A genome for Bidens hawaiensis: a member of a hexaploid Hawaiian plant adaptive radiation

Abstract The plant genus Bidens (Asteraceae or Compositae; Coreopsidae) is
a species-rich and circumglobally distributed taxon. The 19 hexaploid
species endemic to the Hawaiian Islands are considered an iconic example
of adaptive radiation, of which many are imperiled and of high
conservation concern. Until now, no genomic resources were available for
this genus, which may serve as a model system for understanding the
evolutionary genomics of explosive plant diversification. Here, we present
a high-quality reference genome for the Hawai‘i Island endemic species B.
hawaiensis A. Gray reconstructed from long-read, high-fidelity sequences
generated on a Pacific Biosciences Sequel II System. The haplotype-aware,
draft genome assembly consisted of ~6.67 Giga bases (Gb), close to the
holoploid genome size estimate of 7.56 Gb (± 0.44 SD) determined by flow
cytometry. After removal of alternate haplotigs and contaminant filtering,
the consensus haploid reference genome was comprised of 15,904 contigs
containing ~3.48 Gb, with a contig N50 value of 422,594. The high
interspersed repeat content of the genome, approximately 74%, along with
hexaploid status, contributed to assembly fragmentation. Both the
haplotype-aware and consensus haploid assemblies recovered >96% of
Benchmarking Universal Single-copy Orthologs. Yet, the removal of
alternate haplotigs did not substantially reduce the proportion of
duplicated benchmarking genes (~79% versus ~68%). This reference genome
will support future work on the speciation process during adaptive
radiation, including resolving evolutionary relationships, determining the
genomic basis of trait evolution, and supporting ongoing conservation
efforts.

摘要：鬼针草属（Bidens）隶属于菊科（Asteraceae/Compositae）金鸡菊亚族（Coreopsidae），是一个物种丰富且全球广布的分类单元。其中分布于夏威夷群岛的19个六倍体（hexaploid）物种被视为适应性辐射（adaptive radiation）的标志性范例，多数类群濒临灭绝，具有极高的保护价值。此前该属尚无可用的基因组资源（genomic resources），而其本可作为解析植物快速辐射分化进化基因组学（evolutionary genomics）的模式系统。本研究基于PacBio Sequel II测序平台（Pacific Biosciences Sequel II System）产生的长读长高保真序列，对夏威夷群岛特有物种夏威夷鬼针草（B. hawaiensis A. Gray）构建了高质量参考基因组。单倍型解析的草图基因组组装总长度约为6.67吉碱基（Gb），与通过流式细胞术（flow cytometry）测得的全基因组大小估计值7.56 Gb（±0.44 标准差）相近。移除替代单倍型片段（alternate haplotigs）并完成污染物过滤后，最终得到的共识单倍型参考基因组包含15904个重叠群（contig），组装总长度约为3.48 Gb，Contig N50值为422594。该基因组约74%的散在重复序列含量，加之其六倍体属性，导致了组装的碎片化。单倍型解析组装与共识单倍型组装均成功覆盖了超过96%的单拷贝通用直系同源基准基因集（Benchmarking Universal Single-copy Orthologs），但移除替代单倍型片段并未显著降低重复基准基因的占比（约79% vs 约68%）。本研究获得的参考基因组将为后续适应性辐射过程中的物种形成研究提供支撑，包括解析进化关系、明确性状进化的基因组基础，以及助力当前的保护工作。