From 3f650bc03b9716bffbebdf616fd8149b12de71b9 Mon Sep 17 00:00:00 2001 From: "galaxy-social-bot[bot]" <171031730+galaxy-social-bot[bot]@users.noreply.github.com> Date: Fri, 6 Sep 2024 00:32:03 +0000 Subject: [PATCH 1/5] Add Galaxy in Research: Uncovering the evolutionary secrets of wild loquats using comparative chloroplast genomics for group1 --- ...09-05-galaxy-in-research-lin2024-group1.md | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 posts/feed_bot/galaxy_europe/2024-09-05-galaxy-in-research-lin2024-group1.md diff --git a/posts/feed_bot/galaxy_europe/2024-09-05-galaxy-in-research-lin2024-group1.md b/posts/feed_bot/galaxy_europe/2024-09-05-galaxy-in-research-lin2024-group1.md new file mode 100644 index 0000000..807cae8 --- /dev/null +++ b/posts/feed_bot/galaxy_europe/2024-09-05-galaxy-in-research-lin2024-group1.md @@ -0,0 +1,62 @@ +--- +media: +- mastodon-eu-freiburg +- matrix-eu-announce +- linkedin-galaxyproject +mentions: + mastodon-eu-freiburg: + - galaxyproject@mstdn.science +hashtags: + mastodon-eu-freiburg: + - UseGalaxy + - GalaxyProject + - UniFreiburg + - EOSC + - EuroScienceGateway + linkedin-galaxyproject: + - UseGalaxy + - GalaxyProject + - UniFreiburg + - EOSC + - EuroScienceGateway +--- +📝 New blog post Released! +https://galaxyproject.org/news/2024-09-05-galaxy-in-research-lin2024/ + +**Galaxy in Research: Uncovering the evolutionary secrets of wild loquats using comparative chloroplast genomics** +================================================================================================================== + +*A new study has sequenced and analyzed two wild loquat chloroplast genomes, revealing key insights into their evolutionary history and the genetic diversity of loquat species.* + +Researchers have successfully sequenced and assembled the chloroplast genomes of *Eriobotrya elliptica* and an unidentified wild loquat species named “YN\-1\.” Comparative genomic analysis was conducted across six loquat species, including five wild loquats and one cultivated variety. The study identified variations in gene content, repetitive sequences, and RNA editing sites, shedding light on loquats' genetic diversity and evolution. This research contributes to a deeper understanding of species differentiation and adaptation in wild loquats. + +**Key Findings** +---------------- + +* Compared to other loquats, the chloroplast genomes of *E. elliptica* and “YN\-1” have 127 genes, including an extra psbK gene. +* Specific regions such as trnF\-GAA\-ndhJ and petG\-trnP\-UGG showed high variability. +* Positive selection was detected in genes rpl22 and rps12, with chilling stress\-specific RNA editing sites in the rpl2 gene. +* Phylogenetic analysis places “YN\-1” closely related to *E. elliptica*, *E. obovata*, and *E. henryi*, suggesting it is a new wild loquat species. + +![Figure 1 Lin et al., 2024](https://galaxyproject.org/news/2024-09-05-galaxy-in-research-lin2024/Figure_Lin2024.jpeg) + +*Three gene maps: E. elliptica, “YN\-1”, and “JFZ” (Lin et al., 2024\).* + +**Galaxy’s Role** +----------------- + +The Galaxy platform was instrumental in this research, particularly in performing the **Codon Adaptation Index (CAI)** analysis, a crucial step in understanding gene expression levels across different loquat species. CAI measures how efficiently genes are adapted to a species' translational machinery, giving insights into the evolutionary pressure on protein\-coding genes. Using Galaxy, the researchers calculated CAI seamlessly, integrating various genomic tools into a unified workflow. + +**Significance of the Study** +----------------------------- + +This research provides critical insights into the genetic evolution of wild loquats and contributes to a broader understanding of species differentiation and adaptation. The discovery of species\-specific SSRs, along with RNA