High-Throughput Genomic Data Reveal Complex Phylogenetic Relationships in Stylosanthes Sw (Leguminosae)

Maria Alice Silva Oliveira,Brena Van-Lume,Danilo Soares Gissi,Danyelle Ferreira Gomes,Cícero Carlos De Souza Almeida,Gaus S A Lima,Tomáz Nunes,Sarah S Marques Da Silva,Maria Aparecida Dos Santos,Marcelo F Simon,André Marques,Iara Costa,Gustavo Souza,Ronaldo Simão Oliveira

doi:10.3389/fgene.2021.727314

Abstract

Allopolyploidy is widely present across plant lineages. Though estimating the correct phylogenetic relationships and origin of allopolyploids may sometimes become a hard task. In the genus Stylosanthes Sw. (Leguminosae), an important legume crop, allopolyploidy is a key speciation force. This makes difficult adequate species recognition and breeding efforts on the genus. Based on comparative analysis of nine high-throughput sequencing (HTS) samples, including three allopolyploids (S. capitata Vogel cv. “Campo Grande,” S. capitata “RS024” and S. scabra Vogel) and six diploids (S. hamata Taub, S. viscosa (L.) Sw., S. macrocephala M. B. Ferreira and Sousa Costa, S. guianensis (Aubl.) Sw., S. pilosa M. B. Ferreira and Sousa Costa and S. seabrana B. L. Maass & 't Mannetje) we provide a working pipeline to identify organelle and nuclear genome signatures that allowed us to trace the origin and parental genome recognition of allopolyploids. First, organelle genomes were de novo assembled and used to identify maternal genome donors by alignment-based phylogenies and synteny analysis. Second, nuclear-derived reads were subjected to repetitive DNA identification with RepeatExplorer2. Identified repeats were compared based on abundance and presence on diploids in relation to allopolyploids by comparative repeat analysis. Third, reads were extracted and grouped based on the following groups: chloroplast, mitochondrial, satellite DNA, ribosomal DNA, repeat clustered- and total genomic reads. These sets of reads were then subjected to alignment and assembly free phylogenetic analyses and were compared to classical alignment-based phylogenetic methods. Comparative analysis of shared and unique satellite repeats also allowed the tracing of allopolyploid origin in Stylosanthes, especially those with high abundance such as the StyloSat1 in the Scabra complex. This satellite was in situ mapped in the proximal region of the chromosomes and made it possible to identify its previously proposed parents. Hence, with simple genome skimming data we were able to provide evidence for the recognition of parental genomes and understand genome evolution of two Stylosanthes allopolyploids.

Highlights

High-throughput sequencing (HTS) technologies have recently emerged as a versatile source of sequencing data allowing researchers to rapidly access different aspects of biodiversity based on four main approaches: genome skimming, RAD-Seq, RNA-Seq, and Hyb-Seq (Dodsworth et al, 2019)
An extensive variation in the order of approximately 200 Kb was found among Stylosanthes mitogenomes with the following increasing order: S. macrocephala SMA 2707 (350,377 bp), S. viscosa SVI 2702 (353,136 bp), S. capitata SCA 2708 (384,410 bp), S. pilosa SPI 2706 (433,649 bp), S. capitata SCA 2705 (456,448 bp), S. guianensis SGU 2710 (468,896 bp), S. scabra Short Single Copy (SSC) 2703 (492,899 bp), S. hamata SHA 2701 (503,967 bp) and S. seabrana SSE 2709 (523,870 bp) (Supplementary Table S1)
Mitogenomes features of each studied species, including the number of transfer RNA, ribosomal RNA, and protein-coding genes from the annotated regions are shown in Figure 2 and Supplementary Table S2

Summary

Introduction

High-throughput sequencing (HTS) technologies have recently emerged as a versatile source of sequencing data allowing researchers to rapidly access different aspects of biodiversity based on four main approaches: genome skimming, RAD-Seq, RNA-Seq, and Hyb-Seq (Dodsworth et al, 2019). Organelle inheritance mostly maternal for most plant species (Reboud and Zeyl, 1994; Greiner et al, 2014), makes the sequence of organelle genomes ideal for identifying patterns of maternal genome inheritance in hybrid species (Gastony and Yatskievych, 1992; Jankowiak et al, 2005). These different genomic and phylogenomic approaches could be important to characterize the origin and evolution of allopolyploid complexes

Methods

Results

Conclusion