium and Amana.

Cercidiphyllum, the only member of Cercidiphyllaceae, contains two extant species: Cercidiphyllum japonicum and Cercidiphyllum magnificum. Here, we reported their complete chloroplast genomes by de novo assembly. The chloroplast genome sizes of C. japonicum and C. magnificum were 159,871 and 159,899 bp, respectively. The two chloroplast genomes have 99.7% sequence identity and were highly conserved in GC content (37.9%), gene content (132 genes), and gene order. Phylogenetic analysis of the chloroplast genomes confirmed the monophyly of Cercidiphyllum and recovered Cercidiphyllaceae as a member of the 'woody clade' of Saxifragales.