[PDF][PDF] A simple guide to de novo transcriptome assembly and annotation

V Raghavan, L Kraft, F Mesny… - Briefings in …, 2022 - academic.oup.com
A transcriptome constructed from short-read RNA sequencing (RNA-seq) is an easily
attainable proxy catalog of protein-coding genes when genome assembly is unnecessary …

Sequence of the sugar pine megagenome

KA Stevens, JL Wegrzyn, A Zimin, D Puiu, M Crepeau… - Genetics, 2016 - academic.oup.com
Until very recently, complete characterization of the megagenomes of conifers has remained
elusive. The diploid genome of sugar pine (Pinus lambertiana Dougl.) has a highly …

Spruce giga‐genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes

KK Gagalova, RL Warren, L Coombe, J Wong… - The Plant …, 2022 - Wiley Online Library
Spruces (Picea spp.) are coniferous trees widespread in boreal and mountainous forests of
the northern hemisphere, with large economic significance and enormous contributions to …

The Douglas-fir genome sequence reveals specialization of the photosynthetic apparatus in Pinaceae

DB Neale, PE McGuire, NC Wheeler… - G3: Genes …, 2017 - academic.oup.com
A reference genome sequence for Pseudotsuga menziesii var. menziesii (Mirb.) Franco
(Coastal Douglas-fir) is reported, thus providing a reference sequence for a third genus of …

Evolution of protein domain architectures

SK Forslund, M Kaduk, ELL Sonnhammer - … genomics: statistical and …, 2019 - Springer
This chapter reviews current research on how protein domain architectures evolve. We
begin by summarizing work on the phylogenetic distribution of proteins, as this will directly …

Assessing species coverage and assembly quality of rapidly accumulating sequenced genomes

R Feron, RM Waterhouse - GigaScience, 2022 - academic.oup.com
Background Ambitious initiatives to coordinate genome sequencing of Earth's biodiversity
mean that the accumulation of genomic data is growing rapidly. In addition to cataloguing …

A draft genome assembly of the solar-powered sea slug Elysia chlorotica

H Cai, Q Li, X Fang, J Li, NE Curtis, A Altenburger… - Scientific data, 2019 - nature.com
Elysia chlorotica, a sacoglossan sea slug found off the East Coast of the United States, is
well-known for its ability to sequester chloroplasts from its algal prey and survive by …

Global expression pattern of genes containing positively selected sites in European anchovy (Engraulis encrasicolus L.) may shed light on teleost reproduction

V Eldem, G Zararsız, M Erkan - PloS one, 2023 - journals.plos.org
European anchovy is a multiple-spawning and highly fecundate pelagic fish with high
economic and ecological significance. Although fecundity is influenced by nutrition …

Comprehensive Stress‐Based De Novo Transcriptome Assembly and Annotation of Guar (Cyamopsis tetragonoloba (L.) Taub.): An Important Industrial and Forage …

F Al-Qurainy, A Alshameri, AR Gaafar… - … journal of genomics, 2019 - Wiley Online Library
The forage crop Guar (Cyamopsis tetragonoloba (L.) Taub.) has the ability to endure heat,
drought, and mild salinity. A complete image on its genic architecture will promote our …

The modular nature of protein evolution: domain rearrangement rates across eukaryotic life

E Dohmen, S Klasberg, E Bornberg-Bauer… - BMC Evolutionary …, 2020 - Springer
Background Modularity is important for evolutionary innovation. The recombination of
existing units to form larger complexes with new functionalities spares the need to create …