The reference genome and transcriptome of the limestone langur, Trachypithecus leucocephalus, reveal expansion of genes related to alkali tolerance

Abstract

Background Trachypithecus leucocephalus, the white-headed langur, is a critically endangered primate that is endemic to the karst mountains in the southern Guangxi province of China. Studying the genomic and transcriptomic mechanisms underlying its local adaptation could help explain its persistence within a highly specialized ecological niche. Results In this study, we used PacBio sequencing and optical assembly and Hi-C analysis to create a high-quality de novo assembly of the T. leucocephalus genome. Annotation and functional enrichment revealed many genes involved in metabolism, transport, and homeostasis, and almost all of the positively selected genes were related to mineral ion binding. The transcriptomes of 12 tissues from three T. leucocephalus individuals showed that the great majority of genes involved in mineral absorption and calcium signaling were expressed, and their gene families were significantly expanded. For example, FTH1 primarily functions in iron storage and had 20 expanded copies. Conclusions These results increase our understanding of the evolution of alkali tolerance and other traits necessary for the persistence of T. leucocephalus within an ecologically unique limestone karst environment.

Haplotype‐resolved genome assembly of Phanera championii reveals molecular mechanisms of flavonoid synthesis and adaptive evolution

“…For example, a genomic study on P. huaijiensis, a cave plant, showed that the expansion of WRKY genes retained after WGD may have aided its adaptation to karst habitats (Feng et al, 2020). Similarly, in a study of limestone langur adapted to karstic habitats, it was found that nearly all strongly positively selected genes were associated with mineral ion bindings (Que et al, 2021). These findings suggest that gene duplication and selection can contribute to the adaptive evolution of species.…”

Regulation of Root Exudation in Wheat Plants in Response to Alkali Stress

“…To date, multilevel signal networks mediating salt tolerance and Na + compartmentalization mechanisms at the subcellular level have been elucidated [11][12][13][14][15][16]. However, relatively few studies have focused on plant alkali tolerance [3,4,[17][18][19][20][21][22][23][24][25][26][27][28]. Important progress in research on plant alkali tolerance has been made in Arabidopsis [21], maize [25], and wheat [27], in which H + -ATPase was demonstrated to play an important role in alkali tolerance.…”

Antibiotic resistance profiles of gut microbiota across various primate species in Guangxi

“…At present, there are many kinds of NHPs lives in Guangxi, China, including Trachypithecus leucocephalus ( T. leucocephalus ), Trachypithecus francoisi ( T. francoisi ), Macaca multta ( M. multta ), etc., which is reliable resources for the study of non-human primates. Studies on them have focused on genome adaptation, conservation, and behavior ( Huang and Li, 2005 ; Li et al, 2020 ; Liu Z. J. et al, 2020 ; Fan and Pedersen, 2021 ; Que et al, 2021 ), but little is about the diversity and composition of ARGs. Identification of ARGs in NHPs can be used as a proactive method for monitoring antibiotic resistance and as a control measure against infection ( Schuchat et al, 2001 ; Roca et al, 2015 ; Liu et al, 2016 ).…”