Genomics

Genomic decoding of Theobroma grandiflorum (cupuassu) at chromosomal scale: Evolutionary insights for horticultural innovation

1. Rafael Moysés Alves
2. Vinicius A. C. de Abreu
3. Rafaely Pantoja Oliveira
4. João Victor dos Anjos Almeida
5. Mauro de Medeiros de Oliveira
6. Saura R. Silva
7. Alexandre R. Paschoal
8. Sintia S. de Almeida
9. Pedro A. F. de Souza
10. Jesus A. Ferro
11. Vitor F. O. Miranda
12. Antonio Figueira
13. Douglas S. Domingues
14. Alessandro M. Varani

Reviewed by GigaScience

Dimeric ^R25C PTH(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 Gardella
10. Je-Yong Choi
11. Sihoon Lee

• Curated by eLife

  eLife assessment

  The study is noteworthy for its effort to achieve a deeper understanding of PTH-1 Receptor signaling. This molecular pathway which underpins the control of calcium and phosphate metabolism throughout life in land-dwelling animals, can be targeted to the therapeutic benefit of people with osteoporosis. We consider the significance of the findings in this paper to be valuable to the community of investigators working on PTH receptor and PTH ligand signaling. The strength of the evidence is solid and it could become even stronger by addressing a few shortcomings.

Reviewed by eLife

Chromatin accessibility variation provides insights into missing regulation underlying immune-mediated diseases

1. Raehoon Jeong
2. Martha L. Bulyk

• Curated by eLife

  eLife assessment

  This paper addresses a question regarding the low overlap between genetic variants linked to human complex diseases and variants linked to differences in gene expression. Some of the analyses supporting the main claims are convincing, and the key conclusions are valuable and of interest to readers in the fields of human genetics and functional genomics. However, chromatin accessibility QTL (caQTL) also carry the limitation of not identifying the genes that directly mediate the influence on disease phenotypes.

Reviewed by eLife

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