DEAR EDITOR,During the breast-feeding period,infants undergo remarkable changes,including rapid physiological and developmental growth.However,little is known about gene expression features and sex-specific gene expre...DEAR EDITOR,During the breast-feeding period,infants undergo remarkable changes,including rapid physiological and developmental growth.However,little is known about gene expression features and sex-specific gene expression in breast-feeding infants.In this study,we sequenced 32 blood transcriptomes from 16 breast-feeding rhesus macaque(Macaca mulatta)infants and their lactating mothers.We identified 218 differentially expressed genes(DEGs)between infants and mothers,including 91 up-regulated and 127 down-regulated DEGs in the infant group.展开更多
DEAR EDITOR,Changes in gene expression occur as animals,including primates,age.Macaques have long been used as a model species for primate evolution and biomedical studies.Here,to study gene expression in Tibetan maca...DEAR EDITOR,Changes in gene expression occur as animals,including primates,age.Macaques have long been used as a model species for primate evolution and biomedical studies.Here,to study gene expression in Tibetan macaques (Macaca thibetana,TMs) and its differences to humans,we applied RNA-Seq to obtain the blood transcriptomes of 24 TMs.展开更多
The Tibetan macaque, which is endemic to China, is currently listed as a Near Endangered primate species by the International Union for Conservation of Nature (IUCN)(2017). Short tandem repeats (STRs) refer to r...The Tibetan macaque, which is endemic to China, is currently listed as a Near Endangered primate species by the International Union for Conservation of Nature (IUCN)(2017). Short tandem repeats (STRs) refer to repetitive elements of genome sequence that range in length from 1-6 bp. They are found in many organisms and are widely applied in population genetic studies. To clarify the distribution characteristics of genome-wide STRs and understand their variation among Tibetan macaques, we conducted a genome-wide survey of STRs with next-generation sequencing of five macaque samples. A total of 1 077 790 perfect STRs were mined from our assembly, with an N50 of 4 966 bp. Mono-nucleotide repeats were the most abundant, followed by tetra- and di-nucleotide repeats. Analysis of GC content and repeats showed consistent results with other macaques. Furthermore, using STR analysis software (IobSTR), we found that the proportion of base pair deletions in the STRs was greater than that of insertions in the five Tibetan macaque individuals (P〈0.05, t-test). We also found a greater number of homozygous STRs than heterozygous STRs (P〈0.05, t-test), with the Emei and Jianyang Tibetan macaques showing more heterozygous loci than Huangshan Tibetan macaques. The proportion of insertions and mean variation of alleles in the Emei and Jianyang individuals were slightly higher than those in the Huangshan individuals, thus revealing differences in STR allele size between the two populations The polymorphic STR loci identified based on the reference genome showed good amplification efficiency and could be used to study population genetics in Tibetan macaques. The neighbor-joining tree classified the five macaques into two different branches according to their geographical origin, indicating high genetic differentiation between the Huangshan and Sichuan populations. We elucidated the distribution characteristics of STRs in the Tibetan macaque genome and provided an effective method for screening polymorphic STRs. Our results also lay a foundation for future genetic variation studies of macaques.展开更多
Pikas(Lagomorpha: Ochotonidae) are small mouselike lagomorphs. To investigate their adaptation to different ecological environments during their dispersal from the Qinghai-Xizang(Tibet) Plateau(QTP), we collected 226 ...Pikas(Lagomorpha: Ochotonidae) are small mouselike lagomorphs. To investigate their adaptation to different ecological environments during their dispersal from the Qinghai-Xizang(Tibet) Plateau(QTP), we collected 226 pikas and measured 20 morphological characteristics and recorded habitat information. We also sequenced the genome of 81specimens, representing 27 putative pika species.The genome-wide tree based on 4?090 coding genes identified five subgenera, i.e., Alienauroa, Conothoa,Lagotona, Ochotona, and Pika, consistent with morphometric data. Morphologically, Alienauroa and Ochotona had similar traits, including smaller size and earlier divergence time compared to other pikas.Consistently, the habitats of Alienauroa and Ochotona differed from those of the remaining subgenera. Phylogenetic signal analysis detected 83 genes significantly related to morphological characteristics, including several visual and hearingrelated genes. Analysis of shared amino acid substitutions and positively selected genes(PSGs) in Alienauroa and Ochotona identified two genes, i.e.,mitochondrial function-related TSFM(p.Q155E) and low-light visual sensitivity-related PROM1(p.H419Y).Functional experiments demonstrated that TSFM-155E significantly enhanced mitochondrial function compared to TSFM-155Q in other pikas, and PROM1-419Y decreased the modeling of dynamic intracellular chloride efflux upon calcium uptake. Alienauroa and Ochotona individuals mostly inhabit different environments(e.g., subtropical forests) than other pikas, suggesting that a shift from the larger ancestral type and changes in sensory acuity and energy enhancement may have been required in their new environments. This study increases our understanding of the evolutionary history of pikas.展开更多
基金This work was supported by the Sichuan Application Foundation Project(2020YJ0303)Chengdu Giant Panda Breeding Research Foundation(CPF2017-19)。
文摘DEAR EDITOR,During the breast-feeding period,infants undergo remarkable changes,including rapid physiological and developmental growth.However,little is known about gene expression features and sex-specific gene expression in breast-feeding infants.In this study,we sequenced 32 blood transcriptomes from 16 breast-feeding rhesus macaque(Macaca mulatta)infants and their lactating mothers.We identified 218 differentially expressed genes(DEGs)between infants and mothers,including 91 up-regulated and 127 down-regulated DEGs in the infant group.
