Genomics

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

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

Genome assembly of the milky mangrove Excoecaria agallocha

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. Sean T.S. Law
17. Wai Lok So
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. David T.W. Lau
24. Sean T.S. Law
25. Shing Yip Lee
26. 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 milky mangrove Excoecaria agallocha, also known as blind-your-eye mangrove due to its toxic properties of its milky latex that can cause blindness when it comes into contact with the eyes. Living in the brackish water of tropical mangrove forests from India to Australia, they are an extremely important habitat for a diverse variety of aquatic species, including the mangrove jewel bug of which this tree is the sole food source for the larvae. Using PacBio HiFi long-reads and Omni-C technology a 1,332.45 Mb genome was assembled, with 1,402 scaffolds and a scaffold N50 of 58.95 Mb. After feedback the annotations were improved, predicting a very high number (73,740) protein coding genes. The data presented here provides a valuable resource for further investigation in the biosynthesis of phytochemical compounds in its milky latex with the potential of many medicinal and pharmacological properties. As well as increasing the understanding of biology and evolution in genome architecture in the Euphorbiaceae family and mangrove species adapted to high levels of salinity.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

De novo transcriptome assembly and genome annotation of the fat-tailed dunnart ( Sminthopsis crassicaudata )

1. Neke Ibeh
2. Charles Y. Feigin
3. Stephen R. Frankenberg
4. Davis J. McCarthy
5. Andrew J. Pask
6. Irene Gallego Romero

• Curated by GigaByte

  Editors Assessment: Marsupial species are invaluable for comparative studies due to their distinctive modes of reproduction and development, but there are a shortage of genomic resources to do these types of analyses. To help address that data gap multi-tissue transcriptomes and transcriptome assemblies have been sequenced and shared for the fat-tailed dunnart (Sminthopsis crassicaudata), a mouse-like marsupial that due to is ease of breeding is emerging as a useful lab model. Using ONT nanopore and Pacbio long-reads and illumina short reads 2,093,982 transcripts were sequenced and assembled, and functional annotation of the assembled transcripts was also carried out. Some addition work was required to provide more details on the QC metrics and access to the data but this was resolved during review. This work ultimately producing dunnart genome assembly measuring 3.23 Gb in length and organized into 1,848 scaffolds, with a scaffold N50 value of 72.64 Mb. These openly available resources hopefully provide novel insights into the unique genomic architecture of this unusual species and provide valuable tools for future comparative mammalian studies.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte