Mangroves accumulate sedimentary sequences, where cores can provide historical records of mangrove evolution with past climate change and human activity. The study traced the history of mangrove evolution during the p...Mangroves accumulate sedimentary sequences, where cores can provide historical records of mangrove evolution with past climate change and human activity. The study traced the history of mangrove evolution during the past one hundred years in a mangrove swamp of Maowei Sea, SW China. The sedimentation rates(0.38-0.95 cm yr^(-1)) were calculated on the basis of ln(^(210)Pb_(xs)/Al) and mass depth in the core sediments. Chemical tracers, such as δ^(13)C_(org) and C:N values, were utilized to trace the contribution of mangrove-derived organic matter using a ternary mixing model. Because of potential diagenetic alteration and / or overlap in the isotopic signatures of different components, simultaneous use of mangrove pollen diagrams can help to supplement some of these limitations. Combined with mangrove pollen, mangrove evolution was reconstructed and could be divided into three stages: flourishment(1886-1905 AD), slight degradation(1905-1949 AD) and rapid degradation period(1949-2007 AD), which was consistent with previous reports. The reclamation of mangrove swamps to shrimp ponds was the major reason for rapid degradation of mangrove ecosystems in recent years, rather than climate change in the region.展开更多
Mammalian genomes contain tens of thousands of long non-coding RNAs(lnc RNAs) that have been implicated in diverse biological processes. However, the lnc RNA transcriptomes of most mammalian species have not been esta...Mammalian genomes contain tens of thousands of long non-coding RNAs(lnc RNAs) that have been implicated in diverse biological processes. However, the lnc RNA transcriptomes of most mammalian species have not been established, limiting the evolutionary annotation of these novel transcripts. Based on RNA sequencing data from six tissues of nine species, we built comprehensive lnc RNA catalogs(4,142–42,558 lnc RNAs) covering the major mammalian species. Compared to protein-coding RNAs, expression of lnc RNAs exhibits striking lineage specificity. Notably, although 30%–99% human lnc RNAs are conserved across different species on DNA locus level, only 20%–27% of these conserved lnc RNA loci are detected to transcription, which represents a stark contrast to the proportion of conserved protein-coding genes(48%–80%). This finding provides a valuable resource for experimental scientists to study the mechanisms of lnc RNAs. Moreover, we constructed lnc RNA expression phylogenetic trees across nine mammals and demonstrated that lnc RNA expression profiles can reliably determine phylogenic placement in a manner similar to their coding counterparts. Our data also reveal that the evolutionary rate of lnc RNA expression varies among tissues and is significantly higher than those for protein-coding genes. To streamline the processes of browsing lnc RNAs and detecting their evolutionary statuses, we integrate all the data produced in this study into a database named Phylo NONCODE(http://www.bioinfo.org/phylo Noncode). Our work starts to place mammalian lnc RNAs in an evolutionary context and represent a rich resource for comparative and functional analyses of this critical layer of genome.展开更多
基金supported by the National Key Scientific Research Project on Global Climate Change (Grant No. 2010CB 951203)the National Natural Science Foundation of China (Grant Nos. 41206057, 41576067, 41376075 and 41576061)
文摘Mangroves accumulate sedimentary sequences, where cores can provide historical records of mangrove evolution with past climate change and human activity. The study traced the history of mangrove evolution during the past one hundred years in a mangrove swamp of Maowei Sea, SW China. The sedimentation rates(0.38-0.95 cm yr^(-1)) were calculated on the basis of ln(^(210)Pb_(xs)/Al) and mass depth in the core sediments. Chemical tracers, such as δ^(13)C_(org) and C:N values, were utilized to trace the contribution of mangrove-derived organic matter using a ternary mixing model. Because of potential diagenetic alteration and / or overlap in the isotopic signatures of different components, simultaneous use of mangrove pollen diagrams can help to supplement some of these limitations. Combined with mangrove pollen, mangrove evolution was reconstructed and could be divided into three stages: flourishment(1886-1905 AD), slight degradation(1905-1949 AD) and rapid degradation period(1949-2007 AD), which was consistent with previous reports. The reclamation of mangrove swamps to shrimp ponds was the major reason for rapid degradation of mangrove ecosystems in recent years, rather than climate change in the region.
基金supported by Training Program of the Major Research Plan of the National Natural Science Foundation of China(91229120)
文摘Mammalian genomes contain tens of thousands of long non-coding RNAs(lnc RNAs) that have been implicated in diverse biological processes. However, the lnc RNA transcriptomes of most mammalian species have not been established, limiting the evolutionary annotation of these novel transcripts. Based on RNA sequencing data from six tissues of nine species, we built comprehensive lnc RNA catalogs(4,142–42,558 lnc RNAs) covering the major mammalian species. Compared to protein-coding RNAs, expression of lnc RNAs exhibits striking lineage specificity. Notably, although 30%–99% human lnc RNAs are conserved across different species on DNA locus level, only 20%–27% of these conserved lnc RNA loci are detected to transcription, which represents a stark contrast to the proportion of conserved protein-coding genes(48%–80%). This finding provides a valuable resource for experimental scientists to study the mechanisms of lnc RNAs. Moreover, we constructed lnc RNA expression phylogenetic trees across nine mammals and demonstrated that lnc RNA expression profiles can reliably determine phylogenic placement in a manner similar to their coding counterparts. Our data also reveal that the evolutionary rate of lnc RNA expression varies among tissues and is significantly higher than those for protein-coding genes. To streamline the processes of browsing lnc RNAs and detecting their evolutionary statuses, we integrate all the data produced in this study into a database named Phylo NONCODE(http://www.bioinfo.org/phylo Noncode). Our work starts to place mammalian lnc RNAs in an evolutionary context and represent a rich resource for comparative and functional analyses of this critical layer of genome.
