Genomics

The whole blood microbiome of Indonesians reveals translocated and pathogenic microbiota

1. Katalina Bobowik
2. Muhamad Fachrul
3. Chelzie Crenna Darusallam
4. Pradiptajati Kusuma
5. Herawati Sudoyo
6. Clarissa A. Febinia
7. Safarina G. Malik
8. Christine Wells
9. Irene Gallego Romero

Reviewed by Review Commons

Comparative analysis of multiplexed in situ gene expression profiling technologies

1. Austin Hartman
2. Rahul Satija

• Curated by eLife

  eLife assessment

  Hartman et al.'s important research examines six commonly utilized imaging-based multiplexed transcriptomic techniques and introduces a novel specificity metric, "MECR," to streamline platform evaluations. The authors highlight the crucial influence of cell segmentation methodologies on outcomes, offering insight into the field. Nonetheless, the substantiation for the principal assertions remains incomplete, as the comparisons across platforms seem uneven due to variations in gene panels.

Reviewed by eLife

Frequent lack of repressive capacity of promoter DNA methylation identified through genome-wide epigenomic manipulation

1. Ethan Ford
2. Matthew R. Grimmer
3. Sabine Stolzenburg
4. Ozren Bogdanovic
5. Alex de Mendoza
6. Peggy J. Farnham
7. Pilar Blancafort
8. Ryan Lister

Reviewed by PREreview

Unraveling the genetic legacy of commercial whaling in bowhead whales and narwhals

1. Evelien de Greef
2. Claudio Müller
3. Matt J. Thorstensen
4. Steven H. Ferguson
5. Cortney A. Watt
6. Marianne Marcoux
7. Stephen D. Petersen
8. Colin J. Garroway

Reviewed by PREreview

The GC-content at the 5’ends of human protein-coding genes is undergoing mutational decay

1. Yi Qiu
2. Yoon Mo Kang
3. Christopher Korfmann
4. Fanny Pouyet
5. Andrew Eckford
6. Alexander F. Palazzo

Reviewed by Review Commons

Chromosomal-level genome assembly of golden birdwing Troides aeacus (Felder & Felder, 1860)

1. Hong Kong Biodiversity Genomics Consortium
2. Jerome H.L. Hui
3. Ting Fung Chan
4. Leo L. Chan
5. Siu Gin Cheung
6. Chi Chiu Cheang
7. James K.H. Fang
8. Juan D. Gaitan-Espitia
9. Stanley C.K. Lau
10. Yik Hei Sung
11. Chris K.C. Wong
12. Kevin Y.L. Yip
13. Yingying Wei
14. Wai Lok So
15. Wenyan Nong
16. Hydrogen S.F. Pun
17. Wing Kwong Yau
18. Colleen Y.L. Chiu
19. Sammi S.S. Chan
20. Kacy K.L. Man
21. Ho Yin Yip

• Curated by GigaByte

  Editors Assessment:

  This work is part of a series of papers from the Hong Kong Biodiversity Genomics Consortium sequencing the rich biodiversity of species in Hong Kong. This example presents the genome of the golden birdwing butterfly Troides aeacus (Lepidoptera, Papilionidae). A notable and popular species in Asia that faces habitat loss due to urbanization and human activities. The lack of genomic resources impedes conservation efforts based on genetic markers, as well as better understanding of its biology. Using PacBio HiFi long reads and Omni-C a 351Mb genome was assembled genome anchored to 30 pseudo-molecules. After reviewers requested more information on the genome quality it seems there was high sequence continuity with contig length N50 = 11.67 Mb and L50 = 14, and scaffold length N50 = 12.2 Mb and L50 = 13. Allowing a total of 24,946 protein-coding genes were predicted. This study presents the first chromosomal-level genome assembly of the golden birdwing T. aeacus, a potentially useful resource for further phylogenomic studies of birdwing butterfly species in terms of species diversification and conservation. This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Genome sequences of four Ixodes species expands understanding of tick evolution

1. Alexandra Cerqueira de Araujo
2. Benjamin Noël
3. Anthony Bretaudeau
4. Karine Labadie
5. Matéo Boudet
6. Nachida Tadrent
7. Benjamin Istace
8. Salima Kritli
9. Corinne Cruaud
10. Robert Olaso
11. Jean-François Deleuze
12. Maarten Voordouw
13. Caroline Hervet
14. Olivier Plantard
15. Aya Zamoto-Niikura
16. Thomas Chertemps
17. Martine Maïbèche
18. Frédérique Hilliou
19. Gaëlle Le Goff
20. Jindrich Chmelar
21. Vilém Mazák
22. Mohammed Amine Jmel
23. Michalis Kotsyfakis
24. José María Medina
25. Michael Hackenberg
26. Ladislav Šimo
27. Fotini A. Koutroumpa
28. Patrick Wincker
29. Petr Kopacek
30. Jan Perner
31. Jean-Marc Aury
32. Claude Rispe

Reviewed by Arcadia Science

Correction to: Chromosome-level genome assembly of the common chiton, Liolophura japonica (Lischke, 1873)

