Fresh leaves were plucked from a single cultivated alfalfa (cultivar XinJiangDaYe) plant cultivated in a greenhouse kept at 21–23 °C, 16 h light per day (light intensity of 380–450 W per m2) and a relative humidity (RH) of 70%. DNA was extracted from these leaves using a DNeasy Plant Mini Kit (Qiagen). Portions of the DNA were sent to AnnoRoad (Ningbo, China) to construct circular consensus sequencing (CCS) libraries and sequence them using a PacBio Sequal platform, and other portions were sent to Nextomics (Wuhan, China) to construct libraries and sequence them using Nanopore ONT and Illumina Hiseq platforms. These sequencing efforts yielded 70, 99, and 126 Gb of reads, respectively, for de novo assembly of the cultivated alfalfa genome (Supplementary Tables 1 and 2 ).
In addition, tender roots and shoots with leaves were collected, and RNA was extracted from one pooled root and shoot sample (with roughly the same weight of each organ) and four leaf samples using an RNeasy Plant Mini Kit (Qiagen). RNA samples were reverse-transcribed using random primers and sequenced using an Illumina platform. The RNA-seq data obtained are summarized in Supplementary Table9 .
In addition, tender roots and shoots with leaves were collected, and RNA was extracted from one pooled root and shoot sample (with roughly the same weight of each organ) and four leaf samples using an RNeasy Plant Mini Kit (Qiagen). RNA samples were reverse-transcribed using random primers and sequenced using an Illumina platform. The RNA-seq data obtained are summarized in Supplementary Table
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