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| 1 | Speciation with gene flow via cycles of isolation and migration:insights from multiple mangrove taxa显示文摘Allopatric speciation requiring an unbroken period of geographical isolation has been the standard model of neo-Darwinism. While doubts have been repeatedly raised, strict allopatry without any gene flow remains a plausible mechanism in most cases. To rigorously reject strict allopatry, genomic sequences superimposed on the geological records of a well-delineated geographical barrier are necessary. The Strait of Malacca,narrowly connecting the Pacific and Indian Ocean coasts, serves at different times either as a geographical barrier or a conduit of gene flow for coastal/marine species. We surveyed 1700 plants from 29 populations of 5 common mangrove species by large-scale DNA sequencing and added several whole-genome assemblies. Speciation between the two oceans is driven by cycles of isolation and gene flow due to the fluctuations in sea level leading to the opening/closing of the Strait to ocean currents. Because the time required for speciation in mangroves is longer than the isolation phases, speciation in these mangroves has proceeded through many cycles of mixing-isolation-mixing, or MIM, cycles. The MIM mechanism, by relaxing the condition of no gene flow, can promote speciation in many more geographical features than strict allopatry can. Finally, the MIM mechanism of speciation is also efficient, potentially yielding mn(m > 1) species after n cycles. | Ziwen He Xinnian Li Ming Yang Xinfeng Wang Cairong Zhong Norman C.Duke Chung-I Wu Suhua Shi | 2019 | National Science Review2019，6，2： | 14 |
| 2 | 红树植物的胎生现象及其组学研究进展显示文摘红树植物生长于滨海湿地复杂的生境,包括变化的水体盐度、潮汐海浪冲刷的泥滩等,其繁殖体的顺利萌发并成功定植是红树种群世代延续的关键.部分红树植物通过长期进化产生了一种适应于这种独特生境的称为胎生的有性繁殖方式,即种子在母体上萌发形成繁殖体,特别是发达的下胚轴.这种结构使它们能携带足够的能量与淡水,并在落地时迅速生根定植.然而,目前对这种可以稳定传代的胎生现象的遗传本质和分子机制还了解甚少.本文从基因组和转录组水平对红树植物胎生的起源与进化及其机制等方面的研究进展进行综述,并提出待解决的科学问题,为今后研究提供可借鉴的思路. | 李庆顺 乔红梅 周晓旋 | 2021 | 厦门大学学报(自然科学版)2021，60，2： | 4 |
| 3 | Structural variation during dog domestication: insights from gray wolf and dhole genomes显示文摘Several processes like phenotypic evolution, disease susceptibility and environmental adaptations, which fashion the domestication of animals, are largely attributable to structural variations(SVs) in the genome.Here, we present high-quality draft genomes of the gray wolf(Canis lupus) and dhole(Cuon alpinus) with scaffold N50 of 6.04 Mb and 3.96 Mb, respectively. Sequence alignment comprising genomes of three canid species reveals SVs specific to the dog, particularly 16 315 insertions, 2565 deletions, 443 repeats, 16 inversions and 15 translocations. Functional annotation of the dog SVs associated with genes indicates their enrichments in energy metabolisms, neurological processes and immune systems. Interestingly, we identify and verify at population level an insertion fully covering a copy of the AKR1 B1(Aldo-Keto Reductase Family 1 Member B) transcript. Transcriptome analysis reveals a high level of expression of the new AKR1 B1 copy in the small intestine and liver, implying an increase in de novo fatty acid synthesis and antioxidant ability in dog compared to gray wolf, likely in response to dietary shifts during the agricultural revolution. For the first time, we report a comprehensive analysis of the evolutionary dynamics of SVs during the domestication step of dogs. Our findings demonstrate that retroposition can birth new genes to facilitate domestication, and affirm the importance of large-scale genomic variants in domestication studies. | Guo-Dong Wang Xiu-Juan Shao Bing Bai Junlong Wang Xiaobo Wang Xue Cao Yan-Hu Liu Xuan Wang Ting-Ting Yin Shao-Jie Zhang Yan Lu Zechong Wang Lu Wang Wenming Zhao Bing Zhang Jue Ruan Ya-Ping Zhang | 2019 | National Science Review2019，6，1： | 3 |
| 4 | Convergent adaptation of the genomes of woody plants at the land-sea interface显示文摘Sequencing multiple species that share the same ecological niche may be a new frontier for genomic studies.While such studies should shed light on molecular convergence,genomic-level analyses have been unsuccessful,due mainly to the absence of empirical controls.Woody plant species that colonized the global tropical coasts,collectively referred to as mangroves,are ideal for convergence studies.Here,we sequenced the genomes/transcriptomes of 16 species belonging in three major mangrove clades.To detect convergence in a large phylogeny,a CCS+model is implemented,extending the more limited CCS method(convergence at conservative sites).Using the empirical control for reference,the CCS+model reduces the noises drastically,thus permitting the identification of 73 convergent genes with Ptrue(probability of true convergence)>0.9.Products of the convergent genes tend to be on the plasma membrane associated with salinity tolerance.Importantly,convergence is more often manifested at a higher level than at amino-acid(AA)sites.Relative to>50 plant species,mangroves strongly prefer 4 AAs and avoid 5 others across the genome.AA substitutions between mangrove species strongly reflect these tendencies.In conclusion,the selection of taxa,the number of species and,in particular,the empirical control are all crucial for detecting genome-wide convergence.We believe this large study of mangroves is the first successful attempt at detecting genome-wide site convergence. | Ziwen He Shaohua Xu Zhang Zhang Wuxia Guo Haomin Lyu Cairong Zhong David EBoufford Norman CDuke The International Mangrove Consortium Suhua Shi | 2020 | National Science Review2020，7，6： | 3 |