editing patterns linked to environmental stress, offers valuable data for conservation efforts and future studies on the evolutionary biology of loquats. + +**Acknowledgment** +------------------ + +We extend a special thank you to the authors, Zhicong Lin, Qing Guo, Shiwei Ma, Hailan Lin, Shunquan Lin, Shoukai Lin, and Jincheng Wu, for using Galaxy to power their comparative genomic research. Their work showcases Galaxy’s capabilities in advancing plant genomics and evolutionary studies. + +\-\-\- + +Lin, Z., Guo, Q., Ma, S. et al. Chloroplast genomes of Eriobotrya elliptica and an unknown wild loquat “YN\-1”. Sci Rep 14, 18816 (2024\). https://doi.org/10\.1038/s41598\-024\-69882\-7 \ No newline at end of file From 98e555ec49a01e286d78e4f1ddf0572cfbc73aa0 Mon Sep 17 00:00:00 2001 From: "galaxy-social-bot[bot]" <171031730+galaxy-social-bot[bot]@users.noreply.github.com> Date: Fri, 6 Sep 2024 00:32:04 +0000 Subject: [PATCH 2/5] Add Galaxy in Research: Uncovering the evolutionary secrets of wild loquats using comparative chloroplast genomics for group2 --- ...09-05-galaxy-in-research-lin2024-group2.md | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 posts/feed_bot/galaxy_europe/2024-09-05-galaxy-in-research-lin2024-group2.md diff --git a/posts/feed_bot/galaxy_europe/2024-09-05-galaxy-in-research-lin2024-group2.md b/posts/feed_bot/galaxy_europe/2024-09-05-galaxy-in-research-lin2024-group2.md new file mode 100644 index 0000000..8d55266 --- /dev/null +++ b/posts/feed_bot/galaxy_europe/2024-09-05-galaxy-in-research-lin2024-group2.md @@ -0,0 +1,54 @@ +--- +media: +- bluesky-galaxyproject +mentions: + bluesky-galaxyproject: + - galaxyproject.bsky.social +hashtags: + bluesky-galaxyproject: + - UseGalaxy + - GalaxyProject + - UniFreiburg + - EOSC + - EuroScienceGateway +--- +📝 New blog post Released! +https://galaxyproject.org/news/2024-09-05-galaxy-in-research-lin2024/ + +**Galaxy in Research: Uncovering the evolutionary secrets of wild loquats using comparative chloroplast genomics** +================================================================================================================== + +*A new study has sequenced and analyzed two wild loquat chloroplast genomes, revealing key insights into their evolutionary history and the genetic diversity of loquat species.* + +Researchers have successfully sequenced and assembled the chloroplast genomes of *Eriobotrya elliptica* and an unidentified wild loquat species named “YN\-1\.” Comparative genomic analysis was conducted across six loquat species, including five wild loquats and one cultivated variety. The study identified variations in gene content, repetitive sequences, and RNA editing sites, shedding light on loquats' genetic diversity and evolution. This research contributes to a deeper understanding of species differentiation and adaptation in wild loquats. + +**Key Findings** +---------------- + +* Compared to other loquats, the chloroplast genomes of *E. elliptica* and “YN\-1” have 127 genes, including an extra psbK gene. +* Specific regions such as trnF\-GAA\-ndhJ and petG\-trnP\-UGG showed high variability. +* Positive selection was detected in genes rpl22 and rps12, with chilling stress\-specific RNA editing sites in the rpl2 gene. +* Phylogenetic analysis places “YN\-1” closely related to *E. elliptica*, *E. obovata*, and *E. henryi*, suggesting it is a new wild loquat species. + +![Figure 1 Lin et al., 2024](https://galaxyproject.org/news/2024-09-05-galaxy-in-research-lin2024/Figure_Lin2024.jpeg) + +*Three gene maps: E. elliptica, “YN\-1”, and “JFZ” (Lin et al., 2024\).