Genomics

Draft genome of the endangered visayan spotted deer (Rusa alfredi), a Philippine endemic species

1. Ma. Carmel F. Javier
2. Albert C. Noblezada
3. Persie Mark Q. Sienes
4. Robert S. Guino-o
5. Nadia Palomar-Abesamis
6. Maria Celia D. Malay
7. Carmelo S. del Castillo
8. Victor Marco Emmanuel N. Ferriols

• Curated by GigaByte

  Editors Assessment:

  The Visayan spotted deer (Rusa alfredi), is a small, endangered, primarily nocturnal species of deer found in the rainforests of the Visayan Islands in the Philippines. The present study reports the first draft genome assembly for the species, addressing a critical gap in genomic data for this IUCN-redlisted cervid. Using Illumina sequencing, the resulting genome assembly spans 2.52 Gb in size with a BUSCO completeness score of 95.5% and encompasses 24,531 annotated genes. Phylogenetic analysis suggests a close evolutionary relationship between R. alfredi and Cervus species suggesting that the genus Rusa is sister to Cervus. Peer-review teased out more benchmarking results and the annotation files, demonstrating this genomic resource is useful and usable for advancing population genetics and evolutionary studies, thereby informing conservation strategies and enhancing breeding programs for the critically threatened species. Providing whole genome sequences for other native species of Rusa could further provide genomic resources for detecting hybrids, which will also help the management and monitoring of these species, especially for the reintroduction of captive populations in the wild.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

The assembly and annotation of two teinturier grapevine varieties, Dakapo and Rubired

1. Eleanore J. Ritter
2. Noé Cochetel
3. Andrea Minio
4. Peter Cousins
5. Dario Cantu
6. Chad Niederhuth

• Curated by GigaByte

  Editors Assessment:

  Teinturier grapes produce berries with pigmented skin and flesh, and are used in red wine blends, as they provide a deeper colour. This paper presents the genomes of two popular teinturier varieties (Dakapo and Rubired); sequenced, assembled, and annotated to provide additional resources for their use in breeding. Combining Nanopore and Illumina sequencing for Dakapo, scaffolding to the existing grapevine assembly to generate a final assembly of 508.5 Mbp and 36,940 gene annotations. For Rubired PacBio HiFi reads were assembled, scaffolded, and phased to generate a diploid assembly with two haplotypes 474.7-476.0 Mbp long and 56,681 genes annotated. Peer review has helped validate their high quality, these genomes hopefully enabling more insight into the genetics of grapevine berry colour and their other traits like frost and mildew-resistance.

  This evaluation refers to version 1 of the preprint

Reviewed by GigaByte

Genomic evidence for hybridization and introgression between blue peafowl and green peafowl and selection for white plumage

1. Gang Wang
2. Liping Ban
3. Xinye Zhang
4. Xiurong Zhao
5. Xufang Ren
6. Anqi Chen
7. Li Zhang
8. Yan Lu
9. Zhihua Jiang
10. Xiaoyu Zhao
11. Junhui Wen
12. Yalan Zhang
13. Xue Cheng
14. Huie Wang
15. Wenting Dai
16. Yong Liu
17. Zhonghua Ning
18. Lujiang Qu

Reviewed by GigaScience

High-Resolution Genome-Wide Maps Reveal Widespread Presence of Torsional Insulation

1. Porter M Hall
2. Lauren A Mayse
3. Lu Bai
4. Marcus B Smolka
5. B Franklin Pugh
6. Michelle D Wang

• Curated by eLife

  eLife Assessment

  The Twin Domain model proposed by Lui and Wang proposing that twin supercoiling domains of DNA emerge during transcription were first described decades ago, but direct experimental evidence has been challenging to obtain. Here, the authors make a fundamental contribution by directly measuring DNA torsion in cells using a photoactivatable intrastrand cross-linker compared to controls. They gather compelling data using this clever method, which provides direct evidence in support of the twin-supercoiled domain model, for torsional effects at transcription start and end sites, and thereby uncover novel features of higher order structure of chromatin in yeast. These data are exciting, and the tools will be of interest to anyone studying chromosome structure and gene regulation.

Reviewed by eLife

A chromosome-level, haplotype-resolved genome assembly and annotation for the Eurasian minnow (Leuciscidae: Phoxinus phoxinus ) provide evidence of haplotype diversity

1. Temitope Opeyemi Oriowo
2. Ioannis Chrysostomakis
3. Sebastian Martin
4. Sandra Kukowka
5. Thomas Brown
6. Sylke Winkler
7. Eugene W Myers
8. Astrid Böhne
9. Madlen Stange

Reviewed by GigaScience