Author
Hailin Pan
Other affiliations: Kunming Institute of Zoology, Chinese Academy of Sciences, Beijing Genomics Institute
Bio: Hailin Pan is an academic researcher from University of Copenhagen. The author has contributed to research in topics: Genome & Population. The author has an hindex of 15, co-authored 24 publications receiving 2308 citations. Previous affiliations of Hailin Pan include Kunming Institute of Zoology & Chinese Academy of Sciences.
Topics: Genome, Population, Comparative genomics, Pollinator, Honey bee
Papers
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University of Copenhagen1, Beijing Genomics Institute2, Royal Veterinary College3, Seoul National University4, University of Nebraska–Lincoln5, University of Porto6, University of South Carolina7, Montclair State University8, Uppsala University9, National University of Singapore10, University of California, Berkeley11, South China University of Technology12, Chinese Academy of Sciences13, Kunming Institute of Zoology14, Howard Hughes Medical Institute15, Aberystwyth University16, University of Kent17, University of California, Riverside18, Mississippi State University19, Austral University of Chile20, Swedish University of Agricultural Sciences21, China Agricultural University22, Cardiff University23, Copenhagen Zoo24, Louisiana State University25, Washington University in St. Louis26, Xi'an Jiaotong University27, University of California, Santa Cruz28, Nova Southeastern University Oceanographic Center29, Smithsonian Conservation Biology Institute30, National Museum of Natural History31, Natural History Museum32, University of California, San Francisco33, Harvard University34, University of Florida35, University of Edinburgh36, New Mexico State University37, Macau University of Science and Technology38, Curtin University39
TL;DR: This work explored bird macroevolution using full genomes from 48 avian species representing all major extant clades to reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
Abstract: Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits.
872 citations
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University of Illinois at Urbana–Champaign1, Utah State University2, University of Copenhagen3, Johns Hopkins University4, Johns Hopkins University School of Medicine5, University of Chicago6, Hobart and William Smith Colleges7, University of Utah8, United States Department of Agriculture9, Autonomous University of Barcelona10, University of Geneva11, Swiss Institute of Bioinformatics12, Martin Luther University of Halle-Wittenberg13, Queen Mary University of London14, Georgia Institute of Technology15, University of Georgia16, Sao Paulo State University17, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto18, Federal University of São Carlos19, University of São Paulo20, Agricultural Research Service21, East Carolina University22, Ohio Agricultural Research and Development Center23, University of Michigan24, University of Hohenheim25, York University26, Janelia Farm Research Campus27, Texas A&M University28, Harvard University29
TL;DR: There is no single road map to eusociality; independent evolutionary transitions in sociality have independent genetic underpinnings and these transitions do have similar general features, including an increase in constrained protein evolution accompanied by increases in the potential for gene regulation and decreases in diversity and abundance of transposable elements.
Abstract: The evolution of eusociality is one of the major transitions in evolution, but the underlying genomic changes are unknown We compared the genomes of 10 bee species that vary in social complexity, representing multiple independent transitions in social evolution, and report three major findings First, many important genes show evidence of neutral evolution as a consequence of relaxed selection with increasing social complexity Second, there is no single road map to eusociality; independent evolutionary transitions in sociality have independent genetic underpinnings Third, though clearly independent in detail, these transitions do have similar general features, including an increase in constrained protein evolution accompanied by increases in the potential for gene regulation and decreases in diversity and abundance of transposable elements Eusociality may arise through different mechanisms each time, but would likely always involve an increase in the complexity of gene networks
325 citations
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University of Münster1, Aix-Marseille University2, University of Copenhagen3, University of Illinois at Urbana–Champaign4, University of Tulsa5, North Carolina State University6, University of Missouri7, Georgia Institute of Technology8, Arizona State University9, University of Osnabrück10, University of Freiburg11, University of Arizona12, University of Wyoming13, Ludwig Maximilian University of Munich14, Lawrence Berkeley National Laboratory15, Purdue University16, Max Planck Society17, United States Department of Agriculture18, University of Giessen19, Macau University of Science and Technology20
TL;DR: The genome and stage-specific transcriptomes of the dampwood termite Zootermopsis nevadensis (Blattodea) are sequence and similarities in the number and expression of genes related to caste determination mechanisms support a hypothesized epigenetic regulation of caste differentiation.
Abstract: Although eusociality evolved independently within several orders of insects, research into the molecular underpinnings of the transition towards social complexity has been confined primarily to Hymenoptera (for example, ants and bees). Here we sequence the genome and stage-specific transcriptomes of the dampwood termite Zootermopsis nevadensis (Blattodea) and compare them with similar data for eusocial Hymenoptera, to better identify commonalities and differences in achieving this significant transition. We show an expansion of genes related to male fertility, with upregulated gene expression in male reproductive individuals reflecting the profound differences in mating biology relative to the Hymenoptera. For several chemoreceptor families, we show divergent numbers of genes, which may correspond to the more claustral lifestyle of these termites. We also show similarities in the number and expression of genes related to caste determination mechanisms. Finally, patterns of DNA methylation and alternative splicing support a hypothesized epigenetic regulation of caste differentiation.