| 5 | Chromosome-scale assembly of the Kandelia obovata genome显示文摘The mangrove Kandelia obovata(Rhizophoraceae)is an important coastal shelterbelt and landscape tree distributed in tropical and subtropical areas across East Asia and Southeast Asia.Herein,a chromosome-level reference genome of K.obovata based on PacBio,Illumina,and Hi-C data is reported.The high-quality assembled genome size is 177.99 Mb,with a contig N50 value of 5.74 Mb.A large number of contracted gene families and a small number of expanded gene families,as well as a small number of repeated sequences,may account for the small K.obovata genome.We found that K.obovata experienced two whole-genome polyploidization events:one whole-genome duplication shared with other Rhizophoreae and one shared with most eudicots(γevent).We confidently annotated 19,138 protein-coding genes in K.obovata and identified the MADS-box gene class and the RPW8 gene class,which might be related to flowering and resistance to powdery mildew in K.obovata and Rhizophora apiculata,respectively.The reference K.obovata genome described here will be very useful for further molecular elucidation of various traits,the breeding of this coastal shelterbelt species,and evolutionary studies with related taxa. | Min-Jie Hu Wei-Hong Sun Wen-Chieh Tsai Shuang Xiang Xing-Kai Lai De-Qiang Chen Xue-Die Liu Yi-Fan Wang Yi-Xun Le Si-Ming Chen Di-Yang Zhang Xia Yu Wen-Qi Hu Zhuang Zhou Yan-Qiong Chen Shuang-Quan Zou Zhong-Jian Liu | 2020 | Horticulture Research2020，7，1： | 2 |
| 6 | Gene regulatory network stabilized by pervasive weak repressions: micro RNA functions revealed by the May–Wigner theory显示文摘Food web and gene regulatory networks(GRNs)are large biological networks,both of which can be analyzed using the May-Wigner theory.According to the theory,networks as large as mammalian GRNs would require dedicated gene products for stabilization.We propose that microRNAs(miRNAs)are those products.More than 30%of genes are repressed by miRNAs,but m ost repressions are too weak to have a phenotypic consequence.The theory shows that(i)weak repressions cumulatively enhance the stability of GRNs,and(ii)broad and weak repressions confer greater stability than a few strong ones.Hence,the diffuse actions of miRNAs in mammalian cells appear to function mainly in stabilizing GRNs.The postulated link between mRNA repression and GRN stability can be seen in a different light in yeast,which do not have miRNAs.Yeast cells rely on non-specific RNA nucleases to strongly degrade mRNAs for GRN stability.The strategy is suited to GRNs of small and rapidly dividing yeast cells,but not the larger mammalian cells.In conclusion,the May-W igner theory,supplanting the analysis of small motifs,provides a mathematical solution to GRN stability,thus linking miRNAs explicitly to‘developmental canalization’. | Yuxin Chen Yang Shen Pei Lin Ding Tong Yixin Zhao Stefano Allesina Xu Shen Chung-I Wu | 2019 | National Science Review2019，6，6： | 2 |
| 7 | Genomic Convergence in the Adaptation to Extreme Environments显示文摘Convergent evolution is especially common in plants that have independently adapted to the same extreme environments(i.e.,extremophile plants).The recent burst of omics data has alleviated many limitations that have hampered molecular convergence studies of non-model extremophile plants.In this review,we summarize cases of genomic convergence in these taxa to examine the extent and type of genomic convergence during the process of adaptation to extreme environments.Despite being well studied by candidate gene approaches,convergent evolution at individual sites is rare and often has a high false-positive rate when assessed in whole genomes.By contrast,genomic convergence at higher genetic levels has been detected during adaptation to the same extreme environments.Examples include the convergence of biological pathways and changes in gene expression,gene copy number,amino acid usage,and GC content.Higher convergence levels play important roles in the adaptive evolution of extremophiles and may be more frequent and involve more genes.In several cases,multiple types of convergence events have been found to co-occur.However,empirical and theoretical studies of this higher level convergent evolution are still limited.In conclusion,both the development of powerful approaches and the detection of convergence at various genetic levels are needed to further reveal the genetic mechanisms of plant adaptation to extreme environments. | Shaohua Xu Jiayan Wang Zixiao Guo Ziwen He Suhua Shi | 2020 | Plant Communications2020，1，6： | 1 |
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