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Research: Elasmobranch genome sequencing reveals evolutionary trends of vertebrate karyotype organization
- Kazuaki Yamaguchi,
- Yoshinobu Uno,
- Mitsutaka Kadota,
- Osamu Nishimura,
- Ryo Nozu,
- Kiyomi Murakumo,
- Rui Matsumoto,
- Keiichi Sato,
- and Shigehiro Kuraku
Genome Res. September 2023 33: 1527-1540; Published in Advance August 17, 2023, doi:10.1101/gr.276840.122
...as contaminants from other organisms were removed, as previously reported (Hara et al. 2018).Repeat identificationTo obtain a species-specific repeat library, RepeatModeler v2.0.2a was run on the assembly of the individual species with default parameters (Smit and Hubley 2008). Detection of repeat elements...
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Research: Changes in exon–intron structure during vertebrate evolution affect the splicing pattern of exons
- Sahar Gelfman,
- David Burstein,
- Osnat Penn,
- Anna Savchenko,
- Maayan Amit,
- Schraga Schwartz,
- Tal Pupko,
- and Gil Ast
Genome Res. January 2012 22: 35-50; Published in Advance October 5, 2011, doi:10.1101/gr.119834.110
...analyzed 17 vertebrate genomes and reconstructed the ancestral motifs of both 3′ and 5′ splice sites, as also the ancestral length of exons and introns. Our analyses suggest that vertebrate introns increased in length from the shortest ancestral introns to the longest primate introns. An evolutionary...
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LETTER: Comparative Genomic Hybridization Provides New Insights Into the Molecular Taxonomy of the Saccharomyces Sensu Stricto Complex
- Laura C. Edwards-Ingram,
- Manda E. Gent,
- David C. Hoyle,
- Andrew Hayes,
- Lubomira I. Stateva,
- and Stephen G. Oliver
Genome Res. June 2004 14: 1043-1051; doi:10.1101/gr.2114704
...of phylogenetic trees that reflect the evolutionary history of the species in a given clade and thus provide a natural taxonomy. Moreover, the ready acquisition of such sequences from individual specimens, using the polymerase chain reaction (PCR), means that this approach also facilitates identification...
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Research: Genomic analyses of wild argali, domestic sheep, and their hybrids provide insights into chromosome evolution, phenotypic variation, and germplasm innovation
- Xin Li,
- San-Gang He,
- Wen-Rong Li,
- Ling-Yun Luo,
- Ze Yan,
- Dong-Xin Mo,
- Xing Wan,
- Feng-Hua Lv,
- Ji Yang,
- Ya-Xi Xu,
- Juan Deng,
- Qiang-Hui Zhu,
- Xing-Long Xie,
- Song-Song Xu,
- Chen-Xi Liu,
- Xin-Rong Peng,
- Bin Han,
- Zhong-Hui Li,
- Lei Chen,
- Jian-Lin Han,
- Xue-Zhi Ding,
- Renqing Dingkao,
- Yue-Feng Chu,
- Jin-Yan Wu,
- Li-Min Wang,
- Ping Zhou,
- Ming-Jun Liu,
- and Meng-Hua Li
Genome Res. September 2022 32: 1669-1684; Published in Advance August 10, 2022, doi:10.1101/gr.276769.122
...intercross population of 110 individuals. (H) Different phenotypes in the tail configuration for individuals with the CC and AA genotypes of c.334C > A in TBXT; picture credit: Wen-Rong Li. (I) Sequences of sgRNA targeting exon 2 of the TBXT gene and 123-bp single-strand DNA oligonucleotides (ss...
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REVIEW: Multiplex PCR: advantages, development, and applications.
- M C Edwards and
- R A Gibbs
Genome Res. February 1994 3: S65-S75
...variation at highly po lymorph ic markers, and microbial assays may exploit strain- or species-specific variation. The type of $66 PCR Methods and Applications IHIIII Manual Supplement Table 1. Step-by-Step Development of a Multiplex PCR System 1. Choose Loci Determine PCR system. Distribute amplicons...
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