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Tang YZ, Ma Z, Hu Z, Deng Y, Yang A, Lin S, Yi L, Chai Z, Gobler CJ. 3,000 km and 1,500‐year presence of
Aureococcus anophagefferens
reveals indigenous origin of brown tides in China. Mol Ecol 2019; 28:4065-4076. [DOI: 10.1111/mec.15196] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 06/29/2019] [Accepted: 07/08/2019] [Indexed: 02/01/2023]
Affiliation(s)
- Ying Zhong Tang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences Institute of Oceanology Chinese Academy of Sciences Qingdao China
- Laboratory for Marine Ecology and Environmental Science Qingdao National Laboratory for Marine Science and Technology Qingdao China
| | - Zhaopeng Ma
- CAS Key Laboratory of Marine Ecology and Environmental Sciences Institute of Oceanology Chinese Academy of Sciences Qingdao China
- University of Chinese Academy of Sciences Beijing China
| | - Zhangxi Hu
- CAS Key Laboratory of Marine Ecology and Environmental Sciences Institute of Oceanology Chinese Academy of Sciences Qingdao China
| | - Yunyan Deng
- CAS Key Laboratory of Marine Ecology and Environmental Sciences Institute of Oceanology Chinese Academy of Sciences Qingdao China
| | - Aoao Yang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences Institute of Oceanology Chinese Academy of Sciences Qingdao China
- University of Chinese Academy of Sciences Beijing China
| | - Siheng Lin
- CAS Key Laboratory of Marine Ecology and Environmental Sciences Institute of Oceanology Chinese Academy of Sciences Qingdao China
- University of Chinese Academy of Sciences Beijing China
| | - Liang Yi
- State Key Laboratory of Marine Geology Tongji University Shanghai China
| | - Zhaoyang Chai
- CAS Key Laboratory of Marine Ecology and Environmental Sciences Institute of Oceanology Chinese Academy of Sciences Qingdao China
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Zhao L, Zhang N, Ma PF, Liu Q, Li DZ, Guo ZH. Phylogenomic analyses of nuclear genes reveal the evolutionary relationships within the BEP clade and the evidence of positive selection in Poaceae. PLoS One 2013; 8:e64642. [PMID: 23734211 PMCID: PMC3667173 DOI: 10.1371/journal.pone.0064642] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Accepted: 04/16/2013] [Indexed: 11/23/2022] Open
Abstract
BEP clade of the grass family (Poaceae) is composed of three subfamilies, i.e. Bambusoideae, Ehrhartoideae, and Pooideae. Controversies on the phylogenetic relationships among three subfamilies still persist in spite of great efforts. However, previous evidence was mainly provided from plastid genes with only a few nuclear genes utilized. Given different evolutionary histories recorded by plastid and nuclear genes, it is indispensable to uncover their relationships based on nuclear genes. Here, eleven species with whole-sequenced genome and six species with transcriptomic data were included in this study. A total of 121 one-to-one orthologous groups (OGs) were identified and phylogenetic trees were reconstructed by different tree-building methods. Genes which might have undergone positive selection and played important roles in adaptive evolution were also investigated from 314 and 173 one-to-one OGs in two bamboo species and 14 grass species, respectively. Our results support the ((B, P) E) topology with high supporting values. Besides, our findings also indicate that 24 and nine orthologs with statistically significant evidence of positive selection are mainly involved in abiotic and biotic stress response, reproduction and development, plant metabolism and enzyme etc. from two bamboo species and 14 grass species, respectively. In summary, this study demonstrates the power of phylogenomic approach to shed lights on the evolutionary relationships within the BEP clade, and offers valuable insights into adaptive evolution of the grass family.
