Integrating gene annotation with orthology inference at scale

BM Kirilenko, C Munegowda, E Osipova, D Jebb… - Science, 2023 - science.org
Annotating coding genes and inferring orthologs are two classical challenges in genomics
and evolutionary biology that have traditionally been approached separately, limiting …

Genome evolution and the future of phylogenomics of non-avian reptiles

DC Card, WB Jennings, SV Edwards - Animals, 2023 - mdpi.com
Simple Summary As a group of organisms, non-avian reptiles, most of which are the~
11,000 species of lizards and snakes, are an extraordinarily diverse group, displaying a …

The genetic architecture and evolution of the human skeletal form

E Kun, EM Javan, O Smith, F Gulamali, J de la Fuente… - Science, 2023 - science.org
The human skeletal form underlies bipedalism, but the genetic basis of skeletal proportions
(SPs) is not well characterized. We applied deep-learning models to 31,221 x-rays from the …

Blooming balloons: Searching for mechanisms of the inflated calyx

J He, J Van Eck, ZB Lippman - Current Opinion in Plant Biology, 2024 - Elsevier
Studying morphological novelties offers special insights into developmental biology and
evolution. The inflated calyx syndrome (ICS) is a largely unrecognized but fascinating …

The genomes of all lungfish inform on genome expansion and tetrapod evolution

M Schartl, JM Woltering, I Irisarri, K Du, S Kneitz… - Nature, 2024 - nature.com
The genomes of living lungfishes can inform on the molecular-developmental basis of the
Devonian sarcopterygian fish–tetrapod transition. We de novo sequenced the genomes of …

The macroevolutionary singularity of snakes

PO Title, S Singhal, MC Grundler, GC Costa, RA Pyron… - Science, 2024 - science.org
Snakes and lizards (Squamata) represent a third of terrestrial vertebrates and exhibit
spectacular innovations in locomotion, feeding, and sensory processing. However, the …

The state of squamate genomics: past, present, and future of genome research in the most speciose terrestrial vertebrate order

SM Gable, JM Mendez, NA Bushroe, A Wilson… - Genes, 2023 - mdpi.com
Squamates include more than 11,000 extant species of lizards, snakes, and
amphisbaenians, and display a dazzling diversity of phenotypes across their over 200 …

Developmental regulation of conserved non-coding element evolution provides insights into limb loss in squamates

Z Wang, C Peng, W Wu, C Yan, Y Lv, JT Li - Science China Life Sciences, 2023 - Springer
Limb loss shows recurrent phenotypic evolution across squamate lineages. Here, based on
three de novo-assembled genomes of limbless lizards from different lineages, we showed …

[HTML][HTML] Chromosome-level genome assembly of the Muscovy duck provides insight into fatty liver susceptibility

MM Xu, LH Gu, WY Lv, SC Duan, LW Li, Y Du, LZ Lu… - Genomics, 2022 - Elsevier
Abstract The Muscovy duck (Cairina moschata) is an economically important poultry
species, which is susceptible to fatty liver. Thus, the Muscovy duck may serve as an …

Convergent degenerated regulatory elements associated with limb loss in limbless amphibians and reptiles

C Zhu, S Li, D Zhang, J Zhang, G Wang… - Molecular Biology …, 2024 - academic.oup.com
Limbs are a defining characteristic of tetrapods, yet numerous taxa, primarily among
amphibians and reptiles, have independently lost limbs as an adaptation to new ecological …