Genomics

Still waters run deep in large-scale genome rearrangements of morphologically conservative Polyplacophora

1. Julia D Sigwart
2. Yunlong Li
3. Zeyuan Chen
4. Katarzyna Vončina
5. Jin Sun

• Curated by eLife

  eLife Assessment

  This important study advances our understanding of genome annotations for chiton genomes. It provides a solid estimation of syntentic relationships for the chromosomes of the four new genomes plus an analysis linking these to other available chiton genomes, and an update for how these relate to molluscan genomes.

Reviewed by eLife

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

Dimeric R25CPTH(1–34) activates the parathyroid hormone-1 receptor in vitro and stimulates bone formation in osteoporotic female mice

1. Minsoo Noh
2. Xiangguo Che
3. Xian Jin
4. Dong-Kyo Lee
5. Hyun-Ju Kim
6. Doo Ri Park
7. Soo Young Lee
8. Hunsang Lee
9. Thomas J Gardella
10. Je-Yong Choi
11. Sihoon Lee

• Curated by eLife

  eLife Assessment

  This work investigates the functional difference between the most commonly expressed form of PTH, and a mutant form of PTH, identified in a patient with chronic hypocalcemia and hyperphosphatemia which characterizes hypoparathyroidism. The authors investigate the hypothesis that this mutant PTH assumes a dimeric form in vivo and serves anabolic functions in the bone. The data are compelling and the translational aspects are fundamental in understanding PTH-1 Receptor activation.

Reviewed by eLife

Trade-offs in modeling context dependency in complex trait genetics

1. Eric Weine
2. Samuel Pattillo Smith
3. Rebecca Kathryn Knowlton
4. Arbel Harpak

• Curated by eLife

  eLife Assessment

  It is known from model organisms that genes' effects on traits are often modulated by environmental variables, but similar gene-by-environment (GxE) interactions have been difficult to detect using statistical analyses of genomic data, e.g., in humans. This study introduces a new framework to estimate gene-by-environment effects, treating it as a bias-variance tradeoff problem. The authors convincingly show that greater statistical power can be achieved in detecting GxE if an underlying model of polygenic GxE is assumed. This polygenic amplification model is a truly novel view with fundamental promise for the detection of GxE in genomic datasets, especially with continued development to detect more complex signals of amplification.

Reviewed by eLife

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

Discovering root causal genes with high-throughput perturbations

1. Eric V Strobl
2. Eric Gamazon

• Curated by eLife

  eLife Assessment

  This work provides an important framework for understanding the primary causes of disease. While the theoretical results rely on strong assumptions about the underlying causal mechanisms, the authors provide solid empirical evidence that the framework is robust to modest violations of these assumptions.

Reviewed by eLife

Mapping HIV-1 RNA structure, homodimers, long-range interactions and persistent domains by HiCapR

1. Yan Zhang
2. Jingwan Han
3. Xie Dejian
4. Wenlong Shen
5. Ping Li
6. Jian You Lau
7. Jingyun Li
8. Lin Li
9. Grzegorz Kudla
10. Zhihu Zhao

• Curated by eLife

  eLife Assessment

  This manuscript focuses on the identification of RNA crosslinks within the HIV RNA genome under different conditions i.e. in infected cells and in virions using a new method called HiCapR. These cross-links reveal long-range interactions that can be used to determine the structural arrangement of the viral RNA, providing valuable data that show differences in the genomic organization in different conditions. The data analysis, however, is incomplete and based on extensive computational analysis from a limited number of datasets.

Reviewed by eLife