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Affiliation(s)
- Lei Zhao
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ning Zhang
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Peng-Fei Ma
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Qi Liu
- Institute of Genomic Medicine, Wenzhou Medical College, Wenzhou, Zhejiang, China
| | - De-Zhu Li
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhen-Hua Guo
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
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Choi TJ, Lee SS, Yoon DH, Kang HS, Kim CD, Hwang IH, Kim CY, Jin X, Yang CG, Seo KS. Determination of Genetic Diversity among Korean Hanwoo Cattle Based on Physical Characteristics. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2012; 25:1205-15. [PMID: 25049682 PMCID: PMC4092936 DOI: 10.5713/ajas.2012.12124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 06/04/2012] [Accepted: 04/30/2012] [Indexed: 12/04/2022]
Abstract
This study was conducted to establish genetic criteria for phenotypic characteristics of Hanwoo cattle based on allele frequencies and genetic variance analysis using microsatellite markers. Analysis of the genetic diversity among 399 Hanwoo cattle classified according to nose pigmentation and coat color was carried out using 22 microsatellite markers. The results revealed that the INRA035 locus was associated with the highest Fis (0.536). Given that the Fis value for the Hanwoo INRA035 population ranged from 0.533 (white) to 1.000 (white spotted), this finding was consistent with the loci being fixed in Hanwoo cattle. Expected heterozygosities of the Hanwoo groups classified by coat colors and degree of nose pigmentation ranged from 0.689±0.023 (Holstein) to 0.743±0.021 (nose pigmentation level of d). Normal Hanwoo and animals with a mixed white coat showed the closest relationship because the lowest DA value was observed between these groups. However, a pair-wise differentiation test of Fst showed no significant difference among the Hanwoo groups classified by coat color and degree of nose pigmentation (p<0.01). Moreover, results of the neighbor-joining tree based on a DA genetic distance matrix within 399 Hanwoo individuals and principal component analyses confirmed that different groups of cattle with mixed coat color and nose pigmentation formed other specific groups representing Hanwoo genetic and phenotypic characteristics. The results of this study support a relaxation of policies regulating bull selection or animal registration in an effort to minimize financial loss, and could provide basic information that can be used for establishing criteria to classify Hanwoo phenotypes.
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Affiliation(s)
| | | | - D. H. Yoon
- Department of Animal Science, Kyungpook National University, 386 Gajang-dong Sangju, Kyungpook, 742-711,
Korea
| | - H. S. Kang
- Department of Animal Science and Technology, Sunchon National University, Sunchon, 540-742,
Korea
| | | | - I. H. Hwang
- Department of Animal Science, Chonbuk National Univ., 567 Baekje-daero Deokjin-gu Jeonju, Jeollabuk-do 561-756,
Korea
| | - C. Y. Kim
- Hanwoo Improvement Center, National Agricultural Cooperative Federation, 6-10 Wonbul-ri Unsan-Myun Seosan, Chungcheongnam-do, 356-831,
Korea
| | - X. Jin
- College of Agriculture, Yanbian University, Park Road 977 133002 Yanji, Jilin,
China
| | - C. G. Yang
- College of Agriculture, Yanbian University, Park Road 977 133002 Yanji, Jilin,
China
| | - K. S. Seo
- Department of Animal Science and Technology, Sunchon National University, Sunchon, 540-742,
Korea
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Abstract
Multi-sequence alignments of large genomic regions are at the core of many computational genome-annotation approaches aimed at identifying coding regions, RNA genes, regulatory regions, and other functional features. Such alignments also underlie many genome-evolution studies. Here we review recent computational advances in the area of multi-sequence alignment, focusing on methods suitable for aligning whole vertebrate genomes. We introduce the key algorithmic ideas in use today, and identify publicly available resources for computing, accessing, and visualizing genomic alignments. Finally, we describe the latest alignment-based approaches to identify and characterize various types of functional sequences. Key areas of research are identified and directions for future improvements are suggested.
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Affiliation(s)
- Mathieu Blanchette
- McGill Centre for Bioinformatics, McGill University, Montreal, Quebec, Canada.
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