Ramanauskas, K. | bioRxiv Science

bioRxiv2023

Transcriptome data from silica-preserved leaf tissue reveals gene flow patterns in a Caribbean bromeliad

O_LITranscriptome sequencing is a cost-effective approach that allows researchers to study a broad range of questions. However, to preserve RNA for transcriptome sequencing, tissue is often kept under special conditions, such as immediate ultracold freezing. Here, we demonstrate that RNA can be obtained from six-month-old, field collected samples stored in silica gel at room temperature. Using these transcriptomes, we explore the evolutionary relationships of the genus Pitcairnia (Bromeliaceae) in the Dominican Republic and infer barriers to gene flow. C_LIO_LIWe extracted RNA from silica-dried leaf tissue from 19 Pitcairnia individuals collected across the Dominican Republic. We used a series of macro-and micro-evolutionary approaches to examine the relationships and patterns of gene flow among individuals. C_LIO_LIWe produced high-quality transcriptomes from silica-dried material and demonstrated that evolutionary relationships on the island match geography more closely than species delimitation methods. A population genetic examination indicates that a combination of ecological and geographic features are barriers to gene flow in Pitcairnia. C_LIO_LIHigh-quality transcriptomes can be obtained from silica-preserved tissue. The genetic diversity among Pitcairnia populations does not warrant classification as separate species, but the Dominican Republic contains several barriers to gene flow, notably the Cordillera Central mountain range. C_LI

evolutionary biology↗

bioRxiv2023

kakapo: Easy extraction and annotation of genes from raw RNA-seq reads

kakapo (k[a]k[a]p[o]) is a python-based pipeline that allows users to extract and assemble one or more specified genes or gene families. It flexibly uses original RNA-seq read or GenBank SRA accession inputs without performing assembly of entire transcriptomes. The pipeline identifies open reading frames in the assembled gene transcripts and annotates them. It optionally filters raw reads for ribosomal, plastid, and mitochondrial reads, or reads belonging to non-target organisms (e.g., viral, bacterial, human). kakapo can be employed to extract arbitrary loci, such as those commonly used for phylogenetic inference in systematics or candidate genes and gene families in phylogenomic and metagenomic studies. We provide example applications and discuss how its use can offset the declining value of the GenBanks single-gene databases and help assemble datasets for a variety of phylogenetic analyses.

bioinformatics↗