基金supported by the National Natural Science Foundation of China 31501871(Z.X.F.)Department of Science and Technology of Sichuan Province 2019JDZH0029(X.Z.)+1 种基金Department of Science and Technology of Sichuan Province2020JDZH0026(X.Z.)Academy of Medical Sciences&Sichuan Provincial People’s Hospital 2017QN06(X.Z.)。
文摘DEAR EDITOR,Changes in gene expression occur as animals,including primates,age.Macaques have long been used as a model species for primate evolution and biomedical studies.Here,to study gene expression in Tibetan macaques (Macaca thibetana,TMs) and its differences to humans,we applied RNA-Seq to obtain the blood transcriptomes of 24 TMs.
基金supported by the State Key Program of National Natural Science Foundation of China(31530068)National Natural Science Foundation of China(31770415)Sichuan Application Foundation Project(2015JY0268)
文摘The Tibetan macaque, which is endemic to China, is currently listed as a Near Endangered primate species by the International Union for Conservation of Nature (IUCN)(2017). Short tandem repeats (STRs) refer to repetitive elements of genome sequence that range in length from 1-6 bp. They are found in many organisms and are widely applied in population genetic studies. To clarify the distribution characteristics of genome-wide STRs and understand their variation among Tibetan macaques, we conducted a genome-wide survey of STRs with next-generation sequencing of five macaque samples. A total of 1 077 790 perfect STRs were mined from our assembly, with an N50 of 4 966 bp. Mono-nucleotide repeats were the most abundant, followed by tetra- and di-nucleotide repeats. Analysis of GC content and repeats showed consistent results with other macaques. Furthermore, using STR analysis software (IobSTR), we found that the proportion of base pair deletions in the STRs was greater than that of insertions in the five Tibetan macaque individuals (P〈0.05, t-test). We also found a greater number of homozygous STRs than heterozygous STRs (P〈0.05, t-test), with the Emei and Jianyang Tibetan macaques showing more heterozygous loci than Huangshan Tibetan macaques. The proportion of insertions and mean variation of alleles in the Emei and Jianyang individuals were slightly higher than those in the Huangshan individuals, thus revealing differences in STR allele size between the two populations The polymorphic STR loci identified based on the reference genome showed good amplification efficiency and could be used to study population genetics in Tibetan macaques. The neighbor-joining tree classified the five macaques into two different branches according to their geographical origin, indicating high genetic differentiation between the Huangshan and Sichuan populations. We elucidated the distribution characteristics of STRs in the Tibetan macaque genome and provided an effective method for screening polymorphic STRs. Our results also lay a foundation for future genetic variation studies of macaques.
基金supported by the National Natural Science Foundation of China (31470110, 31970399)China National GeneBank (CNGB)。
文摘Pikas(Lagomorpha: Ochotonidae) are small mouselike lagomorphs. To investigate their adaptation to different ecological environments during their dispersal from the Qinghai-Xizang(Tibet) Plateau(QTP), we collected 226 pikas and measured 20 morphological characteristics and recorded habitat information. We also sequenced the genome of 81specimens, representing 27 putative pika species.The genome-wide tree based on 4?090 coding genes identified five subgenera, i.e., Alienauroa, Conothoa,Lagotona, Ochotona, and Pika, consistent with morphometric data. Morphologically, Alienauroa and Ochotona had similar traits, including smaller size and earlier divergence time compared to other pikas.Consistently, the habitats of Alienauroa and Ochotona differed from those of the remaining subgenera. Phylogenetic signal analysis detected 83 genes significantly related to morphological characteristics, including several visual and hearingrelated genes. Analysis of shared amino acid substitutions and positively selected genes(PSGs) in Alienauroa and Ochotona identified two genes, i.e.,mitochondrial function-related TSFM(p.Q155E) and low-light visual sensitivity-related PROM1(p.H419Y).Functional experiments demonstrated that TSFM-155E significantly enhanced mitochondrial function compared to TSFM-155Q in other pikas, and PROM1-419Y decreased the modeling of dynamic intracellular chloride efflux upon calcium uptake. Alienauroa and Ochotona individuals mostly inhabit different environments(e.g., subtropical forests) than other pikas, suggesting that a shift from the larger ancestral type and changes in sensory acuity and energy enhancement may have been required in their new environments. This study increases our understanding of the evolutionary history of pikas.