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Background: Firmiana danxiaensis is a critically endangered and ecologically important tree currently only found in four locations in Danxia or Karst habitats in northern Guangdong Province, China. The specialized habitat preference makes it an ideal model species for study of adaptive evolution. Meanwhile, the phylogenetic relationships of F. danxiaensis in four locations under two landforms are unclear. Therefore, we sequenced its complete chloroplast (cp.) genomes and conducted comprehensive interspecific and intrageneric plastome studies. Results: The F. danxiaensis plastomes in four locations showed a typical quadripartite and circular structure that ranged from 160,832 to 161,206 bp in size, with 112 unique genes encoded. Comparative genomics showed that the plastomes of F. danxiaensis were relatively conserved with high similarity of genome organization, gene number, GC content and SSRs. While the genomes revealed higher biased codon preferences in Karst habitat than those in Danxia habitats. Eighteen and 11 divergent hotpots were identified at interspecific and intrageneric levels for species identification and further phylogenetic studies. Seven genes (clpP, accD, ccsA, ndhH, rpl20, rpoC2, and rps4) were under positive selection and may be related to adaptation. Phylogenetic analysis revealed that F. danxiaensis is sister to F. major and F. simplex. However, the interspecific relationships are not consistent with the habitat types. Conclusions: The characteristics and interspecific relationship of F. danxiaensis plastomes provide new insights into further integration of geographical factors, environmental factors, and genetic variations on the genomic study of F. danxiaensis. Together, our study will contribute to the study of species identification, population genetics, and conservation biology of F. danxiaensis. [ABSTRACT FROM AUTHOR]

[Display omitted] • 169 accessions representing ca. 68 (85% of total) species of Bolbitis are sampled. • Species of Bolbitis are resolved into four major clades. • Six well-supported subclades are identified in the most speciose Asian clade. • Evolution of six characters is analyzed and free venation evolved from anastomosing venation in Bolbitis. • Bolbitis originated from Africa and a dispersal from Asia resulted in continental disjunction between Africa and America. Bolbitis is a pantropical fern genus of Dryopteridaceae with ca. 80 species mainly in tropical Asia. Earlier studies confirmed the monophyly of Bolbitis when Mickelia is excluded and identified three major clades in Bolbitis. However, earlier studies are based on relatively small sampling and the majority of Asian species are not sampled. In this study, DNA sequences of three plastid markers of 169 accessions representing ca. 68 (85 % of total) species of Bolbitis in nine out of the 10 series recognized by Hennipman (1977), and 54 accessions representing the five remaining bolbitidoid genera are used to infer a global phylogeny with a focus on Asian species. The major results include: (1) Bolbitis is strongly supported as monophyletic; (2) species of Bolbitis are resolved into four major clades and their relationships are: the Malagasy/Mascarene clade is sister to the rest, followed by the African clade which is sister to the American clade + the Asian clade; (3) six well-supported subclades are identified in the most speciose Asian clade; (4) the free-veined Egenolfia is embedded in Bolbitis and is paraphyletic in relation to species with anastomosing venation; (5) three series sensu Hennipman (1977), B. ser. Alienae , B. ser. Egenolfianae , and B. ser. Heteroclitae , are paraphyletic or polyphyletic; (6) evolution of six morphological characters is analyzed and free venation is found to have evolved from anastomosing venation and reversed to free venation in Bolbitis ; and (7) biogeographical implications are drawn and it is shown that a single recent dispersal from Asia resulted in continental disjunction of closely related ferns of Bolbitis between Africa and America. [ABSTRACT FROM AUTHOR]

The ferns of Adiantum Series Gravesiana (Pteridaceae) consist of species that occur exclusively on Danxia (A. juxtapositum) and Karst (A. mariesii, A. longzhouensis, A. dentatum, A. obovatum, and A. gravesii) landforms. We cultured representatives of these six species from 20 different populations on both agar and soil to investigate and compare their gametophyte development. All species had the Vittaria-type pattern of spore germination except A. obovatum, for which we missed the best time to observe this developmental phase. However, two different patterns of subsequent development were observed: the Adiantum-type (i.e., naked, cordate mature gametophyte thallus) in A. mariesii, A. longzhouensis, A. juxtapositum, and A. gravesii and the Kaulinia-type (i.e., naked, ribbon-shaped mature gametophyte thallus) in A. dentatum and A. obovatum. All populations from A. juxtapositum and A. gravesii possess the same Adiantum-type, suggesting that Karst and Danxia soils were not the main factor causing the differences in gametophyte development. The Kaulinia-type adult thallus has not been observed previously in Adiantum and may be an adaptive strategy for survival within the relatively harsh micro-habitats experienced by A. dentatum and A. obovatum compared to other members of this series. [ABSTRACT FROM AUTHOR]

Cotton (Gossypium spp.) is a vital global source of renewable fiber and ranks among the world's most important cash crops. While extensive nuclear genomic data of Gossypium has been explored, the organellar genomic resources of allotetraploid cotton, remain largely untapped at the population level. The plastid genome (plastome) is well suited for studying plant species relationships and diversity due to its nonrecombinant uniparental inheritance. Here, we conducted de novo assembly of 336 Gossypium plastomes, mainly from domesticated cultivars, and generated a pan‐plastome level resource for population structure and genetic diversity analyses. The assembled plastomes exhibited a typical quadripartite structure and varied in length from 160 103 to 160 597 bp. At the species level, seven allotetraploid species were resolved into three clades, where Gossypium tomentosum and Gossypium mustelinum formed an early diverging clade rooted by diploids, followed by splitting two sister clades of Gossypium darwinii–Gossypium barbadense and Gossypium hirsutum–Gossypium ekmanianum–Gossypium stephensii. Within the G. hirsutum clade the resolution of cultivated accessions was less polyphyletic with landrace and wild accessions than in G. barbadense suggesting some selection on plastome in the domestication of this adaptable species of cotton. The nucleotide diversity of G. hirsutum was higher than that of G. barbadense. We specifically compared the plastomes of G. hirsutum and G. barbadense to find mutational hotspots within each species as potential molecular markers. These findings contribute a valuable resource for exploring cotton evolution as well as in the breeding of new cotton cultivars and the preservation of wild and cultivated germplasm. [ABSTRACT FROM AUTHOR]