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Sympatric or micro-allopatric speciation in a glacial lake?genomic islands support neither

National Science Review 2022年第12期9卷 37-49页

作者： Ning Sun Liandong Yang Fei Tian Honghui Zeng Ziwen He Kai Zhao Cheng Wang Minghui Meng Chenguang Feng Chengchi Fang Wenqi Lv Jing Bo Yongtao Tang Xiaoni Gan Zuogang Peng Yiyu Chen Shunping He State Key Laboratory of Freshwater Ecology and Biotechnology Institute of Hydrobiology Chinese Academy of Sciences University of Chinese Academy of Sciences Key Laboratory of Adaptation and Evolution of Plateau Biota Northwest Institute of Plateau Biology Chinese Academy of Sciences State Key Laboratory of Biocontrol Guangdong Key Lab of Plant Resources School of Life Sciences Sun Yat-sen University School of Ecology and Environment Northwestern Polytechnical University Institute of Deep-Sea Science and Engineering Chinese Academy of Sciences Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education) Southwest University School of Life Sciences National Natural Science Foundation of China Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences

Apparent cases of sympatric speciation may actually be due to micro-allopatric or micro-parapatric speciation.One way to distinguish between these models is to examine the existence and nature of genomic islands of divergence,wherein divergent DNA segments are interspersed with low-divergence segments.Such islands should be rare or absent under micro-allopatric speciation but common in cases of speciation with gene flow.Sympatric divergence of endemic fishes is known from isolated saline,crater,postglacial,and ancient lakes.Two morphologically distinct cyprinid fishes,Gymnocypris eckloni scoliostomus(GS) and G.eckloni eckloni(GE),in a small glacial lake on the Qinghai-Tibet Plateau,Lake Sunmcuo,match the biogeographic criteria of sympatric speciation.In this study,we examined genome-wide variation in 46individuals from these two groups.The divergence time between the GS and GE lineages was estimated to be 20-60 Kya.We identified 54 large genomic islands(≥100 kb) of speciation,which accounted for 89.4%of the total length of all genomic islands.These islands harboured divergent genes related to olfactory receptors and olfaction signals that may play important roles in food selection and assortative mating in fishes.Although the genomic islands clearly indicated speciation with gene flow and rejected micro-allopatric speciation,they were too large to support the hypothesis of sympatric speciation.Theoretical and recent empirical studies suggested that continual gene flow in sympatry should give rise to many small genomic islands(as small as a few kilobases in size).Thus,the observed pattern is consistent with the extensive evidence on parapatric speciation,in which adjacent habitats facilitate divergent selection but also permit gene flow during speciation.We suggest that many,if not most,of the reported cases of sympatric speciation are likely to be micro-parapatric speciation.

关键词： sympatric speciation gene flow genomic islands micro-parapatric speciation selection olfaction

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Analysis of the 3' ends of tRNA as the cause of insertion sites of foreign DNA in Prochlorococcus

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2010年第9期11卷 708-718页

作者： Hai-lan LIU Jun ZHU Institute of Bioinformaties College of Agriculture and Biotechnology Zhejiang University Hangzhou 310029 China Institute of Maize Research College of Agriculture Sichuan Agricultural University Ya'an 625014 China

The purpose of this study was to investigate the characteristics of transfer RNA(tRNA) responsible for the association between tRNA genes and genes of apparently foreign origin(genomic islands) in five high-light adapted Prochlorococcus strains.Both bidirectional best BLASTP(basic local alignment search tool for proteins) search and the conservation of gene order against each other were utilized to identify genomic islands,and 7 genomic islands were found to be immediately adjacent to tRNAs in Prochlorococcus marinus AS9601,11 in P.marinus MIT9515,8 in P.marinus MED4,6 in P.marinus MIT9301,and 6 in P.marinus MIT9312.Monte Carlo simulation showed that tRNA genes are hotspots for the integration of genomic islands in Prochlorococcus strains.The tRNA genes associated with genomic islands showed the following characteristics:(1) the association was biased towards a specific subset of all iso-accepting tRNA genes;(2) the codon usages of genes within genomic islands appear to be unrelated to the codons recognized by associated tRNAs;and,(3) the majority of the 3' ends of associated tRNAs lack CCA ends.These findings contradict previous hypotheses concerning the molecular basis for the frequent use of tRNA as the insertion site for foreign genetic materials.The analysis of a genomic island associated with a tRNA-Asn gene in P.marinus MIT9301 suggests that foreign genetic material is inserted into the host genomes by means of site-specific recombination,with the 3' end of the tRNA as the target,and during the process,a direct repeat of the 3' end sequence of a boundary tRNA(namely,a scar from the process of insertion) is formed elsewhere in the genomic island.Through the analysis of the sequences of these targets,it can be concluded that a region characterized by both high GC content and a palindromic structure is the preferred insertion site.

关键词： genomic islands Prochlorococcus Transfer RNA(tRNA) Palindromic structure Codon usage

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