* + +**Galaxy’s Role** +----------------- + +The Galaxy platform was instrumental in this research, particularly in performing the **Codon Adaptation Index (CAI)** analysis, a crucial step in understanding gene expression levels across different loquat species. CAI measures how efficiently genes are adapted to a species' translational machinery, giving insights into the evolutionary pressure on protein\-coding genes. Using Galaxy, the researchers calculated CAI seamlessly, integrating various genomic tools into a unified workflow. + +**Significance of the Study** +----------------------------- + +This research provides critical insights into the genetic evolution of wild loquats and contributes to a broader understanding of species differentiation and adaptation. The discovery of species\-specific SSRs, along with RNA editing patterns linked to environmental stress, offers valuable data for conservation efforts and future studies on the evolutionary biology of loquats. + +**Acknowledgment** +------------------ + +We extend a special thank you to the authors, Zhicong Lin, Qing Guo, Shiwei Ma, Hailan Lin, Shunquan Lin, Shoukai Lin, and Jincheng Wu, for using Galaxy to power their comparative genomic research. Their work showcases Galaxy’s capabilities in advancing plant genomics and evolutionary studies. + +\-\-\- + +Lin, Z., Guo, Q., Ma, S. et al. Chloroplast genomes of Eriobotrya elliptica and an unknown wild loquat “YN\-1”. Sci Rep 14, 18816 (2024\). https://doi.org/10\.1038/s41598\-024\-69882\-7 \ No newline at end of file From 34a5aaae9c6205a3742d1a7f4e6101fce91b2174 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Tue, 10 Sep 2024 12:00:22 +0200 Subject: [PATCH 3/5] shorten it --- ...09-05-galaxy-in-research-lin2024-group2.md | 39 +------------------ 1 file changed, 2 insertions(+), 37 deletions(-) diff --git a/posts/feed_bot/galaxy_europe/2024-09-05-galaxy-in-research-lin2024-group2.md b/posts/feed_bot/galaxy_europe/2024-09-05-galaxy-in-research-lin2024-group2.md index 8d55266..4f1cb79 100644 --- a/posts/feed_bot/galaxy_europe/2024-09-05-galaxy-in-research-lin2024-group2.md +++ b/posts/feed_bot/galaxy_europe/2024-09-05-galaxy-in-research-lin2024-group2.md @@ -12,43 +12,8 @@ hashtags: - EOSC - EuroScienceGateway --- -📝 New blog post Released! -https://galaxyproject.org/news/2024-09-05-galaxy-in-research-lin2024/ +📝 New blog post in our *Galaxy in Research* category. Today about "Uncovering the evolutionary secrets of wild loquats using comparative chloroplast genomics" by Lin, Z., Guo, Q., Ma, S. et al. -**Galaxy in Research: Uncovering the evolutionary secrets of wild loquats using comparative chloroplast genomics** -================================================================================================================== - -*A new study has sequenced and analyzed two wild loquat chloroplast genomes, revealing key insights into their evolutionary history and the genetic diversity of loquat species.* - -Researchers have successfully sequenced and assembled the chloroplast genomes of *Eriobotrya elliptica* and an unidentified wild loquat species named “YN\-1\.” Comparative genomic analysis was conducted across six loquat species, including five wild loquats and one cultivated variety. The study identified variations in gene content, repetitive sequences, and RNA editing sites, shedding light on loquats' genetic diversity and evolution. This research contributes to a deeper understanding of species differentiation and adaptation in wild loquats. - -**Key Findings** ----------------- - -* Compared to other loquats, the chloroplast genomes of *E. elliptica* and “YN\-1” have 127 genes, including an extra psbK gene. -* Specific regions such as trnF\-GAA\-ndhJ and petG\-trnP\-UGG showed high variability. -* Positive selection was detected in genes rpl22 and rps12, with chilling stress\-specific RNA editing sites in the rpl2 gene. -* Phylogenetic analysis places “YN\-1” closely related to *E. elliptica*, *E. obovata*, and *E. henryi*, suggesting it is a new wild loquat species. +Read more at https://galaxyproject.org/news/2024-09-05-galaxy-in-research-lin2024/ ![Figure 1 Lin et al., 2024](https://galaxyproject.org/news/2024-09-05-galaxy-in-research-lin2024/Figure_Lin2024.jpeg) - -*Three gene maps: E. elliptica, “YN\-1”, and “JFZ” (Lin et al., 2024\).