Biology subjects

Gao, L.-Z.

Publications and source records attributed to Gao, L.-Z..

6 recordsLinked to original sources

bioRxiv2026

Short repeats rewrite plant mitochondrial evolution: Genomic expansion and hybridization signatures in a taxonomically complex radiation

Plant mitochondrial genomes are paradoxical: structurally dynamic yet functionally conserved. In hybrid-prone lineages like Camellia (Theaceae), the forces shaping mitogenome evolution remain unclear. Here, we assemble mitogenomes of eight Camellia species and an outgroup. We show that short repeats (<100 bp) drive genome expansion (PGLS: R{superscript 2} = 0.97, P = 6.3 x 10-), overturning the long-repeat paradigm. Multichromosomal architectures and extensive horizontal transfer (up to 25.5% plastid DNA) characterize hybrid lineages. Stark phylogenomic conflicts among mitochondrial, chloroplast and nuclear genomes expose genome-wide hybridization signatures. Mitochondria thus act as recorders of historical gene flow, capturing repeat explosions triggered by introgression. This work redefines plant mitogenome evolution and provides a framework to resolve taxonomic complexities in rapidly radiating angiosperms.

genomics↗

bioRxiv2026

An Integrative Phylogenomic Framework Quantifies the Dominant Role of Introgression in Phylogenetic Discordance among Diploid Oryza Species

BackgroundPhylogenomic studies frequently reveal widespread gene tree discordance, primarily arising from incomplete lineage sorting (ILS) and hybridization and/or introgression. Disentangling these processes is especially challenging in rapidly radiating lineages. The genus Oryza, with its rapid diversification and multiple genome types, exemplifies this pervasive phylogenetic incongruence. We integrated multiple genomic datasets including whole-genome resequencing, transcriptomes, and published genomes from diploid Oryza species. Concatenation and multispecies coalescent analyses recovered a robust, congruent species tree, placing the FF and GG genome groups as a monophyletic basal clade, followed by successive divergence of the EE, CC, BB, and AA lineages, a topology differing from some prior hypotheses. ResultsTo assess the sources of discordance, we employed a suite of complementary phylogenomic methods. Quantifying introgression via Branch Lengths (QuIBL)-based model comparisons suggested that [~]74.17% of gene tree-species tree discordance is better explained by post-speciation introgression, whereas only [~]15.56% is consistent with ILS alone. Phylogenetic networks (PhyloNet) and allele-sharing statistics (D-statistics, f-branch) corroborated these results, indicating widespread historical introgression both within and between genome groups. Furthermore, genome-wide scans using the fdM statistic localized introgressed genomic regions, which showed reduced interspecific divergence and were enriched for genes involved in stress responses and metabolism. ConclusionsTaken together, our results demonstrate that historical introgression, not ILS, is the dominant force shaping phylogenetic discordance in diploid Oryza. The integrative phylogenomic framework implemented here, which quantifies the contributions of introgression versus ILS and maps the genomic footprint of gene flow, provides a replicable strategy for resolving complex evolutionary histories in other rapidly radiating lineages.

evolutionary biology↗

bioRxiv2026

Transposable element-mediated co-option drives the evolution of the miRNA regulatory system in Oryza AA-genome species

MicroRNAs (miRNAs) are key post-transcriptional regulators in plants, yet the evolutionary dynamics of the entire miRNA-mediated regulatory system remain poorly understood. We performed small RNA sequencing and comparative genomics analyses across all eight AA-genome species of Oryza within a well-resolved phylogenetic framework. We found that miRNA gene (MIRNA) families evolve with low birth-death rates, while individual paralogous MIRNAs turn over rapidly. We identified a novel mechanism in which transposable element (TE) insertions de novo generates functional miRNA target sites. miRNA target genes are characterized by distinct evolutionary signatures, including greater sequence length, lower GC content, moderately highly expression, reduced expression variability, and higher evolutionary conservation, which is consistent with their role as a conserved kernel regulatory subsystem. In contrast, the majority of recently evolved target genes that have acquired their miRNA binding sites through TE insertions tend to exhibit the opposite set of features. Furthermore, we uncovered co-evolutionary signatures between duplicated MIRNAs and their target genes, as well as between MIRNAs and phased siRNAs (phasiRNAs). Taken together, our study reveals multi-level evolutionary dynamics driven by TEs that rapidly generate new regulatory circuit and proposes a generalizable TE-MIRNA co-option model for regulatory network expansion in plants.

