A draft reference genome assembly of California Pipevine, Aristolochia californica Torr.
Samridhi Chaturvedi, Merly Escalona, Mohan P A Marimuthu, Oanh Nguyen, Noravit Chumchim, Colin W Fairbairn, William Seligmann, Courtney Miller, H Bradley Shaffer, Noah K Whiteman
Author Information
Samridhi Chaturvedi: Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA 70118, United States. ORCID
Merly Escalona: Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, United States. ORCID
Mohan P A Marimuthu: DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States. ORCID
Oanh Nguyen: DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States. ORCID
Noravit Chumchim: DNA Technologies and Expression Analysis Core Laboratory, Genome Center, University of California, Davis, CA 95616, United States. ORCID
Colin W Fairbairn: Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, United States. ORCID
William Seligmann: Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, United States. ORCID
Courtney Miller: Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095-7239, United States. ORCID
H Bradley Shaffer: Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA 90095-7239, United States. ORCID
Noah K Whiteman: Department of Integrative Biology, University of California, 142 Weill Hall #3200, Berkeley, United States. ORCID
The California Pipevine, Aristolochia californica Torr., is the only endemic California species within the cosmopolitan birthwort family Aristolochiaceae. It occurs as an understory vine in riparian and chaparral areas and in forest edges and windrows. The geographic range of this plant species almost entirely overlaps with that of its major specialized herbivore, the California Pipevine Swallowtail Butterfly Battus philenor hirsuta. While this species pair is a useful, ecologically well-understood system to study co-evolution, until recently, genomic resources for both have been lacking. Here, we report a new, chromosome-level assembly of A. californica as part of the California Conservation Genomics Project (CCGP). Following the sequencing and assembly strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin proximity sequencing technology to produce a de novo assembled genome. Our genome assembly, the first for any species in the genus, contains 531 scaffolds spanning 661 megabase (Mb) pairs, with a contig N50 of 6.53 Mb, a scaffold N50 of 42.2 Mb, and BUSCO complete score of 98%. In combination with the recently published B. philenor hirsuta reference genome assembly, the A. californica reference genome assembly will be a powerful tool for studying co-evolution in a rapidly changing California landscape.
