DOI: 10.5061/dryad.7pvmcvf3d
title: Cryptic CAM photosynthesis in Joshua tree (Yucca brevifolia, Y. jaegeriana)

description: Joshua trees are an iconic species of the Mojave Desert, but face threats
 from changes to the climate and land use. Here we uncover cryptic
 Crassulacean acid metabolism (CAM photosynthesis) in Joshua trees via a
 common garden, and use genomic data to understand other metabolic
 differences between populations and the two species of Joshua tree. Our
 Dryad data package includes RNA sequencing data from a common garden
 experiment on Joshua tree species (Yucca brevifolia and Yucca
 jaegeriana). Samples were taken in 2022 from just a single garden and were
 combined with ecophysiological measurements and metabolomics. Our results
 indicate low level CAM activity in all populations of Joshua tree, as well
 as strong differentiation in aspects of carbon metabolism between the two
 species.
description: # Cryptic CAM photosynthesis in Joshua tree (Yucca brevifolia, Y.
 jaegeriana) Dataset DOI:
 [10.5061/dryad.7pvmcvf3d](10.5061/dryad.7pvmcvf3d) ## Description of the
 data and file structure To understand the presence, variability, and
 strength of Crassulacean acid metabolism (CAM) photosynthesis, we
 collected RNA-sequencing data in 2022 from both Joshua tree species
 (*Yucca brevifolia, Yucca jaegeriana*) from plants in a common garden.
 Data package includes only computed read count and transcript per million
 (TPM) values and the reference used for read mapping of samples collected
 in 2022. The 2021 data is available as raw reads on SRA. For raw reads of
 both 2021 and 2022 collections, please see SRA BioProject PRJNA1132710.
 ### Files and variables #### File: 2024-04-17_counts_raw.txt
 **Description:** Raw count data as computed by sleuth from 2022 samples
 mapped to the primary transcript reference file. ##### Variables *
 Columns: Library ID. See "full_RNA_metadata_dryad.csv" for
 information. * Rows: primary transcript ID #### File:
 2024-04-17_tpm_raw.txt **Description:** Raw TPM data as computed by sleuth
 from 2022 samples mapped to the primary transcript reference file. #####
 Variables * Columns: Library ID. See
 "full_RNA_metadata_dryad.csv" for information. * Rows: primary
 transcript ID #### File: 2024-04-17_counts_norm.txt
 **Description:** Normalized count data as computed by sleuth from 2022
 samples mapped to the primary transcript reference file. ##### Variables *
 Columns: Library ID. See "full_RNA_metadata_dryad.csv" for
 information. * Rows: primary transcript ID #### File:
 2024-04-17_tpm_norm.txt **Description:** Normalized TPM data as computed
 by sleuth from 2022 samples mapped to the primary transcript reference
 file. ##### Variables * Columns: Library ID. See
 "full_RNA_metadata_dryad.csv" for information. * Rows: primary
 transcript ID #### File: full_RNA_metadata_dryad.csv
 **Description:** Metadata for each library sequences (headers in the TPM
 and count files). ##### Variables * sample: library ID (internal number) *
 sourcepop: full name of source population * populationcode: Abbreviation
 for the source population from which the individual came. * time: Time of
 day of sample, AM (morning) or PM (night) * species: Which of the two
 species the sample came from (Eastern = *Y. jaegeriana*, Western = *Y.
 brevifolia*, hybrid = hybrid of the two.) * tag: the unique tag identifier
 for the plant * matriline: matriline information for the plant #### File:
 primaryYucca_jaegeriana_transcripts.fa **Description:** Transcript file
 derived from a preliminary annotation of the *Y. jaegeriana* genome.
 Transcripts are only the primary isoforms annotated per locus.  **Genome
 assembly:** A total of 136.8 Gb of PacBio CCS reads were generated using a
 PacBio Sequel 2 at the HudsonAlpha Institute of Biotechnology. PacBio HiFi
 libraries had insert sizes ranging from 17-23.6 Kb. An estimated 44.1X
 coverage of the genome was generated. Initial assembly was completed using
 hifiasm 0.19.8 with default parameters. **Genome annotation:** The
 assembly was annotated using BRAKER v.3.0.4 using gene models from *Yucca
 aloifolia *(Ya24Inoko_839 v.2.1) and *Yucca filamentosa
 *(YfilamentosaC3pri_837_v.2.1) and evidence from transcriptomes generated
 in this manuscript. RepeatModeler v.2.0.3
 [(Flynn](https://paperpile.com/c/8DjyBy/myi31) *[et
 al.](https://paperpile.com/c/8DjyBy/myi31)*[,
 2020)](https://paperpile.com/c/8DjyBy/myi31) and RepeatMasker v.4.1.2-p1
 were run to identify the consensus repeat families and softmasking the
 repeat regions in the genome with default parameters, respectively. TSEBRA
 v.1.1.2.1[(Gabriel](https://paperpile.com/c/8DjyBy/cxOpW) *[et
 al.](https://paperpile.com/c/8DjyBy/cxOpW)*[,
 2021)](https://paperpile.com/c/8DjyBy/cxOpW) was used to retrieve
 BRAKER's filtered single exon genes. We ran InterProScan v.5.19-58.0
 [(Jones](https://paperpile.com/c/8DjyBy/I588O) *[et
 al.](https://paperpile.com/c/8DjyBy/I588O)*[,
 2014)](https://paperpile.com/c/8DjyBy/I588O) to obtain protein evidence of
 the genes provided by TSEBRA output. All the single- exon genes lacking
 any protein evidence were filtered out from the gff3 file using AGAT
 v.0.7.0 [(Dainat, 2021)](https://paperpile.com/c/8DjyBy/Y6aSC). The output
 gff3 file from AGAT was used as the final annotation and for downstream
 analysis.  Dainat J. 2021. AGAT: Another Gff Analysis Toolkit to handle
 annotations in any GTF/GFF format (v0. 8.0). Zenodo. Flynn JM, Hubley R,
 Goubert C, Rosen J, Clark AG, Feschotte C, Smit AF. 2020. RepeatModeler2
 for automated genomic discovery of transposable element families.
 *Proceedings of the National Academy of Sciences of the United States of
 America* 117: 9451–9457.  Gabriel L, Hoff KJ, Brůna T, Borodovsky M,
 Stanke M. 2021. TSEBRA: transcript selector for BRAKER. *BMC
 Bioinformatics* 22: 566.  Jones P, Binns D, Chang H-Y, Fraser M, Li W,
 McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, et al. 2014.
 InterProScan 5: genome-scale protein function classification.
 *Bioinformatics* 30: 1236–1240. ## Code/software All data can be viewed in
 standard text editors. ## Access information Other publicly accessible
 locations of the data: * NCBI SRA BioProject PRJNA1132710