Ma Bin

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Ma
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Bin
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  • Article
    A draft genome sequence of the elusive giant squid, Architeuthis dux
    (Oxford University Press, 2020-01-16) da Fonseca, Rute R. ; Couto, Alvarina ; Machado, Andre M. ; Brejova, Brona ; Albertin, Carolin B. ; Silva, Filipe ; Gardner, Paul ; Baril, Tobias ; Hayward, Alex ; Campos, Alexandre ; Ribeiro, Ângela M. ; Barrio-Hernandez, Inigo ; Hoving, Henk-Jan ; Tafur-Jimenez, Ricardo ; Chu, Chong ; Frazão, Barbara ; Petersen, Bent ; Peñaloza, Fernando ; Musacchia, Francesco ; Alexander, Graham C., Jr. ; Osório, Hugo ; Winkelmann, Inger ; Simakov, Oleg ; Rasmussen, Simon ; Rahman, M. Ziaur ; Pisani, Davide ; Vinther, Jakob ; Jarvis, Erich ; Zhang, Guojie ; Strugnell, Jan M. ; Castro, L. Filipe C. ; Fedrigo, Olivier ; Patricio, Mateus ; Li, Qiye ; Rocha, Sara ; Antunes, Agostinho ; Wu, Yufeng ; Ma, Bin ; Sanges, Remo ; Vinar, Tomas ; Blagoev, Blagoy ; Sicheritz-Ponten, Thomas ; Nielsen, Rasmus ; Gilbert, M. Thomas P.
    Background: The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea–dwelling species will allow several pending evolutionary questions to be unlocked. Findings: We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome. Conclusions: This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.
  • Article
    Distinct biogeographic patterns for archaea, bacteria, and fungi along the vegetation gradient at the continental scale in Eastern China
    (American Society for Microbiology, 2017-02-07) Ma, Bin ; Dai, Zhongmin ; Wang, Haizhen ; Dsouza, Melissa ; Liu, Xingmei ; He, Yan ; Wu, Jianjun ; Rodrigues, Jorge L. M. ; Gilbert, Jack A. ; Brookes, Philip C. ; Xu, Jianming
    The natural forest ecosystem in Eastern China, from tropical forest to boreal forest, has declined due to cropland development during the last 300 years, yet little is known about the historical biogeographic patterns and driving processes for the major domains of microorganisms along this continental-scale natural vegetation gradient. We predicted the biogeographic patterns of soil archaeal, bacterial, and fungal communities across 110 natural forest sites along a transect across four vegetation zones in Eastern China. The distance decay relationships demonstrated the distinct biogeographic patterns of archaeal, bacterial, and fungal communities. While historical processes mainly influenced bacterial community variations, spatially autocorrelated environmental variables mainly influenced the fungal community. Archaea did not display a distance decay pattern along the vegetation gradient. Bacterial community diversity and structure were correlated with the ratio of acid oxalate-soluble Fe to free Fe oxides (Feo/Fed ratio). Fungal community diversity and structure were influenced by dissolved organic carbon (DOC) and free aluminum (Ald), respectively. The role of these environmental variables was confirmed by the correlations between dominant operational taxonomic units (OTUs) and edaphic variables. However, most of the dominant OTUs were not correlated with the major driving variables for the entire communities. These results demonstrate that soil archaea, bacteria, and fungi have different biogeographic patterns and driving processes along this continental-scale natural vegetation gradient, implying different community assembly mechanisms and ecological functions for archaea, bacteria, and fungi in soil ecosystems.