Combining genome-wide and transcriptome-wide analyses reveal the evolutionary conservation and functional diversity of aquaporins in cotton

Published on Dec 1, 2019in BMC Genomics3.50
· DOI :10.1186/s12864-019-5928-2
Weixi Li1
Estimated H-index: 1
(NAU: Nanjing Agricultural University),
Dayong Zhang (NAU: Nanjing Agricultural University)+ 2 AuthorsGUOWangzhen32
Estimated H-index: 32
(NAU: Nanjing Agricultural University)
Background Aquaporins (AQPs) are integral membrane proteins from a larger family of major intrinsic proteins (MIPs) and function in a huge variety of processes such as water transport, plant growth and stress response. The availability of the whole-genome data of different cotton species allows us to study systematic evolution and function of cotton AQPs on a genome-wide level.
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Published on Apr 1, 2019in Nature Genetics25.45
Yan Hu14
Estimated H-index: 14
(ZJU: Zhejiang University),
Jiedan Chen12
Estimated H-index: 12
(ZJU: Zhejiang University)
+ 36 AuthorsJinmin Lian1
Estimated H-index: 1
Allotetraploid cotton is an economically important natural-fiber-producing crop worldwide. After polyploidization, Gossypium hirsutum L. evolved to produce a higher fiber yield and to better survive harsh environments than Gossypium barbadense, which produces superior-quality fibers. The global genetic and molecular bases for these interspecies divergences were unknown. Here we report high-quality de novo–assembled genomes for these two cultivated allotetraploid species with pronounced improveme...
Published on Feb 1, 2019in Nature Genetics25.45
Maojun Wang12
Estimated H-index: 12
(HAU: Huazhong Agricultural University),
Lili Tu25
Estimated H-index: 25
(HAU: Huazhong Agricultural University)
+ 31 AuthorsGuannan Zhao2
Estimated H-index: 2
(HAU: Huazhong Agricultural University)
Allotetraploid cotton species (Gossypium hirsutum and Gossypium barbadense) have long been cultivated worldwide for natural renewable textile fibers. The draft genome sequences of both species are available but they are highly fragmented and incomplete1,2,3,4. Here we report reference-grade genome assemblies and annotations for G. hirsutum accession Texas Marker-1 (TM-1) and G. barbadense accession 3–79 by integrating single-molecule real-time sequencing, BioNano optical mapping and high-through...
Published on Jan 1, 2019in Plant Biology2.39
Christian Zörb26
Estimated H-index: 26
(University of Hohenheim),
Christoph-Martin Geilfus15
Estimated H-index: 15
(Humboldt University of Berlin),
Karl-Josef Dietz67
Estimated H-index: 67
(Bielefeld University)
Published on Jun 1, 2018in Nature Genetics25.45
Xiongming Du10
Estimated H-index: 10
Gai Huang2
Estimated H-index: 2
(PKU: Peking University)
+ 29 AuthorsMin Liu4
Estimated H-index: 4
The ancestors of Gossypium arboreum and Gossypium herbaceum provided the A subgenome for the modern cultivated allotetraploid cotton. Here, we upgraded the G. arboreum genome assembly by integrating different technologies. We resequenced 243 G. arboreum and G. herbaceum accessions to generate a map of genome variations and found that they are equally diverged from Gossypium raimondii. Independent analysis suggested that Chinese G. arboreum originated in South China and was subsequently introduce...
Published on Dec 1, 2017in BMC Plant Biology3.67
Md. Abdul Kayum6
Estimated H-index: 6
(SNU: Sunchon National University),
Jong-In Park16
Estimated H-index: 16
(SNU: Sunchon National University)
+ 3 AuthorsIll-Sup Nou17
Estimated H-index: 17
(SNU: Sunchon National University)
Background Plants contain a range of aquaporin (AQP) proteins, which act as transporter of water and nutrient molecules through living membranes. AQPs also participate in water uptake through the roots and contribute to water homeostasis in leaves.
Published on May 1, 2017in Plant Biology2.39
Zhiwen Chen8
Estimated H-index: 8
(CAU: China Agricultural University),
Hushuai Nie4
Estimated H-index: 4
(CAU: China Agricultural University)
+ 8 AuthorsJonathan F. Wendel82
Estimated H-index: 82
(Iowa State University)
Cotton (Gossypium spp.) is commonly grouped into eight diploid genomic groups, designated A–G and K, and an allotetraploid genomic group, AD. Gossypium raimondii (D5) and G. arboreum (A2) are the putative contributors to the progenitor of G. hirsutum (AD1), the economically important fibre-producing cotton species. Mitochondrial DNA from week-old etiolated seedlings was extracted from isolated organelles using discontinuous sucrose density gradient method. Mitochondrial genomes were sequenced, a...
Published on May 1, 2017in Scientific Reports4.01
S. M. Shivaraj2
Estimated H-index: 2
Rupesh Deshmukh18
Estimated H-index: 18
+ 3 AuthorsPrasanta K. Dash9
Estimated H-index: 9
Genome-wide identification, characterization, and expression profile of aquaporin gene family in flax ( Linum usitatissimum )
Published on Aug 1, 2016in Nature plants13.30
Ayelet Salman-Minkov2
Estimated H-index: 2
Niv Sabath13
Estimated H-index: 13
Itay Mayrose27
Estimated H-index: 27
A study examining a genetic data set including dozens of genera containing crop species and their wild relatives shows that domesticated species experienced more polyploidy events than their wild relatives, and domestication followed polyploidization.
Published on Jul 1, 2016in Molecular Biology and Evolution14.80
Sudhir Kumar63
Estimated H-index: 63
(TU: Temple University),
Glen Stecher6
Estimated H-index: 6
(TU: Temple University),
Koichiro Tamura28
Estimated H-index: 28
(Tokyo Metropolitan University)
Abstract We present the latest version of the Molecular Evolutionary Genetics Analysis (Mega) software, which contains many sophisticated methods and tools for phylogenomics and phylomedicine. In this major upgrade, Mega has been optimized for use on 64-bit computing systems for analyzing larger datasets. Researchers can now explore and analyze tens of thousands of sequences in Mega The new version also provides an advanced wizard for building timetrees and includes a new functionality to automa...
Published on Jun 21, 2016in PLOS ONE2.78
Abul Kalam Azad11
Estimated H-index: 11
(SUST: Shahjalal University of Science and Technology),
Jahed Ahmed3
Estimated H-index: 3
(SUST: Shahjalal University of Science and Technology)
+ 4 AuthorsMaki Katsuhara32
Estimated H-index: 32
(Okayama University)
Major intrinsic proteins (MIPs), commonly known as aquaporins, transport not only water in plants but also other substrates of physiological significance and heavy metals. In most of the higher plants, MIPs are divided into five subfamilies (PIPs, TIPs, NIPs, SIPs and XIPs). Herein, we identified 68, 42, 38 and 28 full-length MIPs, respectively in the genomes of four monocot grass plants, specifically Panicum virgatum, Setaria italica, Sorghum bicolor and Brachypodium distachyon. Phylogenetic an...
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