1. Hong Kong Biodiversity Genomics Consortium
2. Jerome H. L. Hui
3. Ting Fung Chan
4. Leo Lai Chan
5. Siu Gin Cheung
6. Chi Chiu Cheang
7. James Kar-Hei Fang
8. Juan Diego Gaitan-Espitia
9. Stanley Chun Kwan Lau
10. Yik Hei Sung
11. Chris Kong Chu Wong
12. Kevin Yuk-Lap Yip
13. Yingying Wei
14. Ming Fung Franco Au
15. Wai Lok So
16. Wenyan Nong
17. Tin Yan Hui
18. Brian Kai Hin Leung
19. Gray A. Williams

• Curated by GigaByte

  Editors Assessment:

  This work is part of a series of papers from the Hong Kong Biodiversity Genomics Consortium sequencing the rich biodiversity of species in Hong Kong. This example assembles the genome of the common chiton, Liolophura japonica (Lischke, 1873). Chitons are marine molluscs that can be found worldwide from cold waters to the tropics that play important ecological roles in the environment, but to date are lacking in genomes with only a few assemblies available. This data was produced using PacBio HiFi reads and Omni-C sequencing data, the resulting genome assembly being around 609 Mb in size. From this 28,010 protein-coding genes were predicted. After review improved the methodological details the quality metrics look near chromosome-level, having a scaffold N50 length of 37.34 Mb and 96.1% BUSCO score. This high-quality genome should hopefully be a valuable resource for gaining new insights into the environmental adaptations of L. japonica in residing the intertidal zones and for future investigations in the evolutionary biology in Polyplacophorans and other molluscs.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Chromosomal-level genome assembly of the long-spined sea urchin Diadema setosum (Leske, 1778)

1. Hong Kong Biodiversity Genomics Consortium
2. Project Coordinator and Co-Principal Investigators
3. Jerome H.L. Hui
4. Ting Fung Chan
5. Leo L. Chan
6. Siu Gin Cheung
7. Chi Chiu Cheang
8. James K.H. Fang
9. Juan D. Gaitan-Espitia
10. Stanley C.K. Lau
11. Yik Hei Sung
12. Chris K.C. Wong
13. Kevin Y.L. Yip
14. Yingying Wei
15. DNA extraction, library preparation and sequencing
16. Wai Lok So
17. Genome assembly and gene model prediction
18. Wenyan Nong
19. Sample collector, animal culture and logistics
20. Apple P.Y. Chui
21. Thomas H.W. Fong
22. Ho Yin Yip

• Curated by GigaByte

  Editors Assessment:

  This work is part of a series of papers from the Hong Kong Biodiversity Genomics Consortium sequencing the rich biodiversity of species in Hong Kong. This example assembles the genome of the long-spined sea urchin Diadema setosum (Leske, 1778). Using PacBio HiFi long-reads and Omni-C data the assembled genome size was 886 Mb, consistent to the size of other sea urchin genomes. The assembly anchored to 22 pseudo-molecules/chromosomes, and a total of 27,478 genes including 23,030 protein-coding genes were annotated. Peer review added more to the conclusion and future perspectives. The data hopefully providing a valuable resource and foundation for a better understanding of the ecology and evolution of sea urchins.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Genome assembly of the edible jelly fungus Dacryopinax spathularia (Dacrymycetaceae)

1. Hong Kong Biodiversity Genomics Consortium
2. Project Coordinator and Co-Principal Investigators
3. Jerome H.L. Hui
4. Ting Fung Chan
5. Leo L. Chan
6. Siu Gin Cheung
7. Chi Chiu Cheang
8. James K.H. Fang
9. Juan Diego Gaitan-Espitia
10. Stanley C.K. Lau
11. Yik Hei Sung
12. Chris K.C. Wong
13. Kevin Y.L. Yip
14. Yingying Wei
15. DNA extraction, library preparation and sequencing
16. Tze Kiu Chong
17. Sean T.S. Law
18. Genome assembly and gene model prediction
19. Wenyan Nong
20. Genome analysis and quality control
21. Wenyan Nong
22. Sample collector and logistics
23. Tze Kiu Chong
24. Sean T.S. Law
25. Ho Yin Yip

• Curated by GigaByte

  Editors Assessment:

  This work is part of a series of papers from the Hong Kong Biodiversity Genomics Consortium sequencing the rich biodiversity of species in Hong Kong. This example This work is part of a series of papers from the Hong Kong Biodiversity Genomics Consortium sequencing the rich biodiversity of species in Hong Kong. This example presenting the first whole genome assembly of Dacryopinax spathularia, an edible mushroom-forming fungus that is used in the food industry to produce natural preservatives. Using PacBio and Omni-C data a 29.2 Mb genome was assembled, with a scaffold N50 of 1.925 Mb and 92.0% BUSCO score demonstrating the quality (review pushing the authors to provide more detail and QC stats to help better convince on this). This data providing a useful resource for further phylogenomic studies in the family Dacrymycetaceae and investigations on the biosynthesis of glycolipids with potential applications in the food industry.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte