Genomics

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

Korea4K: whole genome sequences of 4,157 Koreans with 107 phenotypes derived from extensive health check-ups

1. Sungwon Jeon
2. Hansol Choi
3. Yeonsu Jeon
4. Whan-Hyuk Choi
5. Hyunjoo Choi
6. Kyungwhan An
7. Hyojung Ryu
8. Jihun Bhak
9. Hyeonjae Lee
10. Yoonsung Kwon
11. Sukyeon Ha
12. Yeo Jin Kim
13. Asta Blazyte
14. Changjae Kim
15. Yeonkyung Kim
16. Younghui Kang
17. Yeong Ju Woo
18. Chanyoung Lee
19. Jeongwoo Seo
20. Changhan Yoon
21. Dan Bolser
22. Orsolya Biro
23. Eun-Seok Shin
24. Byung Chul Kim
25. Seon-Young Kim
26. Ji-Hwan Park
27. Jongbum Jeon
28. Dooyoung Jung
29. Semin Lee
30. Jong Bhak

Reviewed by GigaScience

Deep indel mutagenesis reveals the impact of amino acid insertions and deletions on protein stability and function

1. Magdalena Topolska
2. Antoni Beltran
3. Ben Lehner

Reviewed by PREreview

Signatures of transposon-mediated genome inflation, host specialization, and photoentrainment in Entomophthora muscae and allied entomophthoralean fungi

1. Jason E Stajich
2. Brian Lovett
3. Emily Lee
4. Angie M Macias
5. Ann E Hajek
6. Benjamin L de Bivort
7. Matt T Kasson
8. Henrik H De Fine Licht
9. Carolyn Elya

• Curated by eLife

  eLife assessment

  This important study reports on the genome evolution of a poorly studied fungal group. By combining long-read sequencing and different bioinformatic analyses, the authors show that the giant genome of Entomophthora muscae expanded due to extensive transposable element activity. The strength of evidence is compelling and the authors are to be commended for their multiple comparative analyses of gene content along with transparently written and visualized techniques, data curation, and methods. This paper will be of relevance to fungal biologists as well as to evolutionary biologists interested in the study of genome size dynamics.

Reviewed by eLife

Transcriptional profiling of human brain cortex identifies novel lncRNA-mediated networks dysregulated in amyotrophic lateral sclerosis

1. Alessandro Palma
2. Monica Ballarino

Reviewed by preLights

Global diversity and evolution of Salmonella Panama, an understudied serovar causing gastrointestinal and invasive disease worldwide: a genomic epidemiology study

1. Caisey Victoria Pulford
2. Blanca M Perez-Sepulveda
3. Danielle J Ingle
4. Rebecca J Bengtsson
5. Rebecca J Bennet
6. Ella V Rodwell
7. Maria Pardos de la Gandara
8. Charlotte Chong
9. P. Malaka De Silva
10. Magali Ravel
11. Veronique Guibert
12. Elisabeth Njamkepo
13. Neil Hall
14. Marie A Chattaway
15. Benjamin Howden
16. Deborah A Williamson
17. Jay C. D. Hinton
18. Francois-Xavier Weill
19. Kate S Baker

Reviewed by PREreview

A complex Plasmodium falciparum cryptotype circulating at low frequency across the African continent

1. Olivo Miotto
2. Alfred Amambua-Ngwa
3. Lucas Amenga-Etego
4. Muzamil M Abdel Hamid
5. Ishag Adam
6. Enoch Aninagyei
7. Tobias Apinjoh
8. Gordon A Awandare
9. Philip Bejon
10. Gwladys I Bertin
11. Marielle Bouyou-Akotet
12. Antoine Claessens
13. David J Conway
14. Umberto D’Alessandro
15. Mahamadou Diakite
16. Abdoulaye Djimdé
17. Arjen M Dondorp
18. Patrick Duffy
19. Rick M Fairhurst
20. Caterina I Fanello
21. Anita Ghansah
22. Deus Ishengoma
23. Mara Lawniczak
24. Oumou Maïga-Ascofaré
25. Sarah Auburn
26. Anna Rosanas-Urgell
27. Varanya Wasakul
28. Nina FD White
29. Jacob Almagro-Garcia
30. Richard D Pearson
31. Sonia Goncalves
32. Cristina Ariani
33. Zbynek Bozdech
34. William Hamilton
35. Victoria Simpson
36. Dominic P Kwiatkowski

Reviewed by preLights

Integrated multiplexed assays of variant effect reveal determinants of catechol-O-methyltransferase gene expression

1. Ian Hoskins
2. Shilpa Rao
3. Charisma Tante
4. Can Cenik

Reviewed by Review Commons

Transcription decouples estrogen-dependent changes in enhancer-promoter contact frequencies and spatial proximity

1. Luciana I. Gómez Acuña
2. Ilya Flyamer
3. Shelagh Boyle
4. Elias Friman
5. Wendy A. Bickmore

Reviewed by Review Commons