genomics↗

bioRxiv2020

SMRT sequencing generates the chromosome-scale reference genome of tropical fruit mango, Mangifera indica

Mango (Mangifera indica), a member of the family Anacardiaceae, is one of the worlds most popular tropical fruits. Here we sequenced the variety, "Hong Xiang Ya", and generated a 371.6-Mb mango genome assembly with 34,529 predicted protein-coding genes. Aided with the published genetic map, for the first time, we assembled the M. indica genome to the chromosomes, and finally about 98.77% of the genome assembly was anchored to 20 pseudo-chromosomes. The availability of the chromosome-length genome assembly of M. indica will provide novel insights into genome evolution, understand the genetic basis of specialized phytochemical composites relevant to fruit quality, and enhance allele mining in genomics-assisted breeding for mango genetic improvement.

genomics↗

bioRxiv2020

SMRT sequencing of the Oryza rufipogon genome reveals the genomic basis of rice adaptation

Asian cultivated rice is believed to have been domesticated from an immediate ancestral progenitor, Oryza rufipogon, which provides promising sources of novel alleles for world rice improvement. Here we first present a high-quality de novo assembly of the typical O. rufipogon genome through the integration of single-molecule sequencing (SMRT), 10x and Hi-C technologies. This chromosome-based reference genome allows a multi-species comparative analysis of the annual selfing O. sativa and its two wild progenitors, the annual selfing O. nivara and perennial outcrossing O. rufipogon, identifying massive numbers of dispensable genes that are functionally enriched in reproductive process. Comparative genomic analyses identified millions of genomic variants, of which large-effect mutations (e.g., SVs, CNV and PAVs) may affect the variation of agronomically significant traits. We demonstrate how lineage-specific expansion of rice gene families may have contributed to the formation of reproduction isolation (e.g., the recognition of pollen and male sterility), thus brightening the role in driving mating system evolution during the evolutionary process of recent speciation. We document thousands of positively selected genes that are mainly involved in flower development, ripening, pollination, reproduction and response to biotic- and abiotic stresses. We show that selection pressures may serve as crucial forces to govern substantial genomic alterations among the three rice species that form the genetic basis of rapid evolution of mating and reproductive systems under diverse habitats. This first chromosome-based wild rice genome in the genus Oryza will become powerful to accelerate the exploration of untapped genomic diversity from wild rice for the enhancement of elite rice cultivars.

genomics↗

bioRxiv2020

SMRT sequencing yields the chromosome-scale reference genome of tea tree, Camellia sinensis var. sinensis

Tea is the oldest and most popular nonalcoholic beverage consumed in the world. It provides abundant secondary metabolites that account for its diverse flavors and health benefits. Here we present the first high-quality chromosome-length reference genome of C. sinensis var. sinensis using long read single-molecule real time (SMRT) sequencing and Hi-C technologies to anchor the [~]2.85-Gb genome assembly into 15 pseudo-chromosomes with a scaffold N50 length of [~]195.68 Mb. We annotated at least 2.17 Gb ([~]74.13%) of repetitive sequences and high-confidence prediction of 40,812 protein-coding genes in the [~]2.92-Gb genome assembly. This accurately assembled genome allows us to comprehensively annotate functionally important gene families such as those involved in the biosynthesis of catechins, theanine and caffeine. The contiguous genome assembly provides the first view of the repetitive landscape allowing us to accurately characterize retrotransposon diversity. The large tea tree genome is dominated by a handful of Ty3-gypsy long terminal repeat (LTR) retrotransposon families that recently expanded to high copy numbers. We uncover the latest bursts of numerous non-autonomous LTR retrotransposons that may interfere with the propagation of autonomous retroelements. This reference genome sequence will largely facilitate the improvement of agronomically important traits relevant to the tea quality and production.

genomics↗