324 citations
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TL;DR: These first analyses of the A. echinatior genome indicate that considerable genetic changes are likely to have accompanied the transition from hunter-gathering to agricultural food production 50 million years ago, and the Transition from single to multiple queen mating 10 million years years ago.
Abstract: We present a high-quality (>100 3depth) Illumina genome sequence of the leaf-cutting ant Acromyrmex echinatior, a model speciesforsymbiosisandreproductiveconflictstudies. Wecompare thisgenomewiththreepreviouslysequenced genomes of ants from different subfamilies and focus our analyses on aspects of the genome likely to be associated with known evolutionary changes. The first is the specialized fungal diet of A. echinatior, where we find gene loss in the ant’s arginine synthesis pathway, loss of detoxification genes, and expansion of a group of peptidase proteins. One of these is a unique ant-derived contribution to the fecal fluid, which otherwise consists of ‘‘garden manuring’’ fungal enzymes that are unaffected by antdigestion.Thesecond is multiplemating ofqueens andejaculatecompetition,which maybe associatedwith a greatly expanded nardilysin-like peptidase gene family. The third is sex determination, where we could identify only a single homolog of the feminizer gene. As other ants and the honeybee have duplications of this gene, we hypothesize that this may partly explain the frequent production of diploid male larvae in A. echinatior. The fourth is the evolution of eusociality, where we find a highly conserved ant-specific profile of neuropeptide genes that may be related to caste determination. These first analyses of the A. echinatior genome indicate that considerable genetic changes are likely to have accompaniedthetransitionfromhunter-gathering toagriculturalfoodproduction50millionyearsago,andthetransition from single to multiple queen mating 10 million years ago. [Supplemental material is available for this article.]
245 citations
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TL;DR: The genome of the domestic rock pigeon (Columba livia), along with those of 36 breeds and two feral accessions and its sister species, is sequenced, revealing the underlying genetics of the head crest and suggesting that all crested breeds may have originated from a single mutational event.
Abstract: The geographic origins of breeds and the genetic basis of variation within the widely distributed and phenotypically diverse domestic rock pigeon (Columba livia) remain largely unknown. We generated a rock pigeon reference genome and additional genome sequences representing domestic and feral populations. We found evidence for the origins of major breed groups in the Middle East and contributions from a racing breed to North American feral populations. We identified the gene EphB2 as a strong candidate for the derived head crest phenotype shared by numerous breeds, an important trait in mate selection in many avian species. We also found evidence that this trait evolved just once and spread throughout the species, and that the crest originates early in development by the localized molecular reversal of feather bud polarity.
240 citations
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28 Jul 2005
TL;DR: PfPMP1)与感染红细胞、树突状组胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作�ly.
Abstract: 抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1(PfPMP1)与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员,通过启动转录不同的var基因变异体为抗原变异提供了分子基础。
18,940 citations
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TL;DR: It is suggested that the natural selection against large insertion/deletion is so weak that a large amount of variation is maintained in a population.
11,521 citations
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TL;DR: The approach to utilizing available RNA-Seq and other data types in the authors' manual curation process for vertebrate, plant, and other species is summarized, and a new direction for prokaryotic genomes and protein name management is described.
Abstract: The RefSeq project at the National Center for Biotechnology Information (NCBI) maintains and curates a publicly available database of annotated genomic, transcript, and protein sequence records (http://www.ncbi.nlm.nih.gov/refseq/). The RefSeq project leverages the data submitted to the International Nucleotide Sequence Database Collaboration (INSDC) against a combination of computation, manual curation, and collaboration to produce a standard set of stable, non-redundant reference sequences. The RefSeq project augments these reference sequences with current knowledge including publications, functional features and informative nomenclature. The database currently represents sequences from more than 55,000 organisms (>4800 viruses, >40,000 prokaryotes and >10,000 eukaryotes; RefSeq release 71), ranging from a single record to complete genomes. This paper summarizes the current status of the viral, prokaryotic, and eukaryotic branches of the RefSeq project, reports on improvements to data access and details efforts to further expand the taxonomic representation of the collection. We also highlight diverse functional curation initiatives that support multiple uses of RefSeq data including taxonomic validation, genome annotation, comparative genomics, and clinical testing. We summarize our approach to utilizing available RNA-Seq and other data types in our manual curation process for vertebrate, plant, and other species, and describe a new direction for prokaryotic genomes and protein name management.
4,104 citations
01 Jan 2000
3,536 citations