* - -**Galaxy’s Role** ------------------ - -The Galaxy platform was instrumental in this research, particularly in performing the **Codon Adaptation Index (CAI)** analysis, a crucial step in understanding gene expression levels across different loquat species. CAI measures how efficiently genes are adapted to a species' translational machinery, giving insights into the evolutionary pressure on protein\-coding genes. Using Galaxy, the researchers calculated CAI seamlessly, integrating various genomic tools into a unified workflow. - -**Significance of the Study** ------------------------------ - -This research provides critical insights into the genetic evolution of wild loquats and contributes to a broader understanding of species differentiation and adaptation. The discovery of species\-specific SSRs, along with RNA editing patterns linked to environmental stress, offers valuable data for conservation efforts and future studies on the evolutionary biology of loquats. - -**Acknowledgment** ------------------- - -We extend a special thank you to the authors, Zhicong Lin, Qing Guo, Shiwei Ma, Hailan Lin, Shunquan Lin, Shoukai Lin, and Jincheng Wu, for using Galaxy to power their comparative genomic research. Their work showcases Galaxy’s capabilities in advancing plant genomics and evolutionary studies. - -\-\-\- - -Lin, Z., Guo, Q., Ma, S. et al. Chloroplast genomes of Eriobotrya elliptica and an unknown wild loquat “YN\-1”. Sci Rep 14, 18816 (2024\). https://doi.org/10\.1038/s41598\-024\-69882\-7 \ No newline at end of file From 3e7d67ed83e8bbccbf7865254b9dbb962d8ee275 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Tue, 10 Sep 2024 12:02:11 +0200 Subject: [PATCH 4/5] Update 2024-09-05-galaxy-in-research-lin2024-group2.md --- .../2024-09-05-galaxy-in-research-lin2024-group2.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/posts/feed_bot/galaxy_europe/2024-09-05-galaxy-in-research-lin2024-group2.md b/posts/feed_bot/galaxy_europe/2024-09-05-galaxy-in-research-lin2024-group2.md index 4f1cb79..b868515 100644 --- a/posts/feed_bot/galaxy_europe/2024-09-05-galaxy-in-research-lin2024-group2.md +++ b/posts/feed_bot/galaxy_europe/2024-09-05-galaxy-in-research-lin2024-group2.md @@ -12,7 +12,7 @@ hashtags: - EOSC - EuroScienceGateway --- -📝 New blog post in our *Galaxy in Research* category. Today about "Uncovering the evolutionary secrets of wild loquats using comparative chloroplast genomics" by Lin, Z., Guo, Q., Ma, S. et al. +📝 New blog post about "Uncovering the evolutionary secrets of wild loquats using comparative chloroplast genomics" by Lin, Z., Guo, Q., Ma, S. et al. Read more at https://galaxyproject.org/news/2024-09-05-galaxy-in-research-lin2024/ From fe086c53f61b26c860e437706e96e6b7ff05d60f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Tue, 10 Sep 2024 12:03:26 +0200 Subject: [PATCH 5/5] Update 2024-09-05-galaxy-in-research-lin2024-group2.md --- .../2024-09-05-galaxy-in-research-lin2024-group2.md | 3 --- 1 file changed, 3 deletions(-) diff --git a/posts/feed_bot/galaxy_europe/2024-09-05-galaxy-in-research-lin2024-group2.md b/posts/feed_bot/galaxy_europe/2024-09-05-galaxy-in-research-lin2024-group2.md index b868515..14410b6 100644 --- a/posts/feed_bot/galaxy_europe/2024-09-05-galaxy-in-research-lin2024-group2.md +++ b/posts/feed_bot/galaxy_europe/2024-09-05-galaxy-in-research-lin2024-group2.md @@ -8,9 +8,6 @@ hashtags: bluesky-galaxyproject: - UseGalaxy - GalaxyProject - - UniFreiburg - - EOSC - - EuroScienceGateway --- 📝 New blog post about "Uncovering the evolutionary secrets of wild loquats using comparative chloroplast genomics" by Lin, Z., Guo, Q., Ma, S. et al.