Genomes and demographic histories of the endangeredBretschneidera sinensis(Akaniaceae)

Abstract

Background Bretschneidera sinensis is an endangered relic tree species in the Akaniaceae family and is sporadically distributed in eastern Asia. As opposed to its current narrow and rare distribution, the fossil pollen of B. sinensis has been found to be frequent and widespread in the Northern Hemisphere during the Late Miocene. B. sinensis is also a typical mycorrhizal plant, and its annual seedlings exhibit high mortality rates in absence of mycorrhizal development. The chromosome-level high-quality genome of B. sinensis will help us to more deeply understand the survival and demographic histories of this relic species. Results A total of 25.39 Gb HiFi reads and 109.17 Gb Hi-C reads were used to construct the chromosome-level genome of B. sinensis, which is 1.21 Gb in length with the contig N50 of 64.13 Mb and chromosome N50 of 146.54 Mb. The identified transposable elements account for 55.21% of the genome. A total of 45,839 protein-coding genes were predicted in B. sinensis. A lineage-specific whole-genome duplication was detected, and 7,283 lineage-specific expanded gene families with functions related to the specialized endotrophic mycorrhizal adaptation were identified. The historical effective population size (Ne) of B. sinensis was found to oscillate greatly in response to Quaternary climatic changes. The Ne of B. sinensis has decreased rapidly in the recent past, making its extant Ne extremely lower. Our additional evolutionary genomic analyses suggested that the developed mycorrhizal adaption might have been repeatedly disrupted by environmental changes caused by Quaternary climatic oscillations. The environmental changes and an already decreased population size during the Holocene may have led to the current rarity of B. sinensis. Conclusion This is a detailed report of the genome sequences for the family Akaniaceae distributed in evergreen forests in eastern Asia. Such a high-quality genomic resource may provide critical clues for comparative genomics studies of this family in the future.

Analysis of Carica papaya Informs Lineage-Specific Evolution of the Aquaporin (AQP) Family in Brassicales

“…For species without recent WGDs, i.e., papaya, horseradish, physic nut, and castor bean, six to eight WGD repeats were identified, though a higher E-value cutoff of 1 × 10 −10 instead of 1 × 10 −20 was adopted in this study, which facilitates the detection of microsynteny and ancient WGD repeats [53]. By contrast, higher numbers of 11-26 WGD repeats were identified in poplar, cassava, rubber tree, B. sinensis, spider flower, and Brassicaceae species, corresponding to the occurrence of one to three recent WGDs in these species after the γ event [15,34,43,44,50]. In Arabidopsis, seven, three, and two repeats were shown to arise from the At-α, At-β, and γ events, respectively, most of which are conserved in Brassicaceae species examined in this study, though A. halleri and saltwater cress have retained one more repeat from the At-α WGD (i.e., AhTIP2;1/-2;2 and EsTIP2;1/-2;2) and the ortholog of AtPIP2;8 in saltwater cress is under fractionation.…”

“…By contrast, the last common ancestor of cassava and rubber tree experienced one recent WGD [30,33,50], whereas poplar was proven to experience one Salicaceae-specific p WGD [34]. Interestingly, the amounts of AQP genes were shown to be positively associated with the total gene numbers present in genomes that were mainly contributed by recent WGDs [30,34,44,50], though tandem duplication plays an important role in the family expansion in castor bean [35]. Despite the occurrence of one ancient tetraploidization event in A. coerulea [51,52], only two WGD repeats are retained due to a long time of evolution.…”

“…Brassicales, an economically important order of flowering plants, represents 2.2% of the total extant core eudicot diversity and has been overlooked as a promising system to investigate patterns of disjunct distributions and diversification rates [41]. In addition to the γ event shared by all core eudicots [40], multiple independent WGDs have been described in Brassicales, e.g., one recent WGD in B. sinensis, the Th-α event within Cleomaceae, the At-α event at the base of Brassicaceae, and the At-β event near at the base of the order [15,[42][43][44][45]. Despite the occurrence of two recent WGDs, Arabidopsis harbors a relatively small genome size of approximately 119.7 Mb and serves as a popular model species for research in many aspects of plant biology [16].…”

“…However, whether it is present in other Brassicales families is largely unknown. The accessibility of several representative Brassicales genomes beyond Brassicaceae, i.e., papaya in Caricaceae, horseradish in Moringaceae, B. sinensis in Akaniaceae, and spider flower in Cleomaceae [14,43,44,47], provides a good opportunity to address this issue.…”

Integrating genomics and conservation to safeguard plant diversity

“…Recently, some whole genome sequences were generated with a specific intention to support the conservation of highly endangered plant species such as the eudicot Bretschneidera sinensis (Zhang et al, 2022) and the derived fern Adiantum nelumboides (Zhong et al, 2022). The de novo‐generated genomes enable the study of the demographic history of these plants (Sun et al, 2022; Zhang et al, 2022; Zhong et al, 2022) that will be further integrated, together with ecological field surveys (Yu et al, 2022), into the exploration of the protocols of ex situ and in situ conservation measures